From 2a55e4579aa61107f23305c8d921cfc1a00306ed Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Mon, 10 Jun 2024 11:00:48 +0800
Subject: [PATCH 01/39] add types for bandstructure

---
 .../electronic_structure/bandstructure.py     | 244 ++++++++++--------
 pymatgen/electronic_structure/boltztrap2.py   |  15 +-
 pymatgen/io/lobster/__init__.py               |   2 +-
 3 files changed, 150 insertions(+), 111 deletions(-)

diff --git a/pymatgen/electronic_structure/bandstructure.py b/pymatgen/electronic_structure/bandstructure.py
index f844674be2b..3ce071eb13d 100644
--- a/pymatgen/electronic_structure/bandstructure.py
+++ b/pymatgen/electronic_structure/bandstructure.py
@@ -7,7 +7,7 @@
 import re
 import warnings
 from collections import defaultdict
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, overload
 
 import numpy as np
 from monty.json import MSONable
@@ -20,6 +20,7 @@
 if TYPE_CHECKING:
     from typing import Any
 
+    from numpy.typing import NDArray
     from typing_extensions import Self
 
 __author__ = "Geoffroy Hautier, Shyue Ping Ong, Michael Kocher"
@@ -39,7 +40,7 @@ class Kpoint(MSONable):
 
     def __init__(
         self,
-        coords: np.ndarray,
+        coords: NDArray,
         lattice: Lattice,
         to_unit_cell: bool = False,
         coords_are_cartesian: bool = False,
@@ -67,6 +68,20 @@ def __init__(
 
         self._cart_coords = lattice.get_cartesian_coords(self._frac_coords)
 
+    def __str__(self) -> str:
+        """String with fractional, Cartesian coordinates and label."""
+        return f"{self.frac_coords} {self.cart_coords} {self.label}"
+
+    def __eq__(self, other: object) -> bool:
+        """Check if two Kpoints are equal."""
+        if not isinstance(other, type(self)):
+            return NotImplemented
+        return (
+            np.allclose(self.frac_coords, other.frac_coords)
+            and self.lattice == other.lattice
+            and self.label == other.label
+        )
+
     @property
     def lattice(self) -> Lattice:
         """The lattice associated with the kpoint. It's a
@@ -85,12 +100,12 @@ def label(self, label: str | None) -> None:
         self._label = label
 
     @property
-    def frac_coords(self) -> np.ndarray:
+    def frac_coords(self) -> NDArray:
         """The fractional coordinates of the kpoint as a numpy array."""
         return np.copy(self._frac_coords)
 
     @property
-    def cart_coords(self) -> np.ndarray:
+    def cart_coords(self) -> NDArray:
         """The Cartesian coordinates of the kpoint as a numpy array."""
         return np.copy(self._cart_coords)
 
@@ -109,20 +124,6 @@ def c(self) -> float:
         """Fractional c coordinate of the kpoint."""
         return self._frac_coords[2]
 
-    def __str__(self) -> str:
-        """Get a string with fractional, Cartesian coordinates and label."""
-        return f"{self.frac_coords} {self.cart_coords} {self.label}"
-
-    def __eq__(self, other: object) -> bool:
-        """Check if two kpoints are equal."""
-        if not isinstance(other, Kpoint):
-            return NotImplemented
-        return (
-            np.allclose(self.frac_coords, other.frac_coords)
-            and self.lattice == other.lattice
-            and self.label == other.label
-        )
-
     def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of a kpoint."""
         return {
@@ -150,7 +151,7 @@ def from_dict(cls, dct: dict) -> Self:
 
 class BandStructure:
     """This is the most generic band structure data possible
-    it's defined by a list of kpoints + energies for each of them.
+    it's defined by a list of Kpoints and energies for each of them.
 
     Attributes:
         kpoints (list): The list of kpoints (as Kpoint objects) in the band structure.
@@ -170,18 +171,18 @@ class BandStructure:
 
     def __init__(
         self,
-        kpoints: np.ndarray,
-        eigenvals: dict[Spin, np.ndarray],
+        kpoints: NDArray,
+        eigenvals: dict[Spin, NDArray],
         lattice: Lattice,
         efermi: float,
         labels_dict=None,
         coords_are_cartesian: bool = False,
         structure: Structure | None = None,
-        projections: dict[Spin, np.ndarray] | None = None,
+        projections: dict[Spin, NDArray] | None = None,
     ) -> None:
         """
         Args:
-            kpoints: list of kpoint as numpy arrays, in frac_coords of the
+            kpoints: list of Kpoint as numpy arrays, in frac_coords of the
                 given lattice by default
             eigenvals: dict of energies for spin up and spin down
                 {Spin.up:[][],Spin.down:[][]}, the first index of the array
@@ -215,27 +216,27 @@ def __init__(
         if labels_dict is None:
             labels_dict = {}
 
-        if len(self.projections) != 0 and self.structure is None:
+        if self.projections and self.structure is None:
             raise RuntimeError("if projections are provided a structure object is also required")
 
-        for k in kpoints:
-            # let see if this kpoint has been assigned a label
+        for kpt in kpoints:
+            # Check if this Kpoint has a label
             label = None
             for c in labels_dict:
-                if np.linalg.norm(k - np.array(labels_dict[c])) < 0.0001:
+                if np.linalg.norm(kpt - np.array(labels_dict[c])) < 0.0001:
                     label = c
                     self.labels_dict[label] = Kpoint(
-                        k,
+                        kpt,
                         lattice,
                         label=label,
                         coords_are_cartesian=coords_are_cartesian,
                     )
-            self.kpoints.append(Kpoint(k, lattice, label=label, coords_are_cartesian=coords_are_cartesian))
+            self.kpoints.append(Kpoint(kpt, lattice, label=label, coords_are_cartesian=coords_are_cartesian))
         self.bands = {spin: np.array(v) for spin, v in eigenvals.items()}
         self.nb_bands = len(eigenvals[Spin.up])
         self.is_spin_polarized = len(self.bands) == 2
 
-    def get_projection_on_elements(self):
+    def get_projection_on_elements(self) -> dict[Spin, NDArray]:
         """Get a dictionary of projections on elements.
 
         Returns:
@@ -245,14 +246,14 @@ def get_projection_on_elements(self):
             returns an empty dict
         """
         result = {}
-        for spin, v in self.projections.items():
-            result[spin] = [[defaultdict(float) for i in range(len(self.kpoints))] for j in range(self.nb_bands)]
+        for spin, val in self.projections.items():
+            result[spin] = [[defaultdict(float) for _ in range(len(self.kpoints))] for _ in range(self.nb_bands)]
             for i, j, k in itertools.product(
                 range(self.nb_bands),
                 range(len(self.kpoints)),
                 range(len(self.structure)),
             ):
-                result[spin][i][j][str(self.structure[k].specie)] += np.sum(v[i, j, :, k])
+                result[spin][i][j][str(self.structure[k].specie)] += np.sum(val[i, j, :, k])
         return result
 
     def get_projections_on_elements_and_orbitals(self, el_orb_spec: dict[str, list[str]]):
@@ -274,8 +275,8 @@ def get_projections_on_elements_and_orbitals(self, el_orb_spec: dict[str, list[s
         species_orb_spec = {get_el_sp(el): orbs for el, orbs in el_orb_spec.items()}
         for spin, v in self.projections.items():
             result[spin] = [
-                [{str(e): defaultdict(float) for e in species_orb_spec} for i in range(len(self.kpoints))]
-                for j in range(self.nb_bands)
+                [{str(e): defaultdict(float) for e in species_orb_spec} for _ in range(len(self.kpoints))]
+                for _ in range(self.nb_bands)
             ]
 
             for i, j, k in itertools.product(
@@ -290,7 +291,7 @@ def get_projections_on_elements_and_orbitals(self, el_orb_spec: dict[str, list[s
                         result[spin][i][j][str(sp)][o] += v[i][j][orb_i][k]
         return result
 
-    def is_metal(self, efermi_tol=1e-4) -> bool:
+    def is_metal(self, efermi_tol: float = 1e-4) -> bool:
         """Check if the band structure indicates a metal by looking if the fermi
         level crosses a band.
 
@@ -303,7 +304,7 @@ def is_metal(self, efermi_tol=1e-4) -> bool:
                     return True
         return False
 
-    def get_vbm(self):
+    def get_vbm(self) -> dict[str, Any]:
         """Get data about the VBM.
 
         Returns:
@@ -335,25 +336,26 @@ def get_vbm(self):
         max_tmp = -float("inf")
         index = kpoint_vbm = None
         for value in self.bands.values():
-            for i, j in zip(*np.where(value < self.efermi)):
-                if value[i, j] > max_tmp:
-                    max_tmp = float(value[i, j])
+            for idx, j in zip(*np.where(value < self.efermi)):
+                if value[idx, j] > max_tmp:
+                    max_tmp = float(value[idx, j])
                     index = j
                     kpoint_vbm = self.kpoints[j]
 
         list_ind_kpts = []
         if kpoint_vbm.label is not None:
-            for i, kpt in enumerate(self.kpoints):
+            for idx, kpt in enumerate(self.kpoints):
                 if kpt.label == kpoint_vbm.label:
-                    list_ind_kpts.append(i)
+                    list_ind_kpts.append(idx)
         else:
             list_ind_kpts.append(index)
-        # get all other bands sharing the vbm
+
+        # Get all other bands sharing the vbm
         list_ind_band = defaultdict(list)
         for spin in self.bands:
-            for i in range(self.nb_bands):
-                if math.fabs(self.bands[spin][i][index] - max_tmp) < 0.001:
-                    list_ind_band[spin].append(i)
+            for idx in range(self.nb_bands):
+                if math.fabs(self.bands[spin][idx][index] - max_tmp) < 0.001:
+                    list_ind_band[spin].append(idx)
         proj = {}
         for spin, value in self.projections.items():
             if len(list_ind_band[spin]) == 0:
@@ -367,7 +369,7 @@ def get_vbm(self):
             "projections": proj,
         }
 
-    def get_cbm(self):
+    def get_cbm(self) -> dict[str, Any]:
         """Get data about the CBM.
 
         Returns:
@@ -399,26 +401,26 @@ def get_cbm(self):
 
         index = kpoint_cbm = None
         for value in self.bands.values():
-            for i, j in zip(*np.where(value >= self.efermi)):
-                if value[i, j] < max_tmp:
-                    max_tmp = float(value[i, j])
+            for idx, j in zip(*np.where(value >= self.efermi)):
+                if value[idx, j] < max_tmp:
+                    max_tmp = float(value[idx, j])
                     index = j
                     kpoint_cbm = self.kpoints[j]
 
         list_index_kpoints = []
         if kpoint_cbm.label is not None:
-            for i, kpt in enumerate(self.kpoints):
+            for idx, kpt in enumerate(self.kpoints):
                 if kpt.label == kpoint_cbm.label:
-                    list_index_kpoints.append(i)
+                    list_index_kpoints.append(idx)
         else:
             list_index_kpoints.append(index)
 
         # get all other bands sharing the cbm
         list_index_band = defaultdict(list)
         for spin in self.bands:
-            for i in range(self.nb_bands):
-                if math.fabs(self.bands[spin][i][index] - max_tmp) < 0.001:
-                    list_index_band[spin].append(i)
+            for idx in range(self.nb_bands):
+                if math.fabs(self.bands[spin][idx][index] - max_tmp) < 0.001:
+                    list_index_band[spin].append(idx)
         proj = {}
         for spin, value in self.projections.items():
             if len(list_index_band[spin]) == 0:
@@ -433,22 +435,25 @@ def get_cbm(self):
             "projections": proj,
         }
 
-    def get_band_gap(self):
+    def get_band_gap(self) -> dict[str, Any]:
         r"""Get band gap data.
 
         Returns:
-            A dict {"energy","direct","transition"}:
+            A dict {"energy", "direct", "transition"}:
             "energy": band gap energy
             "direct": A boolean telling if the gap is direct or not
             "transition": kpoint labels of the transition (e.g., "\\Gamma-X")
         """
         if self.is_metal():
             return {"energy": 0.0, "direct": False, "transition": None}
+
         cbm = self.get_cbm()
         vbm = self.get_vbm()
-        result = {"direct": False, "energy": 0.0, "transition": None}
-
-        result["energy"] = cbm["energy"] - vbm["energy"]
+        result = {
+            "direct": False,
+            "transition": None,
+            "energy": cbm["energy"] - vbm["energy"],
+        }
 
         if (cbm["kpoint"].label is not None and cbm["kpoint"].label == vbm["kpoint"].label) or np.linalg.norm(
             cbm["kpoint"].cart_coords - vbm["kpoint"].cart_coords
@@ -464,7 +469,7 @@ def get_band_gap(self):
 
         return result
 
-    def get_direct_band_gap_dict(self):
+    def get_direct_band_gap_dict(self) -> dict[Spin, dict[str, Any]]:
         """Get a dictionary of information about the direct
         band gap.
 
@@ -493,7 +498,7 @@ def get_direct_band_gap_dict(self):
             }
         return direct_gap_dict
 
-    def get_direct_band_gap(self):
+    def get_direct_band_gap(self) -> float:
         """Get the direct band gap.
 
         Returns:
@@ -501,14 +506,20 @@ def get_direct_band_gap(self):
         """
         if self.is_metal():
             return 0.0
+
         dg = self.get_direct_band_gap_dict()
         return min(v["value"] for v in dg.values())
 
-    def get_sym_eq_kpoints(self, kpoint, cartesian=False, tol: float = 1e-2):
-        """Get a list of unique symmetrically equivalent k-points.
+    def get_sym_eq_kpoints(
+        self,
+        kpoint: NDArray,
+        cartesian: bool = False,
+        tol: float = 1e-2,
+    ) -> NDArray:
+        """Get a list of unique symmetrically equivalent Kpoints.
 
         Args:
-            kpoint (1x3 array): coordinate of the k-point
+            kpoint (1x3 array): coordinate of the Kpoint
             cartesian (bool): kpoint is in Cartesian or fractional coordinates
             tol (float): tolerance below which coordinates are considered equal
 
@@ -517,11 +528,12 @@ def get_sym_eq_kpoints(self, kpoint, cartesian=False, tol: float = 1e-2):
         """
         if not self.structure:
             return None
+
         sg = SpacegroupAnalyzer(self.structure)
         symm_ops = sg.get_point_group_operations(cartesian=cartesian)
         points = np.dot(kpoint, [m.rotation_matrix for m in symm_ops])
         rm_list = []
-        # identify and remove duplicates from the list of equivalent k-points:
+        # Identify and remove duplicates from the list of equivalent k-points:
         for i in range(len(points) - 1):
             for j in range(i + 1, len(points)):
                 if np.allclose(pbc_diff(points[i], points[j]), [0, 0, 0], tol):
@@ -529,7 +541,12 @@ def get_sym_eq_kpoints(self, kpoint, cartesian=False, tol: float = 1e-2):
                     break
         return np.delete(points, rm_list, axis=0)
 
-    def get_kpoint_degeneracy(self, kpoint, cartesian=False, tol: float = 1e-2):
+    def get_kpoint_degeneracy(
+        self,
+        kpoint: NDArray,
+        cartesian: bool = False,
+        tol: float = 1e-2,
+    ) -> NDArray | None:
         """Get degeneracy of a given k-point based on structure symmetry.
 
         Args:
@@ -541,11 +558,9 @@ def get_kpoint_degeneracy(self, kpoint, cartesian=False, tol: float = 1e-2):
             int | None: degeneracy or None if structure is not available
         """
         all_kpts = self.get_sym_eq_kpoints(kpoint, cartesian, tol=tol)
-        if all_kpts is not None:
-            return len(all_kpts)
-        return None
+        return len(all_kpts) if all_kpts is not None else None
 
-    def as_dict(self):
+    def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of BandStructure."""
         dct = {
             "@module": type(self).__module__,
@@ -581,7 +596,7 @@ def as_dict(self):
 
         # MongoDB does not accept keys starting with $. Add a blank space to fix the problem
         for c, label in self.labels_dict.items():
-            mongo_key = c if not c.startswith("$") else f" {c}"
+            mongo_key = f" {c}" if c.startswith("$") else c
             dct["labels_dict"][mongo_key] = label.as_dict()["fcoords"]
         dct["projections"] = {}
         if len(self.projections) != 0:
@@ -590,7 +605,7 @@ def as_dict(self):
         return dct
 
     @classmethod
-    def from_dict(cls, dct: dict) -> Self:
+    def from_dict(cls, dct: dict[str, Any]) -> Self:
         """Create from dict.
 
         Args:
@@ -638,7 +653,7 @@ def from_dict(cls, dct: dict) -> Self:
             return cls.from_old_dict(dct)
 
     @classmethod
-    def from_old_dict(cls, dct) -> Self:
+    def from_old_dict(cls, dct: dict[str, Any]) -> Self:
         """
         Args:
             dct (dict): A dict with all data for a band structure symmetry line object.
@@ -687,14 +702,14 @@ class BandStructureSymmLine(BandStructure, MSONable):
 
     def __init__(
         self,
-        kpoints,
-        eigenvals,
-        lattice,
-        efermi,
-        labels_dict,
-        coords_are_cartesian=False,
-        structure=None,
-        projections=None,
+        kpoints: NDArray,
+        eigenvals: dict[Spin, list],
+        lattice: Lattice,
+        efermi: float,
+        labels_dict: dict,
+        coords_are_cartesian: bool = False,
+        structure: Structure | None = None,
+        projections: dict[Spin, NDArray] | None = None,
     ) -> None:
         """
         Args:
@@ -735,7 +750,7 @@ def __init__(
         self.branches = []
         one_group: list = []
         branches_tmp = []
-        # get labels and distance for each kpoint
+        # Get labels and distance for each kpoint
         previous_kpoint = self.kpoints[0]
         previous_distance = 0.0
 
@@ -770,7 +785,7 @@ def __init__(
         if len(self.bands) == 2:
             self.is_spin_polarized = True
 
-    def get_equivalent_kpoints(self, index):
+    def get_equivalent_kpoints(self, index: int) -> list[int]:
         """Get the list of kpoint indices equivalent (meaning they are the
         same frac coords) to the given one.
 
@@ -783,20 +798,20 @@ def get_equivalent_kpoints(self, index):
         TODO: now it uses the label we might want to use coordinates instead
         (in case there was a mislabel)
         """
-        # if the kpoint has no label it can't have a repetition along the band
-        # structure line object
+        # If the kpoint has no label it can't have a repetition
+        # along the band structure line object
 
         if self.kpoints[index].label is None:
             return [index]
 
         list_index_kpoints = []
-        for i, kpt in enumerate(self.kpoints):
+        for idx, kpt in enumerate(self.kpoints):
             if kpt.label == self.kpoints[index].label:
-                list_index_kpoints.append(i)
+                list_index_kpoints.append(idx)
 
         return list_index_kpoints
 
-    def get_branch(self, index):
+    def get_branch(self, index: int) -> list[dict[str, Any]]:
         r"""Get in what branch(es) is the kpoint. There can be several
         branches.
 
@@ -823,7 +838,7 @@ def get_branch(self, index):
                     )
         return to_return
 
-    def apply_scissor(self, new_band_gap):
+    def apply_scissor(self, new_band_gap: float) -> Self:
         """Apply a scissor operator (shift of the CBM) to fit the given band gap.
         If it's a metal, we look for the band crossing the Fermi level
         and shift this one up. This will not work all the time for metals!
@@ -835,7 +850,7 @@ def apply_scissor(self, new_band_gap):
             BandStructureSymmLine: with the applied scissor shift
         """
         if self.is_metal():
-            # moves then the highest index band crossing the Fermi level find this band...
+            # Move then the highest index band crossing the Fermi level find this band...
             max_index = -1000
             # spin_index = None
             for idx in range(self.nb_bands):
@@ -867,6 +882,7 @@ def apply_scissor(self, new_band_gap):
                     for v in range(len(old_dict["bands"][spin][k])):
                         if k >= max_index:
                             old_dict["bands"][spin][k][v] = old_dict["bands"][spin][k][v] + shift
+
         else:
             shift = new_band_gap - self.get_band_gap()["energy"]
             old_dict = self.as_dict()
@@ -876,9 +892,10 @@ def apply_scissor(self, new_band_gap):
                         if old_dict["bands"][spin][k][v] >= old_dict["cbm"]["energy"]:
                             old_dict["bands"][spin][k][v] = old_dict["bands"][spin][k][v] + shift
             old_dict["efermi"] = old_dict["efermi"] + shift
+
         return self.from_dict(old_dict)
 
-    def as_dict(self):
+    def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of BandStructureSymmLine."""
         dct = super().as_dict()
         dct["branches"] = self.branches
@@ -888,7 +905,7 @@ def as_dict(self):
 class LobsterBandStructureSymmLine(BandStructureSymmLine):
     """Lobster subclass of BandStructure with customized functions."""
 
-    def as_dict(self):
+    def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of BandStructureSymmLine."""
         dct = {
             "@module": type(self).__module__,
@@ -921,6 +938,7 @@ def as_dict(self):
         dct["band_gap"] = self.get_band_gap()
         dct["labels_dict"] = {}
         dct["is_spin_polarized"] = self.is_spin_polarized
+
         # MongoDB does not accept keys starting with $. Add a blank space to fix the problem
         for c, label in self.labels_dict.items():
             mongo_key = c if not c.startswith("$") else " " + c
@@ -931,7 +949,7 @@ def as_dict(self):
         return dct
 
     @classmethod
-    def from_dict(cls, dct: dict) -> Self:
+    def from_dict(cls, dct: dict[str, Any]) -> Self:
         """
         Args:
             dct (dict): A dict with all data for a band structure symmetry line
@@ -970,7 +988,7 @@ def from_dict(cls, dct: dict) -> Self:
             return cls.from_old_dict(dct)
 
     @classmethod
-    def from_old_dict(cls, dct) -> Self:
+    def from_old_dict(cls, dct: dict[str, Any]) -> Self:
         """
         Args:
             dct (dict): A dict with all data for a band structure symmetry line
@@ -1005,7 +1023,7 @@ def from_old_dict(cls, dct) -> Self:
             projections=projections,
         )
 
-    def get_projection_on_elements(self):
+    def get_projection_on_elements(self) -> dict[Spin, list]:
         """Get a dictionary of projections on elements. It sums over all available orbitals
         for each element.
 
@@ -1017,7 +1035,7 @@ def get_projection_on_elements(self):
         """
         result = {}
         for spin, v in self.projections.items():
-            result[spin] = [[defaultdict(float) for i in range(len(self.kpoints))] for j in range(self.nb_bands)]
+            result[spin] = [[defaultdict(float) for _ in range(len(self.kpoints))] for _ in range(self.nb_bands)]
             for i, j in itertools.product(range(self.nb_bands), range(len(self.kpoints))):
                 for key, item in v[i][j].items():
                     for item2 in item.values():
@@ -1025,7 +1043,10 @@ def get_projection_on_elements(self):
                         result[spin][i][j][specie] += item2
         return result
 
-    def get_projections_on_elements_and_orbitals(self, el_orb_spec):
+    def get_projections_on_elements_and_orbitals(
+        self,
+        el_orb_spec: dict[Element, list],
+    ) -> dict[Spin, list]:
         """Return a dictionary of projections on elements and specific orbitals.
 
         Args:
@@ -1040,12 +1061,12 @@ def get_projections_on_elements_and_orbitals(self, el_orb_spec):
             if there is no projections in the band structure returns an empty
             dict.
         """
-        result = {}
+        result: dict[Spin, list] = {}
         el_orb_spec = {get_el_sp(el): orbs for el, orbs in el_orb_spec.items()}
         for spin, v in self.projections.items():
             result[spin] = [
-                [{str(e): defaultdict(float) for e in el_orb_spec} for i in range(len(self.kpoints))]
-                for j in range(self.nb_bands)
+                [{str(e): defaultdict(float) for e in el_orb_spec} for _ in range(len(self.kpoints))]
+                for _ in range(self.nb_bands)
             ]
 
             for i, j in itertools.product(range(self.nb_bands), range(len(self.kpoints))):
@@ -1057,7 +1078,26 @@ def get_projections_on_elements_and_orbitals(self, el_orb_spec):
         return result
 
 
-def get_reconstructed_band_structure(list_bs, efermi=None):
+@overload
+def get_reconstructed_band_structure(
+    list_bs: list[BandStructure],
+    efermi: float | None = None,
+) -> BandStructure:
+    pass
+
+
+@overload
+def get_reconstructed_band_structure(
+    list_bs: list[BandStructureSymmLine],
+    efermi: float | None = None,
+) -> BandStructureSymmLine:
+    pass
+
+
+def get_reconstructed_band_structure(
+    list_bs: list[BandStructure] | list[BandStructureSymmLine],
+    efermi: float | None = None,
+) -> BandStructure | BandStructureSymmLine:
     """Take a list of band structures and reconstructs
     one band structure object from all of them.
 
diff --git a/pymatgen/electronic_structure/boltztrap2.py b/pymatgen/electronic_structure/boltztrap2.py
index d3ed99d5167..50d09d116ac 100644
--- a/pymatgen/electronic_structure/boltztrap2.py
+++ b/pymatgen/electronic_structure/boltztrap2.py
@@ -1,10 +1,10 @@
-"""BoltzTraP2 is a python software interpolating band structures and
-computing materials properties from dft band structure using Boltzmann
-semi-classical transport theory.
-This module provides a pymatgen interface to BoltzTraP2.
+"""This module provides a pymatgen interface to BoltzTraP2.
 Some of the code is written following the examples provided in BoltzTraP2.
 
-BoltzTraP2 has been developed by Georg Madsen, Jesús Carrete, Matthieu J. Verstraete.
+BoltzTraP2 is a Python software interpolating band structures and
+computing materials properties from dft band structure using Boltzmann
+semi-classical transport theory, developed by Georg Madsen, Jesús Carrete,
+Matthieu J. Verstraete.
 
 https://gitlab.com/sousaw/BoltzTraP2
 https://www.sciencedirect.com/science/article/pii/S0010465518301632
@@ -21,9 +21,8 @@
     Computer Physics Communications, 175, 67-71
 
 Todo:
-- DONE: spin polarized bands
-- read first derivative of the eigenvalues from vasprun.xml (mommat)
-- handle magnetic moments (magmom)
+- Read first derivative of the eigenvalues from vasprun.xml (mommat)
+- Handle magnetic moments (MAGMOM)
 """
 
 from __future__ import annotations
diff --git a/pymatgen/io/lobster/__init__.py b/pymatgen/io/lobster/__init__.py
index f5e4a5f4234..e4b1100a2d6 100644
--- a/pymatgen/io/lobster/__init__.py
+++ b/pymatgen/io/lobster/__init__.py
@@ -1,5 +1,5 @@
 """
-This package implements modules for input and output to and from Lobster. It
+This package implements modules for input and output to and from LOBSTER. It
 imports the key classes form both lobster.inputs and lobster_outputs to allow most
 classes to be simply called as pymatgen.io.lobster.Lobsterin for example, to retain
 backwards compatibility.

From 1cd0037abc2f19fcef2a28b9dec3614ff7bc9df7 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Mon, 10 Jun 2024 11:45:54 +0800
Subject: [PATCH 02/39] relocate magic methods to top

---
 pymatgen/electronic_structure/dos.py | 83 ++++++++++++++--------------
 1 file changed, 42 insertions(+), 41 deletions(-)

diff --git a/pymatgen/electronic_structure/dos.py b/pymatgen/electronic_structure/dos.py
index be074213ca6..fc7378290a2 100644
--- a/pymatgen/electronic_structure/dos.py
+++ b/pymatgen/electronic_structure/dos.py
@@ -189,6 +189,33 @@ def __init__(
         vol = norm_vol or 1
         self.densities = {k: np.array(d) / vol for k, d in densities.items()}
 
+    def __add__(self, other):
+        """Add two DOS together. Checks that energy scales are the same.
+        Otherwise, a ValueError is thrown.
+
+        Args:
+            other: Another DOS object.
+
+        Returns:
+            Sum of the two DOSs.
+        """
+        if not all(np.equal(self.energies, other.energies)):
+            raise ValueError("Energies of both DOS are not compatible!")
+        densities = {spin: self.densities[spin] + other.densities[spin] for spin in self.densities}
+        return Dos(self.efermi, self.energies, densities)
+
+    def __str__(self) -> str:
+        """Get a string which can be easily plotted (using gnuplot)."""
+        if Spin.down in self.densities:
+            str_arr = [f"#{'Energy':30s} {'DensityUp':30s} {'DensityDown':30s}"]
+            for i, energy in enumerate(self.energies):
+                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f} {self.densities[Spin.down][i]:.5f}")
+        else:
+            str_arr = [f"#{'Energy':30s} {'DensityUp':30s}"]
+            for i, energy in enumerate(self.energies):
+                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f}")
+        return "\n".join(str_arr)
+
     def get_densities(self, spin: Spin | None = None):
         """Get the density of states for a particular spin.
 
@@ -200,8 +227,9 @@ def get_densities(self, spin: Spin | None = None):
             None, the sum of all spins is returned.
         """
         if self.densities is None:
-            result = None
-        elif spin is None:
+            return None
+
+        if spin is None:
             if Spin.down in self.densities:
                 result = self.densities[Spin.up] + self.densities[Spin.down]
             else:
@@ -227,21 +255,6 @@ def get_smeared_densities(self, sigma: float):
             smeared_dens[spin] = gaussian_filter1d(dens, sigma / avg_diff)
         return smeared_dens
 
-    def __add__(self, other):
-        """Add two DOS together. Checks that energy scales are the same.
-        Otherwise, a ValueError is thrown.
-
-        Args:
-            other: Another DOS object.
-
-        Returns:
-            Sum of the two DOSs.
-        """
-        if not all(np.equal(self.energies, other.energies)):
-            raise ValueError("Energies of both DOS are not compatible!")
-        densities = {spin: self.densities[spin] + other.densities[spin] for spin in self.densities}
-        return Dos(self.efermi, self.energies, densities)
-
     def get_interpolated_value(self, energy: float) -> dict[Spin, float]:
         """Get interpolated density for a particular energy.
 
@@ -341,18 +354,6 @@ def get_gap(self, tol: float = 0.001, abs_tol: bool = False, spin: Spin | None =
         cbm, vbm = self.get_cbm_vbm(tol, abs_tol, spin)
         return max(cbm - vbm, 0.0)
 
-    def __str__(self) -> str:
-        """Get a string which can be easily plotted (using gnuplot)."""
-        if Spin.down in self.densities:
-            str_arr = [f"#{'Energy':30s} {'DensityUp':30s} {'DensityDown':30s}"]
-            for i, energy in enumerate(self.energies):
-                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f} {self.densities[Spin.down][i]:.5f}")
-        else:
-            str_arr = [f"#{'Energy':30s} {'DensityUp':30s}"]
-            for i, energy in enumerate(self.energies):
-                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f}")
-        return "\n".join(str_arr)
-
     @classmethod
     def from_dict(cls, dct: dict) -> Self:
         """Get Dos object from dict representation of Dos."""
@@ -626,6 +627,9 @@ def __init__(
         self.pdos = pdoss
         self.structure = structure
 
+    def __str__(self) -> str:
+        return f"Complete DOS for {self.structure}"
+
     def get_normalized(self) -> CompleteDos:
         """Get a normalized version of the CompleteDos."""
         if self.norm_vol is not None:
@@ -775,7 +779,7 @@ def spin_polarization(self) -> float | None:
         n_F_down = n_F[Spin.down]
 
         if (n_F_up + n_F_down) == 0:
-            # only well defined for metals or half-metals
+            # Only well defined for metals or half-metals
             return float("NaN")
 
         spin_polarization = (n_F_up - n_F_down) / (n_F_up + n_F_down)
@@ -1169,7 +1173,7 @@ class fingerprint(NamedTuple):
 
             dos_rebin = np.zeros(ener.shape)
 
-            for ii, e1, e2 in zip(range(len(ener)), ener_bounds[0:-1], ener_bounds[1:]):
+            for ii, e1, e2 in zip(range(len(ener)), ener_bounds[:-1], ener_bounds[1:]):
                 inds = np.where((energies >= e1) & (energies < e2))
                 dos_rebin[ii] = np.sum(densities[inds])
             if normalize:  # scale DOS bins to make area under histogram equal 1
@@ -1291,9 +1295,6 @@ def as_dict(self) -> dict:
             dct["spd_dos"] = {str(orb): dos.as_dict() for orb, dos in self.get_spd_dos().items()}
         return dct
 
-    def __str__(self) -> str:
-        return f"Complete DOS for {self.structure}"
-
 
 class LobsterCompleteDos(CompleteDos):
     """Extended CompleteDOS for Lobster."""
@@ -1312,7 +1313,7 @@ def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos:  # type
         Returns:
             Dos containing densities of an orbital of a specific site.
         """
-        if orbital[1:] not in [
+        if orbital[1:] not in {
             "s",
             "p_y",
             "p_z",
@@ -1329,7 +1330,7 @@ def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos:  # type
             "f_xz^2",
             "f_z(x^2-y^2)",
             "f_x(x^2-3y^2)",
-        ]:
+        }:
             raise ValueError("orbital is not correct")
         return Dos(self.efermi, self.energies, self.pdos[site][orbital])  # type: ignore
 
@@ -1457,8 +1458,8 @@ def _get_orb_type_lobster(orb) -> OrbitalType | None:
     Returns:
         OrbitalType
     """
-    orb_labs = ["s", "p_y", "p_z", "p_x", "d_xy", "d_yz", "d_z^2", "d_xz", "d_x^2-y^2"]
-    orb_labs += ["f_y(3x^2-y^2)", "f_xyz", "f_yz^2", "f_z^3", "f_xz^2", "f_z(x^2-y^2)", "f_x(x^2-3y^2)"]
+    orb_labs = ("s", "p_y", "p_z", "p_x", "d_xy", "d_yz", "d_z^2", "d_xz", "d_x^2-y^2")
+    orb_labs += ("f_y(3x^2-y^2)", "f_xyz", "f_yz^2", "f_z^3", "f_xz^2", "f_z(x^2-y^2)", "f_x(x^2-3y^2)")
 
     try:
         orbital = Orbital(orb_labs.index(orb[1:]))
@@ -1476,7 +1477,7 @@ def _get_orb_lobster(orb):
     Returns:
         Orbital.
     """
-    orb_labs = [
+    orb_labs = (
         "s",
         "p_y",
         "p_z",
@@ -1493,10 +1494,10 @@ def _get_orb_lobster(orb):
         "f_xz^2",
         "f_z(x^2-y^2)",
         "f_x(x^2-3y^2)",
-    ]
+    )
 
     try:
         return Orbital(orb_labs.index(orb[1:]))
     except AttributeError:
         print("Orb not in list")
-    return None
+        return None

From 79e8868a7c21a5877e8193222b6b108779896735 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Mon, 10 Jun 2024 11:46:33 +0800
Subject: [PATCH 03/39] add some types

---
 .../electronic_structure/bandstructure.py     |   2 +-
 pymatgen/electronic_structure/cohp.py         | 198 ++++++++++++------
 pymatgen/electronic_structure/core.py         | 180 ++++++++--------
 3 files changed, 227 insertions(+), 153 deletions(-)

diff --git a/pymatgen/electronic_structure/bandstructure.py b/pymatgen/electronic_structure/bandstructure.py
index 3ce071eb13d..ee12fa1148e 100644
--- a/pymatgen/electronic_structure/bandstructure.py
+++ b/pymatgen/electronic_structure/bandstructure.py
@@ -799,7 +799,7 @@ def get_equivalent_kpoints(self, index: int) -> list[int]:
         (in case there was a mislabel)
         """
         # If the kpoint has no label it can't have a repetition
-        # along the band structure line object
+        # along the BandStructureSymmLine object
 
         if self.kpoints[index].label is None:
             return [index]
diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index bd1fa4b794f..e9eaa928bf7 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -1,6 +1,7 @@
 """This module defines classes to represent crystal orbital Hamilton
-populations (COHP) and integrated COHP (ICOHP), but can also be used
+populations (COHP) and integrated COHP (ICOHP), and can also be used
 for crystal orbital overlap populations (COOP) or crystal orbital bond indices (COBIs).
+
 If you use this module, please cite:
 J. George, G. Petretto, A. Naik, M. Esters, A. J. Jackson, R. Nelson, R. Dronskowski, G.-M. Rignanese, G. Hautier,
 "Automated Bonding Analysis with Crystal Orbital Hamilton Populations",
@@ -29,8 +30,10 @@
 from pymatgen.util.num import round_to_sigfigs
 
 if TYPE_CHECKING:
-    from typing import Any
+    from collections.abc import Sequence
+    from typing import Any, Literal
 
+    from numpy.typing import NDArray
     from typing_extensions import Self
 
 __author__ = "Marco Esters, Janine George"
@@ -50,16 +53,23 @@ class Cohp(MSONable):
     """Basic COHP object."""
 
     def __init__(
-        self, efermi, energies, cohp, are_coops=False, are_cobis=False, are_multi_center_cobis=False, icohp=None
+        self,
+        efermi: float,
+        energies: Sequence[float],
+        cohp: dict[Spin, NDArray],
+        are_coops: bool = False,
+        are_cobis: bool = False,
+        are_multi_center_cobis: bool = False,
+        icohp: dict[Spin, NDArray] | None = None,
     ) -> None:
         """
         Args:
-            are_coops: Indicates whether this object describes COOPs.
-            are_cobis: Indicates whether this object describes COBIs.
-            are_multi_center_cobis: Indicates whether this object describes multi-center COBIs
             efermi: Fermi energy.
             energies: A sequence of energies.
             cohp ({Spin: np.array}): representing the COHP for each spin.
+            are_coops: Indicates whether this object describes COOPs.
+            are_cobis: Indicates whether this object describes COBIs.
+            are_multi_center_cobis: Indicates whether this object describes multi-center COBIs
             icohp ({Spin: np.array}): representing the ICOHP for each spin.
         """
         self.are_coops = are_coops
@@ -97,7 +107,7 @@ def __repr__(self) -> str:
             str_arr.append(format_data.format(*(d[idx] for d in data)))
         return "\n".join(str_arr)
 
-    def as_dict(self):
+    def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of COHP."""
         dct = {
             "@module": type(self).__module__,
@@ -113,11 +123,15 @@ def as_dict(self):
             dct["ICOHP"] = {str(spin): pops.tolist() for spin, pops in self.icohp.items()}
         return dct
 
-    def get_cohp(self, spin=None, integrated=False):
+    def get_cohp(
+        self,
+        spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
+        integrated: bool = False,
+    ) -> dict[Spin, NDArray]:
         """Get the COHP or ICOHP for a particular spin.
 
         Args:
-            spin: Spin. Can be parsed as spin object, integer (-1/1)
+            spin: Can be Spin object, integer (-1/1)
                 or str ("up"/"down")
             integrated: Return COHP (False) or ICOHP (True)
 
@@ -126,7 +140,7 @@ def get_cohp(self, spin=None, integrated=False):
             None and both spins are present, both spins will be returned
             as a dictionary.
         """
-        populations = self.cohp if not integrated else self.icohp
+        populations = self.icohp if integrated else self.cohp
 
         if populations is None:
             return None
@@ -138,11 +152,18 @@ def get_cohp(self, spin=None, integrated=False):
             spin = Spin({"up": 1, "down": -1}[spin.lower()])
         return {spin: populations[spin]}
 
-    def get_icohp(self, spin=None):
-        """Convenient alternative to get the ICOHP for a particular spin."""
+    def get_icohp(
+        self,
+        spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
+    ) -> dict[Spin, NDArray]:
+        """Convenient wrapper to get the ICOHP for a particular spin."""
         return self.get_cohp(spin=spin, integrated=True)
 
-    def get_interpolated_value(self, energy, integrated=False):
+    def get_interpolated_value(
+        self,
+        energy: float,
+        integrated: bool = False,
+    ) -> dict[Spin, float]:
         """Get the COHP for a particular energy.
 
         Args:
@@ -159,7 +180,11 @@ def get_interpolated_value(self, energy, integrated=False):
                 raise ValueError("ICOHP is empty.")
         return inter
 
-    def has_antibnd_states_below_efermi(self, spin=None, limit=0.01):
+    def has_antibnd_states_below_efermi(
+        self,
+        spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
+        limit: float = 0.01,
+    ) -> dict[Spin, bool] | None:
         """Get dict indicating if there are antibonding states below the Fermi level depending on the spin
         spin: Spin
         limit: -COHP smaller -limit will be considered.
@@ -169,23 +194,18 @@ def has_antibnd_states_below_efermi(self, spin=None, limit=0.01):
 
         if populations is None:
             return None
+
+        dict_to_return = {}
         if spin is None:
-            dict_to_return = {}
             for sp, cohp_vals in populations.items():
-                if (max(cohp_vals[0:n_energies_below_efermi])) > limit:
-                    dict_to_return[sp] = True
-                else:
-                    dict_to_return[sp] = False
+                dict_to_return[sp] = (max(cohp_vals[:n_energies_below_efermi])) > limit
+
         else:
-            dict_to_return = {}
             if isinstance(spin, int):
                 spin = Spin(spin)
             elif isinstance(spin, str):
                 spin = Spin({"up": 1, "down": -1}[spin.lower()])
-            if (max(populations[spin][0:n_energies_below_efermi])) > limit:
-                dict_to_return[spin] = True
-            else:
-                dict_to_return[spin] = False
+            dict_to_return[spin] = (max(populations[spin][:n_energies_below_efermi])) > limit
 
         return dict_to_return
 
@@ -223,19 +243,19 @@ class CompleteCohp(Cohp):
 
     def __init__(
         self,
-        structure,
-        avg_cohp,
-        cohp_dict,
-        bonds=None,
-        are_coops=False,
-        are_cobis=False,
-        are_multi_center_cobis=False,
-        orb_res_cohp=None,
+        structure: Structure,
+        avg_cohp: Cohp,
+        cohp_dict: dict[str, Cohp],
+        bonds: dict | None = None,
+        are_coops: bool = False,
+        are_cobis: bool = False,
+        are_multi_center_cobis: bool = False,
+        orb_res_cohp=None,  # TODO: add type
     ) -> None:
         """
         Args:
             structure: Structure associated with this COHP.
-            avg_cohp: The average cohp as a COHP object.
+            avg_cohp: The average COHP as a Cohp object.
             cohp_dict: A dict of COHP objects for individual bonds of the form
                 {label: COHP}
             bonds: A dict containing information on the bonds of the form
@@ -257,6 +277,7 @@ def __init__(
             or (are_cobis and are_multi_center_cobis)
         ):
             raise ValueError("You cannot have info about COOPs, COBIs and/or multi-center COBIS in the same file.")
+
         super().__init__(
             avg_cohp.efermi,
             avg_cohp.energies,
@@ -281,7 +302,7 @@ def __str__(self) -> str:
             return f"Complete COBIs for {self.structure}"
         return f"Complete COHPs for {self.structure}"
 
-    def as_dict(self):
+    def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of CompleteCohp."""
         dct = {
             "@module": type(self).__module__,
@@ -332,11 +353,15 @@ def as_dict(self):
 
         return dct
 
-    def get_cohp_by_label(self, label, summed_spin_channels=False):
+    def get_cohp_by_label(
+        self,
+        label: str,  # TODO: can this be a float/int (according to the following docstring)
+        summed_spin_channels: bool = False,
+    ) -> Cohp:
         """Get specific COHP object.
 
         Args:
-            label: string (for newer Lobster versions: a number)
+            label: string (for newer LOBSTER versions: a number)
             summed_spin_channels: bool, will sum the spin channels and return the sum in Spin.up if true
 
         Returns:
@@ -368,7 +393,12 @@ def get_cohp_by_label(self, label, summed_spin_channels=False):
             icohp=final_icohp,
         )
 
-    def get_summed_cohp_by_label_list(self, label_list, divisor=1, summed_spin_channels=False):
+    def get_summed_cohp_by_label_list(
+        self,
+        label_list,
+        divisor=1,
+        summed_spin_channels=False,
+    ):
         """Get a COHP object that includes a summed COHP divided by divisor.
 
         Args:
@@ -422,7 +452,11 @@ def get_summed_cohp_by_label_list(self, label_list, divisor=1, summed_spin_chann
         )
 
     def get_summed_cohp_by_label_and_orbital_list(
-        self, label_list, orbital_list, divisor=1, summed_spin_channels=False
+        self,
+        label_list,
+        orbital_list,
+        divisor=1,
+        summed_spin_channels=False,
     ):
         """Get a COHP object that includes a summed COHP divided by divisor.
 
@@ -479,7 +513,12 @@ def get_summed_cohp_by_label_and_orbital_list(
             icohp=final_icohp,
         )
 
-    def get_orbital_resolved_cohp(self, label, orbitals, summed_spin_channels=False):
+    def get_orbital_resolved_cohp(
+        self,
+        label,
+        orbitals,
+        summed_spin_channels=False,
+    ):
         """Get orbital-resolved COHP.
 
         Args:
@@ -548,8 +587,10 @@ def get_orbital_resolved_cohp(self, label, orbitals, summed_spin_channels=False)
 
     @classmethod
     def from_dict(cls, dct: dict) -> Self:
-        """Get CompleteCohp object from dict representation."""
-        # TODO: clean that mess up?
+        """Get CompleteCohp object from dict representation.
+
+        TODO: clean that up?
+        """
         cohp_dict = {}
         efermi = dct["efermi"]
         energies = dct["energies"]
@@ -666,7 +707,7 @@ def from_file(
         cls, fmt, filename=None, structure_file=None, are_coops=False, are_cobis=False, are_multi_center_cobis=False
     ) -> Self:
         """
-        Creates a CompleteCohp object from an output file of a COHP
+        Create a CompleteCohp object from an output file of a COHP
         calculation. Valid formats are either LMTO (for the Stuttgart
         LMTO-ASA code) or LOBSTER (for the LOBSTER code).
 
@@ -733,7 +774,7 @@ def from_file(
         cohp_data = cohp_file.cohp_data
         energies = cohp_file.energies
 
-        # Lobster shifts the energies so that the Fermi energy is at zero.
+        # LOBSTER shifts the energies so that the Fermi energy is at zero.
         # Shifting should be done by the plotter object though.
 
         spins = [Spin.up, Spin.down] if cohp_file.is_spin_polarized else [Spin.up]
@@ -866,11 +907,21 @@ class IcohpValue(MSONable):
         are_cobis (bool): Whether the object is a COBIS/ICOBIS or not.
         icohp (dict): A dictionary of the ICOHP/COHP values. The keys are Spin.up and Spin.down.
         summed_icohp (float): The summed ICOHP/COHP values.
-        num_bonds (int): The number of bonds used for the average COHP (relevant for Lobster versions <3.0).
+        num_bonds (int): The number of bonds used for the average COHP (relevant for LOBSTER versions <3.0).
     """
 
     def __init__(
-        self, label, atom1, atom2, length, translation, num, icohp, are_coops=False, are_cobis=False, orbitals=None
+        self,
+        label,
+        atom1,
+        atom2,
+        length,
+        translation,
+        num,
+        icohp,
+        are_coops=False,
+        are_cobis=False,
+        orbitals=None,
     ) -> None:
         """
         Args:
@@ -888,6 +939,7 @@ def __init__(
         """
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
+
         self._are_coops = are_coops
         self._are_cobis = are_cobis
         self._label = label
@@ -898,10 +950,7 @@ def __init__(
         self._num = num
         self._icohp = icohp
         self._orbitals = orbitals
-        if Spin.down in self._icohp:
-            self._is_spin_polarized = True
-        else:
-            self._is_spin_polarized = False
+        self._is_spin_polarized = Spin.down in self._icohp
 
     def __str__(self) -> str:
         """String representation of the ICOHP/ICOOP."""
@@ -915,6 +964,7 @@ def __str__(self) -> str:
                 f"ICOHP {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
                 f"{self._icohp[Spin.up]} eV (Spin up)"
             )
+
         if self._are_coops and not self._are_cobis:
             if self._is_spin_polarized:
                 return (
@@ -925,6 +975,7 @@ def __str__(self) -> str:
                 f"ICOOP {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
                 f"{self._icohp[Spin.up]} eV (Spin up)"
             )
+
         if self._are_cobis and not self._are_coops:
             if self._is_spin_polarized:
                 return (
@@ -940,7 +991,7 @@ def __str__(self) -> str:
 
     @property
     def num_bonds(self):
-        """Tells the number of bonds for which the ICOHP value is an average.
+        """The number of bonds for which the ICOHP value is an average.
 
         Returns:
             Int.
@@ -949,7 +1000,7 @@ def num_bonds(self):
 
     @property
     def are_coops(self) -> bool:
-        """Tells if ICOOPs or not.
+        """Check if ICOOPs or not.
 
         Returns:
             Boolean.
@@ -958,7 +1009,7 @@ def are_coops(self) -> bool:
 
     @property
     def are_cobis(self) -> bool:
-        """Tells if ICOBIs or not.
+        """Check if ICOBIs or not.
 
         Returns:
             Boolean.
@@ -967,7 +1018,7 @@ def are_cobis(self) -> bool:
 
     @property
     def is_spin_polarized(self) -> bool:
-        """Tells if spin polarized calculation or not.
+        """Check if is spin polarized calculation.
 
         Returns:
             Boolean.
@@ -1013,7 +1064,7 @@ def icohp(self):
 
     @property
     def summed_icohp(self):
-        """Sums ICOHPs of both spin channels for spin polarized compounds.
+        """Sum ICOHPs of both spin channels for spin polarized compounds.
 
         Returns:
             float: icohp value in eV.
@@ -1022,7 +1073,7 @@ def summed_icohp(self):
 
     @property
     def summed_orbital_icohp(self):
-        """Sums orbital-resolved ICOHPs of both spin channels for spin-polarized compounds.
+        """Sum orbital-resolved ICOHPs of both spin channels for spin-polarized compounds.
 
         Returns:
             dict[str, float]: "str(Orbital1)-str(Ortibal2)" mapped to ICOHP value in eV.
@@ -1076,6 +1127,7 @@ def __init__(
         """
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
+
         self._are_coops = are_coops
         self._are_cobis = are_cobis
         self._icohplist = {}
@@ -1104,13 +1156,16 @@ def __init__(
             )
 
     def __str__(self) -> str:
-        lst = []
-        for value in self._icohplist.values():
-            lst.append(str(value))
-        return "\n".join(lst)
+        return "\n".join([str(value) for value in self._icohplist.values()])
 
-    def get_icohp_by_label(self, label, summed_spin_channels=True, spin=Spin.up, orbitals=None) -> float:
-        """Get an icohp value for a certain bond as indicated by the label (bond labels starting by "1" as in
+    def get_icohp_by_label(
+        self,
+        label,
+        summed_spin_channels=True,
+        spin=Spin.up,
+        orbitals=None,
+    ) -> float:
+        """Get an ICOHP value for a certain bond as indicated by the label (bond labels starting by "1" as in
         ICOHPLIST/ICOOPLIST).
 
         Args:
@@ -1135,7 +1190,13 @@ def get_icohp_by_label(self, label, summed_spin_channels=True, spin=Spin.up, orb
 
         return icohp_here.icohpvalue_orbital(spin=spin, orbitals=orbitals)
 
-    def get_summed_icohp_by_label_list(self, label_list, divisor=1.0, summed_spin_channels=True, spin=Spin.up) -> float:
+    def get_summed_icohp_by_label_list(
+        self,
+        label_list,
+        divisor=1.0,
+        summed_spin_channels=True,
+        spin=Spin.up,
+    ) -> float:
         """Get the sum of several ICOHP values that are indicated by a list of labels
         (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST).
 
@@ -1162,7 +1223,11 @@ def get_summed_icohp_by_label_list(self, label_list, divisor=1.0, summed_spin_ch
                 sum_icohp = sum_icohp + icohp_here.icohpvalue(spin)
         return sum_icohp / divisor
 
-    def get_icohp_dict_by_bondlengths(self, minbondlength=0.0, maxbondlength=8.0):
+    def get_icohp_dict_by_bondlengths(
+        self,
+        minbondlength=0.0,
+        maxbondlength=8.0,
+    ):
         """Get a dict of IcohpValues corresponding to certain bond lengths.
 
         Args:
@@ -1279,7 +1344,12 @@ def are_cobis(self) -> bool:
 
 
 def get_integrated_cohp_in_energy_range(
-    cohp, label, orbital=None, energy_range=None, relative_E_Fermi=True, summed_spin_channels=True
+    cohp,
+    label,
+    orbital=None,
+    energy_range=None,
+    relative_E_Fermi=True,
+    summed_spin_channels=True,
 ):
     """Integrate CompleteCohp objects which include data on integrated COHPs
     Args:
diff --git a/pymatgen/electronic_structure/core.py b/pymatgen/electronic_structure/core.py
index c10ee208137..bd887f64a25 100644
--- a/pymatgen/electronic_structure/core.py
+++ b/pymatgen/electronic_structure/core.py
@@ -13,6 +13,7 @@
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
+    from numpy.typing import NDArray
     from typing_extensions import Self
 
     from pymatgen.core import Lattice
@@ -77,7 +78,7 @@ def __str__(self) -> str:
         return str(self.name)
 
     @property
-    def orbital_type(self):
+    def orbital_type(self) -> OrbitalType:
         """OrbitalType of an orbital."""
         return OrbitalType[self.name[0]]
 
@@ -127,19 +128,18 @@ class Magmom(MSONable):
     """
 
     def __init__(
-        self, moment: float | Sequence[float] | np.ndarray | Magmom, saxis: Sequence[float] = (0, 0, 1)
+        self,
+        moment: float | Sequence[float] | NDArray | Magmom,
+        saxis: Sequence[float] = (0, 0, 1),
     ) -> None:
         """
         Args:
             moment: magnetic moment, supplied as float or list/np.ndarray
             saxis: spin axis, supplied as list/np.ndarray, parameter will
                 be converted to unit vector (default is [0, 0, 1]).
-
-        Returns:
-            Magmom object
         """
-        # to init from another Magmom instance
-        if isinstance(moment, Magmom):
+        # Init from another Magmom instance
+        if isinstance(moment, type(self)):
             saxis = moment.saxis  # type: ignore[has-type]
             moment = moment.moment  # type: ignore[has-type]
 
@@ -153,6 +153,63 @@ def __init__(
 
         self.saxis = saxis / np.linalg.norm(saxis)
 
+    def __getitem__(self, key):
+        return self.moment[key]
+
+    def __iter__(self):
+        return iter(self.moment)
+
+    def __abs__(self) -> float:
+        return np.linalg.norm(self.moment)
+
+    def __eq__(self, other: object) -> bool:
+        """Equal if 'global' magnetic moments are the same, saxis can differ."""
+        try:
+            other_magmom = type(self)(other)
+        except (TypeError, ValueError):
+            return NotImplemented
+
+        return np.allclose(self.global_moment, other_magmom.global_moment)
+
+    def __lt__(self, other: Self) -> bool:
+        return abs(self) < abs(other)
+
+    def __neg__(self) -> Self:
+        return type(self)(-self.moment, saxis=self.saxis)
+
+    def __hash__(self) -> int:
+        return hash(tuple(self.moment) + tuple(self.saxis))
+
+    def __float__(self) -> float:
+        """Get magnitude of magnetic moment with a sign with respect to
+        an arbitrary direction.
+
+        Should give unsurprising output if Magmom is treated like a
+        scalar or if a set of Magmoms describes a collinear structure.
+
+        Implemented this way rather than simpler abs(self) so that
+        moments will have a consistent sign in case of e.g.
+        antiferromagnetic collinear structures without additional
+        user intervention.
+
+        However, should be used with caution for non-collinear
+        structures and might give nonsensical results except in the case
+        of only slightly non-collinear structures (e.g. small canting).
+
+        This approach is also used to obtain "diff" VolumetricDensity
+        in pymatgen.io.vasp.outputs.VolumetricDensity when processing
+        Chgcars from SOC calculations.
+        """
+        return float(self.get_00t_magmom_with_xyz_saxis()[2])
+
+    def __str__(self) -> str:
+        return str(float(self))
+
+    def __repr__(self) -> str:
+        if np.allclose(self.saxis, (0, 0, 1)):
+            return f"Magnetic moment {self.moment}"
+        return f"Magnetic moment {self.moment} (spin axis = {self.saxis})"
+
     @classmethod
     def from_global_moment_and_saxis(cls, global_moment, saxis) -> Self:
         """Convenience method to initialize Magmom from a given global
@@ -166,7 +223,7 @@ def from_global_moment_and_saxis(cls, global_moment, saxis) -> Self:
             global_moment: global magnetic moment
             saxis: desired saxis
         """
-        magmom = Magmom(global_moment)
+        magmom = cls(global_moment)
         return cls(magmom.get_moment(saxis=saxis), saxis=saxis)
 
     @classmethod
@@ -217,26 +274,26 @@ def get_moment(self, saxis=(0, 0, 1)):
         Returns:
             np.ndarray of length 3
         """
-        # transform back to moment with spin axis [0, 0, 1]
+        # Transform back to moment with spin axis [0, 0, 1]
         trafo_mat_inv = self._get_transformation_matrix_inv(self.saxis)
         moment = np.matmul(self.moment, trafo_mat_inv)
 
-        # transform to new saxis
+        # Transform to new saxis
         trafo_mat = self._get_transformation_matrix(saxis)
         moment = np.matmul(moment, trafo_mat)
 
-        # round small values to zero
+        # Round small values to zero
         moment[np.abs(moment) < 1e-8] = 0
 
         return moment
 
     @property
-    def global_moment(self) -> np.ndarray:
+    def global_moment(self) -> NDArray:
         """The magnetic moment defined in an arbitrary global reference frame as an np.array of length 3."""
         return self.get_moment()
 
     @property
-    def projection(self):
+    def projection(self) -> float:
         """Projects moment along spin quantization axis. Useful for obtaining
         collinear approximation for slightly non-collinear magmoms.
 
@@ -245,16 +302,16 @@ def projection(self):
         """
         return np.dot(self.moment, self.saxis)
 
-    def get_xyz_magmom_with_001_saxis(self):
+    def get_xyz_magmom_with_001_saxis(self) -> Self:
         """Get a Magmom in the default setting of saxis = [0, 0, 1] and
         the magnetic moment rotated as required.
 
         Returns:
             Magmom
         """
-        return Magmom(self.get_moment())
+        return type(self)(self.get_moment())
 
-    def get_00t_magmom_with_xyz_saxis(self):
+    def get_00t_magmom_with_xyz_saxis(self) -> Self:
         """For internal implementation reasons, in non-collinear calculations VASP prefers the following.
 
             MAGMOM = 0 0 total_magnetic_moment
@@ -276,7 +333,7 @@ def get_00t_magmom_with_xyz_saxis(self):
         Returns:
             Magmom
         """
-        # reference direction gives sign of moment
+        # Reference direction gives sign of moment
         # entirely arbitrary, there will always be a pathological case
         # where a consistent sign is not possible if the magnetic moments
         # are aligned along the reference direction, but in practice this
@@ -288,8 +345,8 @@ def get_00t_magmom_with_xyz_saxis(self):
             if np.dot(ref_direction, new_saxis) < 0:
                 t = -t
                 new_saxis = -new_saxis
-            return Magmom([0, 0, t], saxis=new_saxis)
-        return Magmom(self)
+            return type(self)([0, 0, t], saxis=new_saxis)
+        return type(self)(self)
 
     @staticmethod
     def have_consistent_saxis(magmoms) -> bool:
@@ -339,14 +396,14 @@ def get_suggested_saxis(magmoms):
         Returns:
             np.ndarray of length 3
         """
-        # heuristic, will pick largest magmom as reference
+        # Heuristic, will pick largest magmom as reference
         # useful for creating collinear approximations of
         # e.g. slightly canted magnetic structures
         # for fully collinear structures, will return expected
         # result
 
         magmoms = [Magmom(magmom) for magmom in magmoms]
-        # filter only non-zero magmoms
+        # Filter only non-zero magmoms
         magmoms = [magmom for magmom in magmoms if abs(magmom)]
         magmoms.sort(reverse=True)
         if len(magmoms) > 0:
@@ -367,20 +424,24 @@ def are_collinear(magmoms) -> bool:
         if not Magmom.have_consistent_saxis(magmoms):
             magmoms = Magmom.get_consistent_set_and_saxis(magmoms)[0]
 
-        # convert to numpy array for convenience
+        # Convert to numpy array for convenience
         magmoms = np.array([list(magmom) for magmom in magmoms])
         magmoms = magmoms[np.any(magmoms, axis=1)]  # remove zero magmoms
         if len(magmoms) == 0:
             return True
 
-        # use first moment as reference to compare against
+        # Use first moment as reference to compare against
         ref_magmom = magmoms[0]
-        # magnitude of cross products != 0 if non-collinear with reference
+        # Magnitude of cross products != 0 if non-collinear with reference
         num_ncl = np.count_nonzero(np.linalg.norm(np.cross(ref_magmom, magmoms), axis=1))
         return num_ncl == 0
 
     @classmethod
-    def from_moment_relative_to_crystal_axes(cls, moment: list[float], lattice: Lattice) -> Self:
+    def from_moment_relative_to_crystal_axes(
+        cls,
+        moment: list[float],
+        lattice: Lattice,
+    ) -> Self:
         """Obtaining a Magmom object from a magnetic moment provided
         relative to crystal axes.
 
@@ -393,14 +454,14 @@ def from_moment_relative_to_crystal_axes(cls, moment: list[float], lattice: Latt
         Returns:
             Magmom
         """
-        # get matrix representing unit lattice vectors
+        # Get matrix representing unit lattice vectors
         unit_m = lattice.matrix / np.linalg.norm(lattice.matrix, axis=1)[:, None]
         moment = np.matmul(list(moment), unit_m)
-        # round small values to zero
+        # Round small values to zero
         moment[np.abs(moment) < 1e-8] = 0
         return cls(moment)
 
-    def get_moment_relative_to_crystal_axes(self, lattice):
+    def get_moment_relative_to_crystal_axes(self, lattice: Lattice):
         """If scalar magmoms, moments will be given arbitrarily along z.
         Used for writing moments to magCIF file.
 
@@ -410,67 +471,10 @@ def get_moment_relative_to_crystal_axes(self, lattice):
         Returns:
             vector as list of floats
         """
-        # get matrix representing unit lattice vectors
+        # Get matrix representing unit lattice vectors
         unit_m = lattice.matrix / np.linalg.norm(lattice.matrix, axis=1)[:, None]
-        # note np.matmul() requires numpy version >= 1.10
+        # Note np.matmul() requires numpy version >= 1.10
         moment = np.matmul(self.global_moment, np.linalg.inv(unit_m))
-        # round small values to zero
+        # Round small values to zero
         moment[np.abs(moment) < 1e-8] = 0
         return moment
-
-    def __getitem__(self, key):
-        return self.moment[key]
-
-    def __iter__(self):
-        return iter(self.moment)
-
-    def __abs__(self):
-        return np.linalg.norm(self.moment)
-
-    def __eq__(self, other: object) -> bool:
-        """Equal if 'global' magnetic moments are the same, saxis can differ."""
-        try:
-            other_magmom = Magmom(other)
-        except (TypeError, ValueError):
-            return NotImplemented
-
-        return np.allclose(self.global_moment, other_magmom.global_moment)
-
-    def __lt__(self, other):
-        return abs(self) < abs(other)
-
-    def __neg__(self):
-        return Magmom(-self.moment, saxis=self.saxis)
-
-    def __hash__(self) -> int:
-        return hash(tuple(self.moment) + tuple(self.saxis))
-
-    def __float__(self) -> float:
-        """Get magnitude of magnetic moment with a sign with respect to
-        an arbitrary direction.
-
-        Should give unsurprising output if Magmom is treated like a
-        scalar or if a set of Magmoms describes a collinear structure.
-
-        Implemented this way rather than simpler abs(self) so that
-        moments will have a consistent sign in case of e.g.
-        antiferromagnetic collinear structures without additional
-        user intervention.
-
-        However, should be used with caution for non-collinear
-        structures and might give nonsensical results except in the case
-        of only slightly non-collinear structures (e.g. small canting).
-
-        This approach is also used to obtain "diff" VolumetricDensity
-        in pymatgen.io.vasp.outputs.VolumetricDensity when processing
-        Chgcars from SOC calculations.
-        """
-        return float(self.get_00t_magmom_with_xyz_saxis()[2])
-
-    def __str__(self) -> str:
-        return str(float(self))
-
-    def __repr__(self) -> str:
-        if np.allclose(self.saxis, (0, 0, 1)):
-            return f"Magnetic moment {self.moment}"
-        return f"Magnetic moment {self.moment} (spin axis = {self.saxis})"

From 8a4c4b5fa914b9f40684412885cb898d75352bc8 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Mon, 10 Jun 2024 12:20:47 +0800
Subject: [PATCH 04/39] fix type errors in bandstructure

---
 .../electronic_structure/bandstructure.py     | 19 ++++++++++---------
 pymatgen/electronic_structure/plotter.py      | 13 +++++++++----
 2 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/pymatgen/electronic_structure/bandstructure.py b/pymatgen/electronic_structure/bandstructure.py
index ee12fa1148e..602795a866f 100644
--- a/pymatgen/electronic_structure/bandstructure.py
+++ b/pymatgen/electronic_structure/bandstructure.py
@@ -245,7 +245,8 @@ def get_projection_on_elements(self) -> dict[Spin, NDArray]:
             if there is no projections in the band structure
             returns an empty dict
         """
-        result = {}
+        assert self.structure is not None
+        result: dict[Spin, NDArray] = {}
         for spin, val in self.projections.items():
             result[spin] = [[defaultdict(float) for _ in range(len(self.kpoints))] for _ in range(self.nb_bands)]
             for i, j, k in itertools.product(
@@ -343,7 +344,7 @@ def get_vbm(self) -> dict[str, Any]:
                     kpoint_vbm = self.kpoints[j]
 
         list_ind_kpts = []
-        if kpoint_vbm.label is not None:
+        if kpoint_vbm is not None and kpoint_vbm.label is not None:
             for idx, kpt in enumerate(self.kpoints):
                 if kpt.label == kpoint_vbm.label:
                     list_ind_kpts.append(idx)
@@ -408,7 +409,7 @@ def get_cbm(self) -> dict[str, Any]:
                     kpoint_cbm = self.kpoints[j]
 
         list_index_kpoints = []
-        if kpoint_cbm.label is not None:
+        if kpoint_cbm is not None and kpoint_cbm.label is not None:
             for idx, kpt in enumerate(self.kpoints):
                 if kpt.label == kpoint_cbm.label:
                     list_index_kpoints.append(idx)
@@ -562,7 +563,7 @@ def get_kpoint_degeneracy(
 
     def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of BandStructure."""
-        dct = {
+        dct: dict[str, Any] = {
             "@module": type(self).__module__,
             "@class": type(self).__name__,
             "lattice_rec": self.lattice_rec.as_dict(),
@@ -599,7 +600,7 @@ def as_dict(self) -> dict[str, Any]:
             mongo_key = f" {c}" if c.startswith("$") else c
             dct["labels_dict"][mongo_key] = label.as_dict()["fcoords"]
         dct["projections"] = {}
-        if len(self.projections) != 0:
+        if len(self.projections) != 0 and self.structure is not None:
             dct["structure"] = self.structure.as_dict()
             dct["projections"] = {str(int(spin)): np.array(v).tolist() for spin, v in self.projections.items()}
         return dct
@@ -907,7 +908,7 @@ class LobsterBandStructureSymmLine(BandStructureSymmLine):
 
     def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of BandStructureSymmLine."""
-        dct = {
+        dct: dict[str, Any] = {
             "@module": type(self).__module__,
             "@class": type(self).__name__,
             "lattice_rec": self.lattice_rec.as_dict(),
@@ -943,7 +944,7 @@ def as_dict(self) -> dict[str, Any]:
         for c, label in self.labels_dict.items():
             mongo_key = c if not c.startswith("$") else " " + c
             dct["labels_dict"][mongo_key] = label.as_dict()["fcoords"]
-        if len(self.projections) != 0:
+        if len(self.projections) != 0 and self.structure is not None:
             dct["structure"] = self.structure.as_dict()
             dct["projections"] = {str(int(spin)): np.array(v).tolist() for spin, v in self.projections.items()}
         return dct
@@ -1033,7 +1034,7 @@ def get_projection_on_elements(self) -> dict[Spin, list]:
             if there is no projections in the band structure
             returns an empty dict
         """
-        result = {}
+        result: dict[Spin, list] = {}
         for spin, v in self.projections.items():
             result[spin] = [[defaultdict(float) for _ in range(len(self.kpoints))] for _ in range(self.nb_bands)]
             for i, j in itertools.product(range(self.nb_bands), range(len(self.kpoints))):
@@ -1045,7 +1046,7 @@ def get_projection_on_elements(self) -> dict[Spin, list]:
 
     def get_projections_on_elements_and_orbitals(
         self,
-        el_orb_spec: dict[Element, list],
+        el_orb_spec: dict[Element, list],  # type: ignore[override]
     ) -> dict[Spin, list]:
         """Return a dictionary of projections on elements and specific orbitals.
 
diff --git a/pymatgen/electronic_structure/plotter.py b/pymatgen/electronic_structure/plotter.py
index 29dae3e718d..3df16094164 100644
--- a/pymatgen/electronic_structure/plotter.py
+++ b/pymatgen/electronic_structure/plotter.py
@@ -51,22 +51,27 @@
 
 
 class DosPlotter:
-    """Plot DOSs. The interface is extremely flexible given there are many
+    """Plot DOS. The interface is extremely flexible given there are many
     different ways in which people want to view DOS.
     Typical usage is:
-        # Initializes plotter with some optional args. Defaults are usually fine
+        # Initialize plotter with some optional args. Defaults are usually fine
         plotter = PhononDosPlotter().
 
         # Add DOS with a label
         plotter.add_dos("Total DOS", dos)
 
-        # Alternatively, you can add a dict of DOSes. This is the typical form
+        # Alternatively, you can add a dict of DOS. This is the typical form
         # returned by CompletePhononDos.get_element_dos().
         plotter.add_dos_dict({"dos1": dos1, "dos2": dos2})
         plotter.add_dos_dict(complete_dos.get_spd_dos())
     """
 
-    def __init__(self, zero_at_efermi: bool = True, stack: bool = False, sigma: float | None = None) -> None:
+    def __init__(
+        self,
+        zero_at_efermi: bool = True,
+        stack: bool = False,
+        sigma: float | None = None,
+    ) -> None:
         """
         Args:
             zero_at_efermi (bool): Whether to shift all Dos to have zero energy at the

From 51ffc18769801966e375d451e1a3f7f3420a5436 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 11 Jun 2024 09:55:07 +0800
Subject: [PATCH 05/39] temp save

---
 .../electronic_structure/bandstructure.py     |  2 +-
 pymatgen/electronic_structure/cohp.py         | 29 ++++++++++++-------
 2 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/pymatgen/electronic_structure/bandstructure.py b/pymatgen/electronic_structure/bandstructure.py
index 602795a866f..2b466543270 100644
--- a/pymatgen/electronic_structure/bandstructure.py
+++ b/pymatgen/electronic_structure/bandstructure.py
@@ -1080,7 +1080,7 @@ def get_projections_on_elements_and_orbitals(
 
 
 @overload
-def get_reconstructed_band_structure(
+def get_reconstructed_band_structure(  # type: ignore[overload-overlap]
     list_bs: list[BandStructure],
     efermi: float | None = None,
 ) -> BandStructure:
diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index e9eaa928bf7..e1db10a4f00 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -127,7 +127,7 @@ def get_cohp(
         self,
         spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
         integrated: bool = False,
-    ) -> dict[Spin, NDArray]:
+    ) -> dict[Spin, NDArray] | None:
         """Get the COHP or ICOHP for a particular spin.
 
         Args:
@@ -155,7 +155,7 @@ def get_cohp(
     def get_icohp(
         self,
         spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
-    ) -> dict[Spin, NDArray]:
+    ) -> dict[Spin, NDArray] | None:
         """Convenient wrapper to get the ICOHP for a particular spin."""
         return self.get_cohp(spin=spin, integrated=True)
 
@@ -170,15 +170,15 @@ def get_interpolated_value(
             energy: Energy to return the COHP value for.
             integrated: Return COHP (False) or ICOHP (True)
         """
-        inter = {}
+        inters = {}
         for spin in self.cohp:
             if not integrated:
-                inter[spin] = get_linear_interpolated_value(self.energies, self.cohp[spin], energy)
+                inters[spin] = get_linear_interpolated_value(self.energies, self.cohp[spin], energy)
             elif self.icohp is not None:
-                inter[spin] = get_linear_interpolated_value(self.energies, self.icohp[spin], energy)
+                inters[spin] = get_linear_interpolated_value(self.energies, self.icohp[spin], energy)
             else:
                 raise ValueError("ICOHP is empty.")
-        return inter
+        return inters
 
     def has_antibnd_states_below_efermi(
         self,
@@ -339,7 +339,7 @@ def as_dict(self) -> dict[str, Any]:
                 for bond in self.bonds
             }
         if self.orb_res_cohp:
-            orb_dict = {}
+            orb_dict: dict[str, Any] = {}
             for label in self.orb_res_cohp:
                 orb_dict[label] = {}
                 for orbs in self.orb_res_cohp[label]:
@@ -368,14 +368,17 @@ def get_cohp_by_label(
             Returns the COHP object to simplify plotting
         """
         if label.lower() == "average":
-            divided_cohp = self.cohp
-            divided_icohp = self.icohp
+            divided_cohp: dict[Spin, Any] | None = self.cohp
+            divided_icohp: dict[Spin, Any] | None = self.icohp
 
         else:
             divided_cohp = self.all_cohps[label].get_cohp(spin=None, integrated=False)
             divided_icohp = self.all_cohps[label].get_icohp(spin=None)
 
+        assert divided_cohp is not None
+
         if summed_spin_channels and Spin.down in self.cohp:
+            assert divided_icohp is not None
             final_cohp = {}
             final_icohp = {}
             final_cohp[Spin.up] = np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)
@@ -704,7 +707,13 @@ def from_dict(cls, dct: dict) -> Self:
 
     @classmethod
     def from_file(
-        cls, fmt, filename=None, structure_file=None, are_coops=False, are_cobis=False, are_multi_center_cobis=False
+        cls,
+        fmt,
+        filename=None,
+        structure_file=None,
+        are_coops=False,
+        are_cobis=False,
+        are_multi_center_cobis=False,
     ) -> Self:
         """
         Create a CompleteCohp object from an output file of a COHP

From 0d0615cdaac7fc04ad2d3584df86551581312c1d Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 11:31:00 +0800
Subject: [PATCH 06/39] first run of cohp, mypy errors to fix

---
 pymatgen/electronic_structure/cohp.py | 462 +++++++++++++-------------
 pymatgen/io/lobster/outputs.py        |   3 +-
 2 files changed, 239 insertions(+), 226 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index e1db10a4f00..ab9b3c0fa2c 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -1,6 +1,7 @@
-"""This module defines classes to represent crystal orbital Hamilton
-populations (COHP) and integrated COHP (ICOHP), and can also be used
-for crystal orbital overlap populations (COOP) or crystal orbital bond indices (COBIs).
+"""This module defines classes to represent:
+    - Crystal orbital Hamilton population (COHP) and integrated COHP (ICOHP).
+    - Crystal orbital overlap population (COOP).
+    - Crystal orbital bond index (COBI).
 
 If you use this module, please cite:
 J. George, G. Petretto, A. Naik, M. Esters, A. J. Jackson, R. Nelson, R. Dronskowski, G.-M. Rignanese, G. Hautier,
@@ -36,6 +37,8 @@
     from numpy.typing import NDArray
     from typing_extensions import Self
 
+    from pymatgen.util.typing import PathLike
+
 __author__ = "Marco Esters, Janine George"
 __copyright__ = "Copyright 2017, The Materials Project"
 __version__ = "0.2"
@@ -132,11 +135,11 @@ def get_cohp(
 
         Args:
             spin: Can be Spin object, integer (-1/1)
-                or str ("up"/"down")
-            integrated: Return COHP (False) or ICOHP (True)
+                or str ("up"/"down").
+            integrated: Return ICOHP (True) or COHP (False).
 
         Returns:
-            Returns the CHOP or ICOHP for the input spin. If Spin is
+            The CHOP or ICOHP for the selected spin. If Spin is
             None and both spins are present, both spins will be returned
             as a dictionary.
         """
@@ -164,11 +167,11 @@ def get_interpolated_value(
         energy: float,
         integrated: bool = False,
     ) -> dict[Spin, float]:
-        """Get the COHP for a particular energy.
+        """Get the interpolated COHP for a particular energy.
 
         Args:
             energy: Energy to return the COHP value for.
-            integrated: Return COHP (False) or ICOHP (True)
+            integrated: Return ICOHP (True) or COHP (False).
         """
         inters = {}
         for spin in self.cohp:
@@ -185,9 +188,11 @@ def has_antibnd_states_below_efermi(
         spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
         limit: float = 0.01,
     ) -> dict[Spin, bool] | None:
-        """Get dict indicating if there are antibonding states below the Fermi level depending on the spin
-        spin: Spin
-        limit: -COHP smaller -limit will be considered.
+        """Get dict of antibonding states below the Fermi level for the spin.
+
+        Args:
+            spin: Spin.
+            limit: only COHP higher than this value will be considered.
         """
         populations = self.cohp
         n_energies_below_efermi = len([energy for energy in self.energies if energy <= self.efermi])
@@ -211,18 +216,17 @@ def has_antibnd_states_below_efermi(
 
     @classmethod
     def from_dict(cls, dct: dict[str, Any]) -> Self:
-        """Get a COHP object from a dict representation of the COHP."""
+        """Generate Cohp from a dict representation."""
         icohp = {Spin(int(key)): np.array(val) for key, val in dct["ICOHP"].items()} if "ICOHP" in dct else None
-        are_cobis = dct.get("are_cobis", False)
-        are_multi_center_cobis = dct.get("are_multi_center_cobis", False)
+
         return cls(
             dct["efermi"],
             dct["energies"],
             {Spin(int(key)): np.array(val) for key, val in dct["COHP"].items()},
             icohp=icohp,
             are_coops=dct["are_coops"],
-            are_cobis=are_cobis,
-            are_multi_center_cobis=are_multi_center_cobis,
+            are_cobis=dct.get("are_cobis", False),
+            are_multi_center_cobis=dct.get("are_multi_center_cobis", False),
         )
 
 
@@ -250,7 +254,7 @@ def __init__(
         are_coops: bool = False,
         are_cobis: bool = False,
         are_multi_center_cobis: bool = False,
-        orb_res_cohp=None,  # TODO: add type
+        orb_res_cohp: Cohp | None = None,
     ) -> None:
         """
         Args:
@@ -330,6 +334,7 @@ def as_dict(self) -> dict[str, Any]:
                     dct["ICOHP"].update(
                         {label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].icohp.items()}}
                     )
+
         if False in [bond_dict == {} for bond_dict in self.bonds.values()]:
             dct["bonds"] = {
                 bond: {
@@ -338,6 +343,7 @@ def as_dict(self) -> dict[str, Any]:
                 }
                 for bond in self.bonds
             }
+
         if self.orb_res_cohp:
             orb_dict: dict[str, Any] = {}
             for label in self.orb_res_cohp:
@@ -355,14 +361,14 @@ def as_dict(self) -> dict[str, Any]:
 
     def get_cohp_by_label(
         self,
-        label: str,  # TODO: can this be a float/int (according to the following docstring)
+        label: str | float,  # TODO (DanielYang): double-check type of label, perhaps add custom type
         summed_spin_channels: bool = False,
     ) -> Cohp:
-        """Get specific COHP object.
+        """Get specific Cohp object by label.
 
         Args:
-            label: string (for newer LOBSTER versions: a number)
-            summed_spin_channels: bool, will sum the spin channels and return the sum in Spin.up if true
+            label: string (for newer LOBSTER versions: a number)  # TODO: check arg label type
+            summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
             Returns the COHP object to simplify plotting
@@ -398,21 +404,21 @@ def get_cohp_by_label(
 
     def get_summed_cohp_by_label_list(
         self,
-        label_list,
-        divisor=1,
-        summed_spin_channels=False,
-    ):
+        label_list: list[str | float],
+        divisor: float = 1,
+        summed_spin_channels: bool = False,
+    ) -> Cohp:
         """Get a COHP object that includes a summed COHP divided by divisor.
 
         Args:
-            label_list: list of labels for the COHP that should be included in the summed cohp
-            divisor: float/int, the summed cohp will be divided by this divisor
-            summed_spin_channels: bool, will sum the spin channels and return the sum in Spin.up if true
+            label_list: list of labels for the COHP that should be included in the sum.
+            divisor (float): The summed COHP will be divided by this divisor.
+            summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
-            Returns a COHP object including a summed COHP
+            A Cohp object including a summed COHP.
         """
-        # check if cohps are spinpolarized or not
+        # Check if COHPs are spin polarized
         first_cohpobject = self.get_cohp_by_label(label_list[0])
         summed_cohp = first_cohpobject.cohp.copy()
         summed_icohp = first_cohpobject.icohp.copy()
@@ -456,32 +462,33 @@ def get_summed_cohp_by_label_list(
 
     def get_summed_cohp_by_label_and_orbital_list(
         self,
-        label_list,
-        orbital_list,
-        divisor=1,
-        summed_spin_channels=False,
-    ):
-        """Get a COHP object that includes a summed COHP divided by divisor.
+        label_list: list[str | float],
+        orbital_list: list,  # TODO (DanielYang): what is the type of orbital? Add custom type for it
+        divisor: float = 1,
+        summed_spin_channels: bool = False,
+    ) -> Cohp:
+        """Get a Cohp object that includes a summed COHP divided by divisor.
 
         Args:
-            label_list: list of labels for the COHP that should be included in the summed cohp
-            orbital_list: list of orbitals for the COHPs that should be included in the summed cohp (same order as
-                label_list)
-            divisor: float/int, the summed cohp will be divided by this divisor
-            summed_spin_channels: bool, will sum the spin channels and return the sum in Spin.up if true
+            label_list: list of labels for the COHP that should be included.
+            orbital_list: list of orbitals for the COHPs that should be included
+                (same order as label_list)
+            divisor (float): the summed COHP will be divided by this divisor.
+            summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
-            Returns a COHP object including a summed COHP
+            A Cohp object including a summed COHP
         """
-        # check length of label_list and orbital_list:
+        # Check length of label_list and orbital_list
         if not len(label_list) == len(orbital_list):
             raise ValueError("label_list and orbital_list don't have the same length!")
-        # check if cohps are spinpolarized or not
+
+        # Check if COHPs are spin polarized
         first_cohpobject = self.get_orbital_resolved_cohp(label_list[0], orbital_list[0])
         summed_cohp = first_cohpobject.cohp.copy()
         summed_icohp = first_cohpobject.icohp.copy()
-        for ilabel, label in enumerate(label_list[1:], start=1):
-            cohp_here = self.get_orbital_resolved_cohp(label, orbital_list[ilabel])
+        for idx, label in enumerate(label_list[1:], start=1):
+            cohp_here = self.get_orbital_resolved_cohp(label, orbital_list[idx])
             summed_cohp[Spin.up] = np.sum([summed_cohp[Spin.up], cohp_here.cohp.copy()[Spin.up]], axis=0)
             if Spin.down in summed_cohp:
                 summed_cohp[Spin.down] = np.sum([summed_cohp[Spin.down], cohp_here.cohp.copy()[Spin.down]], axis=0)
@@ -500,7 +507,6 @@ def get_summed_cohp_by_label_and_orbital_list(
         if summed_spin_channels and Spin.down in divided_cohp:
             final_cohp = {}
             final_icohp = {}
-
             final_cohp[Spin.up] = np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)
             final_icohp[Spin.up] = np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)
         else:
@@ -518,31 +524,30 @@ def get_summed_cohp_by_label_and_orbital_list(
 
     def get_orbital_resolved_cohp(
         self,
-        label,
-        orbitals,
-        summed_spin_channels=False,
-    ):
+        label: str | float,
+        orbitals: str | list | tuple,
+        summed_spin_channels: bool = False,
+    ) -> Cohp | None:
         """Get orbital-resolved COHP.
 
         Args:
             label: bond label (Lobster: labels as in ICOHPLIST/ICOOPLIST.lobster).
-
-            orbitals: The orbitals as a label, or list or tuple of the form
-                [(n1, orbital1), (n2, orbital2)]. Orbitals can either be str,
-                int, or Orbital.
-
-            summed_spin_channels: bool, will sum the spin channels and return the sum in Spin.up if true
+            orbitals: The orbitals as a label, or list/tuple of
+                [(n1, orbital1), (n2, orbital2), ...].
+                Where each orbital can either be str, int, or Orbital.
+            summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
             A Cohp object if CompleteCohp contains orbital-resolved cohp,
             or None if it doesn't.
 
         Note: It currently assumes that orbitals are str if they aren't the
-            other valid types. This is not ideal, but the easiest way to
-            avoid unicode issues between python 2 and python 3.
+            other valid types. This is not ideal, but is the easiest way to
+            avoid unicode issues between Python 2 and Python 3.
         """
         if self.orb_res_cohp is None:
             return None
+
         if isinstance(orbitals, (list, tuple)):
             cohp_orbs = [d["orbitals"] for d in self.orb_res_cohp[label].values()]
             orbs = []
@@ -561,6 +566,7 @@ def get_orbital_resolved_cohp(
             orb_label = orbitals
         else:
             raise TypeError("Orbitals must be str, list, or tuple.")
+
         try:
             icohp = self.orb_res_cohp[label][orb_label]["ICOHP"]
         except KeyError:
@@ -589,10 +595,10 @@ def get_orbital_resolved_cohp(
         )
 
     @classmethod
-    def from_dict(cls, dct: dict) -> Self:
+    def from_dict(cls, dct: dict[str, Any]) -> Self:
         """Get CompleteCohp object from dict representation.
 
-        TODO: clean that up?
+        TODO: clean that up
         """
         cohp_dict = {}
         efermi = dct["efermi"]
@@ -614,6 +620,7 @@ def from_dict(cls, dct: dict) -> Self:
             }
         else:
             bonds = None
+
         for label in dct["COHP"]:
             cohp = {Spin(int(spin)): np.array(dct["COHP"][label][spin]) for spin in dct["COHP"][label]}
             try:
@@ -692,15 +699,13 @@ def from_dict(cls, dct: dict) -> Self:
         else:
             orb_cohp = {}
 
-        are_cobis = dct.get("are_cobis", False)
-
         return cls(
             structure,
             avg_cohp,
             cohp_dict,
             bonds=bonds,
             are_coops=dct["are_coops"],
-            are_cobis=are_cobis,
+            are_cobis=dct.get("are_cobis", False),
             are_multi_center_cobis=are_multi_center_cobis,
             orb_res_cohp=orb_cohp,
         )
@@ -708,12 +713,12 @@ def from_dict(cls, dct: dict) -> Self:
     @classmethod
     def from_file(
         cls,
-        fmt,
-        filename=None,
-        structure_file=None,
-        are_coops=False,
-        are_cobis=False,
-        are_multi_center_cobis=False,
+        fmt: Literal["LMTO", "LOBSTER"],
+        filename: PathLike | None = None,
+        structure_file: PathLike | None = None,
+        are_coops: bool = False,
+        are_cobis: bool = False,
+        are_multi_center_cobis: bool = False,
     ) -> Self:
         """
         Create a CompleteCohp object from an output file of a COHP
@@ -721,9 +726,7 @@ def from_file(
         LMTO-ASA code) or LOBSTER (for the LOBSTER code).
 
         Args:
-            fmt: A string for the code that was used to calculate
-                the COHPs so that the output file can be handled
-                correctly. Can take the values "LMTO" or "LOBSTER".
+            fmt (Literal["LMTO", "LOBSTER"]): The code used to calculate COHPs.
             filename: Name of the COHP output file. Defaults to COPL
                 for LMTO and COHPCAR.lobster/COOPCAR.lobster for LOBSTER.
             structure_file: Name of the file containing the structure.
@@ -741,9 +744,10 @@ def from_file(
         """
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
+
         fmt = fmt.upper()
         if fmt == "LMTO":
-            # LMTO COOPs and orbital-resolved COHP cannot be handled yet.
+            # LMTO COOPs and orbital-resolved COHP cannot be handled yet
             are_coops = False
             are_cobis = False
             orb_res_cohp = None
@@ -752,6 +756,7 @@ def from_file(
             if filename is None:
                 filename = "COPL"
             cohp_file: LMTOCopl | Cohpcar = LMTOCopl(filename=filename, to_eV=True)
+
         elif fmt == "LOBSTER":
             if (
                 (are_coops and are_cobis)
@@ -775,6 +780,7 @@ def from_file(
                 are_multi_center_cobis=are_multi_center_cobis,
             )
             orb_res_cohp = cohp_file.orb_res_cohp
+
         else:
             raise ValueError(f"Unknown format {fmt}. Valid formats are LMTO and LOBSTER.")
 
@@ -785,7 +791,6 @@ def from_file(
 
         # LOBSTER shifts the energies so that the Fermi energy is at zero.
         # Shifting should be done by the plotter object though.
-
         spins = [Spin.up, Spin.down] if cohp_file.is_spin_polarized else [Spin.up]
         if fmt == "LOBSTER":
             energies += efermi
@@ -795,6 +800,7 @@ def from_file(
             # COHPs from the single-orbital populations. Total COHPs
             # may not be present when the cohpgenerator keyword is used
             # in LOBSTER versions 2.2.0 and earlier.
+
             # TODO: Test this more extensively
 
             for label in orb_res_cohp:
@@ -816,16 +822,16 @@ def from_file(
                     }
 
         if fmt == "LMTO":
-            # Calculate the average COHP for the LMTO file to be
-            # consistent with LOBSTER output.
-            avg_data: dict[str, dict] = {"COHP": {}, "ICOHP": {}}
-            for i in avg_data:
+            # Calculate the average COHP for the LMTO file to be consistent with LOBSTER
+            avg_data: dict[Literal["COHP", "ICOHP"], dict] = {"COHP": {}, "ICOHP": {}}
+            for dtype in avg_data:
                 for spin in spins:
-                    rows = np.array([v[i][spin] for v in cohp_data.values()])
+                    rows = np.array([v[dtype][spin] for v in cohp_data.values()])
                     avg = np.mean(rows, axis=0)
-                    # LMTO COHPs have 5 significant figures
-                    avg_data[i].update({spin: np.array([round_to_sigfigs(a, 5) for a in avg], dtype=float)})
+                    # LMTO COHPs have 5 significant digits
+                    avg_data[dtype] |= {spin: np.array([round_to_sigfigs(a, 5) for a in avg], dtype=float)}
             avg_cohp = Cohp(efermi, energies, avg_data["COHP"], icohp=avg_data["ICOHP"])
+
         elif not are_multi_center_cobis:
             avg_cohp = Cohp(
                 efermi,
@@ -837,9 +843,9 @@ def from_file(
                 are_multi_center_cobis=are_multi_center_cobis,
             )
             del cohp_data["average"]
+
         else:
-            # only include two-center cobis in average
-            # do this for both spin channels
+            # Only include two-center COBIs in average for both spin channels
             cohp = {}
             cohp[Spin.up] = np.array(
                 [np.array(c["COHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
@@ -850,6 +856,7 @@ def from_file(
                 ).mean(axis=0)
             except KeyError:
                 pass
+
             try:
                 icohp = {}
                 icohp[Spin.up] = np.array(
@@ -863,6 +870,7 @@ def from_file(
                     pass
             except KeyError:
                 icohp = None
+
             avg_cohp = Cohp(
                 efermi,
                 energies,
@@ -906,7 +914,7 @@ def from_file(
 
 
 class IcohpValue(MSONable):
-    """Store information on an ICOHP or ICOOP value.
+    """Information for an ICOHP or ICOOP value.
 
     Attributes:
         energies (ndarray): Energy values for the COHP/ICOHP/COOP/ICOOP.
@@ -921,28 +929,28 @@ class IcohpValue(MSONable):
 
     def __init__(
         self,
-        label,
-        atom1,
-        atom2,
-        length,
+        label: str | float,
+        atom1: str,
+        atom2: str,
+        length: float,
         translation,
-        num,
+        num: int,
         icohp,
-        are_coops=False,
-        are_cobis=False,
-        orbitals=None,
+        are_coops: bool = False,
+        are_cobis: bool = False,
+        orbitals: dict | None = None,  # TODO: DanielYang: more specific type
     ) -> None:
         """
         Args:
-            label: label for the icohp
-            atom1: str of atom that is contributing to the bond
-            atom2: str of second atom that is contributing to the bond
-            length: float of bond lengths
-            translation: translation list, e.g. [0,0,0]
-            num: integer describing how often the bond exists
+            label: label for the icohp.
+            atom1 (str): The first atom that contributes to the bond.
+            atom2 (str): The second atom that contributes to the bond.
+            length (float): Bond length.
+            translation: translation list, e.g. [0, 0, 0].  # TODO: DanielYang: use tuple3float?
+            num (int): How often the bond exists.
             icohp: dict={Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}
-            are_coops: if True, this are COOPs
-            are_cobis: if True, this are COBIs
+            are_coops (bool): If True, this are COOPs
+            are_cobis (bool): If True, this are COBIs
             orbitals: {[str(Orbital1)-str(Orbital2)]: {"icohp":{Spin.up: icohpvalue for spin.up, Spin.down:
                 icohpvalue for spin.down}, "orbitals":[Orbital1, Orbital2]}}.
         """
@@ -985,7 +993,7 @@ def __str__(self) -> str:
                 f"{self._icohp[Spin.up]} eV (Spin up)"
             )
 
-        if self._are_cobis and not self._are_coops:
+        if not self._are_coops and self._are_cobis:
             if self._is_spin_polarized:
                 return (
                     f"ICOBI {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
@@ -999,89 +1007,90 @@ def __str__(self) -> str:
         return ""
 
     @property
-    def num_bonds(self):
+    def num_bonds(self) -> int:
         """The number of bonds for which the ICOHP value is an average.
 
         Returns:
-            Int.
+            int
         """
         return self._num
 
     @property
     def are_coops(self) -> bool:
-        """Check if ICOOPs or not.
+        """Whether is ICOOPs.
 
         Returns:
-            Boolean.
+            bool
         """
         return self._are_coops
 
     @property
     def are_cobis(self) -> bool:
-        """Check if ICOBIs or not.
+        """Whether is ICOBIs.
 
         Returns:
-            Boolean.
+            bool
         """
         return self._are_cobis
 
     @property
     def is_spin_polarized(self) -> bool:
-        """Check if is spin polarized calculation.
+        """Whether is spin polarized calculation.
 
         Returns:
-            Boolean.
+            bool
         """
         return self._is_spin_polarized
 
-    def icohpvalue(self, spin=Spin.up):
+    def icohpvalue(self, spin: Spin = Spin.up) -> float:
         """
         Args:
             spin: Spin.up or Spin.down.
 
         Returns:
-            float: corresponding to chosen spin.
+            float: ICOHP value corresponding to chosen spin.
         """
         if not self.is_spin_polarized and spin == Spin.down:
             raise ValueError("The calculation was not performed with spin polarization")
 
         return self._icohp[spin]
 
-    def icohpvalue_orbital(self, orbitals, spin=Spin.up) -> float:
+    def icohpvalue_orbital(self, orbitals: list[Orbital] | str, spin: Spin = Spin.up) -> float:
         """
         Args:
             orbitals: List of Orbitals or "str(Orbital1)-str(Orbital2)"
             spin: Spin.up or Spin.down.
 
         Returns:
-            float: corresponding to chosen spin.
+            float: ICOHP value corresponding to chosen spin.
         """
         if not self.is_spin_polarized and spin == Spin.down:
             raise ValueError("The calculation was not performed with spin polarization")
-        if isinstance(orbitals, list):
+
+        if isinstance(orbitals, list):  # TODO: DanielYang: use tuple of 2
             orbitals = f"{orbitals[0]}-{orbitals[1]}"
         return self._orbitals[orbitals]["icohp"][spin]
 
     @property
-    def icohp(self):
+    def icohp(self) -> dict[Spin, IcohpValue]:
         """Dict with ICOHPs for spin up and spin down.
 
         Returns:
-            dict={Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}.
+            dict: {Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}.
         """
         return self._icohp
 
     @property
-    def summed_icohp(self):
+    def summed_icohp(self) -> float:
         """Sum ICOHPs of both spin channels for spin polarized compounds.
 
         Returns:
-            float: icohp value in eV.
+            float: ICOHP value in eV.
         """
         return self._icohp[Spin.down] + self._icohp[Spin.up] if self._is_spin_polarized else self._icohp[Spin.up]
 
     @property
-    def summed_orbital_icohp(self):
+    def summed_orbital_icohp(self) -> dict[str, float]:
         """Sum orbital-resolved ICOHPs of both spin channels for spin-polarized compounds.
 
         Returns:
@@ -1096,7 +1105,7 @@ def summed_orbital_icohp(self):
 
 
 class IcohpCollection(MSONable):
-    """Store IcohpValues.
+    """Collection of IcohpValues.
 
     Attributes:
         are_coops (bool): Boolean to indicate if these are ICOOPs.
@@ -1106,33 +1115,32 @@ class IcohpCollection(MSONable):
 
     def __init__(
         self,
-        list_labels,
-        list_atom1,
-        list_atom2,
-        list_length,
-        list_translation,
-        list_num,
-        list_icohp,
-        is_spin_polarized,
-        list_orb_icohp=None,
-        are_coops=False,
-        are_cobis=False,
+        list_labels: list,
+        list_atom1: list[str],
+        list_atom2: list[str],
+        list_length: list[float],
+        list_translation: list[list],  # TODO: (DanielYang) more specific type
+        list_num: list,  # TODO: more specific type
+        list_icohp: list[dict[Spin, IcohpValue]],
+        is_spin_polarized: bool,
+        list_orb_icohp: list[dict] | None = None,  # TODO: more specific type
+        are_coops: bool = False,
+        are_cobis: bool = False,
     ) -> None:
         """
         Args:
-            list_labels: list of labels for ICOHP/ICOOP values
-            list_atom1: list of str of atomnames e.g. "O1"
-            list_atom2: list of str of atomnames e.g. "O1"
-            list_length: list of lengths of corresponding bonds in Angstrom
-            list_translation: list of translation list, e.g. [0,0,0]
-            list_num: list of equivalent bonds, usually 1 starting from Lobster 3.0.0
-            list_icohp: list of dict={Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}
-            is_spin_polarized: Boolean to indicate if the Lobster calculation was done spin polarized or not Boolean to
-                indicate if the Lobster calculation was done spin polarized or not
+            list_labels: list of labels for ICOHP/ICOOP values.
+            list_atom1 (list[str]): atom names e.g. "O1".
+            list_atom2 (list[str]): atom names e.g. "O1".
+            list_length: list of lengths of corresponding bonds in Angstrom.
+            list_translation: list of translation list, e.g. [0, 0, 0].
+            list_num: list of equivalent bonds, usually 1 starting from LOBSTER 3.0.0.
+            list_icohp: list of dict={Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}.
+            is_spin_polarized (bool): Whether the LOBSTER calculation was done spin polarized.
             list_orb_icohp: list of dict={[str(Orbital1)-str(Orbital2)]: {"icohp":{Spin.up: icohpvalue for spin.up,
                 Spin.down: icohpvalue for spin.down}, "orbitals":[Orbital1, Orbital2]}}
-            are_coops: Boolean to indicate whether ICOOPs are stored
-            are_cobis: Boolean to indicate whether ICOBIs are stored.
+            are_coops (bool): Whether ICOOPs are stored
+            are_cobis (bool): Whether ICOBIs are stored.
         """
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
@@ -1169,79 +1177,78 @@ def __str__(self) -> str:
 
     def get_icohp_by_label(
         self,
-        label,
-        summed_spin_channels=True,
-        spin=Spin.up,
-        orbitals=None,
+        label: str,
+        summed_spin_channels: bool = True,
+        spin: Spin = Spin.up,
+        orbitals: str | list[Orbital] | None = None,  # TODO: change to tuple of 2
     ) -> float:
-        """Get an ICOHP value for a certain bond as indicated by the label (bond labels starting by "1" as in
-        ICOHPLIST/ICOOPLIST).
+        """Get an ICOHP value for a certain bond as indicated by the label
+        (bond labels starting from "1" as in ICOHPLIST/ICOOPLIST).
 
         Args:
-            label: label in str format (usually the bond number in Icohplist.lobster/Icooplist.lobster
-            summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of both spin channels should be summed
-            spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned
-            orbitals: List of Orbital or "str(Orbital1)-str(Orbital2)"
+            label (str): usually the bond number in Icohplist.lobster/Icooplist.lobster.
+            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
+            spin: If summed_spin_channels is False, this spin indicates which spin channel should be returned.
+            orbitals: List of Orbital or "str(Orbital1)-str(Orbital2)".
 
         Returns:
             float: ICOHP/ICOOP value
         """
-        icohp_here: IcohpValue = self._icohplist[label]
+        icohp: IcohpValue = self._icohplist[label]
+
         if orbitals is None:
-            if summed_spin_channels:
-                return icohp_here.summed_icohp
-            return icohp_here.icohpvalue(spin)
+            return icohp.summed_icohp if summed_spin_channels else icohp.icohpvalue(spin)
 
         if isinstance(orbitals, list):
             orbitals = f"{orbitals[0]}-{orbitals[1]}"
+
         if summed_spin_channels:
-            return icohp_here.summed_orbital_icohp[orbitals]
+            return icohp.summed_orbital_icohp[orbitals]
 
-        return icohp_here.icohpvalue_orbital(spin=spin, orbitals=orbitals)
+        return icohp.icohpvalue_orbital(spin=spin, orbitals=orbitals)
 
     def get_summed_icohp_by_label_list(
         self,
-        label_list,
-        divisor=1.0,
-        summed_spin_channels=True,
-        spin=Spin.up,
+        label_list: list[str | float],
+        divisor: float = 1.0,
+        summed_spin_channels: bool = True,
+        spin: Spin = Spin.up,
     ) -> float:
         """Get the sum of several ICOHP values that are indicated by a list of labels
         (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST).
 
         Args:
-            label_list: list of labels of the ICOHPs/ICOOPs that should be summed
-            divisor: is used to divide the sum
-            summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of both spin channels should be summed
-            spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned
+            label_list: list of labels of the ICOHPs/ICOOPs that should be summed.
+            divisor (float): used to divide the sum.
+            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
+            spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned.
 
         Returns:
-            float: sum of all ICOHPs/ICOOPs as indicated with label_list
+            float: sum of all ICOHPs/ICOOPs as indicated with label_list.
         """
         sum_icohp = 0
         for label in label_list:
             icohp_here = self._icohplist[label]
             if icohp_here.num_bonds != 1:
                 warnings.warn("One of the ICOHP values is an average over bonds. This is currently not considered.")
-            if icohp_here._is_spin_polarized:
-                if summed_spin_channels:
-                    sum_icohp = sum_icohp + icohp_here.summed_icohp
-                else:
-                    sum_icohp = sum_icohp + icohp_here.icohpvalue(spin)
+
+            if icohp_here._is_spin_polarized and summed_spin_channels:
+                sum_icohp = sum_icohp + icohp_here.summed_icohp
             else:
                 sum_icohp = sum_icohp + icohp_here.icohpvalue(spin)
+
         return sum_icohp / divisor
 
     def get_icohp_dict_by_bondlengths(
         self,
-        minbondlength=0.0,
-        maxbondlength=8.0,
-    ):
+        minbondlength: float = 0.0,
+        maxbondlength: float = 8.0,
+    ) -> dict[str | float, IcohpValue]:
         """Get a dict of IcohpValues corresponding to certain bond lengths.
 
         Args:
-            minbondlength: defines the minimum of the bond lengths of the bonds
-            maxbondlength: defines the maximum of the bond lengths of the bonds.
+            minbondlength (float): The minimum bond length.
+            maxbondlength (float): The maximum bond length.
 
         Returns:
             dict of IcohpValues, the keys correspond to the values from the initial list_labels.
@@ -1254,34 +1261,34 @@ def get_icohp_dict_by_bondlengths(
 
     def get_icohp_dict_of_site(
         self,
-        site,
-        minsummedicohp=None,
-        maxsummedicohp=None,
-        minbondlength=0.0,
-        maxbondlength=8.0,
-        only_bonds_to=None,
-    ):
+        site: int,
+        minsummedicohp: float | None = None,
+        maxsummedicohp: float | None = None,
+        minbondlength: float = 0.0,
+        maxbondlength: float = 8.0,
+        only_bonds_to: list[str] | None = None,
+    ) -> dict[str | float, IcohpValue]:
         """Get a dict of IcohpValue for a certain site (indicated by integer).
 
         Args:
-            site: integer describing the site of interest, order as in Icohplist.lobster/Icooplist.lobster, starts at 0
-            minsummedicohp: float, minimal icohp/icoop of the bonds that are considered. It is the summed ICOHP value
+            site (int): The site of interest, order as in Icohplist.lobster/Icooplist.lobster, starts at 0.
+            minsummedicohp (float): Minimal icohp/icoop of the bonds that are considered. It is the summed ICOHP value
                 from both spin channels for spin polarized cases
-            maxsummedicohp: float, maximal icohp/icoop of the bonds that are considered. It is the summed ICOHP value
+            maxsummedicohp (float): Maximal icohp/icoop of the bonds that are considered. It is the summed ICOHP value
                 from both spin channels for spin polarized cases
-            minbondlength: float, defines the minimum of the bond lengths of the bonds
-            maxbondlength: float, defines the maximum of the bond lengths of the bonds
-            only_bonds_to: list of strings describing the bonding partners that are allowed, e.g. ['O']
+            minbondlength (float): The minimum bond length.
+            maxbondlength (float): The maximum bond length.
+            only_bonds_to (list[str]): the bonding partners that are allowed, e.g. ["O"].
 
         Returns:
-            dict of IcohpValues, the keys correspond to the values from the initial list_labels
+            Dict of IcohpValues, the keys correspond to the values from the initial list_labels.
         """
         new_icohp_dict = {}
         for key, value in self._icohplist.items():
             atomnumber1 = int(re.split(r"(\d+)", value._atom1)[1]) - 1
             atomnumber2 = int(re.split(r"(\d+)", value._atom2)[1]) - 1
             if site in (atomnumber1, atomnumber2):
-                # manipulate order of atoms so that searched one is always atom1
+                # Swap order of atoms so that searched one is always atom1
                 if site == atomnumber2:
                     save = value._atom1
                     value._atom1 = value._atom2
@@ -1304,16 +1311,20 @@ def get_icohp_dict_of_site(
 
         return new_icohp_dict
 
-    def extremum_icohpvalue(self, summed_spin_channels=True, spin=Spin.up):
-        """Get ICOHP/ICOOP of strongest bond.
+    def extremum_icohpvalue(
+        self,
+        summed_spin_channels: bool = True,
+        spin: Spin = Spin.up,
+    ) -> float:
+        """Get ICOHP/ICOOP of the strongest bond.
 
         Args:
-            summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of both spin channels should be summed.
+            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
 
             spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned
 
         Returns:
-            lowest ICOHP/largest ICOOP value (i.e. ICOHP/ICOOP value of strongest bond)
+            Lowest ICOHP/largest ICOOP value (i.e. ICOHP/ICOOP value of strongest bond).
         """
         extremum = -sys.float_info.max if self._are_coops or self._are_cobis else sys.float_info.max
 
@@ -1338,56 +1349,56 @@ def extremum_icohpvalue(self, summed_spin_channels=True, spin=Spin.up):
 
     @property
     def is_spin_polarized(self) -> bool:
-        """Whether it is spin polarized."""
+        """Whether this is spin polarized."""
         return self._is_spin_polarized
 
     @property
     def are_coops(self) -> bool:
-        """Whether this is a coop."""
+        """Whether this is COOP."""
         return self._are_coops
 
     @property
     def are_cobis(self) -> bool:
-        """Whether this a cobi."""
+        """Whether this is COBI."""
         return self._are_cobis
 
 
 def get_integrated_cohp_in_energy_range(
-    cohp,
-    label,
-    orbital=None,
-    energy_range=None,
-    relative_E_Fermi=True,
-    summed_spin_channels=True,
-):
-    """Integrate CompleteCohp objects which include data on integrated COHPs
+    cohp: CompleteCohp,
+    label: str | float,
+    orbital: Orbital | None = None,
+    energy_range: float | list[float] | None = None,
+    relative_E_Fermi: bool = True,
+    summed_spin_channels: bool = True,
+) -> float | dict[Spin, float]:
+    """Integrate CompleteCohps which include data of integrated COHPs (ICOHPs).
+
     Args:
-        cohp: CompleteCohp object
-        label: label of the COHP data
-        orbital: If not None, a orbital resolved integrated COHP will be returned
+        cohp: CompleteCohp object.
+        label: label of the COHP data.
+        orbital: If not None, a orbital resolved integrated COHP will be returned.
         energy_range: If None, returns icohp value at Fermi level.
             If float, integrates from this float up to the Fermi level.
-            If [float,float], will integrate in between.
-        relative_E_Fermi: if True, energy scale with E_Fermi at 0 eV is chosen
-        summed_spin_channels: if True, Spin channels will be summed.
+            If [float, float], will integrate in between.
+        relative_E_Fermi (bool): if True, energy scale with E_Fermi at 0 eV is chosen
+        summed_spin_channels (bool): Whether Spin channels will be summed.
 
     Returns:
-        float indicating the integrated COHP if summed_spin_channels==True, otherwise dict of the following form {
-        Spin.up:float, Spin.down:float}
+        If summed_spin_channels:
+            float: the ICOHP.
+        else:
+            dict: {Spin.up: float, Spin.down: float}
     """
     summedicohp = {}
     if orbital is None:
         icohps = cohp.all_cohps[label].get_icohp(spin=None)
-        if summed_spin_channels and Spin.down in icohps:
-            summedicohp[Spin.up] = icohps[Spin.up] + icohps[Spin.down]
-        else:
-            summedicohp = icohps
     else:
         icohps = cohp.get_orbital_resolved_cohp(label=label, orbitals=orbital).icohp
-        if summed_spin_channels and Spin.down in icohps:
-            summedicohp[Spin.up] = icohps[Spin.up] + icohps[Spin.down]
-        else:
-            summedicohp = icohps
+
+    if summed_spin_channels and Spin.down in icohps:
+        summedicohp[Spin.up] = icohps[Spin.up] + icohps[Spin.down]
+    else:
+        summedicohp = icohps
 
     if energy_range is None:
         energies_corrected = cohp.energies - cohp.efermi
@@ -1396,12 +1407,13 @@ def get_integrated_cohp_in_energy_range(
         if not summed_spin_channels and Spin.down in icohps:
             spl_spindown = InterpolatedUnivariateSpline(energies_corrected, summedicohp[Spin.down], ext=0)
             return {Spin.up: spl_spinup(0.0), Spin.down: spl_spindown(0.0)}
+
         if summed_spin_channels:
             return spl_spinup(0.0)
 
         return {Spin.up: spl_spinup(0.0)}
 
-    # returns icohp value at the Fermi level!
+    # Return ICOHP value at the Fermi level
     if isinstance(energy_range, float):
         if relative_E_Fermi:
             energies_corrected = cohp.energies - cohp.efermi
diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index e30308233db..6b18294f62c 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -35,6 +35,7 @@
     from typing import Any
 
     from pymatgen.core.structure import IStructure
+    from pymatgen.util.typing import PathLike
 
 __author__ = "Janine George, Marco Esters"
 __copyright__ = "Copyright 2017, The Materials Project"
@@ -80,7 +81,7 @@ def __init__(
         are_coops: bool = False,
         are_cobis: bool = False,
         are_multi_center_cobis: bool = False,
-        filename: str | None = None,
+        filename: PathLike | None = None,
     ) -> None:
         """
         Args:

From 319dfa86e715faf4bab44aff996de6b8c72e2868 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 11:50:06 +0800
Subject: [PATCH 07/39] fix collection generation

---
 pymatgen/electronic_structure/dos.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/pymatgen/electronic_structure/dos.py b/pymatgen/electronic_structure/dos.py
index fc7378290a2..cdb3074838d 100644
--- a/pymatgen/electronic_structure/dos.py
+++ b/pymatgen/electronic_structure/dos.py
@@ -1458,8 +1458,24 @@ def _get_orb_type_lobster(orb) -> OrbitalType | None:
     Returns:
         OrbitalType
     """
-    orb_labs = ("s", "p_y", "p_z", "p_x", "d_xy", "d_yz", "d_z^2", "d_xz", "d_x^2-y^2")
-    orb_labs += ("f_y(3x^2-y^2)", "f_xyz", "f_yz^2", "f_z^3", "f_xz^2", "f_z(x^2-y^2)", "f_x(x^2-3y^2)")
+    orb_labs = (
+        "s",
+        "p_y",
+        "p_z",
+        "p_x",
+        "d_xy",
+        "d_yz",
+        "d_z^2",
+        "d_xz",
+        "d_x^2-y^2",
+        "f_y(3x^2-y^2)",
+        "f_xyz",
+        "f_yz^2",
+        "f_z^3",
+        "f_xz^2",
+        "f_z(x^2-y^2)",
+        "f_x(x^2-3y^2)",
+    )
 
     try:
         orbital = Orbital(orb_labs.index(orb[1:]))

From a29ef989786e2cd811e26fc83b26dc006bdf0957 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 12:03:26 +0800
Subject: [PATCH 08/39] add type `SpinLike` and case tweaks

---
 pymatgen/electronic_structure/cohp.py | 40 +++++++++++++--------------
 pymatgen/util/typing.py               |  6 +++-
 2 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index ab9b3c0fa2c..a2edc2da928 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -37,7 +37,7 @@
     from numpy.typing import NDArray
     from typing_extensions import Self
 
-    from pymatgen.util.typing import PathLike
+    from pymatgen.util.typing import PathLike, SpinLike
 
 __author__ = "Marco Esters, Janine George"
 __copyright__ = "Copyright 2017, The Materials Project"
@@ -128,14 +128,13 @@ def as_dict(self) -> dict[str, Any]:
 
     def get_cohp(
         self,
-        spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
+        spin: SpinLike | None = None,
         integrated: bool = False,
     ) -> dict[Spin, NDArray] | None:
         """Get the COHP or ICOHP for a particular spin.
 
         Args:
-            spin: Can be Spin object, integer (-1/1)
-                or str ("up"/"down").
+            spin: Spin object, integer (-1/1) or str ("up"/"down").
             integrated: Return ICOHP (True) or COHP (False).
 
         Returns:
@@ -157,7 +156,7 @@ def get_cohp(
 
     def get_icohp(
         self,
-        spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
+        spin: SpinLike | None = None,
     ) -> dict[Spin, NDArray] | None:
         """Convenient wrapper to get the ICOHP for a particular spin."""
         return self.get_cohp(spin=spin, integrated=True)
@@ -185,7 +184,7 @@ def get_interpolated_value(
 
     def has_antibnd_states_below_efermi(
         self,
-        spin: Spin | Literal[-1, 1, "up", "down"] | None = None,
+        spin: SpinLike | None = None,
         limit: float = 0.01,
     ) -> dict[Spin, bool] | None:
         """Get dict of antibonding states below the Fermi level for the spin.
@@ -531,14 +530,14 @@ def get_orbital_resolved_cohp(
         """Get orbital-resolved COHP.
 
         Args:
-            label: bond label (Lobster: labels as in ICOHPLIST/ICOOPLIST.lobster).
+            label: bond labels as in ICOHPLIST/ICOOPLIST.lobster.
             orbitals: The orbitals as a label, or list/tuple of
                 [(n1, orbital1), (n2, orbital2), ...].
                 Where each orbital can either be str, int, or Orbital.
             summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
-            A Cohp object if CompleteCohp contains orbital-resolved cohp,
+            A Cohp object if CompleteCohp contains orbital-resolved COHP,
             or None if it doesn't.
 
         Note: It currently assumes that orbitals are str if they aren't the
@@ -942,17 +941,17 @@ def __init__(
     ) -> None:
         """
         Args:
-            label: label for the icohp.
+            label: label for the ICOHP.
             atom1 (str): The first atom that contributes to the bond.
             atom2 (str): The second atom that contributes to the bond.
             length (float): Bond length.
             translation: translation list, e.g. [0, 0, 0].  # TODO: DanielYang: use tuple3float?
             num (int): How often the bond exists.
-            icohp: dict={Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}
+            icohp: dict={Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}
             are_coops (bool): If True, this are COOPs
             are_cobis (bool): If True, this are COBIs
-            orbitals: {[str(Orbital1)-str(Orbital2)]: {"icohp":{Spin.up: icohpvalue for spin.up, Spin.down:
-                icohpvalue for spin.down}, "orbitals":[Orbital1, Orbital2]}}.
+            orbitals: {[str(Orbital1)-str(Orbital2)]: {"icohp": {Spin.up: IcohpValue for spin.up, Spin.down:
+                IcohpValue for spin.down}, "orbitals": [Orbital1, Orbital2]}}.
         """
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
@@ -1076,7 +1075,7 @@ def icohp(self) -> dict[Spin, IcohpValue]:
         """Dict with ICOHPs for spin up and spin down.
 
         Returns:
-            dict: {Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}.
+            dict: {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
         """
         return self._icohp
 
@@ -1110,7 +1109,7 @@ class IcohpCollection(MSONable):
     Attributes:
         are_coops (bool): Boolean to indicate if these are ICOOPs.
         are_cobis (bool): Boolean to indicate if these are ICOOPs.
-        is_spin_polarized (bool): Boolean to indicate if the Lobster calculation was done spin polarized or not.
+        is_spin_polarized (bool): Boolean to indicate if the LOBSTER calculation was done spin polarized or not.
     """
 
     def __init__(
@@ -1135,10 +1134,10 @@ def __init__(
             list_length: list of lengths of corresponding bonds in Angstrom.
             list_translation: list of translation list, e.g. [0, 0, 0].
             list_num: list of equivalent bonds, usually 1 starting from LOBSTER 3.0.0.
-            list_icohp: list of dict={Spin.up: icohpvalue for spin.up, Spin.down: icohpvalue for spin.down}.
+            list_icohp: list of dict={Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
             is_spin_polarized (bool): Whether the LOBSTER calculation was done spin polarized.
-            list_orb_icohp: list of dict={[str(Orbital1)-str(Orbital2)]: {"icohp":{Spin.up: icohpvalue for spin.up,
-                Spin.down: icohpvalue for spin.down}, "orbitals":[Orbital1, Orbital2]}}
+            list_orb_icohp: list of dict={[str(Orbital1)-str(Orbital2)]: {"icohp": {Spin.up: IcohpValue for spin.up,
+                Spin.down: IcohpValue for spin.down}, "orbitals": [Orbital1, Orbital2]}}
             are_coops (bool): Whether ICOOPs are stored
             are_cobis (bool): Whether ICOBIs are stored.
         """
@@ -1272,9 +1271,9 @@ def get_icohp_dict_of_site(
 
         Args:
             site (int): The site of interest, order as in Icohplist.lobster/Icooplist.lobster, starts at 0.
-            minsummedicohp (float): Minimal icohp/icoop of the bonds that are considered. It is the summed ICOHP value
+            minsummedicohp (float): Minimal ICOHP/ICOOP of the bonds that are considered. It is the summed ICOHP value
                 from both spin channels for spin polarized cases
-            maxsummedicohp (float): Maximal icohp/icoop of the bonds that are considered. It is the summed ICOHP value
+            maxsummedicohp (float): Maximal ICOHP/ICOOP of the bonds that are considered. It is the summed ICOHP value
                 from both spin channels for spin polarized cases
             minbondlength (float): The minimum bond length.
             maxbondlength (float): The maximum bond length.
@@ -1296,6 +1295,7 @@ def get_icohp_dict_of_site(
 
                 second_test = True if only_bonds_to is None else re.split("(\\d+)", value._atom2)[0] in only_bonds_to
                 if value._length >= minbondlength and value._length <= maxbondlength and second_test:
+                    # TODO: DanielYang: merge the following condition blocks
                     if minsummedicohp is not None:
                         if value.summed_icohp >= minsummedicohp:
                             if maxsummedicohp is not None:
@@ -1377,7 +1377,7 @@ def get_integrated_cohp_in_energy_range(
         cohp: CompleteCohp object.
         label: label of the COHP data.
         orbital: If not None, a orbital resolved integrated COHP will be returned.
-        energy_range: If None, returns icohp value at Fermi level.
+        energy_range: If None, returns ICOHP value at Fermi level.
             If float, integrates from this float up to the Fermi level.
             If [float, float], will integrate in between.
         relative_E_Fermi (bool): if True, energy scale with E_Fermi at 0 eV is chosen
diff --git a/pymatgen/util/typing.py b/pymatgen/util/typing.py
index 7f498c5e93f..52246c384df 100644
--- a/pymatgen/util/typing.py
+++ b/pymatgen/util/typing.py
@@ -7,9 +7,10 @@
 
 from collections.abc import Sequence
 from os import PathLike as OsPathLike
-from typing import TYPE_CHECKING, Any, Union
+from typing import TYPE_CHECKING, Any, Literal, Union
 
 from pymatgen.core import Composition, DummySpecies, Element, Species
+from pymatgen.electronic_structure.core import Spin
 
 if TYPE_CHECKING:  # needed to avoid circular imports
     from pymatgen.analysis.cost import CostEntry  # type: ignore[attr-defined]
@@ -25,6 +26,9 @@
 PathLike = Union[str, OsPathLike]
 PbcLike = tuple[bool, bool, bool]
 
+# Things that can be cast to a Spin
+SpinLike = Union[Spin, Literal[-1, 1, "up", "down"]]
+
 # Things that can be cast to a Species-like object using get_el_sp
 SpeciesLike = Union[str, Element, Species, DummySpecies]
 

From d47008cef318dbad75a9e2287169a5e9caf3ec2c Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 16:46:03 +0800
Subject: [PATCH 09/39] reduce repetition for `__str__` of `IcohpValue`

---
 pymatgen/electronic_structure/cohp.py | 98 +++++++++++----------------
 1 file changed, 41 insertions(+), 57 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index a2edc2da928..fcae982d172 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -32,13 +32,16 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
-    from typing import Any, Literal
+    from typing import Any, Literal, Union
 
     from numpy.typing import NDArray
     from typing_extensions import Self
 
     from pymatgen.util.typing import PathLike, SpinLike
 
+    # TODO: double check and clarify this custom type
+    CohpLabel = Union[str, int]
+
 __author__ = "Marco Esters, Janine George"
 __copyright__ = "Copyright 2017, The Materials Project"
 __version__ = "0.2"
@@ -323,16 +326,16 @@ def as_dict(self) -> dict[str, Any]:
             dct["ICOHP"] = {"average": {str(spin): pops.tolist() for spin, pops in self.icohp.items()}}
 
         for label in self.all_cohps:
-            dct["COHP"].update({label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].cohp.items()}})
+            dct["COHP"] |= {label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].cohp.items()}}
             if self.all_cohps[label].icohp is not None:
                 if "ICOHP" not in dct:
                     dct["ICOHP"] = {
                         label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].icohp.items()}
                     }
                 else:
-                    dct["ICOHP"].update(
-                        {label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].icohp.items()}}
-                    )
+                    dct["ICOHP"] |= {
+                        label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].icohp.items()}
+                    }
 
         if False in [bond_dict == {} for bond_dict in self.bonds.values()]:
             dct["bonds"] = {
@@ -360,13 +363,13 @@ def as_dict(self) -> dict[str, Any]:
 
     def get_cohp_by_label(
         self,
-        label: str | float,  # TODO (DanielYang): double-check type of label, perhaps add custom type
+        label: CohpLabel,
         summed_spin_channels: bool = False,
     ) -> Cohp:
         """Get specific Cohp object by label.
 
         Args:
-            label: string (for newer LOBSTER versions: a number)  # TODO: check arg label type
+            label: string (for newer LOBSTER versions: int)
             summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
@@ -523,7 +526,7 @@ def get_summed_cohp_by_label_and_orbital_list(
 
     def get_orbital_resolved_cohp(
         self,
-        label: str | float,
+        label: CohpLabel,
         orbitals: str | list | tuple,
         summed_spin_channels: bool = False,
     ) -> Cohp | None:
@@ -597,7 +600,7 @@ def get_orbital_resolved_cohp(
     def from_dict(cls, dct: dict[str, Any]) -> Self:
         """Get CompleteCohp object from dict representation.
 
-        TODO: clean that up
+        TODO: clean this up
         """
         cohp_dict = {}
         efermi = dct["efermi"]
@@ -719,10 +722,7 @@ def from_file(
         are_cobis: bool = False,
         are_multi_center_cobis: bool = False,
     ) -> Self:
-        """
-        Create a CompleteCohp object from an output file of a COHP
-        calculation. Valid formats are either LMTO (for the Stuttgart
-        LMTO-ASA code) or LOBSTER (for the LOBSTER code).
+        """Create CompleteCohp from an output file of a COHP calculation.
 
         Args:
             fmt (Literal["LMTO", "LOBSTER"]): The code used to calculate COHPs.
@@ -916,25 +916,25 @@ class IcohpValue(MSONable):
     """Information for an ICOHP or ICOOP value.
 
     Attributes:
-        energies (ndarray): Energy values for the COHP/ICOHP/COOP/ICOOP.
-        densities (ndarray): Density of states values for the COHP/ICOHP/COOP/ICOOP.
-        energies_are_cartesian (bool): Whether the energies are cartesian or not.
-        are_coops (bool): Whether the object is a COOP/ICOOP or not.
-        are_cobis (bool): Whether the object is a COBIS/ICOBIS or not.
-        icohp (dict): A dictionary of the ICOHP/COHP values. The keys are Spin.up and Spin.down.
+        energies (NDArray): Energy values for the COHP/ICOHP/COOP/ICOOP.
+        densities (NDArray): Density of states for the COHP/ICOHP/COOP/ICOOP.
+        energies_are_cartesian (bool): Whether the energies are cartesian.
+        are_coops (bool): Whether the object is COOP/ICOOP.
+        are_cobis (bool): Whether the object is COBIS/ICOBIS.
+        icohp (dict): The ICOHP/COHP values, whose keys are Spin.up and Spin.down.
         summed_icohp (float): The summed ICOHP/COHP values.
-        num_bonds (int): The number of bonds used for the average COHP (relevant for LOBSTER versions <3.0).
+        num_bonds (int): The number of bonds used for the average COHP (for LOBSTER versions <3.0).
     """
 
     def __init__(
         self,
-        label: str | float,
+        label: CohpLabel,
         atom1: str,
         atom2: str,
         length: float,
-        translation,
+        translation,  # TODO: DanielYang: use tuple3float?
         num: int,
-        icohp,
+        icohp: dict,  # more specific type
         are_coops: bool = False,
         are_cobis: bool = False,
         orbitals: dict | None = None,  # TODO: DanielYang: more specific type
@@ -945,8 +945,8 @@ def __init__(
             atom1 (str): The first atom that contributes to the bond.
             atom2 (str): The second atom that contributes to the bond.
             length (float): Bond length.
-            translation: translation list, e.g. [0, 0, 0].  # TODO: DanielYang: use tuple3float?
-            num (int): How often the bond exists.
+            translation: translation list, e.g. [0, 0, 0].
+            num (int): How often the bond exists.  # TODO: DanielYang: clarify this description
             icohp: dict={Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}
             are_coops (bool): If True, this are COOPs
             are_cobis (bool): If True, this are COBIs
@@ -971,40 +971,24 @@ def __init__(
     def __str__(self) -> str:
         """String representation of the ICOHP/ICOOP."""
         if not self._are_coops and not self._are_cobis:
-            if self._is_spin_polarized:
-                return (
-                    f"ICOHP {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
-                    f"{self._icohp[Spin.up]} eV (Spin up) and {self._icohp[Spin.down]} eV (Spin down)"
-                )
-            return (
-                f"ICOHP {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
-                f"{self._icohp[Spin.up]} eV (Spin up)"
-            )
+            header = "ICOHP"
+        elif self._are_coops and not self._are_cobis:
+            header = "ICOOP"
+        else:
+            header = "ICOBI"
 
-        if self._are_coops and not self._are_cobis:
-            if self._is_spin_polarized:
-                return (
-                    f"ICOOP {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
-                    f"{self._icohp[Spin.up]} eV (Spin up) and {self._icohp[Spin.down]} eV (Spin down)"
-                )
+        if self._is_spin_polarized:
             return (
-                f"ICOOP {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
-                f"{self._icohp[Spin.up]} eV (Spin up)"
+                f"{header} {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
+                f"{self._icohp[Spin.up]} eV (Spin up) and {self._icohp[Spin.down]} eV (Spin down)"
             )
 
-        if not self._are_coops and self._are_cobis:
-            if self._is_spin_polarized:
-                return (
-                    f"ICOBI {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
-                    f"{self._icohp[Spin.up]} eV (Spin up) and {self._icohp[Spin.down]} eV (Spin down)"
-                )
+        else:
             return (
-                f"ICOBI {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
+                f"{header} {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
                 f"{self._icohp[Spin.up]} eV (Spin up)"
             )
 
-        return ""
-
     @property
     def num_bonds(self) -> int:
         """The number of bonds for which the ICOHP value is an average.
@@ -1016,7 +1000,7 @@ def num_bonds(self) -> int:
 
     @property
     def are_coops(self) -> bool:
-        """Whether is ICOOPs.
+        """Whether are ICOOPs.
 
         Returns:
             bool
@@ -1025,7 +1009,7 @@ def are_coops(self) -> bool:
 
     @property
     def are_cobis(self) -> bool:
-        """Whether is ICOBIs.
+        """Whether are ICOBIs.
 
         Returns:
             bool
@@ -1081,7 +1065,7 @@ def icohp(self) -> dict[Spin, IcohpValue]:
 
     @property
     def summed_icohp(self) -> float:
-        """Sum ICOHPs of both spin channels for spin polarized compounds.
+        """Summed ICOHPs of both spin channels if spin polarized.
 
         Returns:
             float: ICOHP value in eV.
@@ -1090,7 +1074,7 @@ def summed_icohp(self) -> float:
 
     @property
     def summed_orbital_icohp(self) -> dict[str, float]:
-        """Sum orbital-resolved ICOHPs of both spin channels for spin-polarized compounds.
+        """Summed orbital-resolved ICOHPs of both spin channels if spin-polarized.
 
         Returns:
             dict[str, float]: "str(Orbital1)-str(Ortibal2)" mapped to ICOHP value in eV.
@@ -1176,7 +1160,7 @@ def __str__(self) -> str:
 
     def get_icohp_by_label(
         self,
-        label: str,
+        label: CohpLabel,
         summed_spin_channels: bool = True,
         spin: Spin = Spin.up,
         orbitals: str | list[Orbital] | None = None,  # TODO: change to tuple of 2
@@ -1365,7 +1349,7 @@ def are_cobis(self) -> bool:
 
 def get_integrated_cohp_in_energy_range(
     cohp: CompleteCohp,
-    label: str | float,
+    label: CohpLabel,
     orbital: Orbital | None = None,
     energy_range: float | list[float] | None = None,
     relative_E_Fermi: bool = True,

From 0407f52a2aaac2da90a4855454a017179d18e33e Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 16:50:10 +0800
Subject: [PATCH 10/39] simplify condition

---
 pymatgen/electronic_structure/cohp.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index fcae982d172..85310c720f2 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -970,12 +970,13 @@ def __init__(
 
     def __str__(self) -> str:
         """String representation of the ICOHP/ICOOP."""
-        if not self._are_coops and not self._are_cobis:
-            header = "ICOHP"
-        elif self._are_coops and not self._are_cobis:
+        # (are_coops and are_cobis) is never True
+        if self._are_coops:
             header = "ICOOP"
-        else:
+        elif self._are_cobis:
             header = "ICOBI"
+        else:
+            header = "ICOHP"
 
         if self._is_spin_polarized:
             return (

From 3dd5d7c37a55d8ccbb1df3904505cadef92decad Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 16:55:28 +0800
Subject: [PATCH 11/39] reduce indentation level

---
 pymatgen/electronic_structure/cohp.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 85310c720f2..46df286edb5 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -984,11 +984,10 @@ def __str__(self) -> str:
                 f"{self._icohp[Spin.up]} eV (Spin up) and {self._icohp[Spin.down]} eV (Spin down)"
             )
 
-        else:
-            return (
-                f"{header} {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
-                f"{self._icohp[Spin.up]} eV (Spin up)"
-            )
+        return (
+            f"{header} {self._label} between {self._atom1} and {self._atom2} ({self._translation}): "
+            f"{self._icohp[Spin.up]} eV (Spin up)"
+        )
 
     @property
     def num_bonds(self) -> int:

From 0e75e0d6529d1c01b1a7eabc13d008a7f95ced21 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 17:13:48 +0800
Subject: [PATCH 12/39] clarify `translation`

---
 pymatgen/electronic_structure/cohp.py | 30 +++++++++++++--------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 46df286edb5..121ea226481 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -37,7 +37,7 @@
     from numpy.typing import NDArray
     from typing_extensions import Self
 
-    from pymatgen.util.typing import PathLike, SpinLike
+    from pymatgen.util.typing import PathLike, SpinLike, Vector3D
 
     # TODO: double check and clarify this custom type
     CohpLabel = Union[str, int]
@@ -932,7 +932,7 @@ def __init__(
         atom1: str,
         atom2: str,
         length: float,
-        translation,  # TODO: DanielYang: use tuple3float?
+        translation: Vector3D,
         num: int,
         icohp: dict,  # more specific type
         are_coops: bool = False,
@@ -945,7 +945,7 @@ def __init__(
             atom1 (str): The first atom that contributes to the bond.
             atom2 (str): The second atom that contributes to the bond.
             length (float): Bond length.
-            translation: translation list, e.g. [0, 0, 0].
+            translation: cell translation vector, e.g. (0, 0, 0).
             num (int): How often the bond exists.  # TODO: DanielYang: clarify this description
             icohp: dict={Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}
             are_coops (bool): If True, this are COOPs
@@ -1102,7 +1102,7 @@ def __init__(
         list_atom1: list[str],
         list_atom2: list[str],
         list_length: list[float],
-        list_translation: list[list],  # TODO: (DanielYang) more specific type
+        list_translation: list[Vector3D],
         list_num: list,  # TODO: more specific type
         list_icohp: list[dict[Spin, IcohpValue]],
         is_spin_polarized: bool,
@@ -1116,7 +1116,7 @@ def __init__(
             list_atom1 (list[str]): atom names e.g. "O1".
             list_atom2 (list[str]): atom names e.g. "O1".
             list_length: list of lengths of corresponding bonds in Angstrom.
-            list_translation: list of translation list, e.g. [0, 0, 0].
+            list_translation: list of cell translation vectors.
             list_num: list of equivalent bonds, usually 1 starting from LOBSTER 3.0.0.
             list_icohp: list of dict={Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
             is_spin_polarized (bool): Whether the LOBSTER calculation was done spin polarized.
@@ -1141,18 +1141,18 @@ def __init__(
         self._list_icohp = list_icohp
         self._list_orb_icohp = list_orb_icohp
 
-        for ilist, listel in enumerate(list_labels):
-            self._icohplist[listel] = IcohpValue(
-                label=listel,
-                atom1=list_atom1[ilist],
-                atom2=list_atom2[ilist],
-                length=list_length[ilist],
-                translation=list_translation[ilist],
-                num=list_num[ilist],
-                icohp=list_icohp[ilist],
+        for idx, label in enumerate(list_labels):
+            self._icohplist[label] = IcohpValue(
+                label=label,
+                atom1=list_atom1[idx],
+                atom2=list_atom2[idx],
+                length=list_length[idx],
+                translation=list_translation[idx],
+                num=list_num[idx],
+                icohp=list_icohp[idx],
                 are_coops=are_coops,
                 are_cobis=are_cobis,
-                orbitals=None if list_orb_icohp is None else list_orb_icohp[ilist],
+                orbitals=None if list_orb_icohp is None else list_orb_icohp[idx],
             )
 
     def __str__(self) -> str:

From b7c03dac019ba9f895e89966ad3b796ec4303444 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 17:55:56 +0800
Subject: [PATCH 13/39] clarify `list_num` and other docstrings

---
 pymatgen/electronic_structure/cohp.py | 123 +++++++++++++-------------
 1 file changed, 62 insertions(+), 61 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 121ea226481..2ff424e27b5 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -70,7 +70,7 @@ def __init__(
     ) -> None:
         """
         Args:
-            efermi: Fermi energy.
+            efermi: The Fermi level.
             energies: A sequence of energies.
             cohp ({Spin: np.array}): representing the COHP for each spin.
             are_coops: Indicates whether this object describes COOPs.
@@ -137,13 +137,12 @@ def get_cohp(
         """Get the COHP or ICOHP for a particular spin.
 
         Args:
-            spin: Spin object, integer (-1/1) or str ("up"/"down").
+            spin: Spin, integer (-1/1) or str ("up"/"down"). If is None
+                and both spins are present, both will be returned.
             integrated: Return ICOHP (True) or COHP (False).
 
         Returns:
-            The CHOP or ICOHP for the selected spin. If Spin is
-            None and both spins are present, both spins will be returned
-            as a dictionary.
+            dict: The COHP or ICOHP for the selected spin.
         """
         populations = self.icohp if integrated else self.cohp
 
@@ -193,8 +192,8 @@ def has_antibnd_states_below_efermi(
         """Get dict of antibonding states below the Fermi level for the spin.
 
         Args:
-            spin: Spin.
-            limit: only COHP higher than this value will be considered.
+            spin (SpinLike): selected spin.
+            limit (float): Only COHP higher than this value will be considered.
         """
         populations = self.cohp
         n_energies_below_efermi = len([energy for energy in self.energies if energy <= self.efermi])
@@ -233,17 +232,17 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:
 
 
 class CompleteCohp(Cohp):
-    """A wrapper class that defines an average COHP, and individual COHPs.
+    """A wrapper that defines an average COHP, and individual COHPs.
 
     Attributes:
-        are_coops (bool): Indicates whether the object is consisting of COOPs.
-        are_cobis (bool): Indicates whether the object is consisting of COBIs.
-        efermi (float): Fermi energy.
+        are_coops (bool): Whether the object is consisting of COOPs.
+        are_cobis (bool): Whether the object is consisting of COBIs.
+        efermi (float): The Fermi level.
         energies (Sequence[float]): Sequence of energies.
-        structure (pymatgen.Structure): Structure associated with the COHPs.
+        structure (Structure): Structure associated with the COHPs.
         cohp (Sequence[float]): The average COHP.
         icohp (Sequence[float]): The average ICOHP.
-        all_cohps (dict[str, Sequence[float]]): A dict of COHPs for individual bonds of the form {label: COHP}.
+        all_cohps (dict[str, Sequence[float]]): COHPs for individual bonds of the form {label: COHP}.
         orb_res_cohp (dict[str, Dict[str, Sequence[float]]]): Orbital-resolved COHPs.
     """
 
@@ -252,7 +251,7 @@ def __init__(
         structure: Structure,
         avg_cohp: Cohp,
         cohp_dict: dict[str, Cohp],
-        bonds: dict | None = None,
+        bonds: dict | None = None,  # TODO: DanielYang: more specific type
         are_coops: bool = False,
         are_cobis: bool = False,
         are_multi_center_cobis: bool = False,
@@ -262,8 +261,8 @@ def __init__(
         Args:
             structure: Structure associated with this COHP.
             avg_cohp: The average COHP as a Cohp object.
-            cohp_dict: A dict of COHP objects for individual bonds of the form
-                {label: COHP}
+            cohp_dict (dict): COHP objects for individual bonds of the form
+                {label: COHP}.
             bonds: A dict containing information on the bonds of the form
                 {label: {key: val}}. The key-val pair can be any information
                 the user wants to put in, but typically contains the sites,
@@ -366,14 +365,14 @@ def get_cohp_by_label(
         label: CohpLabel,
         summed_spin_channels: bool = False,
     ) -> Cohp:
-        """Get specific Cohp object by label.
+        """Get specific Cohp by label, to simplify plotting.
 
         Args:
             label: string (for newer LOBSTER versions: int)
-            summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
+            summed_spin_channels (bool): Sum the spin channels and return the sum as Spin.up.
 
         Returns:
-            Returns the COHP object to simplify plotting
+            The Cohp.
         """
         if label.lower() == "average":
             divided_cohp: dict[Spin, Any] | None = self.cohp
@@ -788,7 +787,7 @@ def from_file(
         cohp_data = cohp_file.cohp_data
         energies = cohp_file.energies
 
-        # LOBSTER shifts the energies so that the Fermi energy is at zero.
+        # LOBSTER shifts the energies so that the Fermi level is at zero.
         # Shifting should be done by the plotter object though.
         spins = [Spin.up, Spin.down] if cohp_file.is_spin_polarized else [Spin.up]
         if fmt == "LOBSTER":
@@ -1000,7 +999,7 @@ def num_bonds(self) -> int:
 
     @property
     def are_coops(self) -> bool:
-        """Whether are ICOOPs.
+        """Whether these are ICOOPs.
 
         Returns:
             bool
@@ -1009,7 +1008,7 @@ def are_coops(self) -> bool:
 
     @property
     def are_cobis(self) -> bool:
-        """Whether are ICOBIs.
+        """Whether these are ICOBIs.
 
         Returns:
             bool
@@ -1018,7 +1017,7 @@ def are_cobis(self) -> bool:
 
     @property
     def is_spin_polarized(self) -> bool:
-        """Whether is spin polarized calculation.
+        """Whether this is spin polarized calculation.
 
         Returns:
             bool
@@ -1041,7 +1040,7 @@ def icohpvalue(self, spin: Spin = Spin.up) -> float:
     def icohpvalue_orbital(self, orbitals: list[Orbital] | str, spin: Spin = Spin.up) -> float:
         """
         Args:
-            orbitals: List of Orbitals or "str(Orbital1)-str(Orbital2)"
+            orbitals (list[Orbitals]): List of Orbitals or "str(Orbital1)-str(Orbital2)".
             spin: Spin.up or Spin.down.
 
         Returns:
@@ -1091,9 +1090,9 @@ class IcohpCollection(MSONable):
     """Collection of IcohpValues.
 
     Attributes:
-        are_coops (bool): Boolean to indicate if these are ICOOPs.
-        are_cobis (bool): Boolean to indicate if these are ICOOPs.
-        is_spin_polarized (bool): Boolean to indicate if the LOBSTER calculation was done spin polarized or not.
+        are_coops (bool): Whether these are ICOOPs.
+        are_cobis (bool): Whether these are ICOOPs.
+        is_spin_polarized (bool): Whether the calculation is spin polarized.
     """
 
     def __init__(
@@ -1103,7 +1102,7 @@ def __init__(
         list_atom2: list[str],
         list_length: list[float],
         list_translation: list[Vector3D],
-        list_num: list,  # TODO: more specific type
+        list_num: list[int],
         list_icohp: list[dict[Spin, IcohpValue]],
         is_spin_polarized: bool,
         list_orb_icohp: list[dict] | None = None,  # TODO: more specific type
@@ -1112,17 +1111,18 @@ def __init__(
     ) -> None:
         """
         Args:
-            list_labels: list of labels for ICOHP/ICOOP values.
-            list_atom1 (list[str]): atom names e.g. "O1".
-            list_atom2 (list[str]): atom names e.g. "O1".
-            list_length: list of lengths of corresponding bonds in Angstrom.
-            list_translation: list of cell translation vectors.
-            list_num: list of equivalent bonds, usually 1 starting from LOBSTER 3.0.0.
-            list_icohp: list of dict={Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
-            is_spin_polarized (bool): Whether the LOBSTER calculation was done spin polarized.
-            list_orb_icohp: list of dict={[str(Orbital1)-str(Orbital2)]: {"icohp": {Spin.up: IcohpValue for spin.up,
-                Spin.down: IcohpValue for spin.down}, "orbitals": [Orbital1, Orbital2]}}
-            are_coops (bool): Whether ICOOPs are stored
+            list_labels (list): Labels for ICOHP/ICOOP values.
+            list_atom1 (list[str]): Atom names, e.g. "O1".
+            list_atom2 (list[str]): Atom names, e.g. "O1".
+            list_length (list[float]): Bond lengths in Angstrom.
+            list_translation (list[Vector3D]): Cell translation vectors.
+            list_num (list[int]): Numbers of equivalent bonds, usually 1 starting from LOBSTER 3.0.0.
+            list_icohp (list[dict]): Dicts as {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
+            is_spin_polarized (bool): Whether the calculation is spin polarized.
+            list_orb_icohp (list[dict]): Dicts as {[str(Orbital1)-str(Orbital2)]:
+                {"icohp": {Spin.up: IcohpValue for spin.up,
+                Spin.down: IcohpValue for spin.down}, "orbitals": [Orbital1, Orbital2]}}.
+            are_coops (bool): Whether ICOOPs are stored.
             are_cobis (bool): Whether ICOBIs are stored.
         """
         if are_coops and are_cobis:
@@ -1201,10 +1201,10 @@ def get_summed_icohp_by_label_list(
         (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST).
 
         Args:
-            label_list: list of labels of the ICOHPs/ICOOPs that should be summed.
-            divisor (float): used to divide the sum.
+            label_list (list): Labels of the ICOHPs/ICOOPs that should be summed.
+            divisor (float): Divisor used to divide the sum.
             summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
-            spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned.
+            spin: If not summed_spin_channels, indicate which spin channel should be returned.
 
         Returns:
             float: sum of all ICOHPs/ICOOPs as indicated with label_list.
@@ -1251,17 +1251,17 @@ def get_icohp_dict_of_site(
         maxbondlength: float = 8.0,
         only_bonds_to: list[str] | None = None,
     ) -> dict[str | float, IcohpValue]:
-        """Get a dict of IcohpValue for a certain site (indicated by integer).
+        """Get a dict of IcohpValue for a certain site.
 
         Args:
-            site (int): The site of interest, order as in Icohplist.lobster/Icooplist.lobster, starts at 0.
-            minsummedicohp (float): Minimal ICOHP/ICOOP of the bonds that are considered. It is the summed ICOHP value
-                from both spin channels for spin polarized cases
-            maxsummedicohp (float): Maximal ICOHP/ICOOP of the bonds that are considered. It is the summed ICOHP value
-                from both spin channels for spin polarized cases
+            site (int): The site of interest, ordered as in Icohplist.lobster/Icooplist.lobster, starts from 0.
+            minsummedicohp (float): Minimal ICOHP/ICOOP of the bonds that are considered.
+                It is the summed ICOHP value from both spin channels for spin polarized cases
+            maxsummedicohp (float): Maximal ICOHP/ICOOP of the bonds that are considered.
+                It is the summed ICOHP value from both spin channels for spin polarized cases
             minbondlength (float): The minimum bond length.
             maxbondlength (float): The maximum bond length.
-            only_bonds_to (list[str]): the bonding partners that are allowed, e.g. ["O"].
+            only_bonds_to (list[str]): The bonding partners that are allowed, e.g. ["O"].
 
         Returns:
             Dict of IcohpValues, the keys correspond to the values from the initial list_labels.
@@ -1303,9 +1303,10 @@ def extremum_icohpvalue(
         """Get ICOHP/ICOOP of the strongest bond.
 
         Args:
-            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
-
-            spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned
+            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both
+                spin channels should be summed.
+            spin: If not summed_spin_channels, this indicates which
+                spin channel should be returned.
 
         Returns:
             Lowest ICOHP/largest ICOOP value (i.e. ICOHP/ICOOP value of strongest bond).
@@ -1324,11 +1325,14 @@ def extremum_icohpvalue(
                         extremum = value.icohpvalue(spin)
                 elif value.icohpvalue(spin) > extremum:
                     extremum = value.icohpvalue(spin)
+
             elif not self._are_coops and not self._are_cobis:
                 if value.summed_icohp < extremum:
                     extremum = value.summed_icohp
+
             elif value.summed_icohp > extremum:
                 extremum = value.summed_icohp
+
         return extremum
 
     @property
@@ -1351,7 +1355,7 @@ def get_integrated_cohp_in_energy_range(
     cohp: CompleteCohp,
     label: CohpLabel,
     orbital: Orbital | None = None,
-    energy_range: float | list[float] | None = None,
+    energy_range: float | tuple[float, float] | None = None,
     relative_E_Fermi: bool = True,
     summed_spin_channels: bool = True,
 ) -> float | dict[Spin, float]:
@@ -1361,9 +1365,9 @@ def get_integrated_cohp_in_energy_range(
         cohp: CompleteCohp object.
         label: label of the COHP data.
         orbital: If not None, a orbital resolved integrated COHP will be returned.
-        energy_range: If None, returns ICOHP value at Fermi level.
-            If float, integrates from this float up to the Fermi level.
-            If [float, float], will integrate in between.
+        energy_range: If None, return the ICOHP value at Fermi level.
+            If float, integrate from this value up to Fermi level.
+            If (float, float), integrate in between.
         relative_E_Fermi (bool): if True, energy scale with E_Fermi at 0 eV is chosen
         summed_spin_channels (bool): Whether Spin channels will be summed.
 
@@ -1373,12 +1377,12 @@ def get_integrated_cohp_in_energy_range(
         else:
             dict: {Spin.up: float, Spin.down: float}
     """
-    summedicohp = {}
     if orbital is None:
         icohps = cohp.all_cohps[label].get_icohp(spin=None)
     else:
         icohps = cohp.get_orbital_resolved_cohp(label=label, orbitals=orbital).icohp
 
+    summedicohp = {}
     if summed_spin_channels and Spin.down in icohps:
         summedicohp[Spin.up] = icohps[Spin.up] + icohps[Spin.down]
     else:
@@ -1392,10 +1396,7 @@ def get_integrated_cohp_in_energy_range(
             spl_spindown = InterpolatedUnivariateSpline(energies_corrected, summedicohp[Spin.down], ext=0)
             return {Spin.up: spl_spinup(0.0), Spin.down: spl_spindown(0.0)}
 
-        if summed_spin_channels:
-            return spl_spinup(0.0)
-
-        return {Spin.up: spl_spinup(0.0)}
+        return spl_spinup(0.0) if summed_spin_channels else {Spin.up: spl_spinup(0.0)}
 
     # Return ICOHP value at the Fermi level
     if isinstance(energy_range, float):

From 773273684d9ed3c9f821b12629e94d189f8c1e85 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 18:18:58 +0800
Subject: [PATCH 14/39] clarify `label` as str

---
 pymatgen/electronic_structure/cohp.py | 31 ++++++++++++---------------
 pymatgen/electronic_structure/core.py |  1 -
 2 files changed, 14 insertions(+), 18 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 2ff424e27b5..34a02b58d15 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -32,16 +32,13 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
-    from typing import Any, Literal, Union
+    from typing import Any, Literal
 
     from numpy.typing import NDArray
     from typing_extensions import Self
 
     from pymatgen.util.typing import PathLike, SpinLike, Vector3D
 
-    # TODO: double check and clarify this custom type
-    CohpLabel = Union[str, int]
-
 __author__ = "Marco Esters, Janine George"
 __copyright__ = "Copyright 2017, The Materials Project"
 __version__ = "0.2"
@@ -192,7 +189,7 @@ def has_antibnd_states_below_efermi(
         """Get dict of antibonding states below the Fermi level for the spin.
 
         Args:
-            spin (SpinLike): selected spin.
+            spin (SpinLike): Selected spin.
             limit (float): Only COHP higher than this value will be considered.
         """
         populations = self.cohp
@@ -362,13 +359,13 @@ def as_dict(self) -> dict[str, Any]:
 
     def get_cohp_by_label(
         self,
-        label: CohpLabel,
+        label: str,
         summed_spin_channels: bool = False,
     ) -> Cohp:
         """Get specific Cohp by label, to simplify plotting.
 
         Args:
-            label: string (for newer LOBSTER versions: int)
+            label (str): Label for the interaction.
             summed_spin_channels (bool): Sum the spin channels and return the sum as Spin.up.
 
         Returns:
@@ -525,14 +522,14 @@ def get_summed_cohp_by_label_and_orbital_list(
 
     def get_orbital_resolved_cohp(
         self,
-        label: CohpLabel,
+        label: str,
         orbitals: str | list | tuple,
         summed_spin_channels: bool = False,
     ) -> Cohp | None:
         """Get orbital-resolved COHP.
 
         Args:
-            label: bond labels as in ICOHPLIST/ICOOPLIST.lobster.
+            label (str): bond labels as in ICOHPLIST/ICOOPLIST.lobster.
             orbitals: The orbitals as a label, or list/tuple of
                 [(n1, orbital1), (n2, orbital2), ...].
                 Where each orbital can either be str, int, or Orbital.
@@ -927,7 +924,7 @@ class IcohpValue(MSONable):
 
     def __init__(
         self,
-        label: CohpLabel,
+        label: str,
         atom1: str,
         atom2: str,
         length: float,
@@ -940,7 +937,7 @@ def __init__(
     ) -> None:
         """
         Args:
-            label: label for the ICOHP.
+            label (str): Label for the ICOHP.
             atom1 (str): The first atom that contributes to the bond.
             atom2 (str): The second atom that contributes to the bond.
             length (float): Bond length.
@@ -1160,7 +1157,7 @@ def __str__(self) -> str:
 
     def get_icohp_by_label(
         self,
-        label: CohpLabel,
+        label: str,
         summed_spin_channels: bool = True,
         spin: Spin = Spin.up,
         orbitals: str | list[Orbital] | None = None,  # TODO: change to tuple of 2
@@ -1169,7 +1166,7 @@ def get_icohp_by_label(
         (bond labels starting from "1" as in ICOHPLIST/ICOOPLIST).
 
         Args:
-            label (str): usually the bond number in Icohplist.lobster/Icooplist.lobster.
+            label (str): The bond number in Icohplist.lobster/Icooplist.lobster.
             summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
             spin: If summed_spin_channels is False, this spin indicates which spin channel should be returned.
             orbitals: List of Orbital or "str(Orbital1)-str(Orbital2)".
@@ -1353,7 +1350,7 @@ def are_cobis(self) -> bool:
 
 def get_integrated_cohp_in_energy_range(
     cohp: CompleteCohp,
-    label: CohpLabel,
+    label: str,
     orbital: Orbital | None = None,
     energy_range: float | tuple[float, float] | None = None,
     relative_E_Fermi: bool = True,
@@ -1362,13 +1359,13 @@ def get_integrated_cohp_in_energy_range(
     """Integrate CompleteCohps which include data of integrated COHPs (ICOHPs).
 
     Args:
-        cohp: CompleteCohp object.
-        label: label of the COHP data.
+        cohp (CompleteCohp): CompleteCohp object.
+        label (str): Label of the COHP data.
         orbital: If not None, a orbital resolved integrated COHP will be returned.
         energy_range: If None, return the ICOHP value at Fermi level.
             If float, integrate from this value up to Fermi level.
             If (float, float), integrate in between.
-        relative_E_Fermi (bool): if True, energy scale with E_Fermi at 0 eV is chosen
+        relative_E_Fermi (bool): If True, energy scale with E_Fermi at 0 eV is chosen.
         summed_spin_channels (bool): Whether Spin channels will be summed.
 
     Returns:
diff --git a/pymatgen/electronic_structure/core.py b/pymatgen/electronic_structure/core.py
index bd887f64a25..cfac056dd42 100644
--- a/pymatgen/electronic_structure/core.py
+++ b/pymatgen/electronic_structure/core.py
@@ -473,7 +473,6 @@ def get_moment_relative_to_crystal_axes(self, lattice: Lattice):
         """
         # Get matrix representing unit lattice vectors
         unit_m = lattice.matrix / np.linalg.norm(lattice.matrix, axis=1)[:, None]
-        # Note np.matmul() requires numpy version >= 1.10
         moment = np.matmul(self.global_moment, np.linalg.inv(unit_m))
         # Round small values to zero
         moment[np.abs(moment) < 1e-8] = 0

From aaf9f298c6c8a9506a6865c4095f692fdcc314e7 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 19:03:56 +0800
Subject: [PATCH 15/39] more type and docstring improvements

---
 pymatgen/electronic_structure/cohp.py | 250 ++++++++++++++------------
 1 file changed, 131 insertions(+), 119 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 34a02b58d15..0e7b3345a21 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -67,13 +67,13 @@ def __init__(
     ) -> None:
         """
         Args:
-            efermi: The Fermi level.
-            energies: A sequence of energies.
-            cohp ({Spin: np.array}): representing the COHP for each spin.
-            are_coops: Indicates whether this object describes COOPs.
-            are_cobis: Indicates whether this object describes COBIs.
-            are_multi_center_cobis: Indicates whether this object describes multi-center COBIs
-            icohp ({Spin: np.array}): representing the ICOHP for each spin.
+            efermi (float): The Fermi level.
+            energies (Sequence[float]): Energies.
+            cohp ({Spin: NDArrary}): The COHP for each spin.
+            are_coops (bool): Whether this object describes COOPs.
+            are_cobis (bool): Whether this object describes COBIs.
+            are_multi_center_cobis (bool): Whether this object describes multi-center COBIs.
+            icohp ({Spin: NDArrary}): The ICOHP for each spin.
         """
         self.are_coops = are_coops
         self.are_cobis = are_cobis
@@ -84,7 +84,7 @@ def __init__(
         self.icohp = icohp
 
     def __repr__(self) -> str:
-        """Get a string that can be easily plotted (e.g. using gnuplot)."""
+        """A string that can be easily plotted (e.g. using gnuplot)."""
         if self.are_coops:
             cohp_str = "COOP"
         elif self.are_cobis or self.are_multi_center_cobis:
@@ -134,8 +134,8 @@ def get_cohp(
         """Get the COHP or ICOHP for a particular spin.
 
         Args:
-            spin: Spin, integer (-1/1) or str ("up"/"down"). If is None
-                and both spins are present, both will be returned.
+            spin (SpinLike): Selected spin. If is None and both
+                spins are present, both will be returned.
             integrated: Return ICOHP (True) or COHP (False).
 
         Returns:
@@ -168,8 +168,8 @@ def get_interpolated_value(
         """Get the interpolated COHP for a particular energy.
 
         Args:
-            energy: Energy to return the COHP value for.
-            integrated: Return ICOHP (True) or COHP (False).
+            energy (float): Energy to get the COHP value for.
+            integrated (bool): Return ICOHP (True) or COHP (False).
         """
         inters = {}
         for spin in self.cohp:
@@ -248,30 +248,30 @@ def __init__(
         structure: Structure,
         avg_cohp: Cohp,
         cohp_dict: dict[str, Cohp],
-        bonds: dict | None = None,  # TODO: DanielYang: more specific type
+        bonds: dict[str, Any] | None = None,
         are_coops: bool = False,
         are_cobis: bool = False,
         are_multi_center_cobis: bool = False,
-        orb_res_cohp: Cohp | None = None,
+        orb_res_cohp: Cohp | None = None,  # TODO: DanielYang: double check type
     ) -> None:
         """
         Args:
-            structure: Structure associated with this COHP.
-            avg_cohp: The average COHP as a Cohp object.
-            cohp_dict (dict): COHP objects for individual bonds of the form
+            structure (Structure): Structure associated with this COHP.
+            avg_cohp (Cohp): The average COHP.
+            cohp_dict (dict[str, Cohp]): COHP for individual bonds of the form
                 {label: COHP}.
-            bonds: A dict containing information on the bonds of the form
-                {label: {key: val}}. The key-val pair can be any information
-                the user wants to put in, but typically contains the sites,
-                the bond length, and the number of bonds. If nothing is
+            bonds (dict[str, Any]): Information on the bonds of the form
+                {label: {key: val}}. The value can be any information,
+                but typically contains the sites, the bond length,
+                and the number of bonds. If nothing is
                 supplied, it will default to an empty dict.
-            are_coops: indicates whether the Cohp objects are COOPs.
+            are_coops (bool): Whether the Cohp objects are COOPs.
                 Defaults to False for COHPs.
-            are_cobis: indicates whether the Cohp objects are COBIs.
+            are_cobis (bool): Whether the Cohp objects are COBIs.
                 Defaults to False for COHPs.
-            are_multi_center_cobis: indicates whether the Cohp objects are multi-center COBIs.
+            are_multi_center_cobis (bool): Whether the Cohp objects are multi-center COBIs.
                 Defaults to False for COHPs.
-            orb_res_cohp: Orbital-resolved COHPs.
+            orb_res_cohp (Cohp): Orbital-resolved COHPs.
         """
         if (
             (are_coops and are_cobis)
@@ -299,10 +299,13 @@ def __init__(
 
     def __str__(self) -> str:
         if self.are_coops:
-            return f"Complete COOPs for {self.structure}"
-        if self.are_cobis:
-            return f"Complete COBIs for {self.structure}"
-        return f"Complete COHPs for {self.structure}"
+            header = "COOPs"
+        elif self.are_cobis:
+            header = "COBIs"
+        else:
+            header = "COHPs"
+
+        return f"Complete {header} for {self.structure}"
 
     def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of CompleteCohp."""
@@ -362,7 +365,7 @@ def get_cohp_by_label(
         label: str,
         summed_spin_channels: bool = False,
     ) -> Cohp:
-        """Get specific Cohp by label, to simplify plotting.
+        """Get specific Cohp by the label, to simplify plotting.
 
         Args:
             label (str): Label for the interaction.
@@ -382,9 +385,9 @@ def get_cohp_by_label(
         assert divided_cohp is not None
 
         if summed_spin_channels and Spin.down in self.cohp:
-            assert divided_icohp is not None
             final_cohp = {}
             final_icohp = {}
+            assert divided_icohp is not None
             final_cohp[Spin.up] = np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)
             final_icohp[Spin.up] = np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)
         else:
@@ -402,35 +405,35 @@ def get_cohp_by_label(
 
     def get_summed_cohp_by_label_list(
         self,
-        label_list: list[str | float],
+        label_list: list[str],
         divisor: float = 1,
         summed_spin_channels: bool = False,
     ) -> Cohp:
-        """Get a COHP object that includes a summed COHP divided by divisor.
+        """Get a Cohp object that includes a summed COHP divided by divisor.
 
         Args:
-            label_list: list of labels for the COHP that should be included in the sum.
+            label_list (list[str]): Labels for the COHP to include.
             divisor (float): The summed COHP will be divided by this divisor.
             summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
-            A Cohp object including a summed COHP.
+            A Cohp object for the summed COHP.
         """
         # Check if COHPs are spin polarized
         first_cohpobject = self.get_cohp_by_label(label_list[0])
         summed_cohp = first_cohpobject.cohp.copy()
         summed_icohp = first_cohpobject.icohp.copy()
         for label in label_list[1:]:
-            cohp_here = self.get_cohp_by_label(label)
-            summed_cohp[Spin.up] = np.sum([summed_cohp[Spin.up], cohp_here.cohp[Spin.up]], axis=0)
+            cohp = self.get_cohp_by_label(label)
+            summed_cohp[Spin.up] = np.sum([summed_cohp[Spin.up], cohp.cohp[Spin.up]], axis=0)
 
             if Spin.down in summed_cohp:
-                summed_cohp[Spin.down] = np.sum([summed_cohp[Spin.down], cohp_here.cohp[Spin.down]], axis=0)
+                summed_cohp[Spin.down] = np.sum([summed_cohp[Spin.down], cohp.cohp[Spin.down]], axis=0)
 
-            summed_icohp[Spin.up] = np.sum([summed_icohp[Spin.up], cohp_here.icohp[Spin.up]], axis=0)
+            summed_icohp[Spin.up] = np.sum([summed_icohp[Spin.up], cohp.icohp[Spin.up]], axis=0)
 
             if Spin.down in summed_icohp:
-                summed_icohp[Spin.down] = np.sum([summed_icohp[Spin.down], cohp_here.icohp[Spin.down]], axis=0)
+                summed_icohp[Spin.down] = np.sum([summed_icohp[Spin.down], cohp.icohp[Spin.down]], axis=0)
 
         divided_cohp = {}
         divided_icohp = {}
@@ -460,7 +463,7 @@ def get_summed_cohp_by_label_list(
 
     def get_summed_cohp_by_label_and_orbital_list(
         self,
-        label_list: list[str | float],
+        label_list: list[str],
         orbital_list: list,  # TODO (DanielYang): what is the type of orbital? Add custom type for it
         divisor: float = 1,
         summed_spin_channels: bool = False,
@@ -468,14 +471,14 @@ def get_summed_cohp_by_label_and_orbital_list(
         """Get a Cohp object that includes a summed COHP divided by divisor.
 
         Args:
-            label_list: list of labels for the COHP that should be included.
-            orbital_list: list of orbitals for the COHPs that should be included
-                (same order as label_list)
-            divisor (float): the summed COHP will be divided by this divisor.
+            label_list (list[str]): Labels for the COHP that should be included.
+            orbital_list (list): Orbitals for the COHPs that should be included
+                (same order as label_list).
+            divisor (float): The summed COHP will be divided by this divisor.
             summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
 
         Returns:
-            A Cohp object including a summed COHP
+            A Cohp object including the summed COHP.
         """
         # Check length of label_list and orbital_list
         if not len(label_list) == len(orbital_list):
@@ -486,13 +489,13 @@ def get_summed_cohp_by_label_and_orbital_list(
         summed_cohp = first_cohpobject.cohp.copy()
         summed_icohp = first_cohpobject.icohp.copy()
         for idx, label in enumerate(label_list[1:], start=1):
-            cohp_here = self.get_orbital_resolved_cohp(label, orbital_list[idx])
-            summed_cohp[Spin.up] = np.sum([summed_cohp[Spin.up], cohp_here.cohp.copy()[Spin.up]], axis=0)
+            cohp = self.get_orbital_resolved_cohp(label, orbital_list[idx])
+            summed_cohp[Spin.up] = np.sum([summed_cohp[Spin.up], cohp.cohp.copy()[Spin.up]], axis=0)
             if Spin.down in summed_cohp:
-                summed_cohp[Spin.down] = np.sum([summed_cohp[Spin.down], cohp_here.cohp.copy()[Spin.down]], axis=0)
-            summed_icohp[Spin.up] = np.sum([summed_icohp[Spin.up], cohp_here.icohp.copy()[Spin.up]], axis=0)
+                summed_cohp[Spin.down] = np.sum([summed_cohp[Spin.down], cohp.cohp.copy()[Spin.down]], axis=0)
+            summed_icohp[Spin.up] = np.sum([summed_icohp[Spin.up], cohp.icohp.copy()[Spin.up]], axis=0)
             if Spin.down in summed_icohp:
-                summed_icohp[Spin.down] = np.sum([summed_icohp[Spin.down], cohp_here.icohp.copy()[Spin.down]], axis=0)
+                summed_icohp[Spin.down] = np.sum([summed_icohp[Spin.down], cohp.icohp.copy()[Spin.down]], axis=0)
 
         divided_cohp = {}
         divided_icohp = {}
@@ -529,15 +532,16 @@ def get_orbital_resolved_cohp(
         """Get orbital-resolved COHP.
 
         Args:
-            label (str): bond labels as in ICOHPLIST/ICOOPLIST.lobster.
+            label (str): Bond labels as in ICOHPLIST/ICOOPLIST.lobster.
             orbitals: The orbitals as a label, or list/tuple of
                 [(n1, orbital1), (n2, orbital2), ...].
                 Where each orbital can either be str, int, or Orbital.
-            summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
+                # TODO: DanielYang: clarify type
+            summed_spin_channels (bool): Sum the spin channels and return the sum as Spin.up.
 
         Returns:
             A Cohp object if CompleteCohp contains orbital-resolved COHP,
-            or None if it doesn't.
+                or None if it doesn't.
 
         Note: It currently assumes that orbitals are str if they aren't the
             other valid types. This is not ideal, but is the easiest way to
@@ -594,9 +598,9 @@ def get_orbital_resolved_cohp(
 
     @classmethod
     def from_dict(cls, dct: dict[str, Any]) -> Self:
-        """Get CompleteCohp object from dict representation.
+        """Get CompleteCohp object from a dict representation.
 
-        TODO: clean this up
+        TODO: Clean this up.
         """
         cohp_dict = {}
         efermi = dct["efermi"]
@@ -661,9 +665,9 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:
                         "orbitals": orbitals,
                     }
                 # If no total COHPs are present, calculate the total
-                # COHPs from the single-orbital populations. Total COHPs
-                # may not be present when the COHP generator keyword is used
-                # in LOBSTER versions 2.2.0 and earlier.
+                # COHPs from the single-orbital populations.
+                # Total COHPs may not be present when the COHP generator keyword
+                # is used in LOBSTER versions 2.2.0 and earlier.
                 if label not in dct["COHP"] or dct["COHP"][label] is None:
                     cohp = {
                         Spin.up: np.sum(
@@ -722,17 +726,16 @@ def from_file(
 
         Args:
             fmt (Literal["LMTO", "LOBSTER"]): The code used to calculate COHPs.
-            filename: Name of the COHP output file. Defaults to COPL
-                for LMTO and COHPCAR.lobster/COOPCAR.lobster for LOBSTER.
-            structure_file: Name of the file containing the structure.
-                If no file name is given, use CTRL for LMTO and POSCAR
-                for LOBSTER.
-            are_coops: Indicates whether the populations are COOPs or
-                COHPs. Defaults to False for COHPs.
-            are_cobis: Indicates whether the populations are COBIs or
-                COHPs. Defaults to False for COHPs.
-            are_multi_center_cobis: Indicates whether this file
-                includes information on multi-center COBIs
+            filename (PathLike): The COHP output file. Defaults to "COPL"
+                for LMTO and "COHPCAR.lobster/COOPCAR.lobster" for LOBSTER.
+            structure_file (PathLike): The file containing the structure.
+                If None, use "CTRL" for LMTO and "POSCAR" for LOBSTER.
+            are_coops (bool): Whether the populations are COOPs or COHPs.
+                Defaults to False for COHPs.
+            are_cobis (bool): Whether the populations are COBIs or COHPs.
+                Defaults to False for COHPs.
+            are_multi_center_cobis (bool): Whether this file
+                includes information on multi-center COBIs.
 
         Returns:
             A CompleteCohp object.
@@ -740,9 +743,8 @@ def from_file(
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
 
-        fmt = fmt.upper()
-        if fmt == "LMTO":
-            # LMTO COOPs and orbital-resolved COHP cannot be handled yet
+        if fmt.upper() == "LMTO":
+            # TODO: LMTO COOPs and orbital-resolved COHP cannot be handled yet
             are_coops = False
             are_cobis = False
             orb_res_cohp = None
@@ -750,9 +752,10 @@ def from_file(
                 structure_file = "CTRL"
             if filename is None:
                 filename = "COPL"
+
             cohp_file: LMTOCopl | Cohpcar = LMTOCopl(filename=filename, to_eV=True)
 
-        elif fmt == "LOBSTER":
+        elif fmt.upper() == "LOBSTER":
             if (
                 (are_coops and are_cobis)
                 or (are_coops and are_multi_center_cobis)
@@ -930,10 +933,10 @@ def __init__(
         length: float,
         translation: Vector3D,
         num: int,
-        icohp: dict,  # more specific type
+        icohp: dict[Spin, IcohpValue],
         are_coops: bool = False,
         are_cobis: bool = False,
-        orbitals: dict | None = None,  # TODO: DanielYang: more specific type
+        orbitals: dict[str, dict[Literal["icohp", "orbitals"], Any]] | None = None,
     ) -> None:
         """
         Args:
@@ -941,13 +944,17 @@ def __init__(
             atom1 (str): The first atom that contributes to the bond.
             atom2 (str): The second atom that contributes to the bond.
             length (float): Bond length.
-            translation: cell translation vector, e.g. (0, 0, 0).
+            translation (Vector3D): cell translation vector, e.g. (0, 0, 0).
             num (int): How often the bond exists.  # TODO: DanielYang: clarify this description
-            icohp: dict={Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}
-            are_coops (bool): If True, this are COOPs
-            are_cobis (bool): If True, this are COBIs
-            orbitals: {[str(Orbital1)-str(Orbital2)]: {"icohp": {Spin.up: IcohpValue for spin.up, Spin.down:
-                IcohpValue for spin.down}, "orbitals": [Orbital1, Orbital2]}}.
+            icohp (dict): {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}
+            are_coops (bool): Whether these are COOPs.
+            are_cobis (bool): Whether these are COBIs.
+            orbitals (dict): {[str(Orbital1)-str(Orbital2)]: {
+                "icohp": {
+                            Spin.up: IcohpValue for spin.up,
+                            Spin.down: IcohpValue for spin.down
+                        },
+                "orbitals": [Orbital1, Orbital2, ...]}.
         """
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
@@ -1014,7 +1021,7 @@ def are_cobis(self) -> bool:
 
     @property
     def is_spin_polarized(self) -> bool:
-        """Whether this is spin polarized calculation.
+        """Whether this is a spin polarized calculation.
 
         Returns:
             bool
@@ -1038,7 +1045,7 @@ def icohpvalue_orbital(self, orbitals: list[Orbital] | str, spin: Spin = Spin.up
         """
         Args:
             orbitals (list[Orbitals]): List of Orbitals or "str(Orbital1)-str(Orbital2)".
-            spin: Spin.up or Spin.down.
+            spin (Spin): Spin.up or Spin.down.
 
         Returns:
             float: ICOHP value corresponding to chosen spin.
@@ -1073,7 +1080,7 @@ def summed_orbital_icohp(self) -> dict[str, float]:
         """Summed orbital-resolved ICOHPs of both spin channels if spin-polarized.
 
         Returns:
-            dict[str, float]: "str(Orbital1)-str(Ortibal2)" mapped to ICOHP value in eV.
+            dict[str, float]: "str(Orbital1)-str(Ortibal2)": ICOHP value in eV.
         """
         orbital_icohp = {}
         for orb, item in self._orbitals.items():
@@ -1094,7 +1101,7 @@ class IcohpCollection(MSONable):
 
     def __init__(
         self,
-        list_labels: list,
+        list_labels: list[str],
         list_atom1: list[str],
         list_atom2: list[str],
         list_length: list[float],
@@ -1102,13 +1109,13 @@ def __init__(
         list_num: list[int],
         list_icohp: list[dict[Spin, IcohpValue]],
         is_spin_polarized: bool,
-        list_orb_icohp: list[dict] | None = None,  # TODO: more specific type
+        list_orb_icohp: list[dict[str, dict[Literal["icohp", "orbitals"], Any]]] | None = None,
         are_coops: bool = False,
         are_cobis: bool = False,
     ) -> None:
         """
         Args:
-            list_labels (list): Labels for ICOHP/ICOOP values.
+            list_labels (list[str]): Labels for ICOHP/ICOOP values.
             list_atom1 (list[str]): Atom names, e.g. "O1".
             list_atom2 (list[str]): Atom names, e.g. "O1".
             list_length (list[float]): Bond lengths in Angstrom.
@@ -1116,9 +1123,9 @@ def __init__(
             list_num (list[int]): Numbers of equivalent bonds, usually 1 starting from LOBSTER 3.0.0.
             list_icohp (list[dict]): Dicts as {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
             is_spin_polarized (bool): Whether the calculation is spin polarized.
-            list_orb_icohp (list[dict]): Dicts as {[str(Orbital1)-str(Orbital2)]:
-                {"icohp": {Spin.up: IcohpValue for spin.up,
-                Spin.down: IcohpValue for spin.down}, "orbitals": [Orbital1, Orbital2]}}.
+            list_orb_icohp (list[dict]): Dicts as {[str(Orbital1)-str(Orbital2)]: {
+                "icohp": {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down},
+                "orbitals": [Orbital1, Orbital2]}.
             are_coops (bool): Whether ICOOPs are stored.
             are_cobis (bool): Whether ICOBIs are stored.
         """
@@ -1160,19 +1167,21 @@ def get_icohp_by_label(
         label: str,
         summed_spin_channels: bool = True,
         spin: Spin = Spin.up,
-        orbitals: str | list[Orbital] | None = None,  # TODO: change to tuple of 2
+        orbitals: str | list[Orbital] | None = None,  # TODO: DanielYang: use tuple of 2
     ) -> float:
-        """Get an ICOHP value for a certain bond as indicated by the label
-        (bond labels starting from "1" as in ICOHPLIST/ICOOPLIST).
+        """Get an ICOHP value for a certain bond indicated by the label.
 
         Args:
-            label (str): The bond number in Icohplist.lobster/Icooplist.lobster.
-            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
-            spin: If summed_spin_channels is False, this spin indicates which spin channel should be returned.
+            label (str): The bond number in Icohplist.lobster/Icooplist.lobster,
+                starting from "1".
+            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both
+                spin channels should be summed.
+            spin (Spin): If not summed_spin_channels, indicate
+                which spin channel should be returned.
             orbitals: List of Orbital or "str(Orbital1)-str(Orbital2)".
 
         Returns:
-            float: ICOHP/ICOOP value
+            float: ICOHP/ICOOP value.
         """
         icohp: IcohpValue = self._icohplist[label]
 
@@ -1189,33 +1198,35 @@ def get_icohp_by_label(
 
     def get_summed_icohp_by_label_list(
         self,
-        label_list: list[str | float],
+        label_list: list[str],
         divisor: float = 1.0,
         summed_spin_channels: bool = True,
         spin: Spin = Spin.up,
     ) -> float:
-        """Get the sum of several ICOHP values that are indicated by a list of labels
-        (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST).
+        """Get the sum of ICOHP values.
 
         Args:
-            label_list (list): Labels of the ICOHPs/ICOOPs that should be summed.
+            label_list (list[str]): Labels of the ICOHPs/ICOOPs that should be summed,
+                the same as in ICOHPLIST/ICOOPLIST.
             divisor (float): Divisor used to divide the sum.
-            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both spin channels should be summed.
-            spin: If not summed_spin_channels, indicate which spin channel should be returned.
+            summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both
+                spin channels should be summed.
+            spin (Spin): If not summed_spin_channels, indicate
+                which spin channel should be returned.
 
         Returns:
-            float: sum of all ICOHPs/ICOOPs as indicated with label_list.
+            float: Sum of ICOHPs selected with label_list.
         """
         sum_icohp = 0
         for label in label_list:
-            icohp_here = self._icohplist[label]
-            if icohp_here.num_bonds != 1:
+            icohp = self._icohplist[label]
+            if icohp.num_bonds != 1:
                 warnings.warn("One of the ICOHP values is an average over bonds. This is currently not considered.")
 
-            if icohp_here._is_spin_polarized and summed_spin_channels:
-                sum_icohp = sum_icohp + icohp_here.summed_icohp
+            if icohp._is_spin_polarized and summed_spin_channels:
+                sum_icohp = sum_icohp + icohp.summed_icohp
             else:
-                sum_icohp = sum_icohp + icohp_here.icohpvalue(spin)
+                sum_icohp = sum_icohp + icohp.icohpvalue(spin)
 
         return sum_icohp / divisor
 
@@ -1223,19 +1234,19 @@ def get_icohp_dict_by_bondlengths(
         self,
         minbondlength: float = 0.0,
         maxbondlength: float = 8.0,
-    ) -> dict[str | float, IcohpValue]:
-        """Get a dict of IcohpValues corresponding to certain bond lengths.
+    ) -> dict[str, IcohpValue]:
+        """Get IcohpValues within certain bond length range.
 
         Args:
             minbondlength (float): The minimum bond length.
             maxbondlength (float): The maximum bond length.
 
         Returns:
-            dict of IcohpValues, the keys correspond to the values from the initial list_labels.
+            dict[str, IcohpValue]: Keys are the labels from the initial list_labels.
         """
         new_icohp_dict = {}
         for value in self._icohplist.values():
-            if value._length >= minbondlength and value._length <= maxbondlength:
+            if minbondlength <= value._length <= maxbondlength:
                 new_icohp_dict[value._label] = value
         return new_icohp_dict
 
@@ -1248,10 +1259,11 @@ def get_icohp_dict_of_site(
         maxbondlength: float = 8.0,
         only_bonds_to: list[str] | None = None,
     ) -> dict[str | float, IcohpValue]:
-        """Get a dict of IcohpValue for a certain site.
+        """Get IcohpValues for a certain site.
 
         Args:
-            site (int): The site of interest, ordered as in Icohplist.lobster/Icooplist.lobster, starts from 0.
+            site (int): The site of interest, ordered as in Icohplist.lobster/Icooplist.lobster,
+                starts from 0.
             minsummedicohp (float): Minimal ICOHP/ICOOP of the bonds that are considered.
                 It is the summed ICOHP value from both spin channels for spin polarized cases
             maxsummedicohp (float): Maximal ICOHP/ICOOP of the bonds that are considered.
@@ -1275,7 +1287,7 @@ def get_icohp_dict_of_site(
                     value._atom2 = save
 
                 second_test = True if only_bonds_to is None else re.split("(\\d+)", value._atom2)[0] in only_bonds_to
-                if value._length >= minbondlength and value._length <= maxbondlength and second_test:
+                if minbondlength <= value._length <= maxbondlength and second_test:
                     # TODO: DanielYang: merge the following condition blocks
                     if minsummedicohp is not None:
                         if value.summed_icohp >= minsummedicohp:
@@ -1302,7 +1314,7 @@ def extremum_icohpvalue(
         Args:
             summed_spin_channels (bool): Whether the ICOHPs/ICOOPs of both
                 spin channels should be summed.
-            spin: If not summed_spin_channels, this indicates which
+            spin (Spin): If not summed_spin_channels, this indicates which
                 spin channel should be returned.
 
         Returns:
@@ -1365,7 +1377,7 @@ def get_integrated_cohp_in_energy_range(
         energy_range: If None, return the ICOHP value at Fermi level.
             If float, integrate from this value up to Fermi level.
             If (float, float), integrate in between.
-        relative_E_Fermi (bool): If True, energy scale with E_Fermi at 0 eV is chosen.
+        relative_E_Fermi (bool): Whether energy scale with Fermi level at 0 eV is chosen.
         summed_spin_channels (bool): Whether Spin channels will be summed.
 
     Returns:

From 950eb1066f2fcd136915f7560a34ec091b57e6ae Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 19:18:24 +0800
Subject: [PATCH 16/39] fix unit test

---
 pymatgen/electronic_structure/cohp.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 0e7b3345a21..65b49a164ed 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -743,7 +743,8 @@ def from_file(
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
 
-        if fmt.upper() == "LMTO":
+        fmt = fmt.upper()
+        if fmt == "LMTO":
             # TODO: LMTO COOPs and orbital-resolved COHP cannot be handled yet
             are_coops = False
             are_cobis = False
@@ -755,7 +756,7 @@ def from_file(
 
             cohp_file: LMTOCopl | Cohpcar = LMTOCopl(filename=filename, to_eV=True)
 
-        elif fmt.upper() == "LOBSTER":
+        elif fmt == "LOBSTER":
             if (
                 (are_coops and are_cobis)
                 or (are_coops and are_multi_center_cobis)

From 5a2ec9f83f70e9fd8537508ba3fd46fb4abb6847 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 21:05:30 +0800
Subject: [PATCH 17/39] fix most mypy errors

---
 pymatgen/electronic_structure/cohp.py | 109 ++++++++++++++------------
 1 file changed, 61 insertions(+), 48 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 65b49a164ed..7b977becf96 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -39,6 +39,9 @@
 
     from pymatgen.util.typing import PathLike, SpinLike, Vector3D
 
+    # TODO: use more specific type
+    CohpOrbital = str | int | Orbital
+
 __author__ = "Marco Esters, Janine George"
 __copyright__ = "Copyright 2017, The Materials Project"
 __version__ = "0.2"
@@ -252,7 +255,7 @@ def __init__(
         are_coops: bool = False,
         are_cobis: bool = False,
         are_multi_center_cobis: bool = False,
-        orb_res_cohp: Cohp | None = None,  # TODO: DanielYang: double check type
+        orb_res_cohp: dict[str, dict] | None = None,
     ) -> None:
         """
         Args:
@@ -271,7 +274,7 @@ def __init__(
                 Defaults to False for COHPs.
             are_multi_center_cobis (bool): Whether the Cohp objects are multi-center COBIs.
                 Defaults to False for COHPs.
-            orb_res_cohp (Cohp): Orbital-resolved COHPs.
+            orb_res_cohp (dict): Orbital-resolved COHPs.
         """
         if (
             (are_coops and are_cobis)
@@ -326,15 +329,13 @@ def as_dict(self) -> dict[str, Any]:
 
         for label in self.all_cohps:
             dct["COHP"] |= {label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].cohp.items()}}
-            if self.all_cohps[label].icohp is not None:
+            icohp = self.all_cohps[label].icohp
+            if icohp is not None:
+                # TODO: DanielYang59: merge two condition branches with "|=" operator?
                 if "ICOHP" not in dct:
-                    dct["ICOHP"] = {
-                        label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].icohp.items()}
-                    }
+                    dct["ICOHP"] = {label: {str(spin): pops.tolist() for spin, pops in icohp.items()}}
                 else:
-                    dct["ICOHP"] |= {
-                        label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].icohp.items()}
-                    }
+                    dct["ICOHP"] |= {label: {str(spin): pops.tolist() for spin, pops in icohp.items()}}
 
         if False in [bond_dict == {} for bond_dict in self.bonds.values()]:
             dct["bonds"] = {
@@ -350,12 +351,16 @@ def as_dict(self) -> dict[str, Any]:
             for label in self.orb_res_cohp:
                 orb_dict[label] = {}
                 for orbs in self.orb_res_cohp[label]:
-                    cohp = {str(spin): pops.tolist() for spin, pops in self.orb_res_cohp[label][orbs]["COHP"].items()}
-                    orb_dict[label][orbs] = {"COHP": cohp}
-                    icohp = {str(spin): pops.tolist() for spin, pops in self.orb_res_cohp[label][orbs]["ICOHP"].items()}
-                    orb_dict[label][orbs]["ICOHP"] = icohp
-                    orbitals = [[orb[0], orb[1].name] for orb in self.orb_res_cohp[label][orbs]["orbitals"]]
-                    orb_dict[label][orbs]["orbitals"] = orbitals
+                    orb_dict[label][orbs] = {
+                        "COHP": {
+                            str(spin): pops.tolist() for spin, pops in self.orb_res_cohp[label][orbs]["COHP"].items()
+                        },
+                        "ICOHP": {
+                            str(spin): pops.tolist() for spin, pops in self.orb_res_cohp[label][orbs]["ICOHP"].items()
+                        },
+                        "orbitals": [[orb[0], orb[1].name] for orb in self.orb_res_cohp[label][orbs]["orbitals"]],
+                    }
+
             dct["orb_res_cohp"] = orb_dict
 
         return dct
@@ -377,7 +382,6 @@ def get_cohp_by_label(
         if label.lower() == "average":
             divided_cohp: dict[Spin, Any] | None = self.cohp
             divided_icohp: dict[Spin, Any] | None = self.icohp
-
         else:
             divided_cohp = self.all_cohps[label].get_cohp(spin=None, integrated=False)
             divided_icohp = self.all_cohps[label].get_icohp(spin=None)
@@ -385,11 +389,11 @@ def get_cohp_by_label(
         assert divided_cohp is not None
 
         if summed_spin_channels and Spin.down in self.cohp:
-            final_cohp = {}
-            final_icohp = {}
             assert divided_icohp is not None
-            final_cohp[Spin.up] = np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)
-            final_icohp[Spin.up] = np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)
+            final_cohp: dict[Spin, Any] = {Spin.up: np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)}
+            final_icohp: dict[Spin, Any] | None = {
+                Spin.up: np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)
+            }
         else:
             final_cohp = divided_cohp
             final_icohp = divided_icohp
@@ -422,32 +426,31 @@ def get_summed_cohp_by_label_list(
         # Check if COHPs are spin polarized
         first_cohpobject = self.get_cohp_by_label(label_list[0])
         summed_cohp = first_cohpobject.cohp.copy()
+        assert first_cohpobject.icohp is not None
         summed_icohp = first_cohpobject.icohp.copy()
         for label in label_list[1:]:
             cohp = self.get_cohp_by_label(label)
+            icohp = cohp.icohp
+            assert icohp is not None
             summed_cohp[Spin.up] = np.sum([summed_cohp[Spin.up], cohp.cohp[Spin.up]], axis=0)
 
             if Spin.down in summed_cohp:
                 summed_cohp[Spin.down] = np.sum([summed_cohp[Spin.down], cohp.cohp[Spin.down]], axis=0)
 
-            summed_icohp[Spin.up] = np.sum([summed_icohp[Spin.up], cohp.icohp[Spin.up]], axis=0)
+            summed_icohp[Spin.up] = np.sum([summed_icohp[Spin.up], icohp[Spin.up]], axis=0)
 
             if Spin.down in summed_icohp:
-                summed_icohp[Spin.down] = np.sum([summed_icohp[Spin.down], cohp.icohp[Spin.down]], axis=0)
+                summed_icohp[Spin.down] = np.sum([summed_icohp[Spin.down], icohp[Spin.down]], axis=0)
 
-        divided_cohp = {}
-        divided_icohp = {}
-        divided_cohp[Spin.up] = np.divide(summed_cohp[Spin.up], divisor)
-        divided_icohp[Spin.up] = np.divide(summed_icohp[Spin.up], divisor)
+        divided_cohp = {Spin.up: np.divide(summed_cohp[Spin.up], divisor)}
+        divided_icohp = {Spin.up: np.divide(summed_icohp[Spin.up], divisor)}
         if Spin.down in summed_cohp:
             divided_cohp[Spin.down] = np.divide(summed_cohp[Spin.down], divisor)
             divided_icohp[Spin.down] = np.divide(summed_icohp[Spin.down], divisor)
 
         if summed_spin_channels and Spin.down in summed_cohp:
-            final_cohp = {}
-            final_icohp = {}
-            final_cohp[Spin.up] = np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)
-            final_icohp[Spin.up] = np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)
+            final_cohp = {Spin.up: np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)}
+            final_icohp = {Spin.up: np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)}
         else:
             final_cohp = divided_cohp
             final_icohp = divided_icohp
@@ -464,7 +467,7 @@ def get_summed_cohp_by_label_list(
     def get_summed_cohp_by_label_and_orbital_list(
         self,
         label_list: list[str],
-        orbital_list: list,  # TODO (DanielYang): what is the type of orbital? Add custom type for it
+        orbital_list: list,  # TODO (DanielYang): what is its type? Add custom type for it?
         divisor: float = 1,
         summed_spin_channels: bool = False,
     ) -> Cohp:
@@ -486,30 +489,32 @@ def get_summed_cohp_by_label_and_orbital_list(
 
         # Check if COHPs are spin polarized
         first_cohpobject = self.get_orbital_resolved_cohp(label_list[0], orbital_list[0])
+        assert first_cohpobject is not None
+        assert first_cohpobject.icohp is not None
         summed_cohp = first_cohpobject.cohp.copy()
         summed_icohp = first_cohpobject.icohp.copy()
+
         for idx, label in enumerate(label_list[1:], start=1):
             cohp = self.get_orbital_resolved_cohp(label, orbital_list[idx])
+            assert cohp is not None
+            assert cohp.icohp is not None
             summed_cohp[Spin.up] = np.sum([summed_cohp[Spin.up], cohp.cohp.copy()[Spin.up]], axis=0)
             if Spin.down in summed_cohp:
                 summed_cohp[Spin.down] = np.sum([summed_cohp[Spin.down], cohp.cohp.copy()[Spin.down]], axis=0)
+
             summed_icohp[Spin.up] = np.sum([summed_icohp[Spin.up], cohp.icohp.copy()[Spin.up]], axis=0)
             if Spin.down in summed_icohp:
                 summed_icohp[Spin.down] = np.sum([summed_icohp[Spin.down], cohp.icohp.copy()[Spin.down]], axis=0)
 
-        divided_cohp = {}
-        divided_icohp = {}
-        divided_cohp[Spin.up] = np.divide(summed_cohp[Spin.up], divisor)
-        divided_icohp[Spin.up] = np.divide(summed_icohp[Spin.up], divisor)
+        divided_cohp = {Spin.up: np.divide(summed_cohp[Spin.up], divisor)}
+        divided_icohp = {Spin.up: np.divide(summed_icohp[Spin.up], divisor)}
         if Spin.down in summed_cohp:
             divided_cohp[Spin.down] = np.divide(summed_cohp[Spin.down], divisor)
             divided_icohp[Spin.down] = np.divide(summed_icohp[Spin.down], divisor)
 
         if summed_spin_channels and Spin.down in divided_cohp:
-            final_cohp = {}
-            final_icohp = {}
-            final_cohp[Spin.up] = np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)
-            final_icohp[Spin.up] = np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)
+            final_cohp = {Spin.up: np.sum([divided_cohp[Spin.up], divided_cohp[Spin.down]], axis=0)}
+            final_icohp = {Spin.up: np.sum([divided_icohp[Spin.up], divided_icohp[Spin.down]], axis=0)}
         else:
             final_cohp = divided_cohp
             final_icohp = divided_icohp
@@ -526,7 +531,7 @@ def get_summed_cohp_by_label_and_orbital_list(
     def get_orbital_resolved_cohp(
         self,
         label: str,
-        orbitals: str | list | tuple,
+        orbitals: str | list[Orbital] | tuple[Orbital, ...],
         summed_spin_channels: bool = False,
     ) -> Cohp | None:
         """Get orbital-resolved COHP.
@@ -551,7 +556,7 @@ def get_orbital_resolved_cohp(
             return None
 
         if isinstance(orbitals, (list, tuple)):
-            cohp_orbs = [d["orbitals"] for d in self.orb_res_cohp[label].values()]
+            cohp_orbs = [val["orbitals"] for val in self.orb_res_cohp[label].values()]
             orbs = []
             for orbital in orbitals:
                 if isinstance(orbital[1], int):
@@ -564,6 +569,7 @@ def get_orbital_resolved_cohp(
                     raise TypeError("Orbital must be str, int, or Orbital.")
             orb_index = cohp_orbs.index(orbs)
             orb_label = list(self.orb_res_cohp[label])[orb_index]
+
         elif isinstance(orbitals, str):
             orb_label = orbitals
         else:
@@ -643,7 +649,7 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:
                 cohp_dict[label] = Cohp(efermi, energies, cohp, icohp=icohp)
 
         if "orb_res_cohp" in dct:
-            orb_cohp: dict[str, dict] = {}
+            orb_cohp: dict[str, dict[Orbital, dict[str, Any]]] = {}
             for label in dct["orb_res_cohp"]:
                 orb_cohp[label] = {}
                 for orb in dct["orb_res_cohp"][label]:
@@ -701,6 +707,7 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:
         else:
             orb_cohp = {}
 
+        assert avg_cohp is not None
         return cls(
             structure,
             avg_cohp,
@@ -743,7 +750,7 @@ def from_file(
         if are_coops and are_cobis:
             raise ValueError("You cannot have info about COOPs and COBIs in the same file.")
 
-        fmt = fmt.upper()
+        fmt = fmt.upper()  # type: ignore[assignment]
         if fmt == "LMTO":
             # TODO: LMTO COOPs and orbital-resolved COHP cannot be handled yet
             are_coops = False
@@ -1056,6 +1063,8 @@ def icohpvalue_orbital(self, orbitals: list[Orbital] | str, spin: Spin = Spin.up
 
         if isinstance(orbitals, list):  # TODO: DanielYang: use tuple of 2
             orbitals = f"{orbitals[0]}-{orbitals[1]}"
+
+        assert self._orbitals is not None
         return self._orbitals[orbitals]["icohp"][spin]
 
     @property
@@ -1084,6 +1093,7 @@ def summed_orbital_icohp(self) -> dict[str, float]:
             dict[str, float]: "str(Orbital1)-str(Ortibal2)": ICOHP value in eV.
         """
         orbital_icohp = {}
+        assert self._orbitals is not None
         for orb, item in self._orbitals.items():
             orbital_icohp[orb] = (
                 item["icohp"][Spin.up] + item["icohp"][Spin.down] if self._is_spin_polarized else item["icohp"][Spin.up]
@@ -1135,7 +1145,6 @@ def __init__(
 
         self._are_coops = are_coops
         self._are_cobis = are_cobis
-        self._icohplist = {}
         self._is_spin_polarized = is_spin_polarized
         self._list_labels = list_labels
         self._list_atom1 = list_atom1
@@ -1146,6 +1155,7 @@ def __init__(
         self._list_icohp = list_icohp
         self._list_orb_icohp = list_orb_icohp
 
+        self._icohplist: dict[str, IcohpValue] = {}
         for idx, label in enumerate(list_labels):
             self._icohplist[label] = IcohpValue(
                 label=label,
@@ -1218,7 +1228,7 @@ def get_summed_icohp_by_label_list(
         Returns:
             float: Sum of ICOHPs selected with label_list.
         """
-        sum_icohp = 0
+        sum_icohp: float = 0
         for label in label_list:
             icohp = self._icohplist[label]
             if icohp.num_bonds != 1:
@@ -1259,7 +1269,7 @@ def get_icohp_dict_of_site(
         minbondlength: float = 0.0,
         maxbondlength: float = 8.0,
         only_bonds_to: list[str] | None = None,
-    ) -> dict[str | float, IcohpValue]:
+    ) -> dict[str, IcohpValue]:
         """Get IcohpValues for a certain site.
 
         Args:
@@ -1364,7 +1374,7 @@ def are_cobis(self) -> bool:
 def get_integrated_cohp_in_energy_range(
     cohp: CompleteCohp,
     label: str,
-    orbital: Orbital | None = None,
+    orbital: CohpOrbital | None = None,  # TODO: DanielYang: fix type
     energy_range: float | tuple[float, float] | None = None,
     relative_E_Fermi: bool = True,
     summed_spin_channels: bool = True,
@@ -1390,8 +1400,11 @@ def get_integrated_cohp_in_energy_range(
     if orbital is None:
         icohps = cohp.all_cohps[label].get_icohp(spin=None)
     else:
-        icohps = cohp.get_orbital_resolved_cohp(label=label, orbitals=orbital).icohp
+        _icohps = cohp.get_orbital_resolved_cohp(label=label, orbitals=orbital)
+        assert _icohps is not None
+        icohps = _icohps.icohp
 
+    assert icohps is not None
     summedicohp = {}
     if summed_spin_channels and Spin.down in icohps:
         summedicohp[Spin.up] = icohps[Spin.up] + icohps[Spin.down]

From 0afb7c26ff537b714c347cb10c58e51aac7f721a Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 21:11:07 +0800
Subject: [PATCH 18/39] fix remaining mypy errors

---
 pymatgen/electronic_structure/cohp.py | 7 +++----
 pymatgen/io/lobster/outputs.py        | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 7b977becf96..4904ccfc4b9 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -531,7 +531,7 @@ def get_summed_cohp_by_label_and_orbital_list(
     def get_orbital_resolved_cohp(
         self,
         label: str,
-        orbitals: str | list[Orbital] | tuple[Orbital, ...],
+        orbitals: str | list[tuple[str, Orbital]] | tuple[tuple[str, Orbital], ...],
         summed_spin_channels: bool = False,
     ) -> Cohp | None:
         """Get orbital-resolved COHP.
@@ -541,7 +541,6 @@ def get_orbital_resolved_cohp(
             orbitals: The orbitals as a label, or list/tuple of
                 [(n1, orbital1), (n2, orbital2), ...].
                 Where each orbital can either be str, int, or Orbital.
-                # TODO: DanielYang: clarify type
             summed_spin_channels (bool): Sum the spin channels and return the sum as Spin.up.
 
         Returns:
@@ -1374,7 +1373,7 @@ def are_cobis(self) -> bool:
 def get_integrated_cohp_in_energy_range(
     cohp: CompleteCohp,
     label: str,
-    orbital: CohpOrbital | None = None,  # TODO: DanielYang: fix type
+    orbital: str | None = None,
     energy_range: float | tuple[float, float] | None = None,
     relative_E_Fermi: bool = True,
     summed_spin_channels: bool = True,
@@ -1384,7 +1383,7 @@ def get_integrated_cohp_in_energy_range(
     Args:
         cohp (CompleteCohp): CompleteCohp object.
         label (str): Label of the COHP data.
-        orbital: If not None, a orbital resolved integrated COHP will be returned.
+        orbital (str): If not None, a orbital resolved integrated COHP will be returned.
         energy_range: If None, return the ICOHP value at Fermi level.
             If float, integrate from this value up to Fermi level.
             If (float, float), integrate in between.
diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index 6b18294f62c..bad5952e107 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -429,7 +429,7 @@ def __init__(
 
             labels, atoms1, atoms2, lens, translations, nums, icohps = [], [], [], [], [], [], []
 
-            # initialize static variables
+            # Initialize static variables
             label = ""
             atom1 = ""
             atom2 = ""

From 5fcf23619fa804e31b0f7e2d521821a2552c6474 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 21:23:17 +0800
Subject: [PATCH 19/39] add DEBUG tag

---
 pymatgen/io/lobster/outputs.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index bad5952e107..ec4d7d7ae83 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -35,7 +35,7 @@
     from typing import Any
 
     from pymatgen.core.structure import IStructure
-    from pymatgen.util.typing import PathLike
+    from pymatgen.util.typing import PathLike, Vector3D
 
 __author__ = "Janine George, Marco Esters"
 __copyright__ = "Copyright 2017, The Materials Project"
@@ -388,14 +388,14 @@ def __init__(
             if len(data) == 0:
                 raise RuntimeError("ICOHPLIST file contains no data.")
 
-            # Which Lobster version?
+            # Determine LOBSTER version
             if len(data[0].split()) == 8:
                 version = "3.1.1"
             elif len(data[0].split()) == 6:
                 version = "2.2.1"
-                warnings.warn("Please consider using the new Lobster version. See www.cohp.de.")
+                warnings.warn("Please consider using the new LOBSTER version. See www.cohp.de.")
             else:
-                raise ValueError
+                raise ValueError("Unsupported LOBSTER version.")
 
             # If the calculation is spin polarized, the line in the middle
             # of the file will be another header line.
@@ -435,7 +435,7 @@ def __init__(
             atom2 = ""
             length = None
             num = None
-            translation = []
+            translation: Vector3D | None = None
 
             for bond in range(n_bonds):
                 line = data_without_orbitals[bond].split()
@@ -447,16 +447,16 @@ def __init__(
                     length = float(line[3])
                     icohp[Spin.up] = float(line[4])
                     num = int(line[5])
-                    translation = [0, 0, 0]
+                    translation = (0, 0, 0)
                     if self.is_spin_polarized:
                         icohp[Spin.down] = float(data_without_orbitals[bond + n_bonds + 1].split()[4])
 
-                elif version == "3.1.1":
+                else:  # version == "3.1.1"
                     label = f"{line[0]}"
                     atom1 = str(line[1])
                     atom2 = str(line[2])
                     length = float(line[3])
-                    translation = [int(line[4]), int(line[5]), int(line[6])]
+                    translation = (int(line[4]), int(line[5]), int(line[6]))
                     icohp[Spin.up] = float(line[7])
                     num = 1
 
@@ -500,9 +500,9 @@ def __init__(
                 list_atom1=atoms1,
                 list_atom2=atoms2,
                 list_length=lens,
-                list_translation=translations,
+                list_translation=translations,  # type: ignore[arg-type]
                 list_num=nums,
-                list_icohp=icohps,
+                list_icohp=icohps,  # DEBUG: DanielYang: inconsistent type
                 is_spin_polarized=self.is_spin_polarized,
                 list_orb_icohp=list_orb_icohp,
             )

From 796c379d22fe3e173fcc50a0e9ed97136ae5c742 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 21:26:59 +0800
Subject: [PATCH 20/39] reduce code repetition

---
 pymatgen/io/lobster/outputs.py | 38 ++++++++++++++++------------------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index ec4d7d7ae83..e27a040b9e1 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -410,11 +410,11 @@ def __init__(
             if self.orbitalwise:
                 data_without_orbitals = []
                 data_orbitals = []
-                for line in data:
-                    if "_" not in line.split()[1]:
-                        data_without_orbitals += [line]
+                for line_parts in data:
+                    if "_" not in line_parts.split()[1]:
+                        data_without_orbitals += [line_parts]
                     else:
-                        data_orbitals += [line]
+                        data_orbitals += [line_parts]
 
             else:
                 data_without_orbitals = data
@@ -438,26 +438,24 @@ def __init__(
             translation: Vector3D | None = None
 
             for bond in range(n_bonds):
-                line = data_without_orbitals[bond].split()
+                line_parts = data_without_orbitals[bond].split()
+
+                label = f"{line_parts[0]}"
+                atom1 = str(line_parts[1])
+                atom2 = str(line_parts[2])
+                length = float(line_parts[3])
+
                 icohp = {}
                 if version == "2.2.1":
-                    label = f"{line[0]}"
-                    atom1 = str(line[1])
-                    atom2 = str(line[2])
-                    length = float(line[3])
-                    icohp[Spin.up] = float(line[4])
-                    num = int(line[5])
+                    icohp[Spin.up] = float(line_parts[4])
+                    num = int(line_parts[5])
                     translation = (0, 0, 0)
                     if self.is_spin_polarized:
                         icohp[Spin.down] = float(data_without_orbitals[bond + n_bonds + 1].split()[4])
 
                 else:  # version == "3.1.1"
-                    label = f"{line[0]}"
-                    atom1 = str(line[1])
-                    atom2 = str(line[2])
-                    length = float(line[3])
-                    translation = (int(line[4]), int(line[5]), int(line[6]))
-                    icohp[Spin.up] = float(line[7])
+                    translation = (int(line_parts[4]), int(line_parts[5]), int(line_parts[6]))
+                    icohp[Spin.up] = float(line_parts[7])
                     num = 1
 
                     if self.is_spin_polarized:
@@ -479,11 +477,11 @@ def __init__(
                 for i_data_orb in range(n_orbs):
                     data_orb = data_orbitals[i_data_orb]
                     icohp = {}
-                    line = data_orb.split()
-                    label = f"{line[0]}"
+                    line_parts = data_orb.split()
+                    label = f"{line_parts[0]}"
                     orbs = re.findall(r"_(.*?)(?=\s)", data_orb)
                     orb_label, orbitals = get_orb_from_str(orbs)
-                    icohp[Spin.up] = float(line[7])
+                    icohp[Spin.up] = float(line_parts[7])
 
                     if self.is_spin_polarized:
                         icohp[Spin.down] = float(data_orbitals[n_orbs + i_data_orb].split()[7])

From 9551db207ce444119b35b5881e71e26c38527d74 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 21:38:33 +0800
Subject: [PATCH 21/39] Need Confirm: set `translation` as tuple

---
 pymatgen/io/lobster/outputs.py  |  8 ------
 tests/io/lobster/test_inputs.py | 48 ++++++++++++++++-----------------
 2 files changed, 24 insertions(+), 32 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index e27a040b9e1..cc93d889328 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -429,14 +429,6 @@ def __init__(
 
             labels, atoms1, atoms2, lens, translations, nums, icohps = [], [], [], [], [], [], []
 
-            # Initialize static variables
-            label = ""
-            atom1 = ""
-            atom2 = ""
-            length = None
-            num = None
-            translation: Vector3D | None = None
-
             for bond in range(n_bonds):
                 line_parts = data_without_orbitals[bond].split()
 
diff --git a/tests/io/lobster/test_inputs.py b/tests/io/lobster/test_inputs.py
index 574676952d6..ee29a8ba0d4 100644
--- a/tests/io/lobster/test_inputs.py
+++ b/tests/io/lobster/test_inputs.py
@@ -444,77 +444,77 @@ def test_values(self):
                 "length": 2.88231,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -2.18042},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "2": {
                 "length": 3.10144,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -1.14347},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "3": {
                 "length": 2.88231,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -2.18042},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "4": {
                 "length": 3.10144,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -1.14348},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "5": {
                 "length": 3.05001,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -1.30006},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "6": {
                 "length": 2.91676,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -1.96843},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "7": {
                 "length": 3.05001,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -1.30006},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "8": {
                 "length": 2.91676,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -1.96843},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "9": {
                 "length": 3.37522,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.47531},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "10": {
                 "length": 3.07294,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -2.38796},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "11": {
                 "length": 3.37522,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.47531},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
         }
@@ -523,77 +523,77 @@ def test_values(self):
                 "length": 2.88231,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: 0.14245},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "2": {
                 "length": 3.10144,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.04118},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "3": {
                 "length": 2.88231,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: 0.14245},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "4": {
                 "length": 3.10144,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.04118},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "5": {
                 "length": 3.05001,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.03516},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "6": {
                 "length": 2.91676,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: 0.10745},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "7": {
                 "length": 3.05001,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.03516},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "8": {
                 "length": 2.91676,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: 0.10745},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "9": {
                 "length": 3.37522,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.12395},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "10": {
                 "length": 3.07294,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: 0.24714},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "11": {
                 "length": 3.37522,
                 "number_of_bonds": 3,
                 "icohp": {Spin.up: -0.12395},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
         }
@@ -602,14 +602,14 @@ def test_values(self):
                 "length": 2.83189,
                 "number_of_bonds": 2,
                 "icohp": {Spin.up: -0.10218, Spin.down: -0.19701},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
             "2": {
                 "length": 2.45249,
                 "number_of_bonds": 1,
                 "icohp": {Spin.up: -0.28485, Spin.down: -0.58279},
-                "translation": [0, 0, 0],
+                "translation": (0, 0, 0),
                 "orbitals": None,
             },
         }

From c188030470ecee8101665b9581f878dd8b4c1b33 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:39:02 +0000
Subject: [PATCH 22/39] pre-commit auto-fixes

---
 pymatgen/io/lobster/outputs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index cc93d889328..0d855bc60ef 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -35,7 +35,7 @@
     from typing import Any
 
     from pymatgen.core.structure import IStructure
-    from pymatgen.util.typing import PathLike, Vector3D
+    from pymatgen.util.typing import PathLike
 
 __author__ = "Janine George, Marco Esters"
 __copyright__ = "Copyright 2017, The Materials Project"

From e21c5ed367e343e7ca5c111d71e82c8dbf3aaa57 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 12 Jun 2024 22:01:05 +0800
Subject: [PATCH 23/39] more type clarify

---
 pymatgen/electronic_structure/cohp.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 4904ccfc4b9..559a022224b 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -331,7 +331,6 @@ def as_dict(self) -> dict[str, Any]:
             dct["COHP"] |= {label: {str(spin): pops.tolist() for spin, pops in self.all_cohps[label].cohp.items()}}
             icohp = self.all_cohps[label].icohp
             if icohp is not None:
-                # TODO: DanielYang59: merge two condition branches with "|=" operator?
                 if "ICOHP" not in dct:
                     dct["ICOHP"] = {label: {str(spin): pops.tolist() for spin, pops in icohp.items()}}
                 else:
@@ -467,7 +466,7 @@ def get_summed_cohp_by_label_list(
     def get_summed_cohp_by_label_and_orbital_list(
         self,
         label_list: list[str],
-        orbital_list: list,  # TODO (DanielYang): what is its type? Add custom type for it?
+        orbital_list: list[str],
         divisor: float = 1,
         summed_spin_channels: bool = False,
     ) -> Cohp:
@@ -475,7 +474,7 @@ def get_summed_cohp_by_label_and_orbital_list(
 
         Args:
             label_list (list[str]): Labels for the COHP that should be included.
-            orbital_list (list): Orbitals for the COHPs that should be included
+            orbital_list (list[str]): Orbitals for the COHPs that should be included
                 (same order as label_list).
             divisor (float): The summed COHP will be divided by this divisor.
             summed_spin_channels (bool): Sum the spin channels and return the sum in Spin.up.
@@ -1048,10 +1047,14 @@ def icohpvalue(self, spin: Spin = Spin.up) -> float:
 
         return self._icohp[spin]
 
-    def icohpvalue_orbital(self, orbitals: list[Orbital] | str, spin: Spin = Spin.up) -> float:
+    def icohpvalue_orbital(
+        self,
+        orbitals: tuple[Orbital, Orbital] | str,
+        spin: Spin = Spin.up,
+    ) -> float:
         """
         Args:
-            orbitals (list[Orbitals]): List of Orbitals or "str(Orbital1)-str(Orbital2)".
+            orbitals: tuple[Orbital, Orbital] or "str(Orbital0)-str(Orbital1)".
             spin (Spin): Spin.up or Spin.down.
 
         Returns:
@@ -1060,7 +1063,7 @@ def icohpvalue_orbital(self, orbitals: list[Orbital] | str, spin: Spin = Spin.up
         if not self.is_spin_polarized and spin == Spin.down:
             raise ValueError("The calculation was not performed with spin polarization")
 
-        if isinstance(orbitals, list):  # TODO: DanielYang: use tuple of 2
+        if isinstance(orbitals, (tuple, list)):
             orbitals = f"{orbitals[0]}-{orbitals[1]}"
 
         assert self._orbitals is not None
@@ -1177,7 +1180,7 @@ def get_icohp_by_label(
         label: str,
         summed_spin_channels: bool = True,
         spin: Spin = Spin.up,
-        orbitals: str | list[Orbital] | None = None,  # TODO: DanielYang: use tuple of 2
+        orbitals: str | tuple[Orbital, Orbital] | None = None,
     ) -> float:
         """Get an ICOHP value for a certain bond indicated by the label.
 
@@ -1198,7 +1201,7 @@ def get_icohp_by_label(
         if orbitals is None:
             return icohp.summed_icohp if summed_spin_channels else icohp.icohpvalue(spin)
 
-        if isinstance(orbitals, list):
+        if isinstance(orbitals, (tuple, list)):
             orbitals = f"{orbitals[0]}-{orbitals[1]}"
 
         if summed_spin_channels:

From 5b81360cb6563e9d38d246554035695ef029ac46 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 09:57:23 +0800
Subject: [PATCH 24/39] clarify `num` argument

---
 pymatgen/electronic_structure/cohp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 559a022224b..72f15d5a5d8 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -951,7 +951,7 @@ def __init__(
             atom2 (str): The second atom that contributes to the bond.
             length (float): Bond length.
             translation (Vector3D): cell translation vector, e.g. (0, 0, 0).
-            num (int): How often the bond exists.  # TODO: DanielYang: clarify this description
+            num (int): The number of equivalent bonds.
             icohp (dict): {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}
             are_coops (bool): Whether these are COOPs.
             are_cobis (bool): Whether these are COBIs.

From 5f760df63244aab0759edf296c626edf3b6fe915 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 12:37:52 +0800
Subject: [PATCH 25/39] clarify docstring of `bandstructure`

---
 .../electronic_structure/bandstructure.py     | 364 +++++++++---------
 1 file changed, 176 insertions(+), 188 deletions(-)

diff --git a/pymatgen/electronic_structure/bandstructure.py b/pymatgen/electronic_structure/bandstructure.py
index 2b466543270..d77314899d2 100644
--- a/pymatgen/electronic_structure/bandstructure.py
+++ b/pymatgen/electronic_structure/bandstructure.py
@@ -33,9 +33,8 @@
 
 
 class Kpoint(MSONable):
-    """Store kpoint objects. A kpoint is defined with a lattice and frac
-    or Cartesian coordinates syntax similar than the site object in
-    pymatgen.core.structure.
+    """A kpoint is defined with a lattice and frac or Cartesian coordinates,
+    syntax similar than the Site object in pymatgen.core.structure.
     """
 
     def __init__(
@@ -48,15 +47,14 @@ def __init__(
     ) -> None:
         """
         Args:
-            coords: coordinate of the kpoint as a numpy array
-            lattice: A pymatgen.core.Lattice object representing
-                the reciprocal lattice of the kpoint
-            to_unit_cell: Translates fractional coordinate to the basic unit
+            coords (NDArray): Coordinate of the Kpoint.
+            lattice (Lattice): The reciprocal lattice of the kpoint.
+            to_unit_cell (bool): Translate fractional coordinate to the basic unit
                 cell, i.e., all fractional coordinates satisfy 0 <= a < 1.
                 Defaults to False.
-            coords_are_cartesian: Boolean indicating if the coordinates given are
-                in Cartesian or fractional coordinates (by default fractional)
-            label: the label of the kpoint if any (None by default).
+            coords_are_cartesian (bool): Whether the coordinates given are
+                in Cartesian (True) or fractional coordinates (by default fractional).
+            label (str): The label of the Kpoint if any (None by default).
         """
         self._lattice = lattice
         self._frac_coords = lattice.get_fractional_coords(coords) if coords_are_cartesian else coords
@@ -73,9 +71,10 @@ def __str__(self) -> str:
         return f"{self.frac_coords} {self.cart_coords} {self.label}"
 
     def __eq__(self, other: object) -> bool:
-        """Check if two Kpoints are equal."""
+        """Whether two Kpoints are equal."""
         if not isinstance(other, type(self)):
             return NotImplemented
+
         return (
             np.allclose(self.frac_coords, other.frac_coords)
             and self.lattice == other.lattice
@@ -84,9 +83,7 @@ def __eq__(self, other: object) -> bool:
 
     @property
     def lattice(self) -> Lattice:
-        """The lattice associated with the kpoint. It's a
-        pymatgen.core.Lattice object.
-        """
+        """The lattice associated with the kpoint, as a Lattice object."""
         return self._lattice
 
     @property
@@ -101,12 +98,12 @@ def label(self, label: str | None) -> None:
 
     @property
     def frac_coords(self) -> NDArray:
-        """The fractional coordinates of the kpoint as a numpy array."""
+        """The fractional coordinates of the kpoint as a NumPy array."""
         return np.copy(self._frac_coords)
 
     @property
     def cart_coords(self) -> NDArray:
-        """The Cartesian coordinates of the kpoint as a numpy array."""
+        """The Cartesian coordinates of the kpoint as a NumPy array."""
         return np.copy(self._cart_coords)
 
     @property
@@ -125,7 +122,7 @@ def c(self) -> float:
         return self._frac_coords[2]
 
     def as_dict(self) -> dict[str, Any]:
-        """JSON-serializable dict representation of a kpoint."""
+        """JSON-serializable dict representation of the kpoint."""
         return {
             "lattice": self.lattice.as_dict(),
             "fcoords": self.frac_coords.tolist(),
@@ -137,7 +134,7 @@ def as_dict(self) -> dict[str, Any]:
 
     @classmethod
     def from_dict(cls, dct: dict) -> Self:
-        """Create from dict.
+        """Create from a dict.
 
         Args:
             dct (dict): A dict with all data for a kpoint object.
@@ -150,23 +147,23 @@ def from_dict(cls, dct: dict) -> Self:
 
 
 class BandStructure:
-    """This is the most generic band structure data possible
-    it's defined by a list of Kpoints and energies for each of them.
+    """Generic band structure data, defined by a list of Kpoints
+        and corresponding energies for each of them.
 
     Attributes:
-        kpoints (list): The list of kpoints (as Kpoint objects) in the band structure.
+        kpoints (list[Kpoint]): Kpoints in the band structure.
         lattice_rec (Lattice): The reciprocal lattice of the band structure.
-        efermi (float): The Fermi energy.
-        is_spin_polarized (bool): True if the band structure is spin-polarized.
-        bands (dict): The energy eigenvalues as a {spin: array}. Note that the use of an
-            array is necessary for computational as well as memory efficiency due to the large
-            amount of numerical data. The indices of the array are [band_index, kpoint_index].
-        nb_bands (int): Returns the number of bands in the band structure.
-        structure (Structure): Returns the structure.
-        projections (dict): The projections as a {spin: array}. Note that the use of an
-            array is necessary for computational as well as memory efficiency due to the large
-            amount of numerical data. The indices of the array are [band_index, kpoint_index,
-            orbital_index, ion_index].
+        efermi (float): The Fermi level.
+        is_spin_polarized (bool): Whether the band structure is spin-polarized.
+        bands (dict[Spin, NDArray]): The energy eigenvalues. Note that the use of an
+            array is necessary for computational and memory efficiency due to the large
+            amount of numerical data. The indices of the array are (band_index, kpoint_index).
+        nb_bands (int): The number of bands in the band structure.
+        structure (Structure): The structure.
+        projections (dict[Spin, NDArray]): The projections. Note that the use of an
+            array is necessary for computational and memory efficiency due to the large
+            amount of numerical data. The indices of the array are (band_index, kpoint_index,
+            orbital_index, ion_index).
     """
 
     def __init__(
@@ -175,34 +172,32 @@ def __init__(
         eigenvals: dict[Spin, NDArray],
         lattice: Lattice,
         efermi: float,
-        labels_dict=None,
+        labels_dict: dict[Kpoint, str] | None = None,
         coords_are_cartesian: bool = False,
         structure: Structure | None = None,
         projections: dict[Spin, NDArray] | None = None,
     ) -> None:
         """
         Args:
-            kpoints: list of Kpoint as numpy arrays, in frac_coords of the
-                given lattice by default
-            eigenvals: dict of energies for spin up and spin down
-                {Spin.up:[][],Spin.down:[][]}, the first index of the array
-                [][] refers to the band and the second to the index of the
-                kpoint. The kpoints are ordered according to the order of the
-                kpoints array. If the band structure is not spin polarized, we
-                only store one data set under Spin.up
-            lattice: The reciprocal lattice as a pymatgen Lattice object.
-                Pymatgen uses the physics convention of reciprocal lattice vectors
-                WITH a 2*pi coefficient
-            efermi (float): Fermi energy
-            labels_dict: (dict) of {} this links a kpoint (in frac coords or
-                Cartesian coordinates depending on the coords) to a label.
-            coords_are_cartesian: Whether coordinates are cartesian.
-            structure: The crystal structure (as a pymatgen Structure object)
+            kpoints (NDArray): Kpoint as NumPy array, in frac_coords of the
+                given lattice by default.
+            eigenvals (dict): Energies for spin up and spin down as
+                {Spin.up:[][], Spin.down:[][]}, the first index of the array
+                [][] refers to the band and the second to the index of the kpoint.
+                The kpoints are ordered according to the kpoints array.
+                If the band structure is not spin polarized, we
+                only store one data set under Spin.up.
+            lattice (Lattice): The reciprocal lattice. Pymatgen uses the physics
+                convention of reciprocal lattice vectors with a 2*pi coefficient.
+            efermi (float): The Fermi level.
+            labels_dict (dict[Kpoint, str]): Dict mapping kpoint to label.
+            coords_are_cartesian (bool): Whether coordinates are cartesian.
+            structure (Structure): The crystal structure
                 associated with the band structure. This is needed if we
-                provide projections to the band structure
-            projections: dict of orbital projections as {spin: array}. The
-                indices of the array are [band_index, kpoint_index, orbital_index,
-                ion_index].If the band structure is not spin polarized, we only
+                provide projections to the band structure.
+            projections (dict[Spin, NDArray]): Orbital projections. The
+                indices of the array are (band_index, kpoint_index, orbital_index,
+                ion_index). If the band structure is not spin polarized, we only
                 store one data set under Spin.up.
         """
         self.efermi = efermi
@@ -237,13 +232,12 @@ def __init__(
         self.is_spin_polarized = len(self.bands) == 2
 
     def get_projection_on_elements(self) -> dict[Spin, NDArray]:
-        """Get a dictionary of projections on elements.
+        """Get projections on elements.
 
         Returns:
-            a dictionary in the {Spin.up:[][{Element: [values]}],
-            Spin.down:[][{Element: [values]}]} format
-            if there is no projections in the band structure
-            returns an empty dict
+            dict[Spin, NDArray]: Dict in {Spin.up:[][{Element: [values]}],
+                Spin.down: [][{Element: [values]}]} format.
+                If there is no projections in the band structure, return {}.
         """
         assert self.structure is not None
         result: dict[Spin, NDArray] = {}
@@ -258,17 +252,17 @@ def get_projection_on_elements(self) -> dict[Spin, NDArray]:
         return result
 
     def get_projections_on_elements_and_orbitals(self, el_orb_spec: dict[str, list[str]]):
-        """Get a dictionary of projections on elements and specific orbitals.
+        """Get projections on elements and specific orbitals.
 
         Args:
-            el_orb_spec (dict[str, list[str]]): A dictionary of elements and orbitals which
-                to project onto. Format is {Element: [orbitals]}, e.g. {'Cu':['d','s']}.
+            el_orb_spec (dict[str, list[str]]): Elements and orbitals to project onto.
+                Format is {Element: [orbitals]}, e.g. {"Cu": ["d", "s"]}.
 
         Returns:
-            A dictionary of projections on elements in the
-            {Spin.up:[][{Element:{orb:values}}],
-            Spin.down:[][{Element:{orb:values}}]} format
-            if there is no projections in the band structure returns an empty dict.
+            dict[str, list[str]: Projections on elements in the
+                {Spin.up: [][{Element: {orb: values}}],
+                Spin.down: [][{Element: {orb: values}}]} format.
+                If there is no projections in the band structure, return {}.
         """
         if self.structure is None:
             raise ValueError("Structure is required for this method")
@@ -297,7 +291,7 @@ def is_metal(self, efermi_tol: float = 1e-4) -> bool:
         level crosses a band.
 
         Returns:
-            bool: True if a metal.
+            bool: True if is metal.
         """
         for vals in self.bands.values():
             for idx in range(self.nb_bands):
@@ -306,25 +300,25 @@ def is_metal(self, efermi_tol: float = 1e-4) -> bool:
         return False
 
     def get_vbm(self) -> dict[str, Any]:
-        """Get data about the VBM.
+        """Get data about the valence band maximum (VBM).
 
         Returns:
-            dict: With keys "band_index", "kpoint_index", "kpoint", "energy"
-            - "band_index": A dict with spin keys pointing to a list of the
-            indices of the band containing the VBM (please note that you
-            can have several bands sharing the VBM) {Spin.up:[],
-            Spin.down:[]}
-            - "kpoint_index": The list of indices in self.kpoints for the
-            kpoint VBM. Please note that there can be several
-            kpoint_indices relating to the same kpoint (e.g., Gamma can
-            occur at different spots in the band structure line plot)
-            - "kpoint": The kpoint (as a kpoint object)
-            - "energy": The energy of the VBM
-            - "projections": The projections along sites and orbitals of the
-            VBM if any projection data is available (else it is an empty
-            dictionary). The format is similar to the projections field in
-            BandStructure: {spin:{'Orbital': [proj]}} where the array
-            [proj] is ordered according to the sites in structure
+            dict of keys "band_index", "kpoint_index", "kpoint", "energy":
+                - "band_index" (dict): A dict with spin keys pointing to a list of the
+                indices of the band containing the VBM (please note that you
+                can have several bands sharing the VBM) {Spin.up:[],
+                Spin.down:[]}.
+                - "kpoint_index": The list of indices in self.kpoints for the
+                kpoint VBM. Please note that there can be several
+                kpoint_indices relating to the same kpoint (e.g., Gamma can
+                occur at different spots in the band structure line plot).
+                - "kpoint" (Kpoint): The kpoint.
+                - "energy" (float): The energy of the VBM.
+                - "projections": The projections along sites and orbitals of the
+                VBM if any projection data is available (else it is an empty
+                dictionary). The format is similar to the projections field in
+                BandStructure: {spin:{'Orbital': [proj]}} where the array
+                [proj] is ordered according to the sites in structure.
         """
         if self.is_metal():
             return {
@@ -334,6 +328,7 @@ def get_vbm(self) -> dict[str, Any]:
                 "energy": None,
                 "projections": {},
             }
+
         max_tmp = -float("inf")
         index = kpoint_vbm = None
         for value in self.bands.values():
@@ -351,7 +346,7 @@ def get_vbm(self) -> dict[str, Any]:
         else:
             list_ind_kpts.append(index)
 
-        # Get all other bands sharing the vbm
+        # Get all other bands sharing the VBM
         list_ind_band = defaultdict(list)
         for spin in self.bands:
             for idx in range(self.nb_bands):
@@ -362,6 +357,7 @@ def get_vbm(self) -> dict[str, Any]:
             if len(list_ind_band[spin]) == 0:
                 continue
             proj[spin] = value[list_ind_band[spin][0]][list_ind_kpts[0]]
+
         return {
             "band_index": list_ind_band,
             "kpoint_index": list_ind_kpts,
@@ -371,24 +367,24 @@ def get_vbm(self) -> dict[str, Any]:
         }
 
     def get_cbm(self) -> dict[str, Any]:
-        """Get data about the CBM.
+        """Get data about the conduction band minimum (CBM).
 
         Returns:
-            dict[str, Any]: with keys band_index, kpoint_index, kpoint, energy.
-                - "band_index": A dict with spin keys pointing to a list of the
+            dict of keys "band_index", "kpoint_index", "kpoint", "energy":
+                - "band_index" (dict): A dict with spin keys pointing to a list of the
                 indices of the band containing the CBM (please note that you
-                can have several bands sharing the CBM) {Spin.up:[], Spin.down:[]}
+                can have several bands sharing the CBM) {Spin.up:[], Spin.down:[]}.
                 - "kpoint_index": The list of indices in self.kpoints for the
                 kpoint CBM. Please note that there can be several
                 kpoint_indices relating to the same kpoint (e.g., Gamma can
-                occur at different spots in the band structure line plot)
-                - "kpoint": The kpoint (as a kpoint object)
-                - "energy": The energy of the CBM
+                occur at different spots in the band structure line plot).
+                - "kpoint" (Kpoint): The kpoint.
+                - "energy" (float): The energy of the CBM.
                 - "projections": The projections along sites and orbitals of the
                 CBM if any projection data is available (else it is an empty
                 dictionary). The format is similar to the projections field in
                 BandStructure: {spin:{'Orbital': [proj]}} where the array
-                [proj] is ordered according to the sites in structure
+                [proj] is ordered according to the sites in structure.
         """
         if self.is_metal():
             return {
@@ -398,8 +394,8 @@ def get_cbm(self) -> dict[str, Any]:
                 "energy": None,
                 "projections": {},
             }
-        max_tmp = float("inf")
 
+        max_tmp = float("inf")
         index = kpoint_cbm = None
         for value in self.bands.values():
             for idx, j in zip(*np.where(value >= self.efermi)):
@@ -416,7 +412,7 @@ def get_cbm(self) -> dict[str, Any]:
         else:
             list_index_kpoints.append(index)
 
-        # get all other bands sharing the cbm
+        # Get all other bands sharing the CBM
         list_index_band = defaultdict(list)
         for spin in self.bands:
             for idx in range(self.nb_bands):
@@ -437,13 +433,13 @@ def get_cbm(self) -> dict[str, Any]:
         }
 
     def get_band_gap(self) -> dict[str, Any]:
-        r"""Get band gap data.
+        r"""Get band gap.
 
         Returns:
-            A dict {"energy", "direct", "transition"}:
-            "energy": band gap energy
-            "direct": A boolean telling if the gap is direct or not
-            "transition": kpoint labels of the transition (e.g., "\\Gamma-X")
+            dict of keys "energy", "direct", "transition":
+                "energy" (float): Band gap energy.
+                "direct" (bool): Whether the gap is direct.
+                "transition" (str): Kpoint labels of the transition (e.g., "\\Gamma-X").
         """
         if self.is_metal():
             return {"energy": 0.0, "direct": False, "transition": None}
@@ -471,15 +467,15 @@ def get_band_gap(self) -> dict[str, Any]:
         return result
 
     def get_direct_band_gap_dict(self) -> dict[Spin, dict[str, Any]]:
-        """Get a dictionary of information about the direct
-        band gap.
+        """Get information about the direct band gap.
 
         Returns:
-            a dictionary of the band gaps indexed by spin
-            along with their band indices and k-point index
+            dict[Spin, dict[str, Any]]: The band gaps indexed by spin
+                along with their band indices and kpoint index.
         """
         if self.is_metal():
             raise ValueError("get_direct_band_gap_dict should only be used with non-metals")
+
         direct_gap_dict = {}
         for spin, v in self.bands.items():
             above = v[np.all(v > self.efermi, axis=1)]
@@ -503,7 +499,7 @@ def get_direct_band_gap(self) -> float:
         """Get the direct band gap.
 
         Returns:
-            the value of the direct band gap
+            float: The direct band gap value.
         """
         if self.is_metal():
             return 0.0
@@ -517,15 +513,15 @@ def get_sym_eq_kpoints(
         cartesian: bool = False,
         tol: float = 1e-2,
     ) -> NDArray:
-        """Get a list of unique symmetrically equivalent Kpoints.
+        """Get unique symmetrically equivalent Kpoints.
 
         Args:
-            kpoint (1x3 array): coordinate of the Kpoint
-            cartesian (bool): kpoint is in Cartesian or fractional coordinates
-            tol (float): tolerance below which coordinates are considered equal
+            kpoint (1x3 array): Coordinate of the Kpoint.
+            cartesian (bool): Whether kpoint is in Cartesian or fractional coordinates.
+            tol (float): Tolerance below which coordinates are considered equal.
 
         Returns:
-            list[1x3 array] | None: if structure is not available returns None
+            (1x3 NDArray) | None: None if structure is not available.
         """
         if not self.structure:
             return None
@@ -534,7 +530,7 @@ def get_sym_eq_kpoints(
         symm_ops = sg.get_point_group_operations(cartesian=cartesian)
         points = np.dot(kpoint, [m.rotation_matrix for m in symm_ops])
         rm_list = []
-        # Identify and remove duplicates from the list of equivalent k-points:
+        # Identify and remove duplicates from equivalent k-points
         for i in range(len(points) - 1):
             for j in range(i + 1, len(points)):
                 if np.allclose(pbc_diff(points[i], points[j]), [0, 0, 0], tol):
@@ -548,15 +544,15 @@ def get_kpoint_degeneracy(
         cartesian: bool = False,
         tol: float = 1e-2,
     ) -> NDArray | None:
-        """Get degeneracy of a given k-point based on structure symmetry.
+        """Get degeneracy of a given kpoint based on structure symmetry.
 
         Args:
-            kpoint (1x3 array): coordinate of the k-point
-            cartesian (bool): kpoint is in Cartesian or fractional coordinates
-            tol (float): tolerance below which coordinates are considered equal.
+            kpoint (1x3 NDArray): Coordinate of the k-point.
+            cartesian (bool): Whether kpoint is in Cartesian or fractional coordinates.
+            tol (float): Tolerance below which coordinates are considered equal.
 
         Returns:
-            int | None: degeneracy or None if structure is not available
+            int | None: Degeneracy, or None if structure is not available.
         """
         all_kpts = self.get_sym_eq_kpoints(kpoint, cartesian, tol=tol)
         return len(all_kpts) if all_kpts is not None else None
@@ -571,7 +567,7 @@ def as_dict(self) -> dict[str, Any]:
             "kpoints": [],
         }
         # kpoints are not kpoint objects dicts but are frac coords (this makes
-        # the dict smaller and avoids the repetition of the lattice
+        # the dict smaller and avoids the repetition of the lattice).
         for k in self.kpoints:
             dct["kpoints"].append(k.as_dict()["fcoords"])
 
@@ -595,7 +591,7 @@ def as_dict(self) -> dict[str, Any]:
         dct["labels_dict"] = {}
         dct["is_spin_polarized"] = self.is_spin_polarized
 
-        # MongoDB does not accept keys starting with $. Add a blank space to fix the problem
+        # MongoDB does not accept keys starting with "$", add a space to fix this.
         for c, label in self.labels_dict.items():
             mongo_key = f" {c}" if c.startswith("$") else c
             dct["labels_dict"][mongo_key] = label.as_dict()["fcoords"]
@@ -607,27 +603,28 @@ def as_dict(self) -> dict[str, Any]:
 
     @classmethod
     def from_dict(cls, dct: dict[str, Any]) -> Self:
-        """Create from dict.
+        """Create from a dict.
 
         Args:
-            dct: A dict with all data for a band structure object.
+            dct: A dict with all data for a BandStructure.
 
         Returns:
-            A BandStructure object
+            A BandStructure object.
         """
         # Strip the label to recover initial string
-        # (see trick used in as_dict to handle $ chars)
+        # (see trick used in as_dict to handle "$"" chars)
         labels_dict = {k.strip(): v for k, v in dct["labels_dict"].items()}
-        projections = {}
-        structure = None
+
         if isinstance(next(iter(dct["bands"].values())), dict):
             eigenvals = {Spin(int(k)): np.array(dct["bands"][k]["data"]) for k in dct["bands"]}
         else:
             eigenvals = {Spin(int(k)): dct["bands"][k] for k in dct["bands"]}
 
+        structure = None
         if "structure" in dct:
             structure = Structure.from_dict(dct["structure"])
 
+        projections = {}
         try:
             if dct.get("projections"):
                 if isinstance(dct["projections"]["1"][0][0], dict):
@@ -657,12 +654,13 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:
     def from_old_dict(cls, dct: dict[str, Any]) -> Self:
         """
         Args:
-            dct (dict): A dict with all data for a band structure symmetry line object.
+            dct (dict): A dict with all data for a BandStructure object.
 
         Returns:
-            A BandStructureSymmLine object
+            A BandStructure object.
         """
-        # Strip the label to recover initial string (see trick used in as_dict to handle $ chars)
+        # Strip the label to recover initial string
+        # (see trick used in as_dict to handle "$" chars)
         labels_dict = {k.strip(): v for k, v in dct["labels_dict"].items()}
         projections: dict = {}
         structure = None
@@ -707,33 +705,31 @@ def __init__(
         eigenvals: dict[Spin, list],
         lattice: Lattice,
         efermi: float,
-        labels_dict: dict,
+        labels_dict: dict[Kpoint, str],
         coords_are_cartesian: bool = False,
         structure: Structure | None = None,
         projections: dict[Spin, NDArray] | None = None,
     ) -> None:
         """
         Args:
-            kpoints: list of kpoint as numpy arrays, in frac_coords of the
+            kpoints (NDArray): Array of kpoint, in frac_coords of the
                 given lattice by default
-            eigenvals: dict of energies for spin up and spin down
+            eigenvals (dict[Spin, list]): Energies for spin up and spin down
                 {Spin.up:[][],Spin.down:[][]}, the first index of the array
                 [][] refers to the band and the second to the index of the
                 kpoint. The kpoints are ordered according to the order of the
                 kpoints array. If the band structure is not spin polarized, we
                 only store one data set under Spin.up.
-            lattice: The reciprocal lattice.
-                Pymatgen uses the physics convention of reciprocal lattice vectors
-                WITH a 2*pi coefficient
-            efermi: fermi energy
-            labels_dict: (dict) of {} this link a kpoint (in frac coords or
-                Cartesian coordinates depending on the coords).
-            coords_are_cartesian: Whether coordinates are cartesian.
-            structure: The crystal structure (as a pymatgen Structure object)
-                associated with the band structure. This is needed if we
-                provide projections to the band structure.
-            projections: dict of orbital projections as {spin: array}. The
-                indices of the array are [band_index, kpoint_index, orbital_index,
+            lattice (Lattice): The reciprocal lattice. Pymatgen uses the physics
+                convention of reciprocal lattice vectors with a 2*pi coefficient.
+            efermi (float): The Fermi level.
+            labels_dict (dict[Kpoint, str]): Dict mapping kpoint to label.
+            coords_are_cartesian (bool): Whether coordinates are cartesian.
+            structure (Structure): The crystal structure associated with the
+                band structure. This is needed if we provide projections to
+                the band structure.
+            projections (dict[Spin, NDArray]): Orbital projections as {spin: array}.
+                The indices of the array are [band_index, kpoint_index, orbital_index,
                 ion_index].If the band structure is not spin polarized, we only
                 store one data set under Spin.up.
         """
@@ -787,21 +783,19 @@ def __init__(
             self.is_spin_polarized = True
 
     def get_equivalent_kpoints(self, index: int) -> list[int]:
-        """Get the list of kpoint indices equivalent (meaning they are the
-        same frac coords) to the given one.
+        """Get kpoint indices equivalent (having the same coords) to the given one.
 
         Args:
-            index: the kpoint index
+            index (int): The kpoint index
 
         Returns:
-            a list of equivalent indices
+            list[int]: Equivalent indices.
 
-        TODO: now it uses the label we might want to use coordinates instead
+        TODO: now it uses the label, we might want to use coordinates instead.
         (in case there was a mislabel)
         """
         # If the kpoint has no label it can't have a repetition
         # along the BandStructureSymmLine object
-
         if self.kpoints[index].label is None:
             return [index]
 
@@ -813,17 +807,15 @@ def get_equivalent_kpoints(self, index: int) -> list[int]:
         return list_index_kpoints
 
     def get_branch(self, index: int) -> list[dict[str, Any]]:
-        r"""Get in what branch(es) is the kpoint. There can be several
-        branches.
+        """Get what branch(es) is the kpoint. It takes into account the
+            fact that one kpoint (e.g., Gamma) can be in several branches.
 
         Args:
-            index: the kpoint index
+            index (int): The kpoint index.
 
         Returns:
-            A list of dictionaries [{"name","start_index","end_index","index"}]
-            indicating all branches in which the k_point is. It takes into
-            account the fact that one kpoint (e.g., \\Gamma) can be in several
-            branches
+            A list of dicts [{"name", "start_index", "end_index", "index"}]
+                indicating all branches in which the k_point is.
         """
         to_return = []
         for idx in self.get_equivalent_kpoints(index):
@@ -845,10 +837,10 @@ def apply_scissor(self, new_band_gap: float) -> Self:
         and shift this one up. This will not work all the time for metals!
 
         Args:
-            new_band_gap: the band gap the scissor band structure need to have.
+            new_band_gap (float): The band gap the scissor band structure need to have.
 
         Returns:
-            BandStructureSymmLine: with the applied scissor shift
+            BandStructureSymmLine: With the applied scissor shift.
         """
         if self.is_metal():
             # Move then the highest index band crossing the Fermi level find this band...
@@ -904,7 +896,7 @@ def as_dict(self) -> dict[str, Any]:
 
 
 class LobsterBandStructureSymmLine(BandStructureSymmLine):
-    """Lobster subclass of BandStructure with customized functions."""
+    """LOBSTER subclass of BandStructure with customized functions."""
 
     def as_dict(self) -> dict[str, Any]:
         """JSON-serializable dict representation of BandStructureSymmLine."""
@@ -940,9 +932,9 @@ def as_dict(self) -> dict[str, Any]:
         dct["labels_dict"] = {}
         dct["is_spin_polarized"] = self.is_spin_polarized
 
-        # MongoDB does not accept keys starting with $. Add a blank space to fix the problem
+        # MongoDB does not accept keys starting with "$", add a space to fix this.
         for c, label in self.labels_dict.items():
-            mongo_key = c if not c.startswith("$") else " " + c
+            mongo_key = f" {c}" if c.startswith("$") else c
             dct["labels_dict"][mongo_key] = label.as_dict()["fcoords"]
         if len(self.projections) != 0 and self.structure is not None:
             dct["structure"] = self.structure.as_dict()
@@ -953,14 +945,14 @@ def as_dict(self) -> dict[str, Any]:
     def from_dict(cls, dct: dict[str, Any]) -> Self:
         """
         Args:
-            dct (dict): A dict with all data for a band structure symmetry line
-                object.
+            dct (dict): All data for a LobsterBandStructureSymmLine object.
 
         Returns:
-            A BandStructureSymmLine object
+            A LobsterBandStructureSymmLine object.
         """
         try:
-            # Strip the label to recover initial string (see trick used in as_dict to handle $ chars)
+            # Strip the label to recover initial string
+            # (see trick used in as_dict to handle "$" chars)
             labels_dict = {k.strip(): v for k, v in dct["labels_dict"].items()}
             projections = {}
             structure = None
@@ -992,13 +984,13 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:
     def from_old_dict(cls, dct: dict[str, Any]) -> Self:
         """
         Args:
-            dct (dict): A dict with all data for a band structure symmetry line
-                object.
+            dct (dict): All data for a LobsterBandStructureSymmLine object.
 
         Returns:
-            A BandStructureSymmLine object
+            A LobsterBandStructureSymmLine object
         """
-        # Strip the label to recover initial string (see trick used in as_dict to handle $ chars)
+        # Strip the label to recover initial string
+        # (see trick used in as_dict to handle "$" chars)
         labels_dict = {k.strip(): v for k, v in dct["labels_dict"].items()}
         projections: dict = {}
         structure = None
@@ -1025,14 +1017,13 @@ def from_old_dict(cls, dct: dict[str, Any]) -> Self:
         )
 
     def get_projection_on_elements(self) -> dict[Spin, list]:
-        """Get a dictionary of projections on elements. It sums over all available orbitals
+        """Get projections on elements. It sums over all available orbitals
         for each element.
 
         Returns:
-            a dictionary in the {Spin.up:[][{Element:values}],
-            Spin.down:[][{Element:values}]} format
-            if there is no projections in the band structure
-            returns an empty dict
+            dict[Spin, list]: dict in the {Spin.up:[][{Element:values}],
+                Spin.down:[][{Element:values}]} format.
+                If there is no projections in the band structure, return {}.
         """
         result: dict[Spin, list] = {}
         for spin, v in self.projections.items():
@@ -1048,12 +1039,13 @@ def get_projections_on_elements_and_orbitals(
         self,
         el_orb_spec: dict[Element, list],  # type: ignore[override]
     ) -> dict[Spin, list]:
-        """Return a dictionary of projections on elements and specific orbitals.
+        """Get projections on elements and specific orbitals.
 
         Args:
-            el_orb_spec: A dictionary of Elements and Orbitals for which we want
-                to have projections on. It is given as: {Element:[orbitals]},
-                e.g. {'Si':['3s','3p']} or {'Si':['3s','3p_x', '3p_y', '3p_z']} depending on input files
+            el_orb_spec (dict): Elements and Orbitals for which we want
+                to project on. It is given as {Element: [orbitals]},
+                e.g. {"Si": ["3s", "3p"]} or {"Si": ["3s", "3p_x", "3p_y", "3p_z']}
+                depending on input files.
 
         Returns:
             A dictionary of projections on elements in the
@@ -1099,22 +1091,20 @@ def get_reconstructed_band_structure(
     list_bs: list[BandStructure] | list[BandStructureSymmLine],
     efermi: float | None = None,
 ) -> BandStructure | BandStructureSymmLine:
-    """Take a list of band structures and reconstructs
-    one band structure object from all of them.
+    """Merge band structures to one single BandStructure(SymmLine) object.
 
-    This is typically very useful when you split non self consistent
-    band structure runs in several independent jobs and want to merge back
-    the results
+    This is typically useful when you split non self-consistent band
+    structure runs to several independent jobs and want to merge the results.
 
     Args:
-        list_bs: A list of BandStructure or BandStructureSymmLine objects.
-        efermi: The Fermi energy of the reconstructed band structure. If
-            None is assigned an average of all the Fermi energy in each
+        list_bs (list): BandStructure or BandStructureSymmLine objects.
+        efermi (float): The Fermi level of the reconstructed band structure.
+            If None, an average of all the Fermi levels in each
             object in the list_bs is used.
 
     Returns:
         A BandStructure or BandStructureSymmLine object (depending on
-        the type of the list_bs objects)
+        the type of the list_bs objects).
     """
     if efermi is None:
         efermi = sum(b.efermi for b in list_bs) / len(list_bs)
@@ -1128,9 +1118,7 @@ def get_reconstructed_band_structure(
     dicts = [bs.labels_dict for bs in list_bs]
     labels_dict = {k: v.frac_coords for d in dicts for k, v in d.items()}
 
-    eigenvals = {}
-    eigenvals[Spin.up] = np.concatenate([bs.bands[Spin.up][:nb_bands] for bs in list_bs], axis=1)
-
+    eigenvals = {Spin.up: np.concatenate([bs.bands[Spin.up][:nb_bands] for bs in list_bs], axis=1)}
     if list_bs[0].is_spin_polarized:
         eigenvals[Spin.down] = np.concatenate([bs.bands[Spin.down][:nb_bands] for bs in list_bs], axis=1)
 

From e558ac7d99869af913dc68c0b3029f8df9a21629 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 12:42:07 +0800
Subject: [PATCH 26/39] more minor tweaks

---
 pymatgen/electronic_structure/bandstructure.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/pymatgen/electronic_structure/bandstructure.py b/pymatgen/electronic_structure/bandstructure.py
index d77314899d2..9ee8616b8a0 100644
--- a/pymatgen/electronic_structure/bandstructure.py
+++ b/pymatgen/electronic_structure/bandstructure.py
@@ -1,4 +1,4 @@
-"""This module provides classes to define everything related to band structures."""
+"""This module provides classes to define things related to band structures."""
 
 from __future__ import annotations
 
@@ -33,8 +33,8 @@
 
 
 class Kpoint(MSONable):
-    """A kpoint is defined with a lattice and frac or Cartesian coordinates,
-    syntax similar than the Site object in pymatgen.core.structure.
+    """A kpoint defined with a lattice and frac or Cartesian coordinates,
+    similar to the Site object in pymatgen.core.structure.
     """
 
     def __init__(
@@ -287,8 +287,8 @@ def get_projections_on_elements_and_orbitals(self, el_orb_spec: dict[str, list[s
         return result
 
     def is_metal(self, efermi_tol: float = 1e-4) -> bool:
-        """Check if the band structure indicates a metal by looking if the fermi
-        level crosses a band.
+        """Check if the band structure indicates a metal,
+        by looking at if the fermi level crosses a band.
 
         Returns:
             bool: True if is metal.
@@ -1109,8 +1109,6 @@ def get_reconstructed_band_structure(
     if efermi is None:
         efermi = sum(b.efermi for b in list_bs) / len(list_bs)
 
-    kpoints = []
-    labels_dict = {}
     rec_lattice = list_bs[0].lattice_rec
     nb_bands = min(list_bs[i].nb_bands for i in range(len(list_bs)))
 

From 4c0bb04e749af1370d0cadb19a48410617f30777 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 16:59:07 +0800
Subject: [PATCH 27/39] clarify type of labels_dict

---
 .../electronic_structure/bandstructure.py     | 20 +++++++++----------
 pymatgen/io/vasp/outputs.py                   |  2 +-
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/pymatgen/electronic_structure/bandstructure.py b/pymatgen/electronic_structure/bandstructure.py
index 9ee8616b8a0..73378506807 100644
--- a/pymatgen/electronic_structure/bandstructure.py
+++ b/pymatgen/electronic_structure/bandstructure.py
@@ -172,7 +172,7 @@ def __init__(
         eigenvals: dict[Spin, NDArray],
         lattice: Lattice,
         efermi: float,
-        labels_dict: dict[Kpoint, str] | None = None,
+        labels_dict: dict[str, Kpoint] | None = None,
         coords_are_cartesian: bool = False,
         structure: Structure | None = None,
         projections: dict[Spin, NDArray] | None = None,
@@ -190,7 +190,7 @@ def __init__(
             lattice (Lattice): The reciprocal lattice. Pymatgen uses the physics
                 convention of reciprocal lattice vectors with a 2*pi coefficient.
             efermi (float): The Fermi level.
-            labels_dict (dict[Kpoint, str]): Dict mapping kpoint to label.
+            labels_dict (dict[str, Kpoint]): Dict mapping label to Kpoint.
             coords_are_cartesian (bool): Whether coordinates are cartesian.
             structure (Structure): The crystal structure
                 associated with the band structure. This is needed if we
@@ -705,7 +705,7 @@ def __init__(
         eigenvals: dict[Spin, list],
         lattice: Lattice,
         efermi: float,
-        labels_dict: dict[Kpoint, str],
+        labels_dict: dict[str, Kpoint],
         coords_are_cartesian: bool = False,
         structure: Structure | None = None,
         projections: dict[Spin, NDArray] | None = None,
@@ -723,7 +723,7 @@ def __init__(
             lattice (Lattice): The reciprocal lattice. Pymatgen uses the physics
                 convention of reciprocal lattice vectors with a 2*pi coefficient.
             efermi (float): The Fermi level.
-            labels_dict (dict[Kpoint, str]): Dict mapping kpoint to label.
+            labels_dict (dict[str, Kpoint]): Dict mapping label to Kpoint.
             coords_are_cartesian (bool): Whether coordinates are cartesian.
             structure (Structure): The crystal structure associated with the
                 band structure. This is needed if we provide projections to
@@ -791,8 +791,8 @@ def get_equivalent_kpoints(self, index: int) -> list[int]:
         Returns:
             list[int]: Equivalent indices.
 
-        TODO: now it uses the label, we might want to use coordinates instead.
-        (in case there was a mislabel)
+        TODO: now it uses the label, we might want to use coordinates
+        instead in case there was a mislabel.
         """
         # If the kpoint has no label it can't have a repetition
         # along the BandStructureSymmLine object
@@ -1091,7 +1091,7 @@ def get_reconstructed_band_structure(
     list_bs: list[BandStructure] | list[BandStructureSymmLine],
     efermi: float | None = None,
 ) -> BandStructure | BandStructureSymmLine:
-    """Merge band structures to one single BandStructure(SymmLine) object.
+    """Merge multiple BandStructure(SymmLine) objects to a single one.
 
     This is typically useful when you split non self-consistent band
     structure runs to several independent jobs and want to merge the results.
@@ -1104,7 +1104,7 @@ def get_reconstructed_band_structure(
 
     Returns:
         A BandStructure or BandStructureSymmLine object (depending on
-        the type of the list_bs objects).
+        the type of the objects in list_bs).
     """
     if efermi is None:
         efermi = sum(b.efermi for b in list_bs) / len(list_bs)
@@ -1112,9 +1112,9 @@ def get_reconstructed_band_structure(
     rec_lattice = list_bs[0].lattice_rec
     nb_bands = min(list_bs[i].nb_bands for i in range(len(list_bs)))
 
-    kpoints = np.concatenate([[k.frac_coords for k in bs.kpoints] for bs in list_bs])
+    kpoints = np.concatenate([[kpt.frac_coords for kpt in bs.kpoints] for bs in list_bs])
     dicts = [bs.labels_dict for bs in list_bs]
-    labels_dict = {k: v.frac_coords for d in dicts for k, v in d.items()}
+    labels_dict = {key: val.frac_coords for dct in dicts for key, val in dct.items()}
 
     eigenvals = {Spin.up: np.concatenate([bs.bands[Spin.up][:nb_bands] for bs in list_bs], axis=1)}
     if list_bs[0].is_spin_polarized:
diff --git a/pymatgen/io/vasp/outputs.py b/pymatgen/io/vasp/outputs.py
index 7eccca20661..ed9a6fe7aee 100644
--- a/pymatgen/io/vasp/outputs.py
+++ b/pymatgen/io/vasp/outputs.py
@@ -1034,7 +1034,7 @@ def get_band_structure(
                 eigenvals,
                 lattice_new,
                 e_fermi,
-                labels_dict,
+                labels_dict,  # type: ignore[arg-type]
                 structure=self.final_structure,
                 projections=p_eig_vals,
             )

From 8e252388e718415140142a69605896342a5e16c3 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 17:20:22 +0800
Subject: [PATCH 28/39] replace unnecessary single-item list extend with append

---
 pymatgen/io/lobster/outputs.py | 108 +++++++++++++++++----------------
 1 file changed, 57 insertions(+), 51 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index 0d855bc60ef..3a1b00a39cd 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -427,7 +427,13 @@ def __init__(
             else:
                 n_bonds = len(data_without_orbitals)
 
-            labels, atoms1, atoms2, lens, translations, nums, icohps = [], [], [], [], [], [], []
+            labels: list[str] = []
+            atoms1: list[str] = []
+            atoms2: list[str] = []
+            lens: list[float] = []
+            translations: list[tuple[int, int, int]] = []
+            nums: list[int] = []
+            icohps: list[dict[Spin, float]] = []
 
             for bond in range(n_bonds):
                 line_parts = data_without_orbitals[bond].split()
@@ -437,7 +443,7 @@ def __init__(
                 atom2 = str(line_parts[2])
                 length = float(line_parts[3])
 
-                icohp = {}
+                icohp: dict[Spin, float] = {}
                 if version == "2.2.1":
                     icohp[Spin.up] = float(line_parts[4])
                     num = int(line_parts[5])
@@ -453,13 +459,13 @@ def __init__(
                     if self.is_spin_polarized:
                         icohp[Spin.down] = float(data_without_orbitals[bond + n_bonds + 1].split()[7])
 
-                labels += [label]
-                atoms1 += [atom1]
-                atoms2 += [atom2]
-                lens += [length]
-                translations += [translation]
-                nums += [num]
-                icohps += [icohp]
+                labels.append(label)
+                atoms1.append(atom1)
+                atoms2.append(atom2)
+                lens.append(length)
+                translations.append(translation)
+                nums.append(num)
+                icohps.append(icohp)
 
             list_orb_icohp: list[dict] | None = None
             if self.orbitalwise:
@@ -479,7 +485,7 @@ def __init__(
                         icohp[Spin.down] = float(data_orbitals[n_orbs + i_data_orb].split()[7])
 
                     if len(list_orb_icohp) < int(label):
-                        list_orb_icohp += [{orb_label: {"icohp": icohp, "orbitals": orbitals}}]
+                        list_orb_icohp.append({orb_label: {"icohp": icohp, "orbitals": orbitals}})
                     else:
                         list_orb_icohp[int(label) - 1][orb_label] = {"icohp": icohp, "orbitals": orbitals}
 
@@ -561,7 +567,7 @@ def __init__(self, filename: str | None = "NcICOBILIST.lobster"):  # LOBSTER < 4
             data_without_orbitals = []
             for line in data:
                 if "_" not in str(line.split()[3:]) and "s]" not in str(line.split()[3:]):
-                    data_without_orbitals += [line]
+                    data_without_orbitals.append(line)
         else:
             data_without_orbitals = data
 
@@ -592,11 +598,11 @@ def __init__(self, filename: str | None = "NcICOBILIST.lobster"):  # LOBSTER < 4
             if self.is_spin_polarized:
                 ncicobi[Spin.down] = float(data_without_orbitals[bond + n_bonds + 1].split()[2])
 
-            self.list_labels += [label]
-            self.list_n_atoms += [n_atoms]
-            self.list_ncicobi += [ncicobi]
-            self.list_interaction_type += [interaction_type]
-            self.list_num += [num]
+            self.list_labels.append(label)
+            self.list_n_atoms.append(n_atoms)
+            self.list_ncicobi.append(ncicobi)
+            self.list_interaction_type.append(interaction_type)
+            self.list_num.append(num)
 
         # TODO: add functions to get orbital resolved NcICOBIs
 
@@ -677,7 +683,7 @@ def _parse_doscar(self):
                 for nd in range(1, ndos):
                     line = file.readline().split()
                     cdos[nd] = np.array(line)
-                dos += [cdos]
+                dos.append(cdos)
         doshere = np.array(dos[0])
         if len(doshere[0, :]) == 5:
             self._is_spin_polarized = True
@@ -699,7 +705,7 @@ def _parse_doscar(self):
                 for orb_num, j in enumerate(range(1, ncol)):
                     orb = orbitals[atom + 1][orb_num]
                     pdos[orb][spin] = data[:, j]
-                pdoss += [pdos]
+                pdoss.append(pdos)
         else:
             tdensities[Spin.up] = doshere[:, 1]
             tdensities[Spin.down] = doshere[:, 2]
@@ -717,7 +723,7 @@ def _parse_doscar(self):
                     pdos[orb][spin] = data[:, j]
                     if j % 2 == 0:
                         orb_num += 1
-                pdoss += [pdos]
+                pdoss.append(pdos)
 
         self._efermi = efermi
         self._pdos = pdoss
@@ -814,8 +820,8 @@ def __init__(
                 line = data[atom].split()
                 self.atomlist += [line[1] + line[0]]
                 self.types += [line[1]]
-                self.mulliken += [float(line[2])]
-                self.loewdin += [float(line[3])]
+                self.mulliken.append(float(line[2]))
+                self.loewdin.append(float(line[3]))
 
     def get_structure_with_charges(self, structure_filename):
         """Get a Structure with Mulliken and Loewdin charges as site properties
@@ -1087,9 +1093,9 @@ def _get_spillings(data, number_of_spins):
             splitrow = row.split()
             if len(splitrow) > 2 and splitrow[2] == "spilling:":
                 if splitrow[1] == "charge":
-                    charge_spilling += [np.float64(splitrow[3].replace("%", "")) / 100.0]
+                    charge_spilling.append(np.float64(splitrow[3].replace("%", "")) / 100.0)
                 if splitrow[1] == "total":
-                    total_spilling += [np.float64(splitrow[3].replace("%", "")) / 100.0]
+                    total_spilling.append(np.float64(splitrow[3].replace("%", "")) / 100.0)
 
             if len(charge_spilling) == number_of_spins and len(total_spilling) == number_of_spins:
                 break
@@ -1156,7 +1162,7 @@ def _get_warning_orthonormalization(data):
         for row in data:
             splitrow = row.split()
             if "orthonormalized" in splitrow:
-                orthowarning += [" ".join(splitrow[1:])]
+                orthowarning.append(" ".join(splitrow[1:]))
         return orthowarning
 
     @staticmethod
@@ -1165,7 +1171,7 @@ def _get_all_warning_lines(data):
         for row in data:
             splitrow = row.split()
             if len(splitrow) > 0 and splitrow[0] == "WARNING:":
-                ws += [" ".join(splitrow[1:])]
+                ws.append(" ".join(splitrow[1:]))
         return ws
 
     @staticmethod
@@ -1174,7 +1180,7 @@ def _get_all_info_lines(data):
         for row in data:
             splitrow = row.split()
             if len(splitrow) > 0 and splitrow[0] == "INFO:":
-                infos += [" ".join(splitrow[1:])]
+                infos.append(" ".join(splitrow[1:]))
         return infos
 
 
@@ -1257,7 +1263,7 @@ def __init__(
                 filenames = "."
             for name in os.listdir(filenames):
                 if fnmatch.fnmatch(name, "FATBAND_*.lobster"):
-                    filenames_new += [os.path.join(filenames, name)]
+                    filenames_new.append(os.path.join(filenames, name))
             filenames = filenames_new
         if len(filenames) == 0:
             raise ValueError("No FATBAND files in folder or given")
@@ -1310,7 +1316,7 @@ def __init__(
                 linenumbers = []
                 for iline, line in enumerate(contents[1 : self.nbands * 2 + 4]):
                     if line.split()[0] == "#":
-                        linenumbers += [iline]
+                        linenumbers.append(iline)
 
                 if ifilename == 0:
                     self.is_spinpolarized = len(linenumbers) == 2
@@ -1360,7 +1366,7 @@ def __init__(
                         ]
                     )
                     if ifilename == 0:
-                        kpoints_array += [KPOINT]
+                        kpoints_array.append(KPOINT)
 
                     linenumber = 0
                     iband = 0
@@ -1471,7 +1477,7 @@ def _read(self, contents: list, spin_numbers: list):
                 kpoint_array = []
                 for kpointel in kpoint:
                     if kpointel not in {"at", "k-point", ""}:
-                        kpoint_array += [float(kpointel)]
+                        kpoint_array.append(float(kpointel))
 
             elif "maxDeviation" in line:
                 if spin not in self.band_overlaps_dict:
@@ -1483,16 +1489,16 @@ def _read(self, contents: list, spin_numbers: list):
                 if "matrices" not in self.band_overlaps_dict[spin]:
                     self.band_overlaps_dict[spin]["matrices"] = []
                 maxdev = line.split(" ")[2]
-                self.band_overlaps_dict[spin]["max_deviations"] += [float(maxdev)]
+                self.band_overlaps_dict[spin]["max_deviations"].append(float(maxdev))
                 self.band_overlaps_dict[spin]["k_points"] += [kpoint_array]
-                self.max_deviation += [float(maxdev)]
+                self.max_deviation.append(float(maxdev))
                 overlaps = []
 
             else:
                 rows = []
                 for el in line.split(" "):
                     if el != "":
-                        rows += [float(el)]
+                        rows.append(float(el))
                 overlaps += [rows]
                 if len(overlaps) == len(rows):
                     self.band_overlaps_dict[spin]["matrices"] += [np.matrix(overlaps)]
@@ -1603,7 +1609,7 @@ def __init__(self, filename: str = "GROSSPOP.lobster", list_dict_grosspop: list[
                     small_dict["Mulliken GP"][cleanline[0]] = float(cleanline[1])
                     small_dict["Loewdin GP"][cleanline[0]] = float(cleanline[2])
                     if "total" in cleanline[0]:
-                        self.list_dict_grosspop += [small_dict]
+                        self.list_dict_grosspop.append(small_dict)
 
     def get_structure_with_total_grosspop(self, structure_filename: str) -> Structure:
         """Get a Structure with Mulliken and Loewdin total grosspopulations as site properties
@@ -1664,9 +1670,9 @@ def _parse_file(filename):
             splitline = line.split()
             if len(splitline) >= 6:
                 points += [[float(splitline[0]), float(splitline[1]), float(splitline[2])]]
-                distance += [float(splitline[3])]
-                real += [float(splitline[4])]
-                imaginary += [float(splitline[5])]
+                distance.append(float(splitline[3]))
+                real.append(float(splitline[4]))
+                imaginary.append(float(splitline[5]))
 
         if len(real) != grid[0] * grid[1] * grid[2] or len(imaginary) != grid[0] * grid[1] * grid[2]:
             raise ValueError("Something went wrong while reading the file")
@@ -1712,9 +1718,9 @@ def set_volumetric_data(self, grid, structure):
                         "coordinates 0.0 0.0 0.0 coordinates 1.0 1.0 1.0 box bandlist 1 "
                     )
 
-                new_x += [x_here]
-                new_y += [y_here]
-                new_z += [z_here]
+                new_x.append(x_here)
+                new_y.append(y_here)
+                new_z.append(z_here)
 
                 new_real += [self.real[runner]]
                 new_imaginary += [self.imaginary[runner]]
@@ -1909,8 +1915,8 @@ def __init__(
                 line = data[atom].split()
                 self.atomlist += [line[1] + str(line[0])]
                 self.types += [line[1]]
-                self.sitepotentials_mulliken += [float(line[2])]
-                self.sitepotentials_loewdin += [float(line[3])]
+                self.sitepotentials_mulliken.append(float(line[2]))
+                self.sitepotentials_loewdin.append(float(line[3]))
 
             self.madelungenergies_mulliken = float(data[self.num_atoms + 1].split()[3])
             self.madelungenergies_loewdin = float(data[self.num_atoms + 1].split()[4])
@@ -2098,21 +2104,21 @@ def _parse_matrix(file_data, pattern, e_fermi):
         for idx, line in enumerate(file_data):
             line = line.strip()
             if "Real parts" in line:
-                start_inxs_real += [idx + 1]
+                start_inxs_real.append(idx + 1)
                 if idx == 1:  # ignore the first occurrence as files start with real matrices
                     pass
                 else:
-                    end_inxs_imag += [idx - 1]
+                    end_inxs_imag.append(idx - 10)
                 matches = re.search(pattern, file_data[idx - 1])
                 if matches and len(matches.groups()) == 2:
                     k_point = matches.group(2)
                     complex_matrices[k_point] = {}
             if "Imag parts" in line:
-                end_inxs_real += [idx - 1]
-                start_inxs_imag += [idx + 1]
+                end_inxs_real.append(idx - 1)
+                start_inxs_imag.append(idx + 1)
             # explicitly add the last line as files end with imaginary matrix
             if idx == len(file_data) - 1:
-                end_inxs_imag += [len(file_data)]
+                end_inxs_imag.append(len(file_data))
 
         # extract matrix data and store diagonal elements
         matrix_real = []
@@ -2133,13 +2139,13 @@ def _parse_matrix(file_data, pattern, e_fermi):
 
             matches = re.search(pattern, file_data[start_inx_real - 2])
             if matches and len(matches.groups()) == 2:
-                spin = Spin.up if matches.group(1) == "1" else Spin.down
-                k_point = matches.group(2)
+                spin = Spin.up if matches[1] == "1" else Spin.down
+                k_point = matches[2]
                 complex_matrices[k_point].update({spin: comp_matrix})
             elif matches and len(matches.groups()) == 1:
-                k_point = matches.group(1)
+                k_point = matches[1]
                 complex_matrices.update({k_point: comp_matrix})
-            matrix_diagonal_values += [comp_matrix.real.diagonal() - e_fermi]
+            matrix_diagonal_values.append(comp_matrix.real.diagonal() - e_fermi)
 
         # extract elements basis functions as list
         elements_basis_functions = [

From 00b7134352548d2fdb4852fa7aaa32096d4276ab Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 17:22:34 +0800
Subject: [PATCH 29/39] fix typo

---
 pymatgen/io/lobster/outputs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index 3a1b00a39cd..003c43e8554 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -2108,7 +2108,7 @@ def _parse_matrix(file_data, pattern, e_fermi):
                 if idx == 1:  # ignore the first occurrence as files start with real matrices
                     pass
                 else:
-                    end_inxs_imag.append(idx - 10)
+                    end_inxs_imag.append(idx - 1)
                 matches = re.search(pattern, file_data[idx - 1])
                 if matches and len(matches.groups()) == 2:
                     k_point = matches.group(2)

From 952e2060755a53455f38311334fa41fac6e3b2b2 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 17:32:09 +0800
Subject: [PATCH 30/39] relocate magic method

---
 pymatgen/electronic_structure/dos.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/pymatgen/electronic_structure/dos.py b/pymatgen/electronic_structure/dos.py
index cdb3074838d..68f62faf701 100644
--- a/pymatgen/electronic_structure/dos.py
+++ b/pymatgen/electronic_structure/dos.py
@@ -52,6 +52,18 @@ def __init__(self, energies: ArrayLike, densities: ArrayLike, efermi: float) ->
         super().__init__(energies, densities, efermi)
         self.efermi = efermi
 
+    def __str__(self) -> str:
+        """Get a string which can be easily plotted (using gnuplot)."""
+        if Spin.down in self.densities:
+            str_arr = [f"#{'Energy':30s} {'DensityUp':30s} {'DensityDown':30s}"]
+            for idx, energy in enumerate(self.energies):
+                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][idx]:.5f} {self.densities[Spin.down][idx]:.5f}")
+        else:
+            str_arr = [f"#{'Energy':30s} {'DensityUp':30s}"]
+            for idx, energy in enumerate(self.energies):
+                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][idx]:.5f}")
+        return "\n".join(str_arr)
+
     def get_interpolated_gap(self, tol: float = 0.001, abs_tol: bool = False, spin: Spin | None = None):
         """Expects a DOS object and finds the gap.
 
@@ -148,18 +160,6 @@ def get_gap(self, tol: float = 0.001, abs_tol: bool = False, spin: Spin | None =
         cbm, vbm = self.get_cbm_vbm(tol, abs_tol, spin)
         return max(cbm - vbm, 0.0)
 
-    def __str__(self) -> str:
-        """Get a string which can be easily plotted (using gnuplot)."""
-        if Spin.down in self.densities:
-            str_arr = [f"#{'Energy':30s} {'DensityUp':30s} {'DensityDown':30s}"]
-            for i, energy in enumerate(self.energies):
-                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f} {self.densities[Spin.down][i]:.5f}")
-        else:
-            str_arr = [f"#{'Energy':30s} {'DensityUp':30s}"]
-            for i, energy in enumerate(self.energies):
-                str_arr.append(f"{energy:.5f} {self.densities[Spin.up][i]:.5f}")
-        return "\n".join(str_arr)
-
 
 class Dos(MSONable):
     """Basic DOS object. All other DOS objects are extended versions of this

From 4ee908d745f5d39f9b7a856ef9afd26af0ccdba4 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 18:05:33 +0800
Subject: [PATCH 31/39] clarify type of `list_icohp`

---
 pymatgen/electronic_structure/cohp.py | 14 ++++++++------
 pymatgen/io/lobster/outputs.py        |  2 +-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 72f15d5a5d8..f7061a1e951 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -939,7 +939,7 @@ def __init__(
         length: float,
         translation: Vector3D,
         num: int,
-        icohp: dict[Spin, IcohpValue],
+        icohp: dict[Spin, float],
         are_coops: bool = False,
         are_cobis: bool = False,
         orbitals: dict[str, dict[Literal["icohp", "orbitals"], Any]] | None = None,
@@ -952,7 +952,7 @@ def __init__(
             length (float): Bond length.
             translation (Vector3D): cell translation vector, e.g. (0, 0, 0).
             num (int): The number of equivalent bonds.
-            icohp (dict): {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}
+            icohp (dict[Spin, float]): {Spin.up: ICOHP_up, Spin.down: ICOHP_down}
             are_coops (bool): Whether these are COOPs.
             are_cobis (bool): Whether these are COBIs.
             orbitals (dict): {[str(Orbital1)-str(Orbital2)]: {
@@ -1070,11 +1070,11 @@ def icohpvalue_orbital(
         return self._orbitals[orbitals]["icohp"][spin]
 
     @property
-    def icohp(self) -> dict[Spin, IcohpValue]:
+    def icohp(self) -> dict[Spin, float]:
         """Dict with ICOHPs for spin up and spin down.
 
         Returns:
-            dict: {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
+            dict[Spin, float]: {Spin.up: ICOHP_up, Spin.down: ICOHP_down}.
         """
         return self._icohp
 
@@ -1120,7 +1120,7 @@ def __init__(
         list_length: list[float],
         list_translation: list[Vector3D],
         list_num: list[int],
-        list_icohp: list[dict[Spin, IcohpValue]],
+        list_icohp: list[dict[Spin, float]],
         is_spin_polarized: bool,
         list_orb_icohp: list[dict[str, dict[Literal["icohp", "orbitals"], Any]]] | None = None,
         are_coops: bool = False,
@@ -1134,7 +1134,7 @@ def __init__(
             list_length (list[float]): Bond lengths in Angstrom.
             list_translation (list[Vector3D]): Cell translation vectors.
             list_num (list[int]): Numbers of equivalent bonds, usually 1 starting from LOBSTER 3.0.0.
-            list_icohp (list[dict]): Dicts as {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down}.
+            list_icohp (list[dict]): Dicts as {Spin.up: ICOHP_up, Spin.down: ICOHP_down}.
             is_spin_polarized (bool): Whether the calculation is spin polarized.
             list_orb_icohp (list[dict]): Dicts as {[str(Orbital1)-str(Orbital2)]: {
                 "icohp": {Spin.up: IcohpValue for spin.up, Spin.down: IcohpValue for spin.down},
@@ -1157,6 +1157,8 @@ def __init__(
         self._list_icohp = list_icohp
         self._list_orb_icohp = list_orb_icohp
 
+        # TODO: DanielYang: self._icohplist name is misleading
+        # (not list), and confuses with self._list_icohp
         self._icohplist: dict[str, IcohpValue] = {}
         for idx, label in enumerate(list_labels):
             self._icohplist[label] = IcohpValue(
diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index 003c43e8554..6931e44060c 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -498,7 +498,7 @@ def __init__(
                 list_length=lens,
                 list_translation=translations,  # type: ignore[arg-type]
                 list_num=nums,
-                list_icohp=icohps,  # DEBUG: DanielYang: inconsistent type
+                list_icohp=icohps,
                 is_spin_polarized=self.is_spin_polarized,
                 list_orb_icohp=list_orb_icohp,
             )

From 3aef21135aa5faa45da8227dc7e099d11ec93ad3 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Thu, 13 Jun 2024 18:13:16 +0800
Subject: [PATCH 32/39] remove unused type alias

---
 pymatgen/electronic_structure/cohp.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index f7061a1e951..94069a55c22 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -39,9 +39,6 @@
 
     from pymatgen.util.typing import PathLike, SpinLike, Vector3D
 
-    # TODO: use more specific type
-    CohpOrbital = str | int | Orbital
-
 __author__ = "Marco Esters, Janine George"
 __copyright__ = "Copyright 2017, The Materials Project"
 __version__ = "0.2"

From 61379c1d859b3d9b70b7d61a5498721673acb436 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Fri, 14 Jun 2024 10:29:59 +0800
Subject: [PATCH 33/39] revert undesired rename

---
 pymatgen/io/lobster/outputs.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index 6931e44060c..967b6ce7ebb 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -410,11 +410,11 @@ def __init__(
             if self.orbitalwise:
                 data_without_orbitals = []
                 data_orbitals = []
-                for line_parts in data:
-                    if "_" not in line_parts.split()[1]:
-                        data_without_orbitals += [line_parts]
+                for line in data:
+                    if "_" not in line.split()[1]:
+                        data_without_orbitals.append(line)
                     else:
-                        data_orbitals += [line_parts]
+                        data_orbitals.append(line)
 
             else:
                 data_without_orbitals = data

From 92e7df85374955317b75976abf9d6bafb4bb5e51 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Fri, 14 Jun 2024 10:46:42 +0800
Subject: [PATCH 34/39] replace more single item extend with append

---
 pymatgen/io/lobster/outputs.py | 49 +++++++++++++++++-----------------
 1 file changed, 24 insertions(+), 25 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index 967b6ce7ebb..48eb950467b 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -816,12 +816,12 @@ def __init__(
                 raise RuntimeError("CHARGES file contains no data.")
 
             self.num_atoms = len(data)
-            for atom in range(self.num_atoms):
-                line = data[atom].split()
-                self.atomlist += [line[1] + line[0]]
-                self.types += [line[1]]
-                self.mulliken.append(float(line[2]))
-                self.loewdin.append(float(line[3]))
+            for atom_idx in range(self.num_atoms):
+                line_parts = data[atom_idx].split()
+                self.atomlist.append(line_parts[1] + line_parts[0])
+                self.types.append(line_parts[1])
+                self.mulliken.append(float(line_parts[2]))
+                self.loewdin.append(float(line_parts[3]))
 
     def get_structure_with_charges(self, structure_filename):
         """Get a Structure with Mulliken and Loewdin charges as site properties
@@ -1111,8 +1111,8 @@ def _get_elements_basistype_basisfunctions(data):
         basisfunctions = []
         for row in data:
             if begin and not end:
-                splitrow = row.split()
-                if splitrow[0] not in [
+                row_parts = row.split()
+                if row_parts[0] not in {
                     "INFO:",
                     "WARNING:",
                     "setting",
@@ -1121,11 +1121,11 @@ def _get_elements_basistype_basisfunctions(data):
                     "saving",
                     "spillings",
                     "writing",
-                ]:
-                    elements += [splitrow[0]]
-                    basistype += [splitrow[1].replace("(", "").replace(")", "")]
+                }:
+                    elements.append(row_parts[0])
+                    basistype.append(row_parts[1].replace("(", "").replace(")", ""))
                     # last sign is a ''
-                    basisfunctions += [splitrow[2:]]
+                    basisfunctions += [row_parts[2:]]
                 else:
                     end = True
             if "setting up local basis functions..." in row:
@@ -1271,17 +1271,17 @@ def __init__(
             with zopen(name, mode="rt") as file:
                 contents = file.read().split("\n")
 
-            atom_names += [os.path.split(name)[1].split("_")[1].capitalize()]
+            atom_names.append(os.path.split(name)[1].split("_")[1].capitalize())
             parameters = contents[0].split()
-            atom_type += [re.split(r"[0-9]+", parameters[3])[0].capitalize()]
-            orbital_names += [parameters[4]]
+            atom_type.append(re.split(r"[0-9]+", parameters[3])[0].capitalize())
+            orbital_names.append(parameters[4])
 
         # get atomtype orbital dict
         atom_orbital_dict = {}  # type: dict
-        for iatom, atom in enumerate(atom_names):
+        for idx, atom in enumerate(atom_names):
             if atom not in atom_orbital_dict:
                 atom_orbital_dict[atom] = []
-            atom_orbital_dict[atom] += [orbital_names[iatom]]
+            atom_orbital_dict[atom].append(orbital_names[idx])
         # test if there are the same orbitals twice or if two different formats were used or if all necessary orbitals
         # are there
         for items in atom_orbital_dict.values():
@@ -1289,9 +1289,9 @@ def __init__(
                 raise ValueError("The are two FATBAND files for the same atom and orbital. The program will stop.")
             split = []
             for item in items:
-                split += [item.split("_")[0]]
+                split.append(item.split("_")[0])
             for number in collections.Counter(split).values():
-                if number not in (1, 3, 5, 7):
+                if number not in {1, 3, 5, 7}:
                     raise ValueError(
                         "Make sure all relevant orbitals were generated and that no duplicates (2p and 2p_x) are "
                         "present"
@@ -1621,7 +1621,6 @@ def get_structure_with_total_grosspop(self, structure_filename: str) -> Structur
             Structure Object with Mulliken and Loewdin total grosspopulations as site properties.
         """
         struct = Structure.from_file(structure_filename)
-        # site_properties: dict[str, Any] = {}
         mullikengp = []
         loewdingp = []
         for grosspop in self.list_dict_grosspop:
@@ -1912,11 +1911,11 @@ def __init__(
             data = data[5:-1]
             self.num_atoms = len(data) - 2
             for atom in range(self.num_atoms):
-                line = data[atom].split()
-                self.atomlist += [line[1] + str(line[0])]
-                self.types += [line[1]]
-                self.sitepotentials_mulliken.append(float(line[2]))
-                self.sitepotentials_loewdin.append(float(line[3]))
+                line_parts = data[atom].split()
+                self.atomlist.append(line_parts[1] + str(line_parts[0]))
+                self.types.append(line_parts[1])
+                self.sitepotentials_mulliken.append(float(line_parts[2]))
+                self.sitepotentials_loewdin.append(float(line_parts[3]))
 
             self.madelungenergies_mulliken = float(data[self.num_atoms + 1].split()[3])
             self.madelungenergies_loewdin = float(data[self.num_atoms + 1].split()[4])

From c397e1cb5b710ddf2a6a58c7c53ae83106bc23aa Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Fri, 14 Jun 2024 10:56:40 +0800
Subject: [PATCH 35/39] simplify dict generation

---
 pymatgen/io/lobster/outputs.py | 77 +++++++++++++++++-----------------
 1 file changed, 38 insertions(+), 39 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index 48eb950467b..81d65241a1b 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -1003,43 +1003,42 @@ def __init__(self, filename: str | None, **kwargs) -> None:
             raise ValueError("must provide either filename or kwargs to initialize Lobsterout")
 
     def get_doc(self) -> dict[str, Any]:
-        """Get the LobsterDict with all the information stored in lobsterout."""
-        lobster_dict: dict[str, Any] = {}
-        # check if Lobster starts from a projection
-        lobster_dict["restart_from_projection"] = self.is_restart_from_projection
-        lobster_dict["lobster_version"] = self.lobster_version
-        lobster_dict["threads"] = self.number_of_threads
-        lobster_dict["dft_program"] = self.dft_program
-
-        lobster_dict["charge_spilling"] = self.charge_spilling
-        lobster_dict["total_spilling"] = self.total_spilling
-
-        lobster_dict["elements"] = self.elements
-        lobster_dict["basis_type"] = self.basis_type
-        lobster_dict["basis_functions"] = self.basis_functions
-
-        lobster_dict["timing"] = self.timing
-
-        lobster_dict["warning_lines"] = self.warning_lines
-
-        lobster_dict["info_orthonormalization"] = self.info_orthonormalization
-
-        lobster_dict["info_lines"] = self.info_lines
-
-        lobster_dict["has_doscar"] = self.has_doscar
-        lobster_dict["has_doscar_lso"] = self.has_doscar_lso
-        lobster_dict["has_cohpcar"] = self.has_cohpcar
-        lobster_dict["has_coopcar"] = self.has_coopcar
-        lobster_dict["has_cobicar"] = self.has_cobicar
-        lobster_dict["has_charge"] = self.has_charge
-        lobster_dict["has_madelung"] = self.has_madelung
-        lobster_dict["has_projection"] = self.has_projection
-        lobster_dict["has_bandoverlaps"] = self.has_bandoverlaps
-        lobster_dict["has_fatbands"] = self.has_fatbands
-        lobster_dict["has_grosspopulation"] = self.has_grosspopulation
-        lobster_dict["has_density_of_energies"] = self.has_density_of_energies
-
-        return lobster_dict
+        """Get a dict with all the information in lobsterout."""
+        return {
+            # Check if LOBSTER starts from a projection
+            "restart_from_projection": self.is_restart_from_projection,
+            "lobster_version": self.lobster_version,
+            "threads": self.number_of_threads,
+            "dft_program": self.dft_program,
+            #
+            "charge_spilling": self.charge_spilling,
+            "total_spilling": self.total_spilling,
+            #
+            "elements": self.elements,
+            "basis_type": self.basis_type,
+            "basis_functions": self.basis_functions,
+            #
+            "timing": self.timing,
+            #
+            "warning_lines": self.warning_lines,
+            #
+            "info_orthonormalization": self.info_orthonormalization,
+            #
+            "info_lines": self.info_lines,
+            #
+            "has_doscar": self.has_doscar,
+            "has_doscar_lso": self.has_doscar_lso,
+            "has_cohpcar": self.has_cohpcar,
+            "has_coopcar": self.has_coopcar,
+            "has_cobicar": self.has_cobicar,
+            "has_charge": self.has_charge,
+            "has_madelung": self.has_madelung,
+            "has_projection": self.has_projection,
+            "has_bandoverlaps": self.has_bandoverlaps,
+            "has_fatbands": self.has_fatbands,
+            "has_grosspopulation": self.has_grosspopulation,
+            "has_density_of_energies": self.has_density_of_energies,
+        }
 
     def as_dict(self):
         """MSONable dict"""
@@ -1984,7 +1983,7 @@ def get_orb_from_str(orbs):
         list of tw Orbital objects
     """
     # TODO: also useful for plotting of DOS
-    orb_labs = [
+    orb_labs = (
         "s",
         "p_y",
         "p_z",
@@ -2001,7 +2000,7 @@ def get_orb_from_str(orbs):
         "f_xz^2",
         "f_z(x^2-y^2)",
         "f_x(x^2-3y^2)",
-    ]
+    )
     orbitals = [(int(orb[0]), Orbital(orb_labs.index(orb[1:]))) for orb in orbs]
 
     orb_label = ""

From 8cfaa33e1314dd633a07a39ed19a20498efbe156 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Fri, 14 Jun 2024 17:20:42 +0800
Subject: [PATCH 36/39] fix downstream lobsterpy error

---
 pymatgen/electronic_structure/cohp.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/pymatgen/electronic_structure/cohp.py b/pymatgen/electronic_structure/cohp.py
index 94069a55c22..acf4f8f45b5 100644
--- a/pymatgen/electronic_structure/cohp.py
+++ b/pymatgen/electronic_structure/cohp.py
@@ -201,14 +201,16 @@ def has_antibnd_states_below_efermi(
         dict_to_return = {}
         if spin is None:
             for sp, cohp_vals in populations.items():
-                dict_to_return[sp] = (max(cohp_vals[:n_energies_below_efermi])) > limit
+                # NOTE: Casting to bool is necessary, otherwise ended up
+                # getting "bool_" instead of "bool" from NumPy
+                dict_to_return[sp] = bool((max(cohp_vals[:n_energies_below_efermi])) > limit)
 
         else:
             if isinstance(spin, int):
                 spin = Spin(spin)
             elif isinstance(spin, str):
                 spin = Spin({"up": 1, "down": -1}[spin.lower()])
-            dict_to_return[spin] = (max(populations[spin][:n_energies_below_efermi])) > limit
+            dict_to_return[spin] = bool((max(populations[spin][:n_energies_below_efermi])) > limit)
 
         return dict_to_return
 

From 5eefb5326530935fb49a60687b3d2ddd2500dc88 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sun, 16 Jun 2024 17:05:15 +0800
Subject: [PATCH 37/39] tweak module docstring

---
 pymatgen/electronic_structure/boltztrap2.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/pymatgen/electronic_structure/boltztrap2.py b/pymatgen/electronic_structure/boltztrap2.py
index 50d09d116ac..13d7891629e 100644
--- a/pymatgen/electronic_structure/boltztrap2.py
+++ b/pymatgen/electronic_structure/boltztrap2.py
@@ -1,24 +1,23 @@
-"""This module provides a pymatgen interface to BoltzTraP2.
+"""This module provides an interface to BoltzTraP2.
 Some of the code is written following the examples provided in BoltzTraP2.
 
 BoltzTraP2 is a Python software interpolating band structures and
-computing materials properties from dft band structure using Boltzmann
+computing materials properties from DFT band structure using Boltzmann
 semi-classical transport theory, developed by Georg Madsen, Jesús Carrete,
 Matthieu J. Verstraete.
 
 https://gitlab.com/sousaw/BoltzTraP2
 https://www.sciencedirect.com/science/article/pii/S0010465518301632
 
-References are:
-
+References:
     Georg K.H.Madsen, Jesús Carrete, Matthieu J.Verstraete
     BoltzTraP2, a program for interpolating band structures and
     calculating semi-classical transport coefficients
-    Computer Physics Communications 231, 140-145, 2018
+    Computer Physics Communications 231, 140-145, 2018.
 
     Madsen, G. K. H., and Singh, D. J. (2006).
     BoltzTraP. A code for calculating band-structure dependent quantities.
-    Computer Physics Communications, 175, 67-71
+    Computer Physics Communications, 175, 67-71.
 
 Todo:
 - Read first derivative of the eigenvalues from vasprun.xml (mommat)

From eb36650422a3053518fdf8078717062e1d10e64f Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 22 Jun 2024 10:05:09 +0800
Subject: [PATCH 38/39] need confirm: allow efermi to be None

---
 pymatgen/io/lobster/outputs.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pymatgen/io/lobster/outputs.py b/pymatgen/io/lobster/outputs.py
index dd52f024a41..3c7950a9d90 100644
--- a/pymatgen/io/lobster/outputs.py
+++ b/pymatgen/io/lobster/outputs.py
@@ -1225,10 +1225,10 @@ def __init__(
                 "FATBAND_*" files will be read
             kpoints_file (PathLike): KPOINTS file for bandstructure calculation, typically "KPOINTS".
             vasprun_file (PathLike): Corresponding vasprun file.
-                Instead, the Fermi energy from the DFT run can be provided. Then,
+                Instead, the Fermi level from the DFT run can be provided. Then,
                 this value should be set to None.
             structure (Structure): Structure object.
-            efermi (float): fermi energy in eV
+            efermi (float): Fermi level in eV.
         """
         warnings.warn("Make sure all relevant FATBAND files were generated and read in!")
         warnings.warn("Use Lobster 3.2.0 or newer for fatband calculations!")
@@ -1413,7 +1413,7 @@ def get_bandstructure(self) -> LobsterBandStructureSymmLine:
             kpoints=self.kpoints_array,
             eigenvals=self.eigenvals,
             lattice=self.lattice,
-            efermi=self.efermi,
+            efermi=self.efermi,  # type: ignore[arg-type]
             labels_dict=self.label_dict,
             structure=self.structure,
             projections=self.p_eigenvals,

From 220a3981f70ea451649f79a4af2a52c7432d1a1a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 2 Jul 2024 02:04:53 +0000
Subject: [PATCH 39/39] pre-commit auto-fixes

---
 dev_scripts/chemenv/explicit_permutations.py      |  1 -
 .../explicit_permutations_plane_algorithm.py      |  1 -
 .../chemenv/get_plane_permutations_optimized.py   |  1 -
 .../multi_weights_strategy_parameters.py          |  1 -
 dev_scripts/chemenv/test_algos.py                 |  1 -
 dev_scripts/chemenv/view_environment.py           |  1 -
 dev_scripts/potcar_scrambler.py                   |  1 -
 dev_scripts/update_pt_data.py                     |  3 +--
 src/pymatgen/alchemy/filters.py                   |  4 +---
 src/pymatgen/alchemy/materials.py                 |  4 +---
 src/pymatgen/alchemy/transmuters.py               |  3 +--
 src/pymatgen/analysis/adsorption.py               |  6 ++----
 src/pymatgen/analysis/bond_dissociation.py        |  1 -
 src/pymatgen/analysis/bond_valence.py             |  1 -
 .../chemenv/connectivity/connected_components.py  |  1 -
 .../chemenv/connectivity/connectivity_finder.py   |  1 -
 .../connectivity/structure_connectivity.py        |  1 -
 .../chemenv_strategies.py                         |  3 +--
 .../coordination_geometry_finder.py               |  1 -
 .../structure_environments.py                     |  1 -
 .../chemenv/coordination_environments/voronoi.py  |  3 +--
 .../chemenv/utils/coordination_geometry_utils.py  |  3 +--
 src/pymatgen/analysis/chemenv/utils/func_utils.py |  1 -
 .../analysis/chemenv/utils/scripts_utils.py       |  1 -
 src/pymatgen/analysis/chempot_diagram.py          |  3 +--
 src/pymatgen/analysis/cost.py                     |  1 -
 src/pymatgen/analysis/diffraction/core.py         |  1 -
 src/pymatgen/analysis/diffraction/neutron.py      |  1 -
 src/pymatgen/analysis/diffraction/tem.py          |  2 --
 src/pymatgen/analysis/diffraction/xrd.py          |  1 -
 src/pymatgen/analysis/dimensionality.py           |  1 -
 src/pymatgen/analysis/elasticity/elastic.py       | 10 ++++------
 src/pymatgen/analysis/elasticity/strain.py        |  4 +---
 src/pymatgen/analysis/elasticity/stress.py        |  1 -
 src/pymatgen/analysis/energy_models.py            |  4 +---
 src/pymatgen/analysis/eos.py                      |  3 +--
 src/pymatgen/analysis/ewald.py                    |  5 ++---
 .../analysis/ferroelectricity/polarization.py     |  6 ++----
 src/pymatgen/analysis/fragmenter.py               |  1 -
 src/pymatgen/analysis/graphs.py                   |  8 +++-----
 src/pymatgen/analysis/hhi.py                      |  1 -
 src/pymatgen/analysis/interface_reactions.py      |  1 -
 .../analysis/interfaces/coherent_interfaces.py    |  3 +--
 .../analysis/interfaces/substrate_analyzer.py     |  3 +--
 src/pymatgen/analysis/interfaces/zsl.py           |  1 -
 src/pymatgen/analysis/local_env.py                |  8 +++-----
 src/pymatgen/analysis/magnetism/analyzer.py       |  7 +++----
 src/pymatgen/analysis/magnetism/heisenberg.py     |  1 -
 src/pymatgen/analysis/magnetism/jahnteller.py     |  1 -
 src/pymatgen/analysis/molecule_matcher.py         |  4 +---
 .../analysis/molecule_structure_comparator.py     |  1 -
 src/pymatgen/analysis/nmr.py                      |  1 -
 src/pymatgen/analysis/phase_diagram.py            |  9 ++++-----
 src/pymatgen/analysis/piezo.py                    |  1 -
 src/pymatgen/analysis/piezo_sensitivity.py        |  1 -
 src/pymatgen/analysis/pourbaix_diagram.py         |  5 ++---
 src/pymatgen/analysis/prototypes.py               |  1 -
 src/pymatgen/analysis/quasiharmonic.py            |  7 +++----
 src/pymatgen/analysis/quasirrho.py                |  4 +---
 src/pymatgen/analysis/reaction_calculator.py      |  6 ++----
 src/pymatgen/analysis/solar/slme.py               |  3 +--
 src/pymatgen/analysis/structure_analyzer.py       |  3 +--
 src/pymatgen/analysis/structure_matcher.py        |  4 +---
 .../structure_prediction/dopant_predictor.py      |  1 -
 .../substitution_probability.py                   |  1 -
 .../analysis/structure_prediction/substitutor.py  |  1 -
 .../structure_prediction/volume_predictor.py      |  1 -
 src/pymatgen/analysis/surface_analysis.py         |  8 +++-----
 src/pymatgen/analysis/topological/spillage.py     |  1 -
 src/pymatgen/analysis/transition_state.py         |  3 +--
 src/pymatgen/analysis/wulff.py                    |  3 +--
 src/pymatgen/analysis/xas/spectrum.py             |  3 +--
 src/pymatgen/analysis/xps.py                      |  4 +---
 src/pymatgen/apps/battery/analyzer.py             |  1 -
 src/pymatgen/apps/battery/battery_abc.py          |  3 +--
 src/pymatgen/apps/battery/conversion_battery.py   |  6 ++----
 src/pymatgen/apps/battery/insertion_battery.py    |  3 +--
 src/pymatgen/apps/battery/plotter.py              |  1 -
 src/pymatgen/apps/borg/hive.py                    |  1 -
 src/pymatgen/cli/feff_plot_cross_section.py       |  1 -
 src/pymatgen/cli/pmg.py                           |  3 +--
 src/pymatgen/cli/pmg_analyze.py                   |  3 +--
 src/pymatgen/cli/pmg_config.py                    |  3 +--
 src/pymatgen/cli/pmg_plot.py                      |  1 -
 src/pymatgen/cli/pmg_structure.py                 |  3 +--
 src/pymatgen/command_line/bader_caller.py         |  4 +---
 src/pymatgen/command_line/chargemol_caller.py     |  1 -
 src/pymatgen/command_line/critic2_caller.py       |  6 ++----
 src/pymatgen/command_line/enumlib_caller.py       |  1 -
 src/pymatgen/command_line/gulp_caller.py          |  1 -
 src/pymatgen/command_line/mcsqs_caller.py         |  1 -
 src/pymatgen/command_line/vampire_caller.py       |  1 -
 src/pymatgen/core/__init__.py                     |  3 +--
 src/pymatgen/core/composition.py                  |  4 +---
 src/pymatgen/core/interface.py                    |  8 +++-----
 src/pymatgen/core/ion.py                          |  1 -
 src/pymatgen/core/lattice.py                      |  6 ++----
 src/pymatgen/core/operations.py                   |  1 -
 src/pymatgen/core/periodic_table.py               |  4 +---
 src/pymatgen/core/sites.py                        |  4 +---
 src/pymatgen/core/spectrum.py                     |  3 +--
 src/pymatgen/core/structure.py                    | 15 ++++++---------
 src/pymatgen/core/surface.py                      |  8 +++-----
 src/pymatgen/core/tensors.py                      |  6 ++----
 src/pymatgen/core/trajectory.py                   |  4 +---
 src/pymatgen/core/xcfunc.py                       |  1 -
 .../electronic_structure/bandstructure.py         |  1 -
 src/pymatgen/electronic_structure/boltztrap.py    | 10 ++++------
 src/pymatgen/electronic_structure/boltztrap2.py   |  3 +--
 src/pymatgen/electronic_structure/cohp.py         |  6 ++----
 src/pymatgen/electronic_structure/core.py         |  3 +--
 src/pymatgen/electronic_structure/dos.py          | 10 ++++------
 src/pymatgen/electronic_structure/plotter.py      |  2 --
 src/pymatgen/entries/__init__.py                  |  1 -
 src/pymatgen/entries/compatibility.py             |  5 ++---
 src/pymatgen/entries/computed_entries.py          |  8 +++-----
 src/pymatgen/entries/correction_calculator.py     |  5 ++---
 src/pymatgen/entries/entry_tools.py               |  4 +---
 src/pymatgen/entries/exp_entries.py               |  1 -
 src/pymatgen/entries/mixing_scheme.py             |  1 -
 src/pymatgen/ext/cod.py                           |  1 -
 src/pymatgen/ext/matproj.py                       |  4 +---
 src/pymatgen/ext/matproj_legacy.py                |  8 +++-----
 src/pymatgen/ext/optimade.py                      |  3 +--
 src/pymatgen/io/abinit/abiobjects.py              |  1 -
 src/pymatgen/io/abinit/abitimer.py                |  1 -
 src/pymatgen/io/abinit/inputs.py                  |  1 -
 src/pymatgen/io/abinit/netcdf.py                  |  1 -
 src/pymatgen/io/abinit/pseudos.py                 |  6 ++----
 src/pymatgen/io/adf.py                            |  1 -
 src/pymatgen/io/aims/inputs.py                    |  4 +---
 src/pymatgen/io/aims/outputs.py                   |  4 +---
 src/pymatgen/io/aims/parsers.py                   |  1 -
 src/pymatgen/io/aims/sets/base.py                 |  1 -
 src/pymatgen/io/ase.py                            |  4 +---
 src/pymatgen/io/atat.py                           |  1 -
 src/pymatgen/io/babel.py                          |  4 +---
 src/pymatgen/io/cif.py                            |  4 +---
 src/pymatgen/io/common.py                         |  3 +--
 src/pymatgen/io/core.py                           |  3 +--
 src/pymatgen/io/cp2k/inputs.py                    |  4 +---
 src/pymatgen/io/cp2k/outputs.py                   |  1 -
 src/pymatgen/io/cp2k/sets.py                      |  3 +--
 src/pymatgen/io/cssr.py                           |  1 -
 src/pymatgen/io/exciting/inputs.py                |  1 -
 src/pymatgen/io/feff/inputs.py                    |  3 +--
 src/pymatgen/io/feff/outputs.py                   |  1 -
 src/pymatgen/io/feff/sets.py                      |  1 -
 src/pymatgen/io/fiesta.py                         |  4 +---
 src/pymatgen/io/gaussian.py                       |  3 +--
 src/pymatgen/io/lammps/data.py                    |  6 ++----
 src/pymatgen/io/lammps/generators.py              |  1 -
 src/pymatgen/io/lammps/inputs.py                  |  4 +---
 src/pymatgen/io/lammps/outputs.py                 |  1 -
 src/pymatgen/io/lammps/sets.py                    |  3 +--
 src/pymatgen/io/lammps/utils.py                   |  1 -
 src/pymatgen/io/lmto.py                           |  1 -
 src/pymatgen/io/lobster/inputs.py                 |  4 +---
 src/pymatgen/io/lobster/lobsterenv.py             |  4 +---
 src/pymatgen/io/lobster/outputs.py                |  1 -
 src/pymatgen/io/nwchem.py                         |  1 -
 src/pymatgen/io/openff.py                         |  1 -
 src/pymatgen/io/packmol.py                        |  1 -
 src/pymatgen/io/phonopy.py                        |  3 +--
 src/pymatgen/io/pwmat/inputs.py                   |  4 +---
 src/pymatgen/io/pwmat/outputs.py                  |  1 -
 src/pymatgen/io/pwscf.py                          |  1 -
 src/pymatgen/io/qchem/inputs.py                   |  1 -
 src/pymatgen/io/qchem/outputs.py                  |  1 -
 src/pymatgen/io/qchem/sets.py                     |  1 -
 src/pymatgen/io/res.py                            |  4 +---
 src/pymatgen/io/shengbte.py                       |  1 -
 src/pymatgen/io/template.py                       |  1 -
 src/pymatgen/io/vasp/inputs.py                    |  6 ++----
 src/pymatgen/io/vasp/optics.py                    |  6 ++----
 src/pymatgen/io/vasp/outputs.py                   |  4 +---
 src/pymatgen/io/vasp/sets.py                      |  4 +---
 src/pymatgen/io/xr.py                             |  1 -
 src/pymatgen/io/xtb/outputs.py                    |  1 -
 src/pymatgen/io/xyz.py                            |  1 -
 src/pymatgen/io/zeopp.py                          |  1 -
 src/pymatgen/phonon/bandstructure.py              |  4 +---
 src/pymatgen/phonon/dos.py                        |  3 +--
 src/pymatgen/phonon/gruneisen.py                  |  3 +--
 src/pymatgen/phonon/ir_spectra.py                 |  1 -
 src/pymatgen/phonon/plotter.py                    |  2 --
 src/pymatgen/phonon/thermal_displacements.py      |  1 -
 src/pymatgen/symmetry/analyzer.py                 |  1 -
 src/pymatgen/symmetry/bandstructure.py            |  1 -
 src/pymatgen/symmetry/groups.py                   |  4 +---
 src/pymatgen/symmetry/kpath.py                    |  1 -
 src/pymatgen/symmetry/maggroups.py                |  4 +---
 src/pymatgen/symmetry/settings.py                 |  5 ++---
 src/pymatgen/symmetry/site_symmetries.py          |  1 -
 src/pymatgen/symmetry/structure.py                |  6 ++----
 .../transformations/advanced_transformations.py   |  1 -
 .../transformations/site_transformations.py       |  1 -
 .../transformations/standard_transformations.py   |  4 +---
 src/pymatgen/util/coord.py                        |  2 --
 src/pymatgen/util/plotting.py                     |  1 -
 src/pymatgen/util/provenance.py                   |  1 -
 src/pymatgen/util/testing/__init__.py             |  1 -
 src/pymatgen/util/testing/aims.py                 |  1 -
 src/pymatgen/vis/plotters.py                      |  1 -
 src/pymatgen/vis/structure_chemview.py            |  1 -
 src/pymatgen/vis/structure_vtk.py                 |  1 -
 tests/alchemy/test_filters.py                     |  1 -
 tests/alchemy/test_materials.py                   |  1 -
 .../connectivity/test_connected_components.py     |  1 -
 .../test_chemenv_strategies.py                    |  3 +--
 .../test_coordination_geometries.py               |  3 +--
 .../test_coordination_geometry_finder.py          |  3 +--
 .../coordination_environments/test_read_write.py  |  3 +--
 .../test_structure_environments.py                |  3 +--
 .../coordination_environments/test_voronoi.py     |  1 -
 .../coordination_environments/test_weights.py     |  3 +--
 .../utils/test_coordination_geometry_utils.py     |  3 +--
 tests/analysis/chemenv/utils/test_func_utils.py   |  3 +--
 tests/analysis/chemenv/utils/test_graph_utils.py  |  1 -
 tests/analysis/chemenv/utils/test_math_utils.py   |  1 -
 tests/analysis/diffraction/test_neutron.py        |  3 +--
 tests/analysis/diffraction/test_tem.py            |  3 +--
 tests/analysis/diffraction/test_xrd.py            |  3 +--
 tests/analysis/elasticity/test_elastic.py         |  5 ++---
 tests/analysis/elasticity/test_strain.py          |  1 -
 tests/analysis/elasticity/test_stress.py          |  3 +--
 .../ferroelectricity/test_polarization.py         |  3 +--
 .../interfaces/test_coherent_interface.py         |  1 -
 .../interfaces/test_substrate_analyzer.py         |  1 -
 tests/analysis/interfaces/test_zsl.py             |  3 +--
 tests/analysis/magnetism/test_analyzer.py         |  3 +--
 tests/analysis/magnetism/test_heisenberg.py       |  1 -
 tests/analysis/magnetism/test_jahnteller.py       |  3 +--
 tests/analysis/solar/test_slme.py                 |  3 +--
 .../structure_prediction/test_dopant_predictor.py |  3 +--
 .../test_substitution_probability.py              |  3 +--
 .../structure_prediction/test_volume_predictor.py |  3 +--
 tests/analysis/test_adsorption.py                 |  1 -
 tests/analysis/test_bond_dissociation.py          |  1 -
 tests/analysis/test_bond_valence.py               |  3 +--
 tests/analysis/test_chempot_diagram.py            |  3 +--
 tests/analysis/test_cost.py                       |  3 +--
 tests/analysis/test_dimensionality.py             |  1 -
 tests/analysis/test_disorder.py                   |  3 +--
 tests/analysis/test_energy_models.py              |  3 +--
 tests/analysis/test_eos.py                        |  3 +--
 tests/analysis/test_ewald.py                      |  3 +--
 tests/analysis/test_fragmenter.py                 |  1 -
 tests/analysis/test_functional_groups.py          |  1 -
 tests/analysis/test_graphs.py                     |  3 +--
 tests/analysis/test_hhi.py                        |  3 +--
 tests/analysis/test_interface_reactions.py        |  3 +--
 tests/analysis/test_local_env.py                  |  3 +--
 tests/analysis/test_molecule_matcher.py           |  3 +--
 tests/analysis/test_nmr.py                        |  3 +--
 tests/analysis/test_phase_diagram.py              |  3 +--
 tests/analysis/test_piezo.py                      |  1 -
 tests/analysis/test_piezo_sensitivity.py          |  3 +--
 tests/analysis/test_pourbaix_diagram.py           |  3 +--
 .../analysis/test_quasi_harmonic_debye_approx.py  |  1 -
 tests/analysis/test_quasirrho.py                  |  1 -
 tests/analysis/test_reaction_calculator.py        |  3 +--
 tests/analysis/test_structure_analyzer.py         |  3 +--
 tests/analysis/test_structure_matcher.py          |  3 +--
 tests/analysis/test_surface_analysis.py           |  5 ++---
 tests/analysis/test_transition_state.py           |  1 -
 tests/analysis/test_wulff.py                      |  3 +--
 tests/analysis/topological/test_spillage.py       |  3 +--
 tests/analysis/xas/test_spectrum.py               |  3 +--
 tests/apps/battery/test_analyzer.py               |  3 +--
 tests/apps/battery/test_conversion_battery.py     |  3 +--
 tests/apps/battery/test_insertion_battery.py      |  3 +--
 tests/apps/battery/test_plotter.py                |  1 -
 tests/apps/borg/test_hive.py                      |  3 +--
 tests/apps/borg/test_queen.py                     |  3 +--
 tests/command_line/test_bader_caller.py           |  3 +--
 tests/command_line/test_critic2_caller.py         |  3 +--
 tests/command_line/test_enumlib_caller.py         |  3 +--
 tests/command_line/test_gulp_caller.py            |  1 -
 tests/command_line/test_mcsqs_caller.py           |  1 -
 tests/command_line/test_vampire_caller.py         |  3 +--
 tests/core/test_bonds.py                          |  3 +--
 tests/core/test_composition.py                    |  3 +--
 tests/core/test_interface.py                      |  3 +--
 tests/core/test_ion.py                            |  1 -
 tests/core/test_lattice.py                        |  3 +--
 tests/core/test_molecular_orbitals.py             |  1 -
 tests/core/test_operations.py                     |  1 -
 tests/core/test_periodic_table.py                 |  3 +--
 tests/core/test_sites.py                          |  3 +--
 tests/core/test_spectrum.py                       |  5 ++---
 tests/core/test_structure.py                      |  3 +--
 tests/core/test_surface.py                        |  5 ++---
 tests/core/test_tensors.py                        |  3 +--
 tests/core/test_trajectory.py                     |  1 -
 tests/core/test_units.py                          |  3 +--
 tests/core/test_xcfunc.py                         |  1 -
 tests/electronic_structure/test_bandstructure.py  |  3 +--
 tests/electronic_structure/test_boltztrap.py      |  3 +--
 tests/electronic_structure/test_boltztrap2.py     |  3 +--
 tests/electronic_structure/test_cohp.py           |  3 +--
 tests/electronic_structure/test_core.py           |  1 -
 tests/electronic_structure/test_dos.py            |  3 +--
 tests/electronic_structure/test_plotter.py        |  3 +--
 tests/entries/test_compatibility.py               |  5 ++---
 tests/entries/test_computed_entries.py            |  3 +--
 tests/entries/test_correction_calculator.py       |  1 -
 tests/entries/test_entry_tools.py                 |  1 -
 tests/entries/test_exp_entries.py                 |  3 +--
 tests/entries/test_mixing_scheme.py               |  1 -
 tests/ext/test_cod.py                             |  1 -
 tests/ext/test_matproj.py                         |  5 ++---
 tests/ext/test_optimade.py                        |  1 -
 tests/io/abinit/test_abiobjects.py                |  3 +--
 tests/io/abinit/test_inputs.py                    |  1 -
 tests/io/abinit/test_netcdf.py                    |  1 -
 tests/io/abinit/test_pseudos.py                   |  3 +--
 tests/io/aims/conftest.py                         |  1 -
 tests/io/aims/test_aims_inputs.py                 |  1 -
 tests/io/aims/test_aims_outputs.py                |  1 -
 tests/io/aims/test_aims_parsers.py                |  1 -
 tests/io/aims/test_sets/test_input_set.py         |  1 -
 tests/io/cp2k/test_inputs.py                      |  3 +--
 tests/io/cp2k/test_outputs.py                     |  3 +--
 tests/io/cp2k/test_sets.py                        |  3 +--
 tests/io/exciting/test_inputs.py                  |  1 -
 tests/io/feff/test_inputs.py                      |  3 +--
 tests/io/feff/test_sets.py                        |  1 -
 tests/io/lammps/test_data.py                      |  5 ++---
 tests/io/lammps/test_inputs.py                    |  1 -
 tests/io/lammps/test_outputs.py                   |  1 -
 tests/io/lobster/test_inputs.py                   |  3 +--
 tests/io/lobster/test_lobsterenv.py               |  3 +--
 tests/io/pwmat/test_inputs.py                     |  1 -
 tests/io/qchem/test_inputs.py                     |  1 -
 tests/io/qchem/test_outputs.py                    |  3 +--
 tests/io/qchem/test_sets.py                       |  1 -
 tests/io/qchem/test_utils.py                      |  1 -
 tests/io/test_adf.py                              |  3 +--
 tests/io/test_ase.py                              |  1 -
 tests/io/test_atat.py                             |  3 +--
 tests/io/test_babel.py                            |  3 +--
 tests/io/test_cif.py                              |  3 +--
 tests/io/test_core.py                             |  1 -
 tests/io/test_gaussian.py                         |  3 +--
 tests/io/test_jarvis.py                           |  1 -
 tests/io/test_lmto.py                             |  1 -
 tests/io/test_nwchem.py                           |  3 +--
 tests/io/test_openff.py                           |  1 -
 tests/io/test_packmol.py                          |  1 -
 tests/io/test_phonopy.py                          |  3 +--
 tests/io/test_pwscf.py                            |  3 +--
 tests/io/test_res.py                              |  3 +--
 tests/io/test_shengbte.py                         |  1 -
 tests/io/test_template_input.py                   |  1 -
 tests/io/test_wannier90.py                        |  3 +--
 tests/io/test_xcrysden.py                         |  1 -
 tests/io/test_xyz.py                              |  3 +--
 tests/io/test_zeopp.py                            |  3 +--
 tests/io/vasp/test_inputs.py                      |  3 +--
 tests/io/vasp/test_optics.py                      |  1 -
 tests/io/vasp/test_outputs.py                     |  3 +--
 tests/io/vasp/test_sets.py                        |  3 +--
 tests/io/xtb/test_outputs.py                      |  3 +--
 tests/optimization/test_linear_assignment.py      |  3 +--
 tests/optimization/test_neighbors.py              |  1 -
 tests/phonon/test_bandstructure.py                |  3 +--
 tests/phonon/test_dos.py                          |  3 +--
 tests/phonon/test_gruneisen.py                    |  3 +--
 tests/phonon/test_ir_spectra.py                   |  1 -
 tests/phonon/test_plotter.py                      |  1 -
 tests/phonon/test_thermal_displacements.py        |  3 +--
 tests/symmetry/test_analyzer.py                   |  3 +--
 tests/symmetry/test_groups.py                     |  3 +--
 tests/symmetry/test_kpath_hin.py                  |  3 +--
 tests/symmetry/test_kpath_lm.py                   |  3 +--
 tests/symmetry/test_kpath_sc.py                   |  3 +--
 tests/symmetry/test_kpaths.py                     |  1 -
 tests/symmetry/test_maggroups.py                  |  1 -
 tests/symmetry/test_settings.py                   |  1 -
 tests/symmetry/test_site_symmetries.py            |  1 -
 tests/test_cli.py                                 |  1 -
 .../test_advanced_transformations.py              |  3 +--
 .../transformations/test_site_transformations.py  |  1 -
 .../test_standard_transformations.py              |  3 +--
 tests/util/test_coord.py                          |  3 +--
 tests/util/test_num.py                            |  1 -
 tests/util/test_plotting.py                       |  1 -
 tests/util/test_provenance.py                     |  1 -
 tests/util/test_string.py                         |  1 -
 tests/util/test_typing.py                         |  1 -
 tests/vis/test_plotters.py                        |  1 -
 392 files changed, 272 insertions(+), 726 deletions(-)

diff --git a/dev_scripts/chemenv/explicit_permutations.py b/dev_scripts/chemenv/explicit_permutations.py
index f3225fa5293..097e80b25e0 100644
--- a/dev_scripts/chemenv/explicit_permutations.py
+++ b/dev_scripts/chemenv/explicit_permutations.py
@@ -10,7 +10,6 @@
 import os
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     AllCoordinationGeometries,
     ExplicitPermutationsAlgorithm,
diff --git a/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py b/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py
index bd71080c300..689ae58d86a 100644
--- a/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py
+++ b/dev_scripts/chemenv/explicit_permutations_plane_algorithm.py
@@ -9,7 +9,6 @@
 import json
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,
diff --git a/dev_scripts/chemenv/get_plane_permutations_optimized.py b/dev_scripts/chemenv/get_plane_permutations_optimized.py
index 1244d13e487..127ca009f19 100644
--- a/dev_scripts/chemenv/get_plane_permutations_optimized.py
+++ b/dev_scripts/chemenv/get_plane_permutations_optimized.py
@@ -15,7 +15,6 @@
 
 import numpy as np
 import tabulate
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,
diff --git a/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py b/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py
index 495a8bb668e..70449d924f8 100644
--- a/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py
+++ b/dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py
@@ -8,7 +8,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,
diff --git a/dev_scripts/chemenv/test_algos.py b/dev_scripts/chemenv/test_algos.py
index dbffdce27e5..17933a067a3 100644
--- a/dev_scripts/chemenv/test_algos.py
+++ b/dev_scripts/chemenv/test_algos.py
@@ -8,7 +8,6 @@
 from random import shuffle
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,
diff --git a/dev_scripts/chemenv/view_environment.py b/dev_scripts/chemenv/view_environment.py
index 2caa22e9f34..69aa6adc42e 100644
--- a/dev_scripts/chemenv/view_environment.py
+++ b/dev_scripts/chemenv/view_environment.py
@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     SEPARATION_PLANE,
     AllCoordinationGeometries,
diff --git a/dev_scripts/potcar_scrambler.py b/dev_scripts/potcar_scrambler.py
index 0dd2b0190fa..c0793c713d9 100644
--- a/dev_scripts/potcar_scrambler.py
+++ b/dev_scripts/potcar_scrambler.py
@@ -9,7 +9,6 @@
 import numpy as np
 from monty.os.path import zpath
 from monty.serialization import zopen
-
 from pymatgen.core import SETTINGS
 from pymatgen.io.vasp import Potcar, PotcarSingle
 from pymatgen.io.vasp.sets import _load_yaml_config
diff --git a/dev_scripts/update_pt_data.py b/dev_scripts/update_pt_data.py
index 88f321ed712..ee7889c75ea 100644
--- a/dev_scripts/update_pt_data.py
+++ b/dev_scripts/update_pt_data.py
@@ -11,9 +11,8 @@
 import requests
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
-from ruamel import yaml
-
 from pymatgen.core import Element, get_el_sp
+from ruamel import yaml
 
 try:
     from bs4 import BeautifulSoup
diff --git a/src/pymatgen/alchemy/filters.py b/src/pymatgen/alchemy/filters.py
index d133c0289e3..c16c05bf634 100644
--- a/src/pymatgen/alchemy/filters.py
+++ b/src/pymatgen/alchemy/filters.py
@@ -7,15 +7,13 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core import get_el_sp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 
 class AbstractStructureFilter(MSONable, abc.ABC):
diff --git a/src/pymatgen/alchemy/materials.py b/src/pymatgen/alchemy/materials.py
index 2fa8b754721..701133215e3 100644
--- a/src/pymatgen/alchemy/materials.py
+++ b/src/pymatgen/alchemy/materials.py
@@ -12,7 +12,6 @@
 from warnings import warn
 
 from monty.json import MSONable, jsanitize
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.cif import CifParser
 from pymatgen.io.vasp.inputs import Poscar
@@ -24,9 +23,8 @@
     from collections.abc import Sequence
     from typing import Any
 
-    from typing_extensions import Self
-
     from pymatgen.alchemy.filters import AbstractStructureFilter
+    from typing_extensions import Self
 
 
 class TransformedStructure(MSONable):
diff --git a/src/pymatgen/alchemy/transmuters.py b/src/pymatgen/alchemy/transmuters.py
index 802716520fc..d51ea47c247 100644
--- a/src/pymatgen/alchemy/transmuters.py
+++ b/src/pymatgen/alchemy/transmuters.py
@@ -21,9 +21,8 @@
     from collections.abc import Sequence
     from typing import Callable
 
-    from typing_extensions import Self
-
     from pymatgen.alchemy.filters import AbstractStructureFilter
+    from typing_extensions import Self
 
 __author__ = "Shyue Ping Ong, Will Richards"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/src/pymatgen/analysis/adsorption.py b/src/pymatgen/analysis/adsorption.py
index 5fe6b7a3742..88f9f98dc3e 100644
--- a/src/pymatgen/analysis/adsorption.py
+++ b/src/pymatgen/analysis/adsorption.py
@@ -12,8 +12,6 @@
 from matplotlib import patches
 from matplotlib.path import Path
 from monty.serialization import loadfn
-from scipy.spatial import Delaunay
-
 from pymatgen import vis
 from pymatgen.analysis.local_env import VoronoiNN
 from pymatgen.analysis.structure_matcher import StructureMatcher
@@ -22,13 +20,13 @@
 from pymatgen.core.surface import generate_all_slabs
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.coord import in_coord_list_pbc
+from scipy.spatial import Delaunay
 
 if TYPE_CHECKING:
     import matplotlib.pyplot as plt
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.surface import Slab
+    from typing_extensions import Self
 
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2016, The Materials Project"
diff --git a/src/pymatgen/analysis/bond_dissociation.py b/src/pymatgen/analysis/bond_dissociation.py
index 73b9f2d4fe2..cbf6ed83845 100644
--- a/src/pymatgen/analysis/bond_dissociation.py
+++ b/src/pymatgen/analysis/bond_dissociation.py
@@ -8,7 +8,6 @@
 
 import networkx as nx
 from monty.json import MSONable
-
 from pymatgen.analysis.fragmenter import open_ring
 from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
 from pymatgen.analysis.local_env import OpenBabelNN
diff --git a/src/pymatgen/analysis/bond_valence.py b/src/pymatgen/analysis/bond_valence.py
index e9cbe1fc47b..a81a71f5462 100644
--- a/src/pymatgen/analysis/bond_valence.py
+++ b/src/pymatgen/analysis/bond_valence.py
@@ -11,7 +11,6 @@
 
 import numpy as np
 from monty.serialization import loadfn
-
 from pymatgen.core import Element, Species, get_el_sp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
diff --git a/src/pymatgen/analysis/chemenv/connectivity/connected_components.py b/src/pymatgen/analysis/chemenv/connectivity/connected_components.py
index 3e75f758bc8..a7b361eda31 100644
--- a/src/pymatgen/analysis/chemenv/connectivity/connected_components.py
+++ b/src/pymatgen/analysis/chemenv/connectivity/connected_components.py
@@ -13,7 +13,6 @@
 from monty.json import MSONable, jsanitize
 from networkx.algorithms.components import is_connected
 from networkx.algorithms.traversal import bfs_tree
-
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
 from pymatgen.analysis.chemenv.utils.chemenv_errors import ChemenvError
 from pymatgen.analysis.chemenv.utils.graph_utils import get_delta
diff --git a/src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py b/src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py
index 99cb354f89c..26495f4a437 100644
--- a/src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py
+++ b/src/pymatgen/analysis/chemenv/connectivity/connectivity_finder.py
@@ -5,7 +5,6 @@
 import logging
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.connectivity.structure_connectivity import StructureConnectivity
 
 __author__ = "David Waroquiers"
diff --git a/src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py b/src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py
index 7258be9baf4..4fb4c54cc50 100644
--- a/src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py
+++ b/src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py
@@ -9,7 +9,6 @@
 import networkx as nx
 import numpy as np
 from monty.json import MSONable, jsanitize
-
 from pymatgen.analysis.chemenv.connectivity.connected_components import ConnectedComponent
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import get_environment_node
 from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
diff --git a/src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py b/src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py
index 3f814ac3ade..abc7c2b4778 100644
--- a/src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py
+++ b/src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py
@@ -13,8 +13,6 @@
 
 import numpy as np
 from monty.json import MSONable
-from scipy.stats import gmean
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.analysis.chemenv.utils.chemenv_errors import EquivalentSiteSearchError
@@ -29,6 +27,7 @@
 from pymatgen.core.operations import SymmOp
 from pymatgen.core.sites import PeriodicSite
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from scipy.stats import gmean
 
 if TYPE_CHECKING:
     from typing import ClassVar
diff --git a/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py b/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py
index 2e2b91e0066..523448b5bde 100644
--- a/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py
+++ b/src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py
@@ -23,7 +23,6 @@
 
 import numpy as np
 from numpy.linalg import norm, svd
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import MultiWeightsChemenvStrategy
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
diff --git a/src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py b/src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py
index 5d03166f83f..5b81229ced8 100644
--- a/src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py
+++ b/src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py
@@ -17,7 +17,6 @@
 from matplotlib.gridspec import GridSpec
 from matplotlib.patches import Polygon
 from monty.json import MontyDecoder, MSONable, jsanitize
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.analysis.chemenv.utils.chemenv_errors import ChemenvError
diff --git a/src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py b/src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py
index 77fc1ffcbd4..08f257d3ae2 100644
--- a/src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py
+++ b/src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py
@@ -9,8 +9,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from monty.json import MSONable
-from scipy.spatial import Voronoi
-
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import (
     get_lower_and_upper_f,
     rectangle_surface_intersection,
@@ -20,6 +18,7 @@
 from pymatgen.analysis.chemenv.utils.math_utils import normal_cdf_step
 from pymatgen.core.sites import PeriodicSite
 from pymatgen.core.structure import Structure
+from scipy.spatial import Voronoi
 
 if TYPE_CHECKING:
     from typing_extensions import Self
diff --git a/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py b/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py
index edf391b023b..358d03d39a0 100644
--- a/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py
+++ b/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py
@@ -7,12 +7,11 @@
 
 import numpy as np
 from numpy.linalg import norm
+from pymatgen.analysis.chemenv.utils.chemenv_errors import SolidAngleError
 from scipy.integrate import quad
 from scipy.interpolate import UnivariateSpline
 from scipy.spatial import ConvexHull
 
-from pymatgen.analysis.chemenv.utils.chemenv_errors import SolidAngleError
-
 if TYPE_CHECKING:
     from typing import Callable
 
diff --git a/src/pymatgen/analysis/chemenv/utils/func_utils.py b/src/pymatgen/analysis/chemenv/utils/func_utils.py
index 5bae04c94a9..d8437cde208 100644
--- a/src/pymatgen/analysis/chemenv/utils/func_utils.py
+++ b/src/pymatgen/analysis/chemenv/utils/func_utils.py
@@ -5,7 +5,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.utils.math_utils import (
     power2_decreasing_exp,
     power2_inverse_decreasing,
diff --git a/src/pymatgen/analysis/chemenv/utils/scripts_utils.py b/src/pymatgen/analysis/chemenv/utils/scripts_utils.py
index ca0fe90c08c..e153a7fcb63 100644
--- a/src/pymatgen/analysis/chemenv/utils/scripts_utils.py
+++ b/src/pymatgen/analysis/chemenv/utils/scripts_utils.py
@@ -6,7 +6,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     SimpleAbundanceChemenvStrategy,
     SimplestChemenvStrategy,
diff --git a/src/pymatgen/analysis/chempot_diagram.py b/src/pymatgen/analysis/chempot_diagram.py
index a2c6cfc7031..769c3a69b8f 100644
--- a/src/pymatgen/analysis/chempot_diagram.py
+++ b/src/pymatgen/analysis/chempot_diagram.py
@@ -33,13 +33,12 @@
 import plotly.express as px
 from monty.json import MSONable
 from plotly.graph_objects import Figure, Mesh3d, Scatter, Scatter3d
-from scipy.spatial import ConvexHull, HalfspaceIntersection
-
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.core.composition import Composition, Element
 from pymatgen.util.coord import Simplex
 from pymatgen.util.due import Doi, due
 from pymatgen.util.string import htmlify
+from scipy.spatial import ConvexHull, HalfspaceIntersection
 
 if TYPE_CHECKING:
     from pymatgen.entries.computed_entries import ComputedEntry
diff --git a/src/pymatgen/analysis/cost.py b/src/pymatgen/analysis/cost.py
index 458fea711e6..8ed4689301c 100644
--- a/src/pymatgen/analysis/cost.py
+++ b/src/pymatgen/analysis/cost.py
@@ -17,7 +17,6 @@
 
 import scipy.constants as const
 from monty.design_patterns import singleton
-
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.core import Composition, Element
 from pymatgen.util.provenance import is_valid_bibtex
diff --git a/src/pymatgen/analysis/diffraction/core.py b/src/pymatgen/analysis/diffraction/core.py
index 4e852b5e8f8..4a4dce2623a 100644
--- a/src/pymatgen/analysis/diffraction/core.py
+++ b/src/pymatgen/analysis/diffraction/core.py
@@ -8,7 +8,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-
 from pymatgen.core.spectrum import Spectrum
 from pymatgen.util.plotting import add_fig_kwargs, pretty_plot
 
diff --git a/src/pymatgen/analysis/diffraction/neutron.py b/src/pymatgen/analysis/diffraction/neutron.py
index 59d36759ba0..d9ef7328935 100644
--- a/src/pymatgen/analysis/diffraction/neutron.py
+++ b/src/pymatgen/analysis/diffraction/neutron.py
@@ -8,7 +8,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.diffraction.core import (
     AbstractDiffractionPatternCalculator,
     DiffractionPattern,
diff --git a/src/pymatgen/analysis/diffraction/tem.py b/src/pymatgen/analysis/diffraction/tem.py
index 45b8b9f9cf4..98103a22945 100644
--- a/src/pymatgen/analysis/diffraction/tem.py
+++ b/src/pymatgen/analysis/diffraction/tem.py
@@ -11,7 +11,6 @@
 import pandas as pd
 import plotly.graph_objects as go
 import scipy.constants as sc
-
 from pymatgen.analysis.diffraction.core import AbstractDiffractionPatternCalculator
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.string import latexify_spacegroup, unicodeify_spacegroup
@@ -19,7 +18,6 @@
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
-
     from pymatgen.core import Structure
 
 __author__ = "Frank Wan, Jason Liang"
diff --git a/src/pymatgen/analysis/diffraction/xrd.py b/src/pymatgen/analysis/diffraction/xrd.py
index 49eb07e05a0..654cab6d3fe 100644
--- a/src/pymatgen/analysis/diffraction/xrd.py
+++ b/src/pymatgen/analysis/diffraction/xrd.py
@@ -8,7 +8,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.analysis.diffraction.core import (
     AbstractDiffractionPatternCalculator,
     DiffractionPattern,
diff --git a/src/pymatgen/analysis/dimensionality.py b/src/pymatgen/analysis/dimensionality.py
index 7ce19444e03..93746d4f5db 100644
--- a/src/pymatgen/analysis/dimensionality.py
+++ b/src/pymatgen/analysis/dimensionality.py
@@ -29,7 +29,6 @@
 import networkx as nx
 import numpy as np
 from networkx.readwrite import json_graph
-
 from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
 from pymatgen.analysis.local_env import JmolNN
 from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
diff --git a/src/pymatgen/analysis/elasticity/elastic.py b/src/pymatgen/analysis/elasticity/elastic.py
index 7ac2ef19015..805b6017013 100644
--- a/src/pymatgen/analysis/elasticity/elastic.py
+++ b/src/pymatgen/analysis/elasticity/elastic.py
@@ -13,24 +13,22 @@
 
 import numpy as np
 import sympy as sp
-from scipy.integrate import quad
-from scipy.optimize import root
-from scipy.special import factorial
-
 from pymatgen.analysis.elasticity.strain import Strain
 from pymatgen.analysis.elasticity.stress import Stress
 from pymatgen.core.tensors import DEFAULT_QUAD, SquareTensor, Tensor, TensorCollection, get_uvec
 from pymatgen.core.units import Unit
 from pymatgen.util.due import Doi, due
+from scipy.integrate import quad
+from scipy.optimize import root
+from scipy.special import factorial
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Literal
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 
 __author__ = "Joseph Montoya"
diff --git a/src/pymatgen/analysis/elasticity/strain.py b/src/pymatgen/analysis/elasticity/strain.py
index 99fe716a249..13092b5daf2 100644
--- a/src/pymatgen/analysis/elasticity/strain.py
+++ b/src/pymatgen/analysis/elasticity/strain.py
@@ -12,7 +12,6 @@
 
 import numpy as np
 import scipy
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.tensors import SquareTensor, symmetry_reduce
 
@@ -21,9 +20,8 @@
     from typing import Literal
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.structure import Structure
+    from typing_extensions import Self
 
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/src/pymatgen/analysis/elasticity/stress.py b/src/pymatgen/analysis/elasticity/stress.py
index 3e5765130ca..720eb00dc4f 100644
--- a/src/pymatgen/analysis/elasticity/stress.py
+++ b/src/pymatgen/analysis/elasticity/stress.py
@@ -9,7 +9,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.core.tensors import SquareTensor
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/analysis/energy_models.py b/src/pymatgen/analysis/energy_models.py
index fa3c6a1d091..501287f7f01 100644
--- a/src/pymatgen/analysis/energy_models.py
+++ b/src/pymatgen/analysis/energy_models.py
@@ -10,14 +10,12 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.analysis.ewald import EwaldSummation
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 __version__ = "0.1"
 
diff --git a/src/pymatgen/analysis/eos.py b/src/pymatgen/analysis/eos.py
index b5f49e472fa..fc526884537 100644
--- a/src/pymatgen/analysis/eos.py
+++ b/src/pymatgen/analysis/eos.py
@@ -13,10 +13,9 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from scipy.optimize import leastsq, minimize
-
 from pymatgen.core.units import FloatWithUnit
 from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig, pretty_plot
+from scipy.optimize import leastsq, minimize
 
 if TYPE_CHECKING:
     from typing import ClassVar
diff --git a/src/pymatgen/analysis/ewald.py b/src/pymatgen/analysis/ewald.py
index e37d6a4c793..46fb6c523ee 100644
--- a/src/pymatgen/analysis/ewald.py
+++ b/src/pymatgen/analysis/ewald.py
@@ -11,11 +11,10 @@
 
 import numpy as np
 from monty.json import MSONable
-from scipy import constants
-from scipy.special import comb, erfc
-
 from pymatgen.core.structure import Structure
 from pymatgen.util.due import Doi, due
+from scipy import constants
+from scipy.special import comb, erfc
 
 if TYPE_CHECKING:
     from typing import Any
diff --git a/src/pymatgen/analysis/ferroelectricity/polarization.py b/src/pymatgen/analysis/ferroelectricity/polarization.py
index 0ec0e7e1043..2e0175fdf3b 100644
--- a/src/pymatgen/analysis/ferroelectricity/polarization.py
+++ b/src/pymatgen/analysis/ferroelectricity/polarization.py
@@ -48,17 +48,15 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from scipy.interpolate import UnivariateSpline
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
+from scipy.interpolate import UnivariateSpline
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
-    from typing_extensions import Self
-
     from pymatgen.core.sites import PeriodicSite
+    from typing_extensions import Self
 
 
 __author__ = "Tess Smidt"
diff --git a/src/pymatgen/analysis/fragmenter.py b/src/pymatgen/analysis/fragmenter.py
index 7458a46dfeb..98ad92a2b24 100644
--- a/src/pymatgen/analysis/fragmenter.py
+++ b/src/pymatgen/analysis/fragmenter.py
@@ -7,7 +7,6 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
 from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender
 from pymatgen.io.babel import BabelMolAdaptor
diff --git a/src/pymatgen/analysis/graphs.py b/src/pymatgen/analysis/graphs.py
index 9a206c5e578..998db8a72bf 100644
--- a/src/pymatgen/analysis/graphs.py
+++ b/src/pymatgen/analysis/graphs.py
@@ -20,13 +20,12 @@
 from monty.json import MSONable
 from networkx.drawing.nx_agraph import write_dot
 from networkx.readwrite import json_graph
-from scipy.spatial import KDTree
-from scipy.stats import describe
-
 from pymatgen.core import Lattice, Molecule, PeriodicSite, Structure
 from pymatgen.core.structure import FunctionalGroups
 from pymatgen.util.coord import lattice_points_in_supercell
 from pymatgen.vis.structure_vtk import EL_COLORS
+from scipy.spatial import KDTree
+from scipy.stats import describe
 
 try:
     import igraph
@@ -39,11 +38,10 @@
 
     from igraph import Graph
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.analysis.local_env import NearNeighbors
     from pymatgen.core import Species
     from pymatgen.util.typing import Tuple3Ints
+    from typing_extensions import Self
 
 
 logger = logging.getLogger(__name__)
diff --git a/src/pymatgen/analysis/hhi.py b/src/pymatgen/analysis/hhi.py
index 85708e78366..b893fe3a131 100644
--- a/src/pymatgen/analysis/hhi.py
+++ b/src/pymatgen/analysis/hhi.py
@@ -14,7 +14,6 @@
 import os
 
 from monty.design_patterns import singleton
-
 from pymatgen.core import Composition, Element
 
 __author__ = "Anubhav Jain"
diff --git a/src/pymatgen/analysis/interface_reactions.py b/src/pymatgen/analysis/interface_reactions.py
index 9c89adbc8b1..908cd538ff0 100644
--- a/src/pymatgen/analysis/interface_reactions.py
+++ b/src/pymatgen/analysis/interface_reactions.py
@@ -15,7 +15,6 @@
 from monty.json import MSONable
 from pandas import DataFrame
 from plotly.graph_objects import Figure, Scatter
-
 from pymatgen.analysis.phase_diagram import GrandPotentialPhaseDiagram, PhaseDiagram
 from pymatgen.analysis.reaction_calculator import Reaction
 from pymatgen.core.composition import Composition
diff --git a/src/pymatgen/analysis/interfaces/coherent_interfaces.py b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
index 3e145fc5618..e52dab38e04 100644
--- a/src/pymatgen/analysis/interfaces/coherent_interfaces.py
+++ b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
@@ -7,12 +7,11 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from scipy.linalg import polar
-
 from pymatgen.analysis.elasticity.strain import Deformation
 from pymatgen.analysis.interfaces.zsl import ZSLGenerator, fast_norm
 from pymatgen.core.interface import Interface, label_termination
 from pymatgen.core.surface import SlabGenerator
+from scipy.linalg import polar
 
 if TYPE_CHECKING:
     from collections.abc import Iterator, Sequence
diff --git a/src/pymatgen/analysis/interfaces/substrate_analyzer.py b/src/pymatgen/analysis/interfaces/substrate_analyzer.py
index 41746fdd24d..62b2a4a5152 100644
--- a/src/pymatgen/analysis/interfaces/substrate_analyzer.py
+++ b/src/pymatgen/analysis/interfaces/substrate_analyzer.py
@@ -11,10 +11,9 @@
 
 if TYPE_CHECKING:
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
     from pymatgen.util.typing import Tuple3Ints
+    from typing_extensions import Self
 
 
 @dataclass
diff --git a/src/pymatgen/analysis/interfaces/zsl.py b/src/pymatgen/analysis/interfaces/zsl.py
index 8aae62a46c1..fdd17dbcdb0 100644
--- a/src/pymatgen/analysis/interfaces/zsl.py
+++ b/src/pymatgen/analysis/interfaces/zsl.py
@@ -8,7 +8,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.util.due import Doi, due
 from pymatgen.util.numba import njit
 
diff --git a/src/pymatgen/analysis/local_env.py b/src/pymatgen/analysis/local_env.py
index 7d31bf192df..56c5365955e 100644
--- a/src/pymatgen/analysis/local_env.py
+++ b/src/pymatgen/analysis/local_env.py
@@ -19,13 +19,12 @@
 import numpy as np
 from monty.dev import deprecated, requires
 from monty.serialization import loadfn
-from ruamel.yaml import YAML
-from scipy.spatial import Voronoi
-
 from pymatgen.analysis.bond_valence import BV_PARAMS, BVAnalyzer
 from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
 from pymatgen.analysis.molecule_structure_comparator import CovalentRadius
 from pymatgen.core import Element, IStructure, PeriodicNeighbor, PeriodicSite, Site, Species, Structure
+from ruamel.yaml import YAML
+from scipy.spatial import Voronoi
 
 try:
     from openbabel import openbabel
@@ -35,10 +34,9 @@
 if TYPE_CHECKING:
     from typing import Any
 
-    from typing_extensions import Self
-
     from pymatgen.core.composition import SpeciesLike
     from pymatgen.util.typing import Tuple3Ints
+    from typing_extensions import Self
 
 
 __author__ = "Shyue Ping Ong, Geoffroy Hautier, Sai Jayaraman, "
diff --git a/src/pymatgen/analysis/magnetism/analyzer.py b/src/pymatgen/analysis/magnetism/analyzer.py
index 6c10495630b..59359e773fd 100644
--- a/src/pymatgen/analysis/magnetism/analyzer.py
+++ b/src/pymatgen/analysis/magnetism/analyzer.py
@@ -13,10 +13,6 @@
 
 import numpy as np
 from monty.serialization import loadfn
-from ruamel.yaml.error import MarkedYAMLError
-from scipy.signal import argrelextrema
-from scipy.stats import gaussian_kde
-
 from pymatgen.core.structure import DummySpecies, Element, Species, Structure
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
@@ -24,6 +20,9 @@
 from pymatgen.transformations.advanced_transformations import MagOrderingTransformation, MagOrderParameterConstraint
 from pymatgen.transformations.standard_transformations import AutoOxiStateDecorationTransformation
 from pymatgen.util.due import Doi, due
+from ruamel.yaml.error import MarkedYAMLError
+from scipy.signal import argrelextrema
+from scipy.stats import gaussian_kde
 
 if TYPE_CHECKING:
     from typing import Any
diff --git a/src/pymatgen/analysis/magnetism/heisenberg.py b/src/pymatgen/analysis/magnetism/heisenberg.py
index 35f4c12f116..ac627f903b1 100644
--- a/src/pymatgen/analysis/magnetism/heisenberg.py
+++ b/src/pymatgen/analysis/magnetism/heisenberg.py
@@ -15,7 +15,6 @@
 import pandas as pd
 from monty.json import MSONable, jsanitize
 from monty.serialization import dumpfn
-
 from pymatgen.analysis.graphs import StructureGraph
 from pymatgen.analysis.local_env import MinimumDistanceNN
 from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering
diff --git a/src/pymatgen/analysis/magnetism/jahnteller.py b/src/pymatgen/analysis/magnetism/jahnteller.py
index dda2d3b4907..90727f19e15 100644
--- a/src/pymatgen/analysis/magnetism/jahnteller.py
+++ b/src/pymatgen/analysis/magnetism/jahnteller.py
@@ -7,7 +7,6 @@
 from typing import TYPE_CHECKING, Literal, cast
 
 import numpy as np
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.local_env import LocalStructOrderParams, get_neighbors_of_site_with_index
 from pymatgen.core import Species, get_el_sp
diff --git a/src/pymatgen/analysis/molecule_matcher.py b/src/pymatgen/analysis/molecule_matcher.py
index a8da516d5a5..1b779e6898c 100644
--- a/src/pymatgen/analysis/molecule_matcher.py
+++ b/src/pymatgen/analysis/molecule_matcher.py
@@ -22,14 +22,12 @@
 import numpy as np
 from monty.dev import requires
 from monty.json import MSONable
+from pymatgen.core.structure import Molecule
 from scipy.optimize import linear_sum_assignment
 from scipy.spatial.distance import cdist
 
-from pymatgen.core.structure import Molecule
-
 try:
     from openbabel import openbabel
-
     from pymatgen.io.babel import BabelMolAdaptor
 except ImportError:
     openbabel = BabelMolAdaptor = None  # type: ignore[misc]
diff --git a/src/pymatgen/analysis/molecule_structure_comparator.py b/src/pymatgen/analysis/molecule_structure_comparator.py
index 32d603abd28..28400b65a34 100644
--- a/src/pymatgen/analysis/molecule_structure_comparator.py
+++ b/src/pymatgen/analysis/molecule_structure_comparator.py
@@ -14,7 +14,6 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/analysis/nmr.py b/src/pymatgen/analysis/nmr.py
index bf16031f028..91a7ccd21d4 100644
--- a/src/pymatgen/analysis/nmr.py
+++ b/src/pymatgen/analysis/nmr.py
@@ -5,7 +5,6 @@
 from typing import TYPE_CHECKING, NamedTuple
 
 import numpy as np
-
 from pymatgen.core import Site, Species
 from pymatgen.core.tensors import SquareTensor
 from pymatgen.core.units import FloatWithUnit
diff --git a/src/pymatgen/analysis/phase_diagram.py b/src/pymatgen/analysis/phase_diagram.py
index 8411ac64da2..b9d99a7ca44 100644
--- a/src/pymatgen/analysis/phase_diagram.py
+++ b/src/pymatgen/analysis/phase_diagram.py
@@ -21,11 +21,6 @@
 from matplotlib.colors import LinearSegmentedColormap, Normalize
 from matplotlib.font_manager import FontProperties
 from monty.json import MontyDecoder, MSONable
-from scipy import interpolate
-from scipy.optimize import minimize
-from scipy.spatial import ConvexHull
-from tqdm import tqdm
-
 from pymatgen.analysis.reaction_calculator import Reaction, ReactionError
 from pymatgen.core import DummySpecies, Element, get_el_sp
 from pymatgen.core.composition import Composition
@@ -34,6 +29,10 @@
 from pymatgen.util.due import Doi, due
 from pymatgen.util.plotting import pretty_plot
 from pymatgen.util.string import htmlify, latexify
+from scipy import interpolate
+from scipy.optimize import minimize
+from scipy.spatial import ConvexHull
+from tqdm import tqdm
 
 if TYPE_CHECKING:
     from collections.abc import Collection, Iterator, Sequence
diff --git a/src/pymatgen/analysis/piezo.py b/src/pymatgen/analysis/piezo.py
index 2f168e1eef4..7a5b32ac8d0 100644
--- a/src/pymatgen/analysis/piezo.py
+++ b/src/pymatgen/analysis/piezo.py
@@ -6,7 +6,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.core.tensors import Tensor
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/analysis/piezo_sensitivity.py b/src/pymatgen/analysis/piezo_sensitivity.py
index 0a93140dc15..d5b4f232199 100644
--- a/src/pymatgen/analysis/piezo_sensitivity.py
+++ b/src/pymatgen/analysis/piezo_sensitivity.py
@@ -7,7 +7,6 @@
 
 import numpy as np
 from monty.dev import requires
-
 from pymatgen.core.tensors import Tensor
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
diff --git a/src/pymatgen/analysis/pourbaix_diagram.py b/src/pymatgen/analysis/pourbaix_diagram.py
index 74fa89f3d22..dad540db5fb 100644
--- a/src/pymatgen/analysis/pourbaix_diagram.py
+++ b/src/pymatgen/analysis/pourbaix_diagram.py
@@ -16,9 +16,6 @@
 
 import numpy as np
 from monty.json import MontyDecoder, MSONable
-from scipy.spatial import ConvexHull, HalfspaceIntersection
-from scipy.special import comb
-
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.analysis.reaction_calculator import Reaction, ReactionError
 from pymatgen.core import Composition, Element
@@ -29,6 +26,8 @@
 from pymatgen.util.due import Doi, due
 from pymatgen.util.plotting import pretty_plot
 from pymatgen.util.string import Stringify
+from scipy.spatial import ConvexHull, HalfspaceIntersection
+from scipy.special import comb
 
 if TYPE_CHECKING:
     from typing import Any
diff --git a/src/pymatgen/analysis/prototypes.py b/src/pymatgen/analysis/prototypes.py
index a9cdf29c70c..6423e53170c 100644
--- a/src/pymatgen/analysis/prototypes.py
+++ b/src/pymatgen/analysis/prototypes.py
@@ -17,7 +17,6 @@
 from typing import TYPE_CHECKING
 
 from monty.serialization import loadfn
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.util.due import Doi, due
 
diff --git a/src/pymatgen/analysis/quasiharmonic.py b/src/pymatgen/analysis/quasiharmonic.py
index d1c7612fecf..f7b8aa08a05 100644
--- a/src/pymatgen/analysis/quasiharmonic.py
+++ b/src/pymatgen/analysis/quasiharmonic.py
@@ -15,15 +15,14 @@
 
 import numpy as np
 from monty.dev import deprecated
+from pymatgen.analysis.eos import EOS, PolynomialEOS
+from pymatgen.core.units import FloatWithUnit
+from pymatgen.util.due import Doi, due
 from scipy.constants import physical_constants
 from scipy.integrate import quadrature
 from scipy.misc import derivative
 from scipy.optimize import minimize
 
-from pymatgen.analysis.eos import EOS, PolynomialEOS
-from pymatgen.core.units import FloatWithUnit
-from pymatgen.util.due import Doi, due
-
 __author__ = "Kiran Mathew, Brandon Bocklund"
 __credits__ = "Cormac Toher"
 
diff --git a/src/pymatgen/analysis/quasirrho.py b/src/pymatgen/analysis/quasirrho.py
index 0c66f730db3..5846f19339b 100644
--- a/src/pymatgen/analysis/quasirrho.py
+++ b/src/pymatgen/analysis/quasirrho.py
@@ -15,16 +15,14 @@
 
 import numpy as np
 import scipy.constants as const
-
 from pymatgen.core.units import kb as kb_ev
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.core import Molecule
     from pymatgen.io.gaussian import GaussianOutput
     from pymatgen.io.qchem.outputs import QCOutput
+    from typing_extensions import Self
 
 __author__ = "Alex Epstein"
 __copyright__ = "Copyright 2020, The Materials Project"
diff --git a/src/pymatgen/analysis/reaction_calculator.py b/src/pymatgen/analysis/reaction_calculator.py
index 456e6ea97d9..638e9189318 100644
--- a/src/pymatgen/analysis/reaction_calculator.py
+++ b/src/pymatgen/analysis/reaction_calculator.py
@@ -10,18 +10,16 @@
 import numpy as np
 from monty.fractions import gcd_float
 from monty.json import MontyDecoder, MSONable
-from uncertainties import ufloat
-
 from pymatgen.core.composition import Composition
 from pymatgen.entries.computed_entries import ComputedEntry
+from uncertainties import ufloat
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
 
-    from typing_extensions import Self
-
     from pymatgen.core import Element, Species
     from pymatgen.util.typing import CompositionLike
+    from typing_extensions import Self
 
 __author__ = "Shyue Ping Ong, Anubhav Jain"
 __copyright__ = "Copyright 2011, The Materials Project"
diff --git a/src/pymatgen/analysis/solar/slme.py b/src/pymatgen/analysis/solar/slme.py
index cc7fdf2dabf..976ef49b701 100644
--- a/src/pymatgen/analysis/solar/slme.py
+++ b/src/pymatgen/analysis/solar/slme.py
@@ -22,10 +22,9 @@
     from scipy.integrate import simpson
 except ImportError:
     from scipy.integrate import simps as simpson
-from scipy.interpolate import interp1d
-
 from pymatgen.io.vasp.outputs import Vasprun
 from pymatgen.util.due import Doi, due
+from scipy.interpolate import interp1d
 
 due.cite(
     Doi("10.1021/acs.chemmater.9b02166"),
diff --git a/src/pymatgen/analysis/structure_analyzer.py b/src/pymatgen/analysis/structure_analyzer.py
index 45bc60da98d..a044216444a 100644
--- a/src/pymatgen/analysis/structure_analyzer.py
+++ b/src/pymatgen/analysis/structure_analyzer.py
@@ -10,11 +10,10 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from scipy.spatial import Voronoi
-
 from pymatgen.analysis.local_env import JmolNN, VoronoiNN
 from pymatgen.core import Composition, Element, PeriodicSite, Species
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from scipy.spatial import Voronoi
 
 if TYPE_CHECKING:
     from pymatgen.core import Structure
diff --git a/src/pymatgen/analysis/structure_matcher.py b/src/pymatgen/analysis/structure_matcher.py
index 0ad9c9db788..7a2650bef71 100644
--- a/src/pymatgen/analysis/structure_matcher.py
+++ b/src/pymatgen/analysis/structure_matcher.py
@@ -8,7 +8,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.core import Composition, Lattice, Structure, get_el_sp
 from pymatgen.optimization.linear_assignment import LinearAssignment
 from pymatgen.util.coord import lattice_points_in_supercell
@@ -18,9 +17,8 @@
     from collections.abc import Mapping, Sequence
     from typing import Literal
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import SpeciesLike
+    from typing_extensions import Self
 
 __author__ = "William Davidson Richards, Stephen Dacek, Shyue Ping Ong"
 __copyright__ = "Copyright 2011, The Materials Project"
diff --git a/src/pymatgen/analysis/structure_prediction/dopant_predictor.py b/src/pymatgen/analysis/structure_prediction/dopant_predictor.py
index e21603e13ee..dcc750ec9f3 100644
--- a/src/pymatgen/analysis/structure_prediction/dopant_predictor.py
+++ b/src/pymatgen/analysis/structure_prediction/dopant_predictor.py
@@ -5,7 +5,6 @@
 import warnings
 
 import numpy as np
-
 from pymatgen.analysis.structure_prediction.substitution_probability import SubstitutionPredictor
 from pymatgen.core import Element, Species
 
diff --git a/src/pymatgen/analysis/structure_prediction/substitution_probability.py b/src/pymatgen/analysis/structure_prediction/substitution_probability.py
index 210e218d2b1..75720ce9419 100644
--- a/src/pymatgen/analysis/structure_prediction/substitution_probability.py
+++ b/src/pymatgen/analysis/structure_prediction/substitution_probability.py
@@ -13,7 +13,6 @@
 from typing import TYPE_CHECKING
 
 from monty.design_patterns import cached_class
-
 from pymatgen.core import Species, get_el_sp
 from pymatgen.util.due import Doi, due
 
diff --git a/src/pymatgen/analysis/structure_prediction/substitutor.py b/src/pymatgen/analysis/structure_prediction/substitutor.py
index 2921355d637..c36df98f030 100644
--- a/src/pymatgen/analysis/structure_prediction/substitutor.py
+++ b/src/pymatgen/analysis/structure_prediction/substitutor.py
@@ -9,7 +9,6 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.alchemy.filters import RemoveDuplicatesFilter, RemoveExistingFilter
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.alchemy.transmuters import StandardTransmuter
diff --git a/src/pymatgen/analysis/structure_prediction/volume_predictor.py b/src/pymatgen/analysis/structure_prediction/volume_predictor.py
index dd749e8416a..5ce74b652f4 100644
--- a/src/pymatgen/analysis/structure_prediction/volume_predictor.py
+++ b/src/pymatgen/analysis/structure_prediction/volume_predictor.py
@@ -7,7 +7,6 @@
 
 import numpy as np
 from monty.serialization import loadfn
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import Structure
diff --git a/src/pymatgen/analysis/surface_analysis.py b/src/pymatgen/analysis/surface_analysis.py
index ff49d82088f..f395f90afd0 100644
--- a/src/pymatgen/analysis/surface_analysis.py
+++ b/src/pymatgen/analysis/surface_analysis.py
@@ -42,9 +42,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from sympy import Symbol
-from sympy.solvers import linsolve, solve
-
 from pymatgen.analysis.wulff import WulffShape
 from pymatgen.core import Structure
 from pymatgen.core.composition import Composition
@@ -54,11 +51,12 @@
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.due import Doi, due
 from pymatgen.util.plotting import pretty_plot
+from sympy import Symbol
+from sympy.solvers import linsolve, solve
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.util.typing import Tuple3Ints
+    from typing_extensions import Self
 
 EV_PER_ANG2_TO_JOULES_PER_M2 = 16.0217656
 
diff --git a/src/pymatgen/analysis/topological/spillage.py b/src/pymatgen/analysis/topological/spillage.py
index d0da47ccfe1..e088b98553b 100644
--- a/src/pymatgen/analysis/topological/spillage.py
+++ b/src/pymatgen/analysis/topological/spillage.py
@@ -8,7 +8,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.io.vasp.outputs import Wavecar
 
 
diff --git a/src/pymatgen/analysis/transition_state.py b/src/pymatgen/analysis/transition_state.py
index 5dbbe1fbb54..e7c6d9b2924 100644
--- a/src/pymatgen/analysis/transition_state.py
+++ b/src/pymatgen/analysis/transition_state.py
@@ -15,12 +15,11 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from monty.json import MSONable, jsanitize
-from scipy.interpolate import CubicSpline
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import Structure
 from pymatgen.io.vasp import Outcar
 from pymatgen.util.plotting import pretty_plot
+from scipy.interpolate import CubicSpline
 
 if TYPE_CHECKING:
     from typing_extensions import Self
diff --git a/src/pymatgen/analysis/wulff.py b/src/pymatgen/analysis/wulff.py
index 420d77c4161..23a6986d87f 100644
--- a/src/pymatgen/analysis/wulff.py
+++ b/src/pymatgen/analysis/wulff.py
@@ -25,11 +25,10 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import plotly.graph_objects as go
-from scipy.spatial import ConvexHull
-
 from pymatgen.core.structure import Structure
 from pymatgen.util.coord import get_angle
 from pymatgen.util.string import unicodeify_spacegroup
+from scipy.spatial import ConvexHull
 
 if TYPE_CHECKING:
     from pymatgen.core.lattice import Lattice
diff --git a/src/pymatgen/analysis/xas/spectrum.py b/src/pymatgen/analysis/xas/spectrum.py
index 007c4596642..97af8b85282 100644
--- a/src/pymatgen/analysis/xas/spectrum.py
+++ b/src/pymatgen/analysis/xas/spectrum.py
@@ -7,11 +7,10 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from scipy.interpolate import interp1d
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core.spectrum import Spectrum
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from scipy.interpolate import interp1d
 
 if TYPE_CHECKING:
     from typing import Literal
diff --git a/src/pymatgen/analysis/xps.py b/src/pymatgen/analysis/xps.py
index 1aca37a1eee..4e9acff9540 100644
--- a/src/pymatgen/analysis/xps.py
+++ b/src/pymatgen/analysis/xps.py
@@ -25,15 +25,13 @@
 
 import numpy as np
 import pandas as pd
-
 from pymatgen.core import Element
 from pymatgen.core.spectrum import Spectrum
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.electronic_structure.dos import CompleteDos
+    from typing_extensions import Self
 
 
 due.cite(
diff --git a/src/pymatgen/apps/battery/analyzer.py b/src/pymatgen/apps/battery/analyzer.py
index 2543b44da92..3d08e147c35 100644
--- a/src/pymatgen/apps/battery/analyzer.py
+++ b/src/pymatgen/apps/battery/analyzer.py
@@ -6,7 +6,6 @@
 from collections import defaultdict
 
 import scipy.constants as const
-
 from pymatgen.core import Composition, Element, Species
 
 __author__ = "Anubhav Jain"
diff --git a/src/pymatgen/apps/battery/battery_abc.py b/src/pymatgen/apps/battery/battery_abc.py
index 78f4d984498..8465f85445f 100644
--- a/src/pymatgen/apps/battery/battery_abc.py
+++ b/src/pymatgen/apps/battery/battery_abc.py
@@ -12,9 +12,8 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-from scipy.constants import N_A
-
 from pymatgen.core import Composition, Element
+from scipy.constants import N_A
 
 if TYPE_CHECKING:
     from pymatgen.entries.computed_entries import ComputedEntry
diff --git a/src/pymatgen/apps/battery/conversion_battery.py b/src/pymatgen/apps/battery/conversion_battery.py
index b84da63efd6..ee274bcd40d 100644
--- a/src/pymatgen/apps/battery/conversion_battery.py
+++ b/src/pymatgen/apps/battery/conversion_battery.py
@@ -5,20 +5,18 @@
 from dataclasses import dataclass
 from typing import TYPE_CHECKING
 
-from scipy.constants import N_A
-
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.analysis.reaction_calculator import BalancedReaction
 from pymatgen.apps.battery.battery_abc import AbstractElectrode, AbstractVoltagePair
 from pymatgen.core import Composition, Element
 from pymatgen.core.units import Charge, Time
+from scipy.constants import N_A
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
 
-    from typing_extensions import Self
-
     from pymatgen.entries.computed_entries import ComputedEntry
+    from typing_extensions import Self
 
 
 @dataclass
diff --git a/src/pymatgen/apps/battery/insertion_battery.py b/src/pymatgen/apps/battery/insertion_battery.py
index 76631f53368..5f073fbc916 100644
--- a/src/pymatgen/apps/battery/insertion_battery.py
+++ b/src/pymatgen/apps/battery/insertion_battery.py
@@ -9,13 +9,12 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MontyDecoder
-from scipy.constants import N_A
-
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.apps.battery.battery_abc import AbstractElectrode, AbstractVoltagePair
 from pymatgen.core import Composition, Element
 from pymatgen.core.units import Charge, Time
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
+from scipy.constants import N_A
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
diff --git a/src/pymatgen/apps/battery/plotter.py b/src/pymatgen/apps/battery/plotter.py
index f8725ef25e6..150f413784b 100644
--- a/src/pymatgen/apps/battery/plotter.py
+++ b/src/pymatgen/apps/battery/plotter.py
@@ -6,7 +6,6 @@
 
 import matplotlib.pyplot as plt
 import plotly.graph_objects as go
-
 from pymatgen.util.plotting import pretty_plot
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/apps/borg/hive.py b/src/pymatgen/apps/borg/hive.py
index a90380d0dee..87aaeeb2500 100644
--- a/src/pymatgen/apps/borg/hive.py
+++ b/src/pymatgen/apps/borg/hive.py
@@ -12,7 +12,6 @@
 
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 from pymatgen.io.gaussian import GaussianOutput
 from pymatgen.io.vasp.inputs import Incar, Poscar, Potcar
diff --git a/src/pymatgen/cli/feff_plot_cross_section.py b/src/pymatgen/cli/feff_plot_cross_section.py
index a9a59f3a650..2bf9d89fe23 100755
--- a/src/pymatgen/cli/feff_plot_cross_section.py
+++ b/src/pymatgen/cli/feff_plot_cross_section.py
@@ -7,7 +7,6 @@
 import argparse
 
 import matplotlib.pyplot as plt
-
 from pymatgen.io.feff.outputs import Xmu
 from pymatgen.util.plotting import pretty_plot
 
diff --git a/src/pymatgen/cli/pmg.py b/src/pymatgen/cli/pmg.py
index 491d4ab2c11..1ee6a93ed7e 100755
--- a/src/pymatgen/cli/pmg.py
+++ b/src/pymatgen/cli/pmg.py
@@ -7,8 +7,6 @@
 import argparse
 import itertools
 
-from tabulate import tabulate, tabulate_formats
-
 from pymatgen.cli.pmg_analyze import analyze
 from pymatgen.cli.pmg_config import configure_pmg
 from pymatgen.cli.pmg_plot import plot
@@ -17,6 +15,7 @@
 from pymatgen.core import SETTINGS
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp import Incar, Potcar
+from tabulate import tabulate, tabulate_formats
 
 
 def parse_view(args):
diff --git a/src/pymatgen/cli/pmg_analyze.py b/src/pymatgen/cli/pmg_analyze.py
index c12ef4186ef..4db3fbcb2f6 100644
--- a/src/pymatgen/cli/pmg_analyze.py
+++ b/src/pymatgen/cli/pmg_analyze.py
@@ -7,11 +7,10 @@
 import os
 import re
 
-from tabulate import tabulate
-
 from pymatgen.apps.borg.hive import SimpleVaspToComputedEntryDrone, VaspToComputedEntryDrone
 from pymatgen.apps.borg.queen import BorgQueen
 from pymatgen.io.vasp import Outcar
+from tabulate import tabulate
 
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/src/pymatgen/cli/pmg_config.py b/src/pymatgen/cli/pmg_config.py
index d8253983e19..8a0f4a04317 100755
--- a/src/pymatgen/cli/pmg_config.py
+++ b/src/pymatgen/cli/pmg_config.py
@@ -13,11 +13,10 @@
 
 from monty.json import jsanitize
 from monty.serialization import dumpfn, loadfn
-from ruamel import yaml
-
 from pymatgen.core import OLD_SETTINGS_FILE, SETTINGS_FILE, Element
 from pymatgen.io.cp2k.inputs import GaussianTypeOrbitalBasisSet, GthPotential
 from pymatgen.io.cp2k.utils import chunk
+from ruamel import yaml
 
 if TYPE_CHECKING:
     from argparse import Namespace
diff --git a/src/pymatgen/cli/pmg_plot.py b/src/pymatgen/cli/pmg_plot.py
index 89d0fa269ae..56e7d629660 100755
--- a/src/pymatgen/cli/pmg_plot.py
+++ b/src/pymatgen/cli/pmg_plot.py
@@ -5,7 +5,6 @@
 from __future__ import annotations
 
 import matplotlib.pyplot as plt
-
 from pymatgen.analysis.diffraction.xrd import XRDCalculator
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.plotter import DosPlotter
diff --git a/src/pymatgen/cli/pmg_structure.py b/src/pymatgen/cli/pmg_structure.py
index 3f85040fede..b8046b699ce 100755
--- a/src/pymatgen/cli/pmg_structure.py
+++ b/src/pymatgen/cli/pmg_structure.py
@@ -4,11 +4,10 @@
 
 from __future__ import annotations
 
-from tabulate import tabulate
-
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from tabulate import tabulate
 
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/src/pymatgen/command_line/bader_caller.py b/src/pymatgen/command_line/bader_caller.py
index dbbb743acc9..c85baf861ed 100644
--- a/src/pymatgen/command_line/bader_caller.py
+++ b/src/pymatgen/command_line/bader_caller.py
@@ -27,7 +27,6 @@
 from monty.dev import deprecated
 from monty.shutil import decompress_file
 from monty.tempfile import ScratchDir
-
 from pymatgen.io.common import VolumetricData
 from pymatgen.io.vasp.inputs import Potcar
 from pymatgen.io.vasp.outputs import Chgcar
@@ -35,9 +34,8 @@
 if TYPE_CHECKING:
     from typing import Any
 
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 __author__ = "shyuepingong"
 __version__ = "0.1"
diff --git a/src/pymatgen/command_line/chargemol_caller.py b/src/pymatgen/command_line/chargemol_caller.py
index d9b17a27404..a22e4b345a0 100644
--- a/src/pymatgen/command_line/chargemol_caller.py
+++ b/src/pymatgen/command_line/chargemol_caller.py
@@ -51,7 +51,6 @@
 
 import numpy as np
 from monty.tempfile import ScratchDir
-
 from pymatgen.core import Element
 from pymatgen.io.vasp.inputs import Potcar
 from pymatgen.io.vasp.outputs import Chgcar
diff --git a/src/pymatgen/command_line/critic2_caller.py b/src/pymatgen/command_line/critic2_caller.py
index 4f6261afe3e..9855345d7ff 100644
--- a/src/pymatgen/command_line/critic2_caller.py
+++ b/src/pymatgen/command_line/critic2_caller.py
@@ -52,18 +52,16 @@
 from monty.json import MSONable
 from monty.serialization import loadfn
 from monty.tempfile import ScratchDir
-from scipy.spatial import KDTree
-
 from pymatgen.analysis.graphs import StructureGraph
 from pymatgen.core import DummySpecies
 from pymatgen.io.vasp.inputs import Potcar
 from pymatgen.io.vasp.outputs import Chgcar, VolumetricData
 from pymatgen.util.due import Doi, due
+from scipy.spatial import KDTree
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
diff --git a/src/pymatgen/command_line/enumlib_caller.py b/src/pymatgen/command_line/enumlib_caller.py
index bdae0256e0e..619060b8386 100644
--- a/src/pymatgen/command_line/enumlib_caller.py
+++ b/src/pymatgen/command_line/enumlib_caller.py
@@ -39,7 +39,6 @@
 from monty.dev import requires
 from monty.fractions import lcm
 from monty.tempfile import ScratchDir
-
 from pymatgen.core import DummySpecies, PeriodicSite, Structure
 from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
diff --git a/src/pymatgen/command_line/gulp_caller.py b/src/pymatgen/command_line/gulp_caller.py
index b13912f2433..fa3e250b99a 100644
--- a/src/pymatgen/command_line/gulp_caller.py
+++ b/src/pymatgen/command_line/gulp_caller.py
@@ -10,7 +10,6 @@
 import subprocess
 
 from monty.tempfile import ScratchDir
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.core import Element, Lattice, Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
diff --git a/src/pymatgen/command_line/mcsqs_caller.py b/src/pymatgen/command_line/mcsqs_caller.py
index dd1cca70b1c..980f04e2f13 100644
--- a/src/pymatgen/command_line/mcsqs_caller.py
+++ b/src/pymatgen/command_line/mcsqs_caller.py
@@ -13,7 +13,6 @@
 from typing import TYPE_CHECKING, NamedTuple
 
 from monty.dev import requires
-
 from pymatgen.core.structure import Structure
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/command_line/vampire_caller.py b/src/pymatgen/command_line/vampire_caller.py
index 8709088514d..44aa50c3895 100644
--- a/src/pymatgen/command_line/vampire_caller.py
+++ b/src/pymatgen/command_line/vampire_caller.py
@@ -21,7 +21,6 @@
 import pandas as pd
 from monty.dev import requires
 from monty.json import MSONable
-
 from pymatgen.analysis.magnetism.heisenberg import HeisenbergMapper
 
 __author__ = "ncfrey"
diff --git a/src/pymatgen/core/__init__.py b/src/pymatgen/core/__init__.py
index 2b160c6b793..c1f047de11c 100644
--- a/src/pymatgen/core/__init__.py
+++ b/src/pymatgen/core/__init__.py
@@ -7,8 +7,6 @@
 from importlib.metadata import PackageNotFoundError, version
 from typing import Any
 
-from ruamel.yaml import YAML
-
 from pymatgen.core.composition import Composition
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.operations import SymmOp
@@ -16,6 +14,7 @@
 from pymatgen.core.sites import PeriodicSite, Site
 from pymatgen.core.structure import IMolecule, IStructure, Molecule, PeriodicNeighbor, SiteCollection, Structure
 from pymatgen.core.units import ArrayWithUnit, FloatWithUnit, Unit
+from ruamel.yaml import YAML
 
 __author__ = "Pymatgen Development Team"
 __email__ = "pymatgen@googlegroups.com"
diff --git a/src/pymatgen/core/composition.py b/src/pymatgen/core/composition.py
index a387dafd12c..8eaa6a5400d 100644
--- a/src/pymatgen/core/composition.py
+++ b/src/pymatgen/core/composition.py
@@ -18,7 +18,6 @@
 from monty.fractions import gcd, gcd_float
 from monty.json import MSONable
 from monty.serialization import loadfn
-
 from pymatgen.core.periodic_table import DummySpecies, Element, ElementType, Species, get_el_sp
 from pymatgen.core.units import Mass
 from pymatgen.util.string import Stringify, formula_double_format
@@ -27,9 +26,8 @@
     from collections.abc import Generator, Iterator
     from typing import Any, ClassVar
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import SpeciesLike
+    from typing_extensions import Self
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
 
diff --git a/src/pymatgen/core/interface.py b/src/pymatgen/core/interface.py
index 0ac14fd1453..2856130e014 100644
--- a/src/pymatgen/core/interface.py
+++ b/src/pymatgen/core/interface.py
@@ -15,9 +15,6 @@
 import numpy as np
 from monty.fractions import lcm
 from numpy.testing import assert_allclose
-from scipy.cluster.hierarchy import fcluster, linkage
-from scipy.spatial.distance import squareform
-
 from pymatgen.analysis.adsorption import AdsorbateSiteFinder
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.sites import PeriodicSite, Site
@@ -25,16 +22,17 @@
 from pymatgen.core.surface import Slab
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.typing import Tuple3Ints
+from scipy.cluster.hierarchy import fcluster, linkage
+from scipy.spatial.distance import squareform
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Any, Callable
 
     from numpy.typing import ArrayLike, NDArray
-    from typing_extensions import Self
-
     from pymatgen.core import Element
     from pymatgen.util.typing import CompositionLike, Matrix3D, MillerIndex, Tuple3Floats, Vector3D
+    from typing_extensions import Self
 
 Tuple4Ints = tuple[int, int, int, int]
 logger = logging.getLogger(__name__)
diff --git a/src/pymatgen/core/ion.py b/src/pymatgen/core/ion.py
index ec246d1ca34..c3d7cf3271c 100644
--- a/src/pymatgen/core/ion.py
+++ b/src/pymatgen/core/ion.py
@@ -7,7 +7,6 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.core.composition import Composition, reduce_formula
 from pymatgen.util.string import Stringify, charge_string, formula_double_format
 
diff --git a/src/pymatgen/core/lattice.py b/src/pymatgen/core/lattice.py
index 5448c09813a..89f28628e6d 100644
--- a/src/pymatgen/core/lattice.py
+++ b/src/pymatgen/core/lattice.py
@@ -16,19 +16,17 @@
 import numpy as np
 from monty.dev import deprecated
 from monty.json import MSONable
-from scipy.spatial import Voronoi
-
 from pymatgen.util.coord import pbc_shortest_vectors
 from pymatgen.util.due import Doi, due
+from scipy.spatial import Voronoi
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.operations import SymmOp
     from pymatgen.util.typing import MillerIndex, PbcLike, Vector3D
+    from typing_extensions import Self
 
 __author__ = "Shyue Ping Ong, Michael Kocher"
 __copyright__ = "Copyright 2011, The Materials Project"
diff --git a/src/pymatgen/core/operations.py b/src/pymatgen/core/operations.py
index 54f24f8515b..c67603c288f 100644
--- a/src/pymatgen/core/operations.py
+++ b/src/pymatgen/core/operations.py
@@ -10,7 +10,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.util.due import Doi, due
 from pymatgen.util.string import transformation_to_string
diff --git a/src/pymatgen/core/periodic_table.py b/src/pymatgen/core/periodic_table.py
index f26cff49a01..d1be4dd4795 100644
--- a/src/pymatgen/core/periodic_table.py
+++ b/src/pymatgen/core/periodic_table.py
@@ -17,7 +17,6 @@
 import numpy as np
 from monty.dev import deprecated
 from monty.json import MSONable
-
 from pymatgen.core.units import SUPPORTED_UNIT_NAMES, FloatWithUnit, Ha_to_eV, Length, Mass, Unit
 from pymatgen.io.core import ParseError
 from pymatgen.util.string import Stringify, formula_double_format
@@ -25,9 +24,8 @@
 if TYPE_CHECKING:
     from typing import Any, Callable, Literal
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import SpeciesLike
+    from typing_extensions import Self
 
 # Load element data from JSON file
 with open(Path(__file__).absolute().parent / "periodic_table.json", encoding="utf-8") as ptable_json:
diff --git a/src/pymatgen/core/sites.py b/src/pymatgen/core/sites.py
index a703c79a335..fd8a61118ef 100644
--- a/src/pymatgen/core/sites.py
+++ b/src/pymatgen/core/sites.py
@@ -8,7 +8,6 @@
 
 import numpy as np
 from monty.json import MontyDecoder, MontyEncoder, MSONable
-
 from pymatgen.core.composition import Composition
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.periodic_table import DummySpecies, Element, Species, get_el_sp
@@ -18,9 +17,8 @@
     from typing import Any
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.util.typing import CompositionLike, SpeciesLike, Vector3D
+    from typing_extensions import Self
 
 
 class Site(collections.abc.Hashable, MSONable):
diff --git a/src/pymatgen/core/spectrum.py b/src/pymatgen/core/spectrum.py
index 6567f3a63a2..94ade3ce43e 100644
--- a/src/pymatgen/core/spectrum.py
+++ b/src/pymatgen/core/spectrum.py
@@ -8,11 +8,10 @@
 
 import numpy as np
 from monty.json import MSONable
+from pymatgen.util.coord import get_linear_interpolated_value
 from scipy import stats
 from scipy.ndimage import convolve1d
 
-from pymatgen.util.coord import get_linear_interpolated_value
-
 if TYPE_CHECKING:
     from typing import Callable, Literal
 
diff --git a/src/pymatgen/core/structure.py b/src/pymatgen/core/structure.py
index 9886d3035d0..f0d7d477ad6 100644
--- a/src/pymatgen/core/structure.py
+++ b/src/pymatgen/core/structure.py
@@ -31,12 +31,6 @@
 from monty.json import MSONable
 from numpy import cross, eye
 from numpy.linalg import norm
-from ruamel.yaml import YAML
-from scipy.cluster.hierarchy import fcluster, linkage
-from scipy.linalg import expm, polar
-from scipy.spatial.distance import squareform
-from tabulate import tabulate
-
 from pymatgen.core.bonds import CovalentBond, get_bond_length
 from pymatgen.core.composition import Composition
 from pymatgen.core.lattice import Lattice, get_points_in_spheres
@@ -47,6 +41,11 @@
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.symmetry.maggroups import MagneticSpaceGroup
 from pymatgen.util.coord import all_distances, get_angle, lattice_points_in_supercell
+from ruamel.yaml import YAML
+from scipy.cluster.hierarchy import fcluster, linkage
+from scipy.linalg import expm, polar
+from scipy.spatial.distance import squareform
+from tabulate import tabulate
 
 if TYPE_CHECKING:
     from collections.abc import Iterable, Iterator, Sequence
@@ -59,9 +58,8 @@
     from ase.optimize.optimize import Optimizer
     from matgl.ext.ase import TrajectoryObserver
     from numpy.typing import ArrayLike, NDArray
-    from typing_extensions import Self
-
     from pymatgen.util.typing import CompositionLike, MillerIndex, PathLike, PbcLike, SpeciesLike
+    from typing_extensions import Self
 
 FileFormats = Literal["cif", "poscar", "cssr", "json", "yaml", "yml", "xsf", "mcsqs", "res", "pwmat", ""]
 StructureSources = Literal["Materials Project", "COD"]
@@ -829,7 +827,6 @@ def _relax(
         from ase.constraints import ExpCellFilter
         from ase.io import read
         from ase.optimize.optimize import Optimizer
-
         from pymatgen.io.ase import AseAtomsAdaptor
 
         opt_kwargs = opt_kwargs or {}
diff --git a/src/pymatgen/core/surface.py b/src/pymatgen/core/surface.py
index 7e8e969e405..f59d3a3cbc0 100644
--- a/src/pymatgen/core/surface.py
+++ b/src/pymatgen/core/surface.py
@@ -27,26 +27,24 @@
 
 import numpy as np
 from monty.fractions import lcm
-from scipy.cluster.hierarchy import fcluster, linkage
-from scipy.spatial.distance import squareform
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import Lattice, PeriodicSite, Structure, get_el_sp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.coord import in_coord_list
 from pymatgen.util.due import Doi, due
 from pymatgen.util.typing import Tuple3Ints
+from scipy.cluster.hierarchy import fcluster, linkage
+from scipy.spatial.distance import squareform
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Any
 
     from numpy.typing import ArrayLike, NDArray
-    from typing_extensions import Self
-
     from pymatgen.core.composition import Element, Species
     from pymatgen.symmetry.groups import CrystalSystem
     from pymatgen.util.typing import MillerIndex
+    from typing_extensions import Self
 
 __author__ = "Richard Tran, Wenhao Sun, Zihan Xu, Shyue Ping Ong"
 
diff --git a/src/pymatgen/core/tensors.py b/src/pymatgen/core/tensors.py
index cb7234cc6ed..feacea08c43 100644
--- a/src/pymatgen/core/tensors.py
+++ b/src/pymatgen/core/tensors.py
@@ -15,21 +15,19 @@
 import numpy as np
 from monty.json import MSONable
 from monty.serialization import loadfn
-from scipy.linalg import polar
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.operations import SymmOp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from scipy.linalg import polar
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Any
 
     from numpy.typing import NDArray
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 __author__ = "Joseph Montoya"
 __credits__ = "Maarten de Jong, Shyam Dwaraknath, Wei Chen, Mark Asta, Anubhav Jain, Terence Lew"
diff --git a/src/pymatgen/core/trajectory.py b/src/pymatgen/core/trajectory.py
index ad595bb0e45..1d50e2a8df5 100644
--- a/src/pymatgen/core/trajectory.py
+++ b/src/pymatgen/core/trajectory.py
@@ -13,7 +13,6 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core.structure import Composition, DummySpecies, Element, Lattice, Molecule, Species, Structure
 from pymatgen.io.ase import AseAtomsAdaptor
 
@@ -21,9 +20,8 @@
     from collections.abc import Iterator
     from typing import Any
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import Matrix3D, PathLike, SitePropsType, Vector3D
+    from typing_extensions import Self
 
 
 __author__ = "Eric Sivonxay, Shyam Dwaraknath, Mingjian Wen, Evan Spotte-Smith"
diff --git a/src/pymatgen/core/xcfunc.py b/src/pymatgen/core/xcfunc.py
index a17d9c939fb..4b2e46d7376 100644
--- a/src/pymatgen/core/xcfunc.py
+++ b/src/pymatgen/core/xcfunc.py
@@ -6,7 +6,6 @@
 
 from monty.functools import lazy_property
 from monty.json import MSONable
-
 from pymatgen.core.libxcfunc import LibxcFunc
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/electronic_structure/bandstructure.py b/src/pymatgen/electronic_structure/bandstructure.py
index 73378506807..7f6e304b51b 100644
--- a/src/pymatgen/electronic_structure/bandstructure.py
+++ b/src/pymatgen/electronic_structure/bandstructure.py
@@ -11,7 +11,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.core import Element, Lattice, Structure, get_el_sp
 from pymatgen.electronic_structure.core import Orbital, Spin
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
diff --git a/src/pymatgen/electronic_structure/boltztrap.py b/src/pymatgen/electronic_structure/boltztrap.py
index fe4d8ce2649..980ccb4f1a7 100644
--- a/src/pymatgen/electronic_structure/boltztrap.py
+++ b/src/pymatgen/electronic_structure/boltztrap.py
@@ -31,10 +31,6 @@
 from monty.dev import requires
 from monty.json import MSONable, jsanitize
 from monty.os import cd
-from scipy import constants
-from scipy.optimize import fsolve
-from scipy.spatial import distance
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.units import Energy, Length
 from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine, Kpoint
@@ -42,15 +38,17 @@
 from pymatgen.electronic_structure.dos import CompleteDos, Dos, Spin
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.symmetry.bandstructure import HighSymmKpath
+from scipy import constants
+from scipy.optimize import fsolve
+from scipy.spatial import distance
 
 if TYPE_CHECKING:
     from typing import Literal
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.sites import PeriodicSite
     from pymatgen.core.structure import Structure
+    from typing_extensions import Self
 
 __author__ = "Geoffroy Hautier, Zachary Gibbs, Francesco Ricci, Anubhav Jain"
 __copyright__ = "Copyright 2013, The Materials Project"
diff --git a/src/pymatgen/electronic_structure/boltztrap2.py b/src/pymatgen/electronic_structure/boltztrap2.py
index 13d7891629e..41b622827f9 100644
--- a/src/pymatgen/electronic_structure/boltztrap2.py
+++ b/src/pymatgen/electronic_structure/boltztrap2.py
@@ -32,8 +32,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from monty.serialization import dumpfn, loadfn
-from tqdm import tqdm
-
 from pymatgen.electronic_structure.bandstructure import BandStructure, BandStructureSymmLine, Spin
 from pymatgen.electronic_structure.boltztrap import BoltztrapError
 from pymatgen.electronic_structure.dos import CompleteDos, Dos, Orbital
@@ -41,6 +39,7 @@
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.io.vasp import Vasprun
 from pymatgen.symmetry.bandstructure import HighSymmKpath
+from tqdm import tqdm
 
 if TYPE_CHECKING:
     from pathlib import Path
diff --git a/src/pymatgen/electronic_structure/cohp.py b/src/pymatgen/electronic_structure/cohp.py
index acf4f8f45b5..2b5e9c1cd2d 100644
--- a/src/pymatgen/electronic_structure/cohp.py
+++ b/src/pymatgen/electronic_structure/cohp.py
@@ -19,8 +19,6 @@
 
 import numpy as np
 from monty.json import MSONable
-from scipy.interpolate import InterpolatedUnivariateSpline
-
 from pymatgen.core.sites import PeriodicSite
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.core import Orbital, Spin
@@ -29,15 +27,15 @@
 from pymatgen.util.coord import get_linear_interpolated_value
 from pymatgen.util.due import Doi, due
 from pymatgen.util.num import round_to_sigfigs
+from scipy.interpolate import InterpolatedUnivariateSpline
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Any, Literal
 
     from numpy.typing import NDArray
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike, SpinLike, Vector3D
+    from typing_extensions import Self
 
 __author__ = "Marco Esters, Janine George"
 __copyright__ = "Copyright 2017, The Materials Project"
diff --git a/src/pymatgen/electronic_structure/core.py b/src/pymatgen/electronic_structure/core.py
index cfac056dd42..e513ee5c62e 100644
--- a/src/pymatgen/electronic_structure/core.py
+++ b/src/pymatgen/electronic_structure/core.py
@@ -14,9 +14,8 @@
     from collections.abc import Sequence
 
     from numpy.typing import NDArray
-    from typing_extensions import Self
-
     from pymatgen.core import Lattice
+    from typing_extensions import Self
 
 
 @unique
diff --git a/src/pymatgen/electronic_structure/dos.py b/src/pymatgen/electronic_structure/dos.py
index 3f1ed3feebe..07e42c998b3 100644
--- a/src/pymatgen/electronic_structure/dos.py
+++ b/src/pymatgen/electronic_structure/dos.py
@@ -8,23 +8,21 @@
 
 import numpy as np
 from monty.json import MSONable
-from scipy.constants import value as _cd
-from scipy.ndimage import gaussian_filter1d
-from scipy.signal import hilbert
-
 from pymatgen.core import Structure, get_el_sp
 from pymatgen.core.spectrum import Spectrum
 from pymatgen.electronic_structure.core import Orbital, OrbitalType, Spin
 from pymatgen.util.coord import get_linear_interpolated_value
+from scipy.constants import value as _cd
+from scipy.ndimage import gaussian_filter1d
+from scipy.signal import hilbert
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
 
     from numpy.typing import ArrayLike, NDArray
-    from typing_extensions import Self
-
     from pymatgen.core.sites import PeriodicSite
     from pymatgen.util.typing import SpeciesLike, Tuple3Floats
+    from typing_extensions import Self
 
 
 class DOS(Spectrum):
diff --git a/src/pymatgen/electronic_structure/plotter.py b/src/pymatgen/electronic_structure/plotter.py
index d7737e80a32..65709fb4cb8 100644
--- a/src/pymatgen/electronic_structure/plotter.py
+++ b/src/pymatgen/electronic_structure/plotter.py
@@ -20,7 +20,6 @@
 from matplotlib.gridspec import GridSpec
 from monty.dev import requires
 from monty.json import jsanitize
-
 from pymatgen.core import Element
 from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine
 from pymatgen.electronic_structure.boltztrap import BoltztrapError
@@ -37,7 +36,6 @@
     from typing import Literal
 
     from numpy.typing import ArrayLike
-
     from pymatgen.electronic_structure.dos import CompleteDos, Dos
 
 logger = logging.getLogger(__name__)
diff --git a/src/pymatgen/entries/__init__.py b/src/pymatgen/entries/__init__.py
index 51e6d6cee5a..fd0471b8416 100644
--- a/src/pymatgen/entries/__init__.py
+++ b/src/pymatgen/entries/__init__.py
@@ -12,7 +12,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.core.composition import Composition
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/entries/compatibility.py b/src/pymatgen/entries/compatibility.py
index 8108b788b7b..ba2ef68dd07 100644
--- a/src/pymatgen/entries/compatibility.py
+++ b/src/pymatgen/entries/compatibility.py
@@ -15,9 +15,6 @@
 from monty.design_patterns import cached_class
 from monty.json import MSONable
 from monty.serialization import loadfn
-from tqdm import tqdm
-from uncertainties import ufloat
-
 from pymatgen.analysis.structure_analyzer import oxide_type, sulfide_type
 from pymatgen.core import SETTINGS, Composition, Element
 from pymatgen.entries.computed_entries import (
@@ -30,6 +27,8 @@
 )
 from pymatgen.io.vasp.sets import MITRelaxSet, MPRelaxSet, VaspInputSet
 from pymatgen.util.due import Doi, due
+from tqdm import tqdm
+from uncertainties import ufloat
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
diff --git a/src/pymatgen/entries/computed_entries.py b/src/pymatgen/entries/computed_entries.py
index d17eb36bbe6..b80a45f8b29 100644
--- a/src/pymatgen/entries/computed_entries.py
+++ b/src/pymatgen/entries/computed_entries.py
@@ -17,19 +17,17 @@
 
 import numpy as np
 from monty.json import MontyDecoder, MontyEncoder, MSONable
-from scipy.interpolate import interp1d
-from uncertainties import ufloat
-
 from pymatgen.core.composition import Composition
 from pymatgen.entries import Entry
 from pymatgen.util.due import Doi, due
+from scipy.interpolate import interp1d
+from uncertainties import ufloat
 
 if TYPE_CHECKING:
     from typing import Literal
 
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 __author__ = "Ryan Kingsbury, Matt McDermott, Shyue Ping Ong, Anubhav Jain"
 __copyright__ = "Copyright 2011-2020, The Materials Project"
diff --git a/src/pymatgen/entries/correction_calculator.py b/src/pymatgen/entries/correction_calculator.py
index e832a0576c0..778c3885752 100644
--- a/src/pymatgen/entries/correction_calculator.py
+++ b/src/pymatgen/entries/correction_calculator.py
@@ -10,12 +10,11 @@
 import numpy as np
 import plotly.graph_objects as go
 from monty.serialization import loadfn
-from ruamel import yaml
-from scipy.optimize import curve_fit
-
 from pymatgen.analysis.reaction_calculator import ComputedReaction
 from pymatgen.analysis.structure_analyzer import sulfide_type
 from pymatgen.core import Composition, Element
+from ruamel import yaml
+from scipy.optimize import curve_fit
 
 
 class CorrectionCalculator:
diff --git a/src/pymatgen/entries/entry_tools.py b/src/pymatgen/entries/entry_tools.py
index 6fe98612ca5..fc6eb821891 100644
--- a/src/pymatgen/entries/entry_tools.py
+++ b/src/pymatgen/entries/entry_tools.py
@@ -16,7 +16,6 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MontyDecoder, MontyEncoder, MSONable
-
 from pymatgen.analysis.phase_diagram import PDEntry
 from pymatgen.analysis.structure_matcher import SpeciesComparator, StructureMatcher
 from pymatgen.core import Composition, Element
@@ -25,10 +24,9 @@
     from collections.abc import Iterable
     from typing import Literal
 
-    from typing_extensions import Self
-
     from pymatgen.entries import Entry
     from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
+    from typing_extensions import Self
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/pymatgen/entries/exp_entries.py b/src/pymatgen/entries/exp_entries.py
index e012ed7a9fb..78adad7a6ef 100644
--- a/src/pymatgen/entries/exp_entries.py
+++ b/src/pymatgen/entries/exp_entries.py
@@ -5,7 +5,6 @@
 from typing import TYPE_CHECKING
 
 from monty.json import MSONable
-
 from pymatgen.analysis.phase_diagram import PDEntry
 from pymatgen.analysis.thermochemistry import ThermoData
 from pymatgen.core.composition import Composition
diff --git a/src/pymatgen/entries/mixing_scheme.py b/src/pymatgen/entries/mixing_scheme.py
index 8f8fb637ab5..8a4a50fb214 100644
--- a/src/pymatgen/entries/mixing_scheme.py
+++ b/src/pymatgen/entries/mixing_scheme.py
@@ -11,7 +11,6 @@
 
 import numpy as np
 import pandas as pd
-
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.entries.compatibility import (
diff --git a/src/pymatgen/ext/cod.py b/src/pymatgen/ext/cod.py
index 21983b6891f..0bc9966c2dc 100644
--- a/src/pymatgen/ext/cod.py
+++ b/src/pymatgen/ext/cod.py
@@ -34,7 +34,6 @@
 
 import requests
 from monty.dev import requires
-
 from pymatgen.core.composition import Composition
 from pymatgen.core.structure import Structure
 
diff --git a/src/pymatgen/ext/matproj.py b/src/pymatgen/ext/matproj.py
index a7c4318a440..71a4cff7a7a 100644
--- a/src/pymatgen/ext/matproj.py
+++ b/src/pymatgen/ext/matproj.py
@@ -20,7 +20,6 @@
 
 import requests
 from monty.json import MontyDecoder
-
 from pymatgen.core import SETTINGS
 from pymatgen.core import __version__ as PMG_VERSION
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
@@ -29,11 +28,10 @@
     from typing import Callable
 
     from mp_api.client import MPRester as _MPResterNew
-    from typing_extensions import Self
-
     from pymatgen.core.structure import Structure
     from pymatgen.entries.computed_entries import ComputedStructureEntry
     from pymatgen.ext.matproj_legacy import _MPResterLegacy
+    from typing_extensions import Self
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/pymatgen/ext/matproj_legacy.py b/src/pymatgen/ext/matproj_legacy.py
index 26b28e3ed42..ff3ea075ec3 100644
--- a/src/pymatgen/ext/matproj_legacy.py
+++ b/src/pymatgen/ext/matproj_legacy.py
@@ -20,9 +20,6 @@
 
 import requests
 from monty.json import MontyDecoder, MontyEncoder
-from ruamel.yaml import YAML
-from tqdm import tqdm
-
 from pymatgen.core import SETTINGS, Composition, Element, Structure
 from pymatgen.core import __version__ as PMG_VERSION
 from pymatgen.core.surface import get_symmetrically_equivalent_miller_indices
@@ -31,15 +28,16 @@
 from pymatgen.entries.exp_entries import ExpEntry
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.due import Doi, due
+from ruamel.yaml import YAML
+from tqdm import tqdm
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Any, Literal
 
-    from typing_extensions import Self
-
     from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
     from pymatgen.phonon.dos import CompletePhononDos
+    from typing_extensions import Self
 
 logger = logging.getLogger(__name__)
 MP_LOG_FILE = os.path.join(os.path.expanduser("~"), ".mprester.log.yaml")
diff --git a/src/pymatgen/ext/optimade.py b/src/pymatgen/ext/optimade.py
index 2f5c1345429..fa7e9fb3d3c 100644
--- a/src/pymatgen/ext/optimade.py
+++ b/src/pymatgen/ext/optimade.py
@@ -8,11 +8,10 @@
 from urllib.parse import urljoin, urlparse
 
 import requests
-from tqdm import tqdm
-
 from pymatgen.core import DummySpecies, Structure
 from pymatgen.util.due import Doi, due
 from pymatgen.util.provenance import StructureNL
+from tqdm import tqdm
 
 if TYPE_CHECKING:
     from typing import ClassVar
diff --git a/src/pymatgen/io/abinit/abiobjects.py b/src/pymatgen/io/abinit/abiobjects.py
index 2057f79543f..46482f44b3a 100644
--- a/src/pymatgen/io/abinit/abiobjects.py
+++ b/src/pymatgen/io/abinit/abiobjects.py
@@ -13,7 +13,6 @@
 from monty.collections import AttrDict
 from monty.design_patterns import singleton
 from monty.json import MontyDecoder, MontyEncoder, MSONable
-
 from pymatgen.core import ArrayWithUnit, Lattice, Species, Structure, units
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/io/abinit/abitimer.py b/src/pymatgen/io/abinit/abitimer.py
index 036d8ef1911..ceb86f03207 100644
--- a/src/pymatgen/io/abinit/abitimer.py
+++ b/src/pymatgen/io/abinit/abitimer.py
@@ -14,7 +14,6 @@
 import numpy as np
 import pandas as pd
 from matplotlib.gridspec import GridSpec
-
 from pymatgen.io.core import ParseError
 from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig
 
diff --git a/src/pymatgen/io/abinit/inputs.py b/src/pymatgen/io/abinit/inputs.py
index 180fabff915..1382f819d7a 100644
--- a/src/pymatgen/io/abinit/inputs.py
+++ b/src/pymatgen/io/abinit/inputs.py
@@ -18,7 +18,6 @@
 import numpy as np
 from monty.collections import AttrDict
 from monty.json import MSONable
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.abinit import abiobjects as aobj
 from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable
diff --git a/src/pymatgen/io/abinit/netcdf.py b/src/pymatgen/io/abinit/netcdf.py
index fbde8ef1477..8c7538e46c8 100644
--- a/src/pymatgen/io/abinit/netcdf.py
+++ b/src/pymatgen/io/abinit/netcdf.py
@@ -12,7 +12,6 @@
 from monty.dev import requires
 from monty.functools import lazy_property
 from monty.string import marquee
-
 from pymatgen.core.structure import Structure
 from pymatgen.core.units import ArrayWithUnit
 from pymatgen.core.xcfunc import XcFunc
diff --git a/src/pymatgen/io/abinit/pseudos.py b/src/pymatgen/io/abinit/pseudos.py
index 5a56b93e1d3..b0927fe0484 100644
--- a/src/pymatgen/io/abinit/pseudos.py
+++ b/src/pymatgen/io/abinit/pseudos.py
@@ -24,12 +24,11 @@
 from monty.itertools import iterator_from_slice
 from monty.json import MontyDecoder, MSONable
 from monty.os.path import find_exts
-from tabulate import tabulate
-
 from pymatgen.core import Element
 from pymatgen.core.xcfunc import XcFunc
 from pymatgen.io.core import ParseError
 from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig
+from tabulate import tabulate
 
 if TYPE_CHECKING:
     from collections.abc import Iterator, Sequence
@@ -37,9 +36,8 @@
 
     import matplotlib.pyplot as plt
     from numpy.typing import NDArray
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
+    from typing_extensions import Self
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/pymatgen/io/adf.py b/src/pymatgen/io/adf.py
index 865493b697f..59a3d8bfabc 100644
--- a/src/pymatgen/io/adf.py
+++ b/src/pymatgen/io/adf.py
@@ -10,7 +10,6 @@
 from monty.itertools import chunks
 from monty.json import MSONable
 from monty.serialization import zopen
-
 from pymatgen.core.structure import Molecule
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/io/aims/inputs.py b/src/pymatgen/io/aims/inputs.py
index 489de5390ec..342c01b40d0 100644
--- a/src/pymatgen/io/aims/inputs.py
+++ b/src/pymatgen/io/aims/inputs.py
@@ -17,16 +17,14 @@
 from monty.io import zopen
 from monty.json import MontyDecoder, MSONable
 from monty.os.path import zpath
-
 from pymatgen.core import SETTINGS, Element, Lattice, Molecule, Structure
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Any
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import Tuple3Floats, Tuple3Ints
+    from typing_extensions import Self
 
 __author__ = "Thomas A. R. Purcell"
 __version__ = "1.0"
diff --git a/src/pymatgen/io/aims/outputs.py b/src/pymatgen/io/aims/outputs.py
index 45f680f6d84..f6012472ac5 100644
--- a/src/pymatgen/io/aims/outputs.py
+++ b/src/pymatgen/io/aims/outputs.py
@@ -6,7 +6,6 @@
 
 import numpy as np
 from monty.json import MontyDecoder, MSONable
-
 from pymatgen.io.aims.parsers import (
     read_aims_header_info,
     read_aims_header_info_from_content,
@@ -19,10 +18,9 @@
     from pathlib import Path
     from typing import Any
 
-    from typing_extensions import Self
-
     from pymatgen.core import Molecule, Structure
     from pymatgen.util.typing import Matrix3D, Vector3D
+    from typing_extensions import Self
 
 __author__ = "Andrey Sobolev and Thomas A. R. Purcell"
 __version__ = "1.0"
diff --git a/src/pymatgen/io/aims/parsers.py b/src/pymatgen/io/aims/parsers.py
index 005a78f8aeb..3021c49279c 100644
--- a/src/pymatgen/io/aims/parsers.py
+++ b/src/pymatgen/io/aims/parsers.py
@@ -8,7 +8,6 @@
 from typing import TYPE_CHECKING, cast
 
 import numpy as np
-
 from pymatgen.core import Lattice, Molecule, Structure
 from pymatgen.core.tensors import Tensor
 from pymatgen.util.typing import Tuple3Floats
diff --git a/src/pymatgen/io/aims/sets/base.py b/src/pymatgen/io/aims/sets/base.py
index 52ceed9b182..c15385d9a2e 100644
--- a/src/pymatgen/io/aims/sets/base.py
+++ b/src/pymatgen/io/aims/sets/base.py
@@ -12,7 +12,6 @@
 
 import numpy as np
 from monty.json import MontyDecoder, MontyEncoder
-
 from pymatgen.core import Molecule, Structure
 from pymatgen.io.aims.inputs import AimsControlIn, AimsGeometryIn
 from pymatgen.io.aims.parsers import AimsParseError, read_aims_output
diff --git a/src/pymatgen/io/ase.py b/src/pymatgen/io/ase.py
index 7058a9d2eee..bae2dbc5a62 100644
--- a/src/pymatgen/io/ase.py
+++ b/src/pymatgen/io/ase.py
@@ -12,7 +12,6 @@
 
 import numpy as np
 from monty.json import MontyDecoder, MSONable, jsanitize
-
 from pymatgen.core.structure import Molecule, Structure
 
 try:
@@ -36,9 +35,8 @@ def __init__(self, *args, **kwargs):
     from typing import Any
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.structure import SiteCollection
+    from typing_extensions import Self
 
 __author__ = "Shyue Ping Ong, Andrew S. Rosen"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/src/pymatgen/io/atat.py b/src/pymatgen/io/atat.py
index 7badcab828c..98660051d6b 100644
--- a/src/pymatgen/io/atat.py
+++ b/src/pymatgen/io/atat.py
@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.core import Lattice, Structure, get_el_sp
 
 __author__ = "Matthew Horton"
diff --git a/src/pymatgen/io/babel.py b/src/pymatgen/io/babel.py
index 0d0e19871c4..a648a783831 100644
--- a/src/pymatgen/io/babel.py
+++ b/src/pymatgen/io/babel.py
@@ -11,7 +11,6 @@
 from typing import TYPE_CHECKING
 
 from monty.dev import requires
-
 from pymatgen.core.structure import IMolecule, Molecule
 
 try:
@@ -20,9 +19,8 @@
     openbabel = pybel = None
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.analysis.graphs import MoleculeGraph
+    from typing_extensions import Self
 
 
 __author__ = "Shyue Ping Ong, Qi Wang"
diff --git a/src/pymatgen/io/cif.py b/src/pymatgen/io/cif.py
index 6b0a2453a71..5020d66d83b 100644
--- a/src/pymatgen/io/cif.py
+++ b/src/pymatgen/io/cif.py
@@ -19,7 +19,6 @@
 from monty.dev import deprecated
 from monty.io import zopen
 from monty.serialization import loadfn
-
 from pymatgen.core import Composition, DummySpecies, Element, Lattice, PeriodicSite, Species, Structure, get_el_sp
 from pymatgen.core.operations import MagSymmOp, SymmOp
 from pymatgen.electronic_structure.core import Magmom
@@ -33,9 +32,8 @@
     from typing import Any
 
     from numpy.typing import NDArray
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike, Vector3D
+    from typing_extensions import Self
 
 __author__ = "Shyue Ping Ong, Will Richards, Matthew Horton"
 
diff --git a/src/pymatgen/io/common.py b/src/pymatgen/io/common.py
index 00a0cac7932..0949bf08306 100644
--- a/src/pymatgen/io/common.py
+++ b/src/pymatgen/io/common.py
@@ -11,11 +11,10 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-from scipy.interpolate import RegularGridInterpolator
-
 from pymatgen.core import Element, Site, Structure
 from pymatgen.core.units import ang_to_bohr, bohr_to_angstrom
 from pymatgen.electronic_structure.core import Spin
+from scipy.interpolate import RegularGridInterpolator
 
 if TYPE_CHECKING:
     from pathlib import Path
diff --git a/src/pymatgen/io/core.py b/src/pymatgen/io/core.py
index 1392e8a564e..c4c944706eb 100644
--- a/src/pymatgen/io/core.py
+++ b/src/pymatgen/io/core.py
@@ -37,9 +37,8 @@
 from monty.json import MSONable
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike
+    from typing_extensions import Self
 
 
 __author__ = "Ryan Kingsbury"
diff --git a/src/pymatgen/io/cp2k/inputs.py b/src/pymatgen/io/cp2k/inputs.py
index 8076e51d09c..83054d4380b 100644
--- a/src/pymatgen/io/cp2k/inputs.py
+++ b/src/pymatgen/io/cp2k/inputs.py
@@ -37,7 +37,6 @@
 from monty.dev import deprecated
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core import Element
 from pymatgen.io.cp2k.utils import chunk, postprocessor, preprocessor
 from pymatgen.io.vasp.inputs import Kpoints as VaspKpoints
@@ -48,11 +47,10 @@
     from collections.abc import Sequence
     from typing import Any, Literal
 
-    from typing_extensions import Self
-
     from pymatgen.core.lattice import Lattice
     from pymatgen.core.structure import Molecule, Structure
     from pymatgen.util.typing import Kpoint, Tuple3Ints
+    from typing_extensions import Self
 
 __author__ = "Nicholas Winner"
 __version__ = "2.0"
diff --git a/src/pymatgen/io/cp2k/outputs.py b/src/pymatgen/io/cp2k/outputs.py
index 19c63761eba..0fecc2bd98b 100644
--- a/src/pymatgen/io/cp2k/outputs.py
+++ b/src/pymatgen/io/cp2k/outputs.py
@@ -17,7 +17,6 @@
 from monty.io import zopen
 from monty.json import MSONable, jsanitize
 from monty.re import regrep
-
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.core.units import Ha_to_eV
 from pymatgen.electronic_structure.bandstructure import BandStructure, BandStructureSymmLine
diff --git a/src/pymatgen/io/cp2k/sets.py b/src/pymatgen/io/cp2k/sets.py
index d6fc950a583..9af72d01594 100644
--- a/src/pymatgen/io/cp2k/sets.py
+++ b/src/pymatgen/io/cp2k/sets.py
@@ -24,8 +24,6 @@
 import warnings
 
 import numpy as np
-from ruamel.yaml import YAML
-
 from pymatgen.core import SETTINGS
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Element, Molecule, Structure
@@ -67,6 +65,7 @@
 from pymatgen.io.cp2k.utils import get_truncated_coulomb_cutoff, get_unique_site_indices
 from pymatgen.io.vasp.inputs import Kpoints as VaspKpoints
 from pymatgen.io.vasp.inputs import KpointsSupportedModes
+from ruamel.yaml import YAML
 
 __author__ = "Nicholas Winner"
 __version__ = "2.0"
diff --git a/src/pymatgen/io/cssr.py b/src/pymatgen/io/cssr.py
index 97631f3bf28..52d02996815 100644
--- a/src/pymatgen/io/cssr.py
+++ b/src/pymatgen/io/cssr.py
@@ -6,7 +6,6 @@
 from typing import TYPE_CHECKING
 
 from monty.io import zopen
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 
diff --git a/src/pymatgen/io/exciting/inputs.py b/src/pymatgen/io/exciting/inputs.py
index 13f280c8fa0..2a61fa77184 100644
--- a/src/pymatgen/io/exciting/inputs.py
+++ b/src/pymatgen/io/exciting/inputs.py
@@ -10,7 +10,6 @@
 import scipy.constants as const
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core import Element, Lattice, Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.symmetry.bandstructure import HighSymmKpath
diff --git a/src/pymatgen/io/feff/inputs.py b/src/pymatgen/io/feff/inputs.py
index 5a3ed16ac35..52e95a14521 100644
--- a/src/pymatgen/io/feff/inputs.py
+++ b/src/pymatgen/io/feff/inputs.py
@@ -15,14 +15,13 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-from tabulate import tabulate
-
 from pymatgen.core import Element, Lattice, Molecule, Structure
 from pymatgen.io.cif import CifParser
 from pymatgen.io.core import ParseError
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.io_utils import clean_lines
 from pymatgen.util.string import str_delimited
+from tabulate import tabulate
 
 if TYPE_CHECKING:
     from typing_extensions import Self
diff --git a/src/pymatgen/io/feff/outputs.py b/src/pymatgen/io/feff/outputs.py
index 133a28c7821..4337ee78741 100644
--- a/src/pymatgen/io/feff/outputs.py
+++ b/src/pymatgen/io/feff/outputs.py
@@ -13,7 +13,6 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core import Element
 from pymatgen.electronic_structure.core import Orbital, Spin
 from pymatgen.electronic_structure.dos import CompleteDos, Dos
diff --git a/src/pymatgen/io/feff/sets.py b/src/pymatgen/io/feff/sets.py
index 55ddd7fd588..4231f1772ad 100644
--- a/src/pymatgen/io/feff/sets.py
+++ b/src/pymatgen/io/feff/sets.py
@@ -20,7 +20,6 @@
 from monty.json import MSONable
 from monty.os.path import zpath
 from monty.serialization import loadfn
-
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags
 
diff --git a/src/pymatgen/io/fiesta.py b/src/pymatgen/io/fiesta.py
index 45ad8954c72..dc75893c37a 100644
--- a/src/pymatgen/io/fiesta.py
+++ b/src/pymatgen/io/fiesta.py
@@ -17,15 +17,13 @@
 
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core.structure import Molecule
 
 if TYPE_CHECKING:
     from pathlib import Path
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import Tuple3Ints
+    from typing_extensions import Self
 
 __author__ = "ndardenne"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/src/pymatgen/io/gaussian.py b/src/pymatgen/io/gaussian.py
index ca150bab18a..36102e6c334 100644
--- a/src/pymatgen/io/gaussian.py
+++ b/src/pymatgen/io/gaussian.py
@@ -9,14 +9,13 @@
 import numpy as np
 import scipy.constants as cst
 from monty.io import zopen
-from scipy.stats import norm
-
 from pymatgen.core import Composition, Element, Molecule
 from pymatgen.core.operations import SymmOp
 from pymatgen.core.units import Ha_to_eV
 from pymatgen.electronic_structure.core import Spin
 from pymatgen.util.coord import get_angle
 from pymatgen.util.plotting import pretty_plot
+from scipy.stats import norm
 
 if TYPE_CHECKING:
     from pathlib import Path
diff --git a/src/pymatgen/io/lammps/data.py b/src/pymatgen/io/lammps/data.py
index 69d9d834853..46ac9b97765 100644
--- a/src/pymatgen/io/lammps/data.py
+++ b/src/pymatgen/io/lammps/data.py
@@ -27,20 +27,18 @@
 from monty.io import zopen
 from monty.json import MSONable
 from monty.serialization import loadfn
-from ruamel.yaml import YAML
-
 from pymatgen.core import Element, Lattice, Molecule, Structure
 from pymatgen.core.operations import SymmOp
 from pymatgen.util.io_utils import clean_lines
+from ruamel.yaml import YAML
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from typing import Any, Literal
 
-    from typing_extensions import Self
-
     from pymatgen.core.sites import Site
     from pymatgen.core.structure import SiteCollection
+    from typing_extensions import Self
 
 __author__ = "Kiran Mathew, Zhi Deng, Tingzheng Hou"
 __copyright__ = "Copyright 2018, The Materials Virtual Lab"
diff --git a/src/pymatgen/io/lammps/generators.py b/src/pymatgen/io/lammps/generators.py
index afc2f39b5dc..5e1c0a30950 100644
--- a/src/pymatgen/io/lammps/generators.py
+++ b/src/pymatgen/io/lammps/generators.py
@@ -15,7 +15,6 @@
 from string import Template
 
 from monty.io import zopen
-
 from pymatgen.core import Structure
 from pymatgen.io.core import InputGenerator
 from pymatgen.io.lammps.data import CombinedData, LammpsData
diff --git a/src/pymatgen/io/lammps/inputs.py b/src/pymatgen/io/lammps/inputs.py
index 565feea80bf..5ea8477d5fd 100644
--- a/src/pymatgen/io/lammps/inputs.py
+++ b/src/pymatgen/io/lammps/inputs.py
@@ -19,7 +19,6 @@
 from monty.dev import deprecated
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core import __version__ as CURRENT_VER
 from pymatgen.io.core import InputFile
 from pymatgen.io.lammps.data import CombinedData, LammpsData
@@ -28,9 +27,8 @@
 if TYPE_CHECKING:
     from os import PathLike
 
-    from typing_extensions import Self
-
     from pymatgen.io.core import InputSet
+    from typing_extensions import Self
 
 __author__ = "Kiran Mathew, Brandon Wood, Zhi Deng, Manas Likhit, Guillaume Brunin (Matgenix)"
 __copyright__ = "Copyright 2018, The Materials Virtual Lab"
diff --git a/src/pymatgen/io/lammps/outputs.py b/src/pymatgen/io/lammps/outputs.py
index 033a7d58b4a..b8e9688c06d 100644
--- a/src/pymatgen/io/lammps/outputs.py
+++ b/src/pymatgen/io/lammps/outputs.py
@@ -14,7 +14,6 @@
 import pandas as pd
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.io.lammps.data import LammpsBox
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/io/lammps/sets.py b/src/pymatgen/io/lammps/sets.py
index d61510f3d67..54e63afd5f2 100644
--- a/src/pymatgen/io/lammps/sets.py
+++ b/src/pymatgen/io/lammps/sets.py
@@ -18,9 +18,8 @@
 from pymatgen.io.lammps.inputs import LammpsInputFile
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike
+    from typing_extensions import Self
 
 __author__ = "Ryan Kingsbury, Guillaume Brunin (Matgenix)"
 __copyright__ = "Copyright 2021, The Materials Project"
diff --git a/src/pymatgen/io/lammps/utils.py b/src/pymatgen/io/lammps/utils.py
index 2ccca0ea2e0..cc8537d8af6 100644
--- a/src/pymatgen/io/lammps/utils.py
+++ b/src/pymatgen/io/lammps/utils.py
@@ -11,7 +11,6 @@
 import numpy as np
 from monty.dev import deprecated
 from monty.tempfile import ScratchDir
-
 from pymatgen.core.operations import SymmOp
 from pymatgen.core.structure import Molecule
 from pymatgen.io.babel import BabelMolAdaptor
diff --git a/src/pymatgen/io/lmto.py b/src/pymatgen/io/lmto.py
index 747a65ca42e..5c6057d8190 100644
--- a/src/pymatgen/io/lmto.py
+++ b/src/pymatgen/io/lmto.py
@@ -11,7 +11,6 @@
 
 import numpy as np
 from monty.io import zopen
-
 from pymatgen.core.structure import Structure
 from pymatgen.core.units import Ry_to_eV, bohr_to_angstrom
 from pymatgen.electronic_structure.core import Spin
diff --git a/src/pymatgen/io/lobster/inputs.py b/src/pymatgen/io/lobster/inputs.py
index 9eef7c654a0..f3759a38b93 100644
--- a/src/pymatgen/io/lobster/inputs.py
+++ b/src/pymatgen/io/lobster/inputs.py
@@ -22,7 +22,6 @@
 from monty.io import zopen
 from monty.json import MSONable
 from monty.serialization import loadfn
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp import Vasprun
 from pymatgen.io.vasp.inputs import Incar, Kpoints, Potcar
@@ -32,10 +31,9 @@
 if TYPE_CHECKING:
     from typing import Any, ClassVar, Literal
 
-    from typing_extensions import Self
-
     from pymatgen.core.composition import Composition
     from pymatgen.util.typing import PathLike, Tuple3Ints
+    from typing_extensions import Self
 
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
 
diff --git a/src/pymatgen/io/lobster/lobsterenv.py b/src/pymatgen/io/lobster/lobsterenv.py
index 919ea6bb678..7982b025c99 100644
--- a/src/pymatgen/io/lobster/lobsterenv.py
+++ b/src/pymatgen/io/lobster/lobsterenv.py
@@ -20,7 +20,6 @@
 
 import numpy as np
 from monty.dev import deprecated
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
 from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
@@ -32,10 +31,9 @@
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.core import Structure
     from pymatgen.core.periodic_table import Element
+    from typing_extensions import Self
 
 __author__ = "Janine George"
 __copyright__ = "Copyright 2021, The Materials Project"
diff --git a/src/pymatgen/io/lobster/outputs.py b/src/pymatgen/io/lobster/outputs.py
index 31ebe16b04d..266e42096c5 100644
--- a/src/pymatgen/io/lobster/outputs.py
+++ b/src/pymatgen/io/lobster/outputs.py
@@ -22,7 +22,6 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.bandstructure import LobsterBandStructureSymmLine
 from pymatgen.electronic_structure.core import Orbital, Spin
diff --git a/src/pymatgen/io/nwchem.py b/src/pymatgen/io/nwchem.py
index 04686e878f7..8b39dcb40e3 100644
--- a/src/pymatgen/io/nwchem.py
+++ b/src/pymatgen/io/nwchem.py
@@ -29,7 +29,6 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.analysis.excitation import ExcitationSpectrum
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.core.units import Energy, FloatWithUnit
diff --git a/src/pymatgen/io/openff.py b/src/pymatgen/io/openff.py
index 37e610409c0..bef308811d5 100644
--- a/src/pymatgen/io/openff.py
+++ b/src/pymatgen/io/openff.py
@@ -6,7 +6,6 @@
 from pathlib import Path
 
 import numpy as np
-
 import pymatgen
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender
diff --git a/src/pymatgen/io/packmol.py b/src/pymatgen/io/packmol.py
index ed159029864..d1f1f7f6c6a 100644
--- a/src/pymatgen/io/packmol.py
+++ b/src/pymatgen/io/packmol.py
@@ -26,7 +26,6 @@ class that provides a run() method for running packmol locally.
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.core import Molecule
 from pymatgen.io.core import InputGenerator, InputSet
 
diff --git a/src/pymatgen/io/phonopy.py b/src/pymatgen/io/phonopy.py
index d0d39f014e4..6e156b2e2e5 100644
--- a/src/pymatgen/io/phonopy.py
+++ b/src/pymatgen/io/phonopy.py
@@ -5,14 +5,13 @@
 import numpy as np
 from monty.dev import requires
 from monty.serialization import loadfn
-from scipy.interpolate import InterpolatedUnivariateSpline
-
 from pymatgen.core import Lattice, Structure
 from pymatgen.phonon.bandstructure import PhononBandStructure, PhononBandStructureSymmLine
 from pymatgen.phonon.dos import CompletePhononDos, PhononDos
 from pymatgen.phonon.gruneisen import GruneisenParameter, GruneisenPhononBandStructureSymmLine
 from pymatgen.phonon.thermal_displacements import ThermalDisplacementMatrices
 from pymatgen.symmetry.bandstructure import HighSymmKpath
+from scipy.interpolate import InterpolatedUnivariateSpline
 
 try:
     from phonopy import Phonopy
diff --git a/src/pymatgen/io/pwmat/inputs.py b/src/pymatgen/io/pwmat/inputs.py
index a0330270d00..1051405ffe9 100644
--- a/src/pymatgen/io/pwmat/inputs.py
+++ b/src/pymatgen/io/pwmat/inputs.py
@@ -8,14 +8,12 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core import Lattice, Structure
 from pymatgen.symmetry.kpath import KPathSeek
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike
+    from typing_extensions import Self
 
 __author__ = "Hanyu Liu"
 __email__ = "domainofbuaa@gmail.com"
diff --git a/src/pymatgen/io/pwmat/outputs.py b/src/pymatgen/io/pwmat/outputs.py
index 3daf32b57c0..0ebd966efd2 100644
--- a/src/pymatgen/io/pwmat/outputs.py
+++ b/src/pymatgen/io/pwmat/outputs.py
@@ -8,7 +8,6 @@
 import numpy as np
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.io.pwmat.inputs import ACstrExtractor, AtomConfig, LineLocator
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/io/pwscf.py b/src/pymatgen/io/pwscf.py
index 73aa43f4a55..2af861b9941 100644
--- a/src/pymatgen/io/pwscf.py
+++ b/src/pymatgen/io/pwscf.py
@@ -8,7 +8,6 @@
 
 from monty.io import zopen
 from monty.re import regrep
-
 from pymatgen.core import Element, Lattice, Structure
 from pymatgen.util.io_utils import clean_lines
 
diff --git a/src/pymatgen/io/qchem/inputs.py b/src/pymatgen/io/qchem/inputs.py
index 27f2816103e..bb20603c8bd 100644
--- a/src/pymatgen/io/qchem/inputs.py
+++ b/src/pymatgen/io/qchem/inputs.py
@@ -7,7 +7,6 @@
 from typing import TYPE_CHECKING
 
 from monty.io import zopen
-
 from pymatgen.core import Molecule
 from pymatgen.io.core import InputFile
 
diff --git a/src/pymatgen/io/qchem/outputs.py b/src/pymatgen/io/qchem/outputs.py
index c2cccd2ddc9..6db29b910ac 100644
--- a/src/pymatgen/io/qchem/outputs.py
+++ b/src/pymatgen/io/qchem/outputs.py
@@ -16,7 +16,6 @@
 import pandas as pd
 from monty.io import zopen
 from monty.json import MSONable, jsanitize
-
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.analysis.local_env import OpenBabelNN
 from pymatgen.core import Molecule
diff --git a/src/pymatgen/io/qchem/sets.py b/src/pymatgen/io/qchem/sets.py
index 1b40d49fb4c..7be1ddbc67a 100644
--- a/src/pymatgen/io/qchem/sets.py
+++ b/src/pymatgen/io/qchem/sets.py
@@ -8,7 +8,6 @@
 from typing import TYPE_CHECKING
 
 from monty.io import zopen
-
 from pymatgen.io.qchem.inputs import QCInput
 from pymatgen.io.qchem.utils import lower_and_check_unique
 
diff --git a/src/pymatgen/io/res.py b/src/pymatgen/io/res.py
index d43efbaaf00..6218392ed1e 100644
--- a/src/pymatgen/io/res.py
+++ b/src/pymatgen/io/res.py
@@ -17,7 +17,6 @@
 
 from monty.io import zopen
 from monty.json import MSONable
-
 from pymatgen.core import Element, Lattice, PeriodicSite, Structure
 from pymatgen.entries.computed_entries import ComputedStructureEntry
 from pymatgen.io.core import ParseError
@@ -28,9 +27,8 @@
     from pathlib import Path
     from typing import Any, Callable, Literal
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import Tuple3Ints, Vector3D
+    from typing_extensions import Self
 
 
 @dataclass(frozen=True)
diff --git a/src/pymatgen/io/shengbte.py b/src/pymatgen/io/shengbte.py
index bd8009d93cb..7ccdee00c23 100644
--- a/src/pymatgen/io/shengbte.py
+++ b/src/pymatgen/io/shengbte.py
@@ -8,7 +8,6 @@
 import numpy as np
 from monty.dev import requires
 from monty.json import MSONable
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp import Kpoints
 
diff --git a/src/pymatgen/io/template.py b/src/pymatgen/io/template.py
index 2ee08031ede..6103f09d105 100644
--- a/src/pymatgen/io/template.py
+++ b/src/pymatgen/io/template.py
@@ -9,7 +9,6 @@
 from typing import TYPE_CHECKING
 
 from monty.io import zopen
-
 from pymatgen.io.core import InputGenerator, InputSet
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/io/vasp/inputs.py b/src/pymatgen/io/vasp/inputs.py
index cda9ff18cf6..25572a2b1ab 100644
--- a/src/pymatgen/io/vasp/inputs.py
+++ b/src/pymatgen/io/vasp/inputs.py
@@ -31,23 +31,21 @@
 from monty.os import cd
 from monty.os.path import zpath
 from monty.serialization import dumpfn, loadfn
-from tabulate import tabulate
-
 from pymatgen.core import SETTINGS, Element, Lattice, Structure, get_el_sp
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.util.io_utils import clean_lines
 from pymatgen.util.string import str_delimited
 from pymatgen.util.typing import Kpoint, Tuple3Floats, Tuple3Ints, Vector3D
+from tabulate import tabulate
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
     from typing import Any, ClassVar, Literal
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.symmetry.bandstructure import HighSymmKpath
     from pymatgen.util.typing import PathLike
+    from typing_extensions import Self
 
 
 __author__ = "Shyue Ping Ong, Geoffroy Hautier, Rickard Armiento, Vincent L Chevrier, Stephen Dacek"
diff --git a/src/pymatgen/io/vasp/optics.py b/src/pymatgen/io/vasp/optics.py
index 9e1e1b66cf7..bc52f8ec197 100644
--- a/src/pymatgen/io/vasp/optics.py
+++ b/src/pymatgen/io/vasp/optics.py
@@ -10,16 +10,14 @@
 import scipy.constants
 import scipy.special
 from monty.json import MSONable
-from tqdm import tqdm
-
 from pymatgen.electronic_structure.core import Spin
 from pymatgen.io.vasp.outputs import Vasprun, Waveder
+from tqdm import tqdm
 
 if TYPE_CHECKING:
     from numpy.typing import ArrayLike, NDArray
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike
+    from typing_extensions import Self
 
 __author__ = "Jimmy-Xuan Shen"
 __copyright__ = "Copyright 2022, The Materials Project"
diff --git a/src/pymatgen/io/vasp/outputs.py b/src/pymatgen/io/vasp/outputs.py
index f321fdfe40a..ed9e013ecc9 100644
--- a/src/pymatgen/io/vasp/outputs.py
+++ b/src/pymatgen/io/vasp/outputs.py
@@ -24,7 +24,6 @@
 from monty.os.path import zpath
 from monty.re import regrep
 from numpy.testing import assert_allclose
-
 from pymatgen.core import Composition, Element, Lattice, Structure
 from pymatgen.core.trajectory import Trajectory
 from pymatgen.core.units import unitized
@@ -51,9 +50,8 @@
     from xml.etree.ElementTree import Element as XML_Element
 
     from numpy.typing import NDArray
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike
+    from typing_extensions import Self
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/pymatgen/io/vasp/sets.py b/src/pymatgen/io/vasp/sets.py
index 08ce0dedb18..5bc09f6d46b 100644
--- a/src/pymatgen/io/vasp/sets.py
+++ b/src/pymatgen/io/vasp/sets.py
@@ -45,7 +45,6 @@
 from monty.dev import deprecated
 from monty.json import MSONable
 from monty.serialization import loadfn
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import Element, PeriodicSite, SiteCollection, Species, Structure
 from pymatgen.io.core import InputGenerator
@@ -59,9 +58,8 @@
 if TYPE_CHECKING:
     from typing import Callable, Literal, Union
 
-    from typing_extensions import Self
-
     from pymatgen.util.typing import PathLike, Tuple3Ints, Vector3D
+    from typing_extensions import Self
 
     UserPotcarFunctional = Union[
         Literal["PBE", "PBE_52", "PBE_54", "LDA", "LDA_52", "LDA_54", "PW91", "LDA_US", "PW91_US"], None
diff --git a/src/pymatgen/io/xr.py b/src/pymatgen/io/xr.py
index 645c8a6910c..3fb644c11bd 100644
--- a/src/pymatgen/io/xr.py
+++ b/src/pymatgen/io/xr.py
@@ -15,7 +15,6 @@
 
 import numpy as np
 from monty.io import zopen
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 
diff --git a/src/pymatgen/io/xtb/outputs.py b/src/pymatgen/io/xtb/outputs.py
index 4751c251a8f..60ca8c52834 100644
--- a/src/pymatgen/io/xtb/outputs.py
+++ b/src/pymatgen/io/xtb/outputs.py
@@ -7,7 +7,6 @@
 import re
 
 from monty.json import MSONable
-
 from pymatgen.core import Molecule
 from pymatgen.io.xyz import XYZ
 
diff --git a/src/pymatgen/io/xyz.py b/src/pymatgen/io/xyz.py
index 81430321a28..28914a47010 100644
--- a/src/pymatgen/io/xyz.py
+++ b/src/pymatgen/io/xyz.py
@@ -8,7 +8,6 @@
 
 import pandas as pd
 from monty.io import zopen
-
 from pymatgen.core import Molecule, Structure
 from pymatgen.core.structure import SiteCollection
 
diff --git a/src/pymatgen/io/zeopp.py b/src/pymatgen/io/zeopp.py
index fa8299a2925..5ebee530013 100644
--- a/src/pymatgen/io/zeopp.py
+++ b/src/pymatgen/io/zeopp.py
@@ -31,7 +31,6 @@
 from monty.dev import requires
 from monty.io import zopen
 from monty.tempfile import ScratchDir
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.io.cssr import Cssr
diff --git a/src/pymatgen/phonon/bandstructure.py b/src/pymatgen/phonon/bandstructure.py
index d56ff99df89..17cb899b948 100644
--- a/src/pymatgen/phonon/bandstructure.py
+++ b/src/pymatgen/phonon/bandstructure.py
@@ -7,7 +7,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.bandstructure import Kpoint
@@ -18,9 +17,8 @@
     from typing import Any
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.util.typing import Tuple3Ints
+    from typing_extensions import Self
 
 
 def get_reasonable_repetitions(n_atoms: int) -> Tuple3Ints:
diff --git a/src/pymatgen/phonon/dos.py b/src/pymatgen/phonon/dos.py
index e4e26c192d4..0e3e0ea2296 100644
--- a/src/pymatgen/phonon/dos.py
+++ b/src/pymatgen/phonon/dos.py
@@ -8,10 +8,9 @@
 import scipy.constants as const
 from monty.functools import lazy_property
 from monty.json import MSONable
-from scipy.ndimage import gaussian_filter1d
-
 from pymatgen.core.structure import Structure
 from pymatgen.util.coord import get_linear_interpolated_value
+from scipy.ndimage import gaussian_filter1d
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
diff --git a/src/pymatgen/phonon/gruneisen.py b/src/pymatgen/phonon/gruneisen.py
index a4aee2cc443..67517b4faa7 100644
--- a/src/pymatgen/phonon/gruneisen.py
+++ b/src/pymatgen/phonon/gruneisen.py
@@ -8,13 +8,12 @@
 import scipy.constants as const
 from monty.dev import requires
 from monty.json import MSONable
-from scipy.interpolate import UnivariateSpline
-
 from pymatgen.core import Structure
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.units import amu_to_kg
 from pymatgen.phonon.bandstructure import PhononBandStructure, PhononBandStructureSymmLine
 from pymatgen.phonon.dos import PhononDos
+from scipy.interpolate import UnivariateSpline
 
 try:
     import phonopy
diff --git a/src/pymatgen/phonon/ir_spectra.py b/src/pymatgen/phonon/ir_spectra.py
index 462f4fa94b9..9626e6c5726 100644
--- a/src/pymatgen/phonon/ir_spectra.py
+++ b/src/pymatgen/phonon/ir_spectra.py
@@ -11,7 +11,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.core.spectrum import Spectrum
 from pymatgen.core.structure import Structure
 from pymatgen.util.plotting import add_fig_kwargs
diff --git a/src/pymatgen/phonon/plotter.py b/src/pymatgen/phonon/plotter.py
index 4fe7295fe15..abbd219d530 100644
--- a/src/pymatgen/phonon/plotter.py
+++ b/src/pymatgen/phonon/plotter.py
@@ -10,7 +10,6 @@
 import scipy.constants as const
 from matplotlib.collections import LineCollection
 from monty.json import jsanitize
-
 from pymatgen.electronic_structure.plotter import BSDOSPlotter, plot_brillouin_zone
 from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
 from pymatgen.phonon.gruneisen import GruneisenPhononBandStructureSymmLine
@@ -23,7 +22,6 @@
 
     from matplotlib.axes import Axes
     from matplotlib.figure import Figure
-
     from pymatgen.core import Structure
     from pymatgen.phonon.dos import PhononDos
     from pymatgen.phonon.gruneisen import GruneisenParameter
diff --git a/src/pymatgen/phonon/thermal_displacements.py b/src/pymatgen/phonon/thermal_displacements.py
index b021cbc57b3..818b5f6f911 100644
--- a/src/pymatgen/phonon/thermal_displacements.py
+++ b/src/pymatgen/phonon/thermal_displacements.py
@@ -8,7 +8,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core.structure import Structure
 from pymatgen.io.cif import CifFile, CifParser, CifWriter, str2float
diff --git a/src/pymatgen/symmetry/analyzer.py b/src/pymatgen/symmetry/analyzer.py
index 1f08b8f6904..17b29e3e69e 100644
--- a/src/pymatgen/symmetry/analyzer.py
+++ b/src/pymatgen/symmetry/analyzer.py
@@ -25,7 +25,6 @@
 import numpy as np
 import scipy.cluster
 import spglib
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.operations import SymmOp
 from pymatgen.core.structure import Molecule, PeriodicSite, Structure
diff --git a/src/pymatgen/symmetry/bandstructure.py b/src/pymatgen/symmetry/bandstructure.py
index 05d416a0fbe..c37009792e1 100644
--- a/src/pymatgen/symmetry/bandstructure.py
+++ b/src/pymatgen/symmetry/bandstructure.py
@@ -9,7 +9,6 @@
 
 import networkx as nx
 import numpy as np
-
 from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine
 from pymatgen.electronic_structure.core import Spin
 from pymatgen.symmetry.analyzer import cite_conventional_cell_algo
diff --git a/src/pymatgen/symmetry/groups.py b/src/pymatgen/symmetry/groups.py
index 3ecaf8ac1d1..a0c3e79ab87 100644
--- a/src/pymatgen/symmetry/groups.py
+++ b/src/pymatgen/symmetry/groups.py
@@ -17,19 +17,17 @@
 import numpy as np
 from monty.design_patterns import cached_class
 from monty.serialization import loadfn
-
 from pymatgen.util.string import Stringify
 
 if TYPE_CHECKING:
     from typing import ClassVar, Literal
 
     from numpy.typing import ArrayLike
-    from typing_extensions import Self
-
     from pymatgen.core.lattice import Lattice
 
     # Don't import at runtime to avoid circular import
     from pymatgen.core.operations import SymmOp  # noqa: TCH004
+    from typing_extensions import Self
 
     CrystalSystem = Literal["cubic", "hexagonal", "monoclinic", "orthorhombic", "tetragonal", "triclinic", "trigonal"]
 
diff --git a/src/pymatgen/symmetry/kpath.py b/src/pymatgen/symmetry/kpath.py
index 222dab404d3..a1983f5047d 100644
--- a/src/pymatgen/symmetry/kpath.py
+++ b/src/pymatgen/symmetry/kpath.py
@@ -12,7 +12,6 @@
 import numpy as np
 import spglib
 from monty.dev import requires
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.operations import MagSymmOp, SymmOp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer, cite_conventional_cell_algo
diff --git a/src/pymatgen/symmetry/maggroups.py b/src/pymatgen/symmetry/maggroups.py
index 33270ee8c82..1b7b72ee33a 100644
--- a/src/pymatgen/symmetry/maggroups.py
+++ b/src/pymatgen/symmetry/maggroups.py
@@ -11,7 +11,6 @@
 
 import numpy as np
 from monty.design_patterns import cached_class
-
 from pymatgen.core.operations import MagSymmOp
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.symmetry.groups import SymmetryGroup, in_array_list
@@ -21,9 +20,8 @@
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
-    from typing_extensions import Self
-
     from pymatgen.core.lattice import Lattice
+    from typing_extensions import Self
 
 __author__ = "Matthew Horton, Shyue Ping Ong"
 
diff --git a/src/pymatgen/symmetry/settings.py b/src/pymatgen/symmetry/settings.py
index 3abd7f547f3..99597c1cbe3 100644
--- a/src/pymatgen/symmetry/settings.py
+++ b/src/pymatgen/symmetry/settings.py
@@ -7,12 +7,11 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from sympy import Matrix
-from sympy.parsing.sympy_parser import parse_expr
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.operations import MagSymmOp, SymmOp
 from pymatgen.util.string import transformation_to_string
+from sympy import Matrix
+from sympy.parsing.sympy_parser import parse_expr
 
 if TYPE_CHECKING:
     from typing_extensions import Self
diff --git a/src/pymatgen/symmetry/site_symmetries.py b/src/pymatgen/symmetry/site_symmetries.py
index c73a321270a..ed889cb5f72 100644
--- a/src/pymatgen/symmetry/site_symmetries.py
+++ b/src/pymatgen/symmetry/site_symmetries.py
@@ -5,7 +5,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from pymatgen.core.operations import SymmOp
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
diff --git a/src/pymatgen/symmetry/structure.py b/src/pymatgen/symmetry/structure.py
index 22d975c9b53..093b5f8af39 100644
--- a/src/pymatgen/symmetry/structure.py
+++ b/src/pymatgen/symmetry/structure.py
@@ -5,16 +5,14 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from tabulate import tabulate
-
 from pymatgen.core.structure import PeriodicSite, Structure
+from tabulate import tabulate
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
-    from typing_extensions import Self
-
     from pymatgen.symmetry.analyzer import SpacegroupOperations
+    from typing_extensions import Self
 
 
 class SymmetrizedStructure(Structure):
diff --git a/src/pymatgen/transformations/advanced_transformations.py b/src/pymatgen/transformations/advanced_transformations.py
index fa1b209915f..57b89c43efe 100644
--- a/src/pymatgen/transformations/advanced_transformations.py
+++ b/src/pymatgen/transformations/advanced_transformations.py
@@ -16,7 +16,6 @@
 from monty.dev import requires
 from monty.fractions import lcm
 from monty.json import MSONable
-
 from pymatgen.analysis.adsorption import AdsorbateSiteFinder
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.energy_models import SymmetryModel
diff --git a/src/pymatgen/transformations/site_transformations.py b/src/pymatgen/transformations/site_transformations.py
index 220769fd0f4..7ba3151fc90 100644
--- a/src/pymatgen/transformations/site_transformations.py
+++ b/src/pymatgen/transformations/site_transformations.py
@@ -14,7 +14,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation
 from pymatgen.analysis.local_env import MinimumDistanceNN
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
diff --git a/src/pymatgen/transformations/standard_transformations.py b/src/pymatgen/transformations/standard_transformations.py
index 92bbe883da7..616c7de84a7 100644
--- a/src/pymatgen/transformations/standard_transformations.py
+++ b/src/pymatgen/transformations/standard_transformations.py
@@ -12,7 +12,6 @@
 
 import numpy as np
 from numpy import around
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.analysis.elasticity.strain import Deformation
 from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation
@@ -25,10 +24,9 @@
 from pymatgen.transformations.transformation_abc import AbstractTransformation
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
-
     from pymatgen.core.sites import PeriodicSite
     from pymatgen.util.typing import SpeciesLike
+    from typing_extensions import Self
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/pymatgen/util/coord.py b/src/pymatgen/util/coord.py
index eabbc2dadfa..e00dceb5655 100644
--- a/src/pymatgen/util/coord.py
+++ b/src/pymatgen/util/coord.py
@@ -11,7 +11,6 @@
 
 import numpy as np
 from monty.json import MSONable
-
 from pymatgen.util import coord_cython
 
 if TYPE_CHECKING:
@@ -19,7 +18,6 @@
     from typing import Literal
 
     from numpy.typing import ArrayLike
-
     from pymatgen.util.typing import PbcLike
 
 
diff --git a/src/pymatgen/util/plotting.py b/src/pymatgen/util/plotting.py
index 13958cc9b22..b94cba844e0 100644
--- a/src/pymatgen/util/plotting.py
+++ b/src/pymatgen/util/plotting.py
@@ -12,7 +12,6 @@
 import numpy as np
 import palettable.colorbrewer.diverging
 from matplotlib import cm, colors
-
 from pymatgen.core import Element
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/util/provenance.py b/src/pymatgen/util/provenance.py
index 7fcb5c54a4b..0e72704b1cc 100644
--- a/src/pymatgen/util/provenance.py
+++ b/src/pymatgen/util/provenance.py
@@ -10,7 +10,6 @@
 from typing import TYPE_CHECKING, NamedTuple
 
 from monty.json import MontyDecoder, MontyEncoder
-
 from pymatgen.core.structure import Molecule, Structure
 
 try:
diff --git a/src/pymatgen/util/testing/__init__.py b/src/pymatgen/util/testing/__init__.py
index 9ec92a8ee25..211690effa9 100644
--- a/src/pymatgen/util/testing/__init__.py
+++ b/src/pymatgen/util/testing/__init__.py
@@ -17,7 +17,6 @@
 import pytest
 from monty.json import MontyDecoder, MontyEncoder, MSONable
 from monty.serialization import loadfn
-
 from pymatgen.core import ROOT, SETTINGS, Structure
 
 if TYPE_CHECKING:
diff --git a/src/pymatgen/util/testing/aims.py b/src/pymatgen/util/testing/aims.py
index 057df663083..ce5b85525a7 100644
--- a/src/pymatgen/util/testing/aims.py
+++ b/src/pymatgen/util/testing/aims.py
@@ -10,7 +10,6 @@
 
 import numpy as np
 from monty.io import zopen
-
 from pymatgen.core import Molecule, Structure
 
 
diff --git a/src/pymatgen/vis/plotters.py b/src/pymatgen/vis/plotters.py
index 5670e24f8ae..e77d4c92ccb 100644
--- a/src/pymatgen/vis/plotters.py
+++ b/src/pymatgen/vis/plotters.py
@@ -5,7 +5,6 @@
 import importlib
 
 import matplotlib.pyplot as plt
-
 from pymatgen.util.plotting import pretty_plot
 
 
diff --git a/src/pymatgen/vis/structure_chemview.py b/src/pymatgen/vis/structure_chemview.py
index 9007bb9446f..73069535a91 100644
--- a/src/pymatgen/vis/structure_chemview.py
+++ b/src/pymatgen/vis/structure_chemview.py
@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.analysis.molecule_structure_comparator import CovalentRadius
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
diff --git a/src/pymatgen/vis/structure_vtk.py b/src/pymatgen/vis/structure_vtk.py
index c2329591744..cdb15313a80 100644
--- a/src/pymatgen/vis/structure_vtk.py
+++ b/src/pymatgen/vis/structure_vtk.py
@@ -12,7 +12,6 @@
 import numpy as np
 from monty.dev import requires
 from monty.serialization import loadfn
-
 from pymatgen.core import PeriodicSite, Species, Structure
 from pymatgen.util.coord import in_coord_list
 
diff --git a/tests/alchemy/test_filters.py b/tests/alchemy/test_filters.py
index 16737ae67fa..418213e1dd3 100644
--- a/tests/alchemy/test_filters.py
+++ b/tests/alchemy/test_filters.py
@@ -4,7 +4,6 @@
 from unittest import TestCase
 
 from monty.json import MontyDecoder
-
 from pymatgen.alchemy.filters import (
     ContainsSpecieFilter,
     RemoveDuplicatesFilter,
diff --git a/tests/alchemy/test_materials.py b/tests/alchemy/test_materials.py
index c667b27277e..0ec5c800f01 100644
--- a/tests/alchemy/test_materials.py
+++ b/tests/alchemy/test_materials.py
@@ -4,7 +4,6 @@
 from copy import deepcopy
 
 import pytest
-
 from pymatgen.alchemy.filters import ContainsSpecieFilter
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.core import SETTINGS
diff --git a/tests/analysis/chemenv/connectivity/test_connected_components.py b/tests/analysis/chemenv/connectivity/test_connected_components.py
index 2768fc5b815..dc9b01e62ea 100644
--- a/tests/analysis/chemenv/connectivity/test_connected_components.py
+++ b/tests/analysis/chemenv/connectivity/test_connected_components.py
@@ -7,7 +7,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.chemenv.connectivity.connected_components import ConnectedComponent
 from pymatgen.analysis.chemenv.connectivity.connectivity_finder import ConnectivityFinder
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
diff --git a/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py b/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py
index 631aed31b01..ef2109769e5 100644
--- a/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py
+++ b/tests/analysis/chemenv/coordination_environments/test_chemenv_strategies.py
@@ -1,8 +1,6 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AdditionalConditionInt,
     AngleCutoffFloat,
@@ -11,6 +9,7 @@
     SimplestChemenvStrategy,
 )
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 
diff --git a/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py b/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py
index 3cbda25a5fe..03a323c65e9 100644
--- a/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py
+++ b/tests/analysis/chemenv/coordination_environments/test_coordination_geometries.py
@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     AllCoordinationGeometries,
     CoordinationGeometry,
@@ -12,6 +10,7 @@
     SeparationPlane,
 )
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 
diff --git a/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py b/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py
index fc26a3c33af..2428253b876 100644
--- a/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py
+++ b/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py
@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,
@@ -13,6 +11,7 @@
 )
 from pymatgen.core.structure import Lattice, Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 
diff --git a/tests/analysis/chemenv/coordination_environments/test_read_write.py b/tests/analysis/chemenv/coordination_environments/test_read_write.py
index 42ee8b8cb91..0bb61b6163a 100644
--- a/tests/analysis/chemenv/coordination_environments/test_read_write.py
+++ b/tests/analysis/chemenv/coordination_environments/test_read_write.py
@@ -3,8 +3,6 @@
 import json
 
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,
@@ -23,6 +21,7 @@
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 
diff --git a/tests/analysis/chemenv/coordination_environments/test_structure_environments.py b/tests/analysis/chemenv/coordination_environments/test_structure_environments.py
index b9a8ec160d7..8ce3f92ec4b 100644
--- a/tests/analysis/chemenv/coordination_environments/test_structure_environments.py
+++ b/tests/analysis/chemenv/coordination_environments/test_structure_environments.py
@@ -5,8 +5,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     MultiWeightsChemenvStrategy,
     SimplestChemenvStrategy,
@@ -18,6 +16,7 @@
 )
 from pymatgen.core import Species, Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 
diff --git a/tests/analysis/chemenv/coordination_environments/test_voronoi.py b/tests/analysis/chemenv/coordination_environments/test_voronoi.py
index cfe7b6af420..2adaa1f343c 100644
--- a/tests/analysis/chemenv/coordination_environments/test_voronoi.py
+++ b/tests/analysis/chemenv/coordination_environments/test_voronoi.py
@@ -3,7 +3,6 @@
 import random
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
diff --git a/tests/analysis/chemenv/coordination_environments/test_weights.py b/tests/analysis/chemenv/coordination_environments/test_weights.py
index f4f117dbe38..5295d47c635 100644
--- a/tests/analysis/chemenv/coordination_environments/test_weights.py
+++ b/tests/analysis/chemenv/coordination_environments/test_weights.py
@@ -3,8 +3,6 @@
 import json
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,
@@ -17,6 +15,7 @@
 )
 from pymatgen.analysis.chemenv.coordination_environments.structure_environments import StructureEnvironments
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "waroquiers"
 
diff --git a/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py b/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py
index 10e8ff8eb2e..7124904f7cd 100644
--- a/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py
+++ b/tests/analysis/chemenv/utils/test_coordination_geometry_utils.py
@@ -5,10 +5,9 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "David Waroquiers"
 
diff --git a/tests/analysis/chemenv/utils/test_func_utils.py b/tests/analysis/chemenv/utils/test_func_utils.py
index 265c26d39f4..e01c3d66cc8 100644
--- a/tests/analysis/chemenv/utils/test_func_utils.py
+++ b/tests/analysis/chemenv/utils/test_func_utils.py
@@ -2,13 +2,12 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.chemenv.utils.func_utils import (
     CSMFiniteRatioFunction,
     CSMInfiniteRatioFunction,
     DeltaCSMRatioFunction,
 )
+from pytest import approx
 
 __author__ = "waroquiers"
 
diff --git a/tests/analysis/chemenv/utils/test_graph_utils.py b/tests/analysis/chemenv/utils/test_graph_utils.py
index 54ca8e9ef08..cf7ef01fa30 100644
--- a/tests/analysis/chemenv/utils/test_graph_utils.py
+++ b/tests/analysis/chemenv/utils/test_graph_utils.py
@@ -2,7 +2,6 @@
 
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
 from pymatgen.analysis.chemenv.utils.graph_utils import MultiGraphCycle, SimpleGraphCycle, get_delta
 from pymatgen.util.testing import PymatgenTest
diff --git a/tests/analysis/chemenv/utils/test_math_utils.py b/tests/analysis/chemenv/utils/test_math_utils.py
index 87420c9c61e..3b0cab7d229 100644
--- a/tests/analysis/chemenv/utils/test_math_utils.py
+++ b/tests/analysis/chemenv/utils/test_math_utils.py
@@ -2,7 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.chemenv.utils.math_utils import (
     _cartesian_product,
     cosinus_step,
diff --git a/tests/analysis/diffraction/test_neutron.py b/tests/analysis/diffraction/test_neutron.py
index f9f54d9d4fa..5256710bae1 100644
--- a/tests/analysis/diffraction/test_neutron.py
+++ b/tests/analysis/diffraction/test_neutron.py
@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.diffraction.neutron import NDCalculator
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 """
 These calculated values were verified with VESTA and FullProf.
diff --git a/tests/analysis/diffraction/test_tem.py b/tests/analysis/diffraction/test_tem.py
index 7b5a79cea67..edbe77256ca 100644
--- a/tests/analysis/diffraction/test_tem.py
+++ b/tests/analysis/diffraction/test_tem.py
@@ -6,12 +6,11 @@
 import pandas as pd
 import plotly.graph_objects as go
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.diffraction.tem import TEMCalculator
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "Frank Wan, Jason Liang"
 __copyright__ = "Copyright 2019, The Materials Project"
diff --git a/tests/analysis/diffraction/test_xrd.py b/tests/analysis/diffraction/test_xrd.py
index 9663d6fbf7d..ed4f9bcb2d2 100644
--- a/tests/analysis/diffraction/test_xrd.py
+++ b/tests/analysis/diffraction/test_xrd.py
@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.diffraction.xrd import XRDCalculator
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 """
 TODO: Modify unittest doc.
diff --git a/tests/analysis/elasticity/test_elastic.py b/tests/analysis/elasticity/test_elastic.py
index 4fe8ecdc5da..85de3ac4728 100644
--- a/tests/analysis/elasticity/test_elastic.py
+++ b/tests/analysis/elasticity/test_elastic.py
@@ -8,9 +8,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-from scipy.misc import central_diff_weights
-
 from pymatgen.analysis.elasticity.elastic import (
     ComplianceTensor,
     ElasticTensor,
@@ -29,6 +26,8 @@
 from pymatgen.core.tensors import Tensor
 from pymatgen.core.units import FloatWithUnit
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
+from scipy.misc import central_diff_weights
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/elasticity"
 
diff --git a/tests/analysis/elasticity/test_strain.py b/tests/analysis/elasticity/test_strain.py
index e64de89f18d..2ffadf975e5 100644
--- a/tests/analysis/elasticity/test_strain.py
+++ b/tests/analysis/elasticity/test_strain.py
@@ -3,7 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.elasticity.strain import Deformation, DeformedStructureSet, Strain, convert_strain_to_deformation
 from pymatgen.core.structure import Structure
 from pymatgen.core.tensors import Tensor
diff --git a/tests/analysis/elasticity/test_stress.py b/tests/analysis/elasticity/test_stress.py
index cc79322de83..66a656243ed 100644
--- a/tests/analysis/elasticity/test_stress.py
+++ b/tests/analysis/elasticity/test_stress.py
@@ -3,11 +3,10 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.elasticity.strain import Deformation
 from pymatgen.analysis.elasticity.stress import Stress
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestStress(PymatgenTest):
diff --git a/tests/analysis/ferroelectricity/test_polarization.py b/tests/analysis/ferroelectricity/test_polarization.py
index 8c5de6645fc..67f90933990 100644
--- a/tests/analysis/ferroelectricity/test_polarization.py
+++ b/tests/analysis/ferroelectricity/test_polarization.py
@@ -2,8 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.ferroelectricity.polarization import (
     EnergyTrend,
     Polarization,
@@ -14,6 +12,7 @@
 from pymatgen.io.vasp.inputs import Potcar
 from pymatgen.io.vasp.outputs import Outcar
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/vasp/fixtures/BTO_221_99_polarization"
 bto_folders = ["nonpolar_polarization"]
diff --git a/tests/analysis/interfaces/test_coherent_interface.py b/tests/analysis/interfaces/test_coherent_interface.py
index 081cc3c4b62..1284bc8c731 100644
--- a/tests/analysis/interfaces/test_coherent_interface.py
+++ b/tests/analysis/interfaces/test_coherent_interface.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.interfaces.coherent_interfaces import (
     CoherentInterfaceBuilder,
     from_2d_to_3d,
diff --git a/tests/analysis/interfaces/test_substrate_analyzer.py b/tests/analysis/interfaces/test_substrate_analyzer.py
index a842cd4dad7..39e75ea53f5 100644
--- a/tests/analysis/interfaces/test_substrate_analyzer.py
+++ b/tests/analysis/interfaces/test_substrate_analyzer.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.elasticity.elastic import ElasticTensor
 from pymatgen.analysis.interfaces.substrate_analyzer import SubstrateAnalyzer
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
diff --git a/tests/analysis/interfaces/test_zsl.py b/tests/analysis/interfaces/test_zsl.py
index 3cc7732eb73..d4fc0bdef2a 100644
--- a/tests/analysis/interfaces/test_zsl.py
+++ b/tests/analysis/interfaces/test_zsl.py
@@ -2,8 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_array_equal
-from pytest import approx
-
 from pymatgen.analysis.interfaces.zsl import (
     ZSLGenerator,
     fast_norm,
@@ -14,6 +12,7 @@
 )
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 __author__ = "Shyam Dwaraknath"
 __copyright__ = "Copyright 2016, The Materials Project"
diff --git a/tests/analysis/magnetism/test_analyzer.py b/tests/analysis/magnetism/test_analyzer.py
index bcdd02f1970..12e0f3029a6 100644
--- a/tests/analysis/magnetism/test_analyzer.py
+++ b/tests/analysis/magnetism/test_analyzer.py
@@ -6,8 +6,6 @@
 import pytest
 from monty.serialization import loadfn
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.magnetism import (
     CollinearMagneticStructureAnalyzer,
     MagneticStructureEnumerator,
@@ -16,6 +14,7 @@
 )
 from pymatgen.core import Element, Lattice, Species, Structure
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/magnetic_orderings"
 
diff --git a/tests/analysis/magnetism/test_heisenberg.py b/tests/analysis/magnetism/test_heisenberg.py
index 3eea3bd6782..968e28524ce 100644
--- a/tests/analysis/magnetism/test_heisenberg.py
+++ b/tests/analysis/magnetism/test_heisenberg.py
@@ -3,7 +3,6 @@
 from unittest import TestCase
 
 import pandas as pd
-
 from pymatgen.analysis.magnetism.heisenberg import HeisenbergMapper
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR
diff --git a/tests/analysis/magnetism/test_jahnteller.py b/tests/analysis/magnetism/test_jahnteller.py
index 6cc3356b4aa..3a5da6a5ef4 100644
--- a/tests/analysis/magnetism/test_jahnteller.py
+++ b/tests/analysis/magnetism/test_jahnteller.py
@@ -3,11 +3,10 @@
 from unittest import TestCase
 
 import numpy as np
-from pytest import approx
-
 from pymatgen.analysis.magnetism.jahnteller import JahnTellerAnalyzer, Species
 from pymatgen.core import Structure
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 
 class TestJahnTeller(TestCase):
diff --git a/tests/analysis/solar/test_slme.py b/tests/analysis/solar/test_slme.py
index 4d2e12c1ef0..906dba63bc7 100644
--- a/tests/analysis/solar/test_slme.py
+++ b/tests/analysis/solar/test_slme.py
@@ -1,9 +1,8 @@
 from __future__ import annotations
 
-from pytest import approx
-
 from pymatgen.analysis.solar.slme import optics, slme
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/solar"
 
diff --git a/tests/analysis/structure_prediction/test_dopant_predictor.py b/tests/analysis/structure_prediction/test_dopant_predictor.py
index f19d032624d..a763421b0bb 100644
--- a/tests/analysis/structure_prediction/test_dopant_predictor.py
+++ b/tests/analysis/structure_prediction/test_dopant_predictor.py
@@ -2,14 +2,13 @@
 
 from unittest import TestCase
 
-from pytest import approx
-
 from pymatgen.analysis.local_env import CrystalNN
 from pymatgen.analysis.structure_prediction.dopant_predictor import (
     get_dopants_from_shannon_radii,
     get_dopants_from_substitution_probabilities,
 )
 from pymatgen.core import Species, Structure
+from pytest import approx
 
 
 class TestDopantPrediction(TestCase):
diff --git a/tests/analysis/structure_prediction/test_substitution_probability.py b/tests/analysis/structure_prediction/test_substitution_probability.py
index e6c5f9786d0..eb9115995a3 100644
--- a/tests/analysis/structure_prediction/test_substitution_probability.py
+++ b/tests/analysis/structure_prediction/test_substitution_probability.py
@@ -3,14 +3,13 @@
 import json
 from unittest import TestCase
 
-from pytest import approx
-
 from pymatgen.analysis.structure_prediction.substitution_probability import (
     SubstitutionPredictor,
     SubstitutionProbability,
 )
 from pymatgen.core import Composition, Species
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/struct_predictor"
 
diff --git a/tests/analysis/structure_prediction/test_volume_predictor.py b/tests/analysis/structure_prediction/test_volume_predictor.py
index 9f6a150aeb7..069a9dbc86f 100644
--- a/tests/analysis/structure_prediction/test_volume_predictor.py
+++ b/tests/analysis/structure_prediction/test_volume_predictor.py
@@ -1,11 +1,10 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.structure_prediction.volume_predictor import DLSVolumePredictor, RLSVolumePredictor
 from pymatgen.core import Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/structure_prediction"
 
diff --git a/tests/analysis/test_adsorption.py b/tests/analysis/test_adsorption.py
index 9f611a2feaa..76fdc09a0cd 100644
--- a/tests/analysis/test_adsorption.py
+++ b/tests/analysis/test_adsorption.py
@@ -2,7 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.adsorption import AdsorbateSiteFinder, generate_all_slabs, get_rot, reorient_z
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Molecule, Structure
diff --git a/tests/analysis/test_bond_dissociation.py b/tests/analysis/test_bond_dissociation.py
index b29081413c9..6dd0d7f9af6 100644
--- a/tests/analysis/test_bond_dissociation.py
+++ b/tests/analysis/test_bond_dissociation.py
@@ -4,7 +4,6 @@
 
 import pytest
 from monty.serialization import loadfn
-
 from pymatgen.analysis.bond_dissociation import BondDissociationEnergies
 from pymatgen.util.testing import TEST_FILES_DIR
 
diff --git a/tests/analysis/test_bond_valence.py b/tests/analysis/test_bond_valence.py
index 8bfc158a574..5a0202e075b 100644
--- a/tests/analysis/test_bond_valence.py
+++ b/tests/analysis/test_bond_valence.py
@@ -1,11 +1,10 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.bond_valence import BVAnalyzer, calculate_bv_sum, calculate_bv_sum_unordered
 from pymatgen.core import Composition, Species, Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/bond_valence"
 
diff --git a/tests/analysis/test_chempot_diagram.py b/tests/analysis/test_chempot_diagram.py
index 648d6a5a164..5465e1d050d 100644
--- a/tests/analysis/test_chempot_diagram.py
+++ b/tests/analysis/test_chempot_diagram.py
@@ -2,8 +2,6 @@
 
 import numpy as np
 from plotly.graph_objects import Figure
-from pytest import approx
-
 from pymatgen.analysis.chempot_diagram import (
     ChemicalPotentialDiagram,
     get_2d_orthonormal_vector,
@@ -13,6 +11,7 @@
 from pymatgen.core.composition import Element
 from pymatgen.entries.entry_tools import EntrySet
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis"
 
diff --git a/tests/analysis/test_cost.py b/tests/analysis/test_cost.py
index c20bed2fd54..4aa598bc5fa 100644
--- a/tests/analysis/test_cost.py
+++ b/tests/analysis/test_cost.py
@@ -2,10 +2,9 @@
 
 from unittest import TestCase
 
-from pytest import approx
-
 from pymatgen.analysis.cost import CostAnalyzer, CostDBCSV, CostDBElements
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/cost"
 
diff --git a/tests/analysis/test_dimensionality.py b/tests/analysis/test_dimensionality.py
index 8b99c6fd5e2..b83c2cb5748 100644
--- a/tests/analysis/test_dimensionality.py
+++ b/tests/analysis/test_dimensionality.py
@@ -3,7 +3,6 @@
 import networkx as nx
 import pytest
 from monty.serialization import loadfn
-
 from pymatgen.analysis.dimensionality import (
     calculate_dimensionality_of_site,
     get_dimensionality_cheon,
diff --git a/tests/analysis/test_disorder.py b/tests/analysis/test_disorder.py
index a4b930096ac..2384bc4e296 100644
--- a/tests/analysis/test_disorder.py
+++ b/tests/analysis/test_disorder.py
@@ -1,10 +1,9 @@
 from __future__ import annotations
 
-from pytest import approx
-
 from pymatgen.analysis.disorder import get_warren_cowley_parameters
 from pymatgen.core import Element, Structure
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestOrderParameter(PymatgenTest):
diff --git a/tests/analysis/test_energy_models.py b/tests/analysis/test_energy_models.py
index 36d3024ac75..a2c4aa40612 100644
--- a/tests/analysis/test_energy_models.py
+++ b/tests/analysis/test_energy_models.py
@@ -1,12 +1,11 @@
 from __future__ import annotations
 
-from pytest import approx
-
 from pymatgen.analysis.energy_models import EwaldElectrostaticModel, IsingModel, SymmetryModel
 from pymatgen.core import Species
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 
 class TestEwaldElectrostaticModel:
diff --git a/tests/analysis/test_eos.py b/tests/analysis/test_eos.py
index 4c02d040fd4..f31c3723eb7 100644
--- a/tests/analysis/test_eos.py
+++ b/tests/analysis/test_eos.py
@@ -2,10 +2,9 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.eos import EOS, NumericalEOS
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestEOS(PymatgenTest):
diff --git a/tests/analysis/test_ewald.py b/tests/analysis/test_ewald.py
index 285152bb8fd..7ada2e539dc 100644
--- a/tests/analysis/test_ewald.py
+++ b/tests/analysis/test_ewald.py
@@ -4,11 +4,10 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.ewald import EwaldMinimizer, EwaldSummation
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import VASP_IN_DIR
+from pytest import approx
 
 
 class TestEwaldSummation(TestCase):
diff --git a/tests/analysis/test_fragmenter.py b/tests/analysis/test_fragmenter.py
index 611edcf58dd..26b2840b3ae 100644
--- a/tests/analysis/test_fragmenter.py
+++ b/tests/analysis/test_fragmenter.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import pytest
-
 from pymatgen.analysis.fragmenter import Fragmenter
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.analysis.local_env import OpenBabelNN
diff --git a/tests/analysis/test_functional_groups.py b/tests/analysis/test_functional_groups.py
index e53a62960a0..bc59a7da57d 100644
--- a/tests/analysis/test_functional_groups.py
+++ b/tests/analysis/test_functional_groups.py
@@ -3,7 +3,6 @@
 from unittest import TestCase
 
 import pytest
-
 from pymatgen.analysis.functional_groups import FunctionalGroupExtractor
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.analysis.local_env import OpenBabelNN
diff --git a/tests/analysis/test_graphs.py b/tests/analysis/test_graphs.py
index dcb8809a818..f196cde29ad 100644
--- a/tests/analysis/test_graphs.py
+++ b/tests/analysis/test_graphs.py
@@ -10,8 +10,6 @@
 import networkx.algorithms.isomorphism as iso
 import pytest
 from monty.serialization import loadfn
-from pytest import approx
-
 from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError, PeriodicSite, StructureGraph
 from pymatgen.analysis.local_env import (
     CovalentBondNN,
@@ -25,6 +23,7 @@
 from pymatgen.core import Lattice, Molecule, Site, Structure
 from pymatgen.core.structure import FunctionalGroups
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 try:
     from openbabel import openbabel
diff --git a/tests/analysis/test_hhi.py b/tests/analysis/test_hhi.py
index 105072426fb..d1c95587124 100644
--- a/tests/analysis/test_hhi.py
+++ b/tests/analysis/test_hhi.py
@@ -1,8 +1,7 @@
 from __future__ import annotations
 
-from pytest import approx
-
 from pymatgen.analysis.hhi import HHIModel
+from pytest import approx
 
 
 class TestHHIModel:
diff --git a/tests/analysis/test_interface_reactions.py b/tests/analysis/test_interface_reactions.py
index 3c47a6f9f3c..0b9665fef4f 100644
--- a/tests/analysis/test_interface_reactions.py
+++ b/tests/analysis/test_interface_reactions.py
@@ -8,13 +8,12 @@
 from numpy.testing import assert_allclose
 from pandas import DataFrame
 from plotly.graph_objects import Figure
-from scipy.spatial import ConvexHull
-
 from pymatgen.analysis.interface_reactions import GrandPotentialInterfacialReactivity, InterfacialReactivity
 from pymatgen.analysis.phase_diagram import GrandPotentialPhaseDiagram, PhaseDiagram
 from pymatgen.analysis.reaction_calculator import Reaction
 from pymatgen.core.composition import Composition, Element
 from pymatgen.entries.computed_entries import ComputedEntry
+from scipy.spatial import ConvexHull
 
 
 class TestInterfaceReaction(TestCase):
diff --git a/tests/analysis/test_local_env.py b/tests/analysis/test_local_env.py
index ed8b72c677d..1fbed74da82 100644
--- a/tests/analysis/test_local_env.py
+++ b/tests/analysis/test_local_env.py
@@ -7,8 +7,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
 from pymatgen.analysis.local_env import (
     BrunnerNNReal,
@@ -38,6 +36,7 @@
 )
 from pymatgen.core import Element, Lattice, Molecule, Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/local_env/fragmenter_files"
 
diff --git a/tests/analysis/test_molecule_matcher.py b/tests/analysis/test_molecule_matcher.py
index 485e3c75f2f..cca70ae1c2c 100644
--- a/tests/analysis/test_molecule_matcher.py
+++ b/tests/analysis/test_molecule_matcher.py
@@ -4,8 +4,6 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.molecule_matcher import (
     BruteForceOrderMatcher,
     GeneticOrderMatcher,
@@ -19,6 +17,7 @@
 from pymatgen.core.structure import Lattice, Molecule, Structure
 from pymatgen.io.xyz import XYZ
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 try:
     from openbabel import openbabel
diff --git a/tests/analysis/test_nmr.py b/tests/analysis/test_nmr.py
index 14490ec7a0c..86961996a71 100644
--- a/tests/analysis/test_nmr.py
+++ b/tests/analysis/test_nmr.py
@@ -2,10 +2,9 @@
 
 import numpy as np
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.analysis.nmr import ChemicalShielding, ElectricFieldGradient
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestChemicalShieldingNotation(PymatgenTest):
diff --git a/tests/analysis/test_phase_diagram.py b/tests/analysis/test_phase_diagram.py
index c42ca82ab6e..e05464d774d 100644
--- a/tests/analysis/test_phase_diagram.py
+++ b/tests/analysis/test_phase_diagram.py
@@ -12,8 +12,6 @@
 import pytest
 from monty.serialization import dumpfn, loadfn
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.phase_diagram import (
     CompoundPhaseDiagram,
     GrandPotentialPhaseDiagram,
@@ -32,6 +30,7 @@
 from pymatgen.entries.computed_entries import ComputedEntry
 from pymatgen.entries.entry_tools import EntrySet
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis"
 
diff --git a/tests/analysis/test_piezo.py b/tests/analysis/test_piezo.py
index 62569975053..559d1a3cc75 100644
--- a/tests/analysis/test_piezo.py
+++ b/tests/analysis/test_piezo.py
@@ -5,7 +5,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-
 from pymatgen.analysis.piezo import PiezoTensor
 from pymatgen.util.testing import PymatgenTest
 
diff --git a/tests/analysis/test_piezo_sensitivity.py b/tests/analysis/test_piezo_sensitivity.py
index eafaaddc6b4..19f2444f028 100644
--- a/tests/analysis/test_piezo_sensitivity.py
+++ b/tests/analysis/test_piezo_sensitivity.py
@@ -5,10 +5,9 @@
 import pickle
 
 import numpy as np
+import pymatgen
 import pytest
 from numpy.testing import assert_allclose
-
-import pymatgen
 from pymatgen.analysis.piezo_sensitivity import (
     BornEffectiveCharge,
     ForceConstantMatrix,
diff --git a/tests/analysis/test_pourbaix_diagram.py b/tests/analysis/test_pourbaix_diagram.py
index 3119877f33b..6ea90a801b3 100644
--- a/tests/analysis/test_pourbaix_diagram.py
+++ b/tests/analysis/test_pourbaix_diagram.py
@@ -7,13 +7,12 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from monty.serialization import dumpfn, loadfn
-from pytest import approx
-
 from pymatgen.analysis.pourbaix_diagram import IonEntry, MultiEntry, PourbaixDiagram, PourbaixEntry, PourbaixPlotter
 from pymatgen.core.composition import Composition
 from pymatgen.core.ion import Ion
 from pymatgen.entries.computed_entries import ComputedEntry
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/pourbaix_diagram"
 
diff --git a/tests/analysis/test_quasi_harmonic_debye_approx.py b/tests/analysis/test_quasi_harmonic_debye_approx.py
index 9a9aa86bce5..fce94e37d44 100644
--- a/tests/analysis/test_quasi_harmonic_debye_approx.py
+++ b/tests/analysis/test_quasi_harmonic_debye_approx.py
@@ -4,7 +4,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.eos import EOS
 from pymatgen.analysis.quasiharmonic import QuasiHarmonicDebyeApprox
 from pymatgen.core.structure import Structure
diff --git a/tests/analysis/test_quasirrho.py b/tests/analysis/test_quasirrho.py
index 63cd0015ad4..37829e37a75 100644
--- a/tests/analysis/test_quasirrho.py
+++ b/tests/analysis/test_quasirrho.py
@@ -3,7 +3,6 @@
 from unittest import TestCase
 
 import pytest
-
 from pymatgen.analysis.quasirrho import QuasiRRHO, get_avg_mom_inertia
 from pymatgen.io.gaussian import GaussianOutput
 from pymatgen.io.qchem.outputs import QCOutput
diff --git a/tests/analysis/test_reaction_calculator.py b/tests/analysis/test_reaction_calculator.py
index dcb06819574..f8584fd5549 100644
--- a/tests/analysis/test_reaction_calculator.py
+++ b/tests/analysis/test_reaction_calculator.py
@@ -6,11 +6,10 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.reaction_calculator import BalancedReaction, ComputedReaction, Reaction, ReactionError
 from pymatgen.core.composition import Composition
 from pymatgen.entries.computed_entries import ComputedEntry
+from pytest import approx
 
 
 class TestReaction:
diff --git a/tests/analysis/test_structure_analyzer.py b/tests/analysis/test_structure_analyzer.py
index 12a0c02f991..1639729a56a 100644
--- a/tests/analysis/test_structure_analyzer.py
+++ b/tests/analysis/test_structure_analyzer.py
@@ -4,8 +4,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.structure_analyzer import (
     RelaxationAnalyzer,
     VoronoiAnalyzer,
@@ -19,6 +17,7 @@
 from pymatgen.core import Element, Lattice, Structure
 from pymatgen.io.vasp.outputs import Xdatcar
 from pymatgen.util.testing import VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import approx
 
 
 class TestVoronoiAnalyzer(PymatgenTest):
diff --git a/tests/analysis/test_structure_matcher.py b/tests/analysis/test_structure_matcher.py
index c658585cf75..28707ef44de 100644
--- a/tests/analysis/test_structure_matcher.py
+++ b/tests/analysis/test_structure_matcher.py
@@ -6,8 +6,6 @@
 import pytest
 from monty.json import MontyDecoder
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.analysis.structure_matcher import (
     ElementComparator,
     FrameworkComparator,
@@ -18,6 +16,7 @@
 from pymatgen.core import Element, Lattice, Structure, SymmOp
 from pymatgen.util.coord import find_in_coord_list_pbc
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/structure_matcher"
 
diff --git a/tests/analysis/test_surface_analysis.py b/tests/analysis/test_surface_analysis.py
index 0e58a2099d5..07195437d80 100644
--- a/tests/analysis/test_surface_analysis.py
+++ b/tests/analysis/test_surface_analysis.py
@@ -3,12 +3,11 @@
 import json
 
 from numpy.testing import assert_allclose
-from pytest import approx
-from sympy import Number, Symbol
-
 from pymatgen.analysis.surface_analysis import NanoscaleStability, SlabEntry, SurfaceEnergyPlotter, WorkFunctionAnalyzer
 from pymatgen.entries.computed_entries import ComputedStructureEntry
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
+from sympy import Number, Symbol
 
 __author__ = "Richard Tran"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/tests/analysis/test_transition_state.py b/tests/analysis/test_transition_state.py
index 96841bc482a..0e404e02fc8 100644
--- a/tests/analysis/test_transition_state.py
+++ b/tests/analysis/test_transition_state.py
@@ -4,7 +4,6 @@
 
 from matplotlib import pyplot as plt
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.transition_state import NEBAnalysis, combine_neb_plots
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
diff --git a/tests/analysis/test_wulff.py b/tests/analysis/test_wulff.py
index 11109c1e746..c4656a79097 100644
--- a/tests/analysis/test_wulff.py
+++ b/tests/analysis/test_wulff.py
@@ -2,14 +2,13 @@
 
 import json
 
-from pytest import approx
-
 from pymatgen.analysis.wulff import WulffShape
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.coord import in_coord_list
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "Zihan Xu, Richard Tran, Balachandran Radhakrishnan"
 __copyright__ = "Copyright 2013, The Materials Virtual Lab"
diff --git a/tests/analysis/topological/test_spillage.py b/tests/analysis/topological/test_spillage.py
index 39224cdfc52..61652c97696 100644
--- a/tests/analysis/topological/test_spillage.py
+++ b/tests/analysis/topological/test_spillage.py
@@ -1,9 +1,8 @@
 from __future__ import annotations
 
-from pytest import approx
-
 from pymatgen.analysis.topological.spillage import SOCSpillage
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/topological"
 
diff --git a/tests/analysis/xas/test_spectrum.py b/tests/analysis/xas/test_spectrum.py
index ccc1c3812a5..25772d15fb7 100644
--- a/tests/analysis/xas/test_spectrum.py
+++ b/tests/analysis/xas/test_spectrum.py
@@ -6,11 +6,10 @@
 import pytest
 from monty.json import MontyDecoder
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.analysis.xas.spectrum import XAS, site_weighted_spectrum
 from pymatgen.core import Element
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/spectrum_test"
 
diff --git a/tests/apps/battery/test_analyzer.py b/tests/apps/battery/test_analyzer.py
index 61426c65510..a7a22ccf015 100644
--- a/tests/apps/battery/test_analyzer.py
+++ b/tests/apps/battery/test_analyzer.py
@@ -1,11 +1,10 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.apps.battery.analyzer import BatteryAnalyzer
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 
 class TestBatteryAnalyzer(PymatgenTest):
diff --git a/tests/apps/battery/test_conversion_battery.py b/tests/apps/battery/test_conversion_battery.py
index ae17c969353..041702625a4 100644
--- a/tests/apps/battery/test_conversion_battery.py
+++ b/tests/apps/battery/test_conversion_battery.py
@@ -4,11 +4,10 @@
 from unittest import TestCase
 
 from monty.json import MontyDecoder
-from pytest import approx
-
 from pymatgen.apps.battery.conversion_battery import ConversionElectrode, ConversionVoltagePair
 from pymatgen.core.composition import Composition
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/apps/battery"
 
diff --git a/tests/apps/battery/test_insertion_battery.py b/tests/apps/battery/test_insertion_battery.py
index 4c6b9caa951..06c6ef0802f 100644
--- a/tests/apps/battery/test_insertion_battery.py
+++ b/tests/apps/battery/test_insertion_battery.py
@@ -4,11 +4,10 @@
 from unittest import TestCase
 
 from monty.json import MontyDecoder, MontyEncoder
-from pytest import approx
-
 from pymatgen.apps.battery.insertion_battery import InsertionElectrode, InsertionVoltagePair
 from pymatgen.entries.computed_entries import ComputedEntry
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/apps/battery"
 
diff --git a/tests/apps/battery/test_plotter.py b/tests/apps/battery/test_plotter.py
index 8b93b20f8bf..c9e14875e25 100644
--- a/tests/apps/battery/test_plotter.py
+++ b/tests/apps/battery/test_plotter.py
@@ -4,7 +4,6 @@
 from unittest import TestCase
 
 from monty.json import MontyDecoder
-
 from pymatgen.apps.battery.conversion_battery import ConversionElectrode
 from pymatgen.apps.battery.insertion_battery import InsertionElectrode
 from pymatgen.apps.battery.plotter import VoltageProfilePlotter
diff --git a/tests/apps/borg/test_hive.py b/tests/apps/borg/test_hive.py
index 766086d429b..64b64814c70 100644
--- a/tests/apps/borg/test_hive.py
+++ b/tests/apps/borg/test_hive.py
@@ -3,8 +3,6 @@
 import os
 from unittest import TestCase
 
-from pytest import approx
-
 from pymatgen.apps.borg.hive import (
     GaussianToComputedEntryDrone,
     SimpleVaspToComputedEntryDrone,
@@ -12,6 +10,7 @@
 )
 from pymatgen.entries.computed_entries import ComputedStructureEntry
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/apps/borg"
 
diff --git a/tests/apps/borg/test_queen.py b/tests/apps/borg/test_queen.py
index b95e660f7f8..14cc20679a9 100644
--- a/tests/apps/borg/test_queen.py
+++ b/tests/apps/borg/test_queen.py
@@ -1,10 +1,9 @@
 from __future__ import annotations
 
-from pytest import approx
-
 from pymatgen.apps.borg.hive import VaspToComputedEntryDrone
 from pymatgen.apps.borg.queen import BorgQueen
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/tests/command_line/test_bader_caller.py b/tests/command_line/test_bader_caller.py
index c3d9b609946..5bff1599c62 100644
--- a/tests/command_line/test_bader_caller.py
+++ b/tests/command_line/test_bader_caller.py
@@ -8,10 +8,9 @@
 import pytest
 from monty.shutil import copy_r
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.command_line.bader_caller import BaderAnalysis, bader_analysis_from_path
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/command_line/bader"
 
diff --git a/tests/command_line/test_critic2_caller.py b/tests/command_line/test_critic2_caller.py
index 46218f94e8c..4f1a7cf648f 100644
--- a/tests/command_line/test_critic2_caller.py
+++ b/tests/command_line/test_critic2_caller.py
@@ -4,11 +4,10 @@
 from unittest import TestCase
 
 import pytest
-from pytest import approx
-
 from pymatgen.command_line.critic2_caller import Critic2Analysis, Critic2Caller
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 __author__ = "Matthew Horton"
 __version__ = "0.1"
diff --git a/tests/command_line/test_enumlib_caller.py b/tests/command_line/test_enumlib_caller.py
index 010bb0bd1b8..d21b5b67986 100644
--- a/tests/command_line/test_enumlib_caller.py
+++ b/tests/command_line/test_enumlib_caller.py
@@ -5,14 +5,13 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.command_line.enumlib_caller import EnumError, EnumlibAdaptor
 from pymatgen.core import Element, Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.transformations.site_transformations import RemoveSitesTransformation
 from pymatgen.transformations.standard_transformations import SubstitutionTransformation
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 enum_cmd = which("enum.x") or which("multienum.x")
 makestr_cmd = which("makestr.x") or which("makeStr.x") or which("makeStr.py")
diff --git a/tests/command_line/test_gulp_caller.py b/tests/command_line/test_gulp_caller.py
index 054d0e7c023..aa0faf1d16e 100644
--- a/tests/command_line/test_gulp_caller.py
+++ b/tests/command_line/test_gulp_caller.py
@@ -14,7 +14,6 @@
 
 import numpy as np
 import pytest
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.command_line.gulp_caller import (
     BuckinghamPotential,
diff --git a/tests/command_line/test_mcsqs_caller.py b/tests/command_line/test_mcsqs_caller.py
index 39714b1f4f1..9dd6303a1dc 100644
--- a/tests/command_line/test_mcsqs_caller.py
+++ b/tests/command_line/test_mcsqs_caller.py
@@ -4,7 +4,6 @@
 
 import pytest
 from monty.serialization import loadfn
-
 from pymatgen.command_line.mcsqs_caller import run_mcsqs
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
diff --git a/tests/command_line/test_vampire_caller.py b/tests/command_line/test_vampire_caller.py
index 19efe2eef1f..e8cc2330f02 100644
--- a/tests/command_line/test_vampire_caller.py
+++ b/tests/command_line/test_vampire_caller.py
@@ -4,11 +4,10 @@
 
 import pandas as pd
 import pytest
-from pytest import approx
-
 from pymatgen.command_line.vampire_caller import VampireCaller
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/magnetic_orderings"
 
diff --git a/tests/core/test_bonds.py b/tests/core/test_bonds.py
index 777d938619a..9154207aba6 100644
--- a/tests/core/test_bonds.py
+++ b/tests/core/test_bonds.py
@@ -1,10 +1,9 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.core import Element, Site
 from pymatgen.core.bonds import CovalentBond, get_bond_length, get_bond_order, obtain_all_bond_lengths
+from pytest import approx
 
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
diff --git a/tests/core/test_composition.py b/tests/core/test_composition.py
index f520438c15b..1cf2c688e31 100644
--- a/tests/core/test_composition.py
+++ b/tests/core/test_composition.py
@@ -10,11 +10,10 @@
 
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core import Composition, DummySpecies, Element, Species
 from pymatgen.core.composition import ChemicalPotential
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestComposition(PymatgenTest):
diff --git a/tests/core/test_interface.py b/tests/core/test_interface.py
index 22cd178dd5b..1757265fd27 100644
--- a/tests/core/test_interface.py
+++ b/tests/core/test_interface.py
@@ -2,13 +2,12 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core.interface import GrainBoundary, GrainBoundaryGenerator, Interface
 from pymatgen.core.structure import Structure
 from pymatgen.core.surface import SlabGenerator
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/core/grain_boundary"
 
diff --git a/tests/core/test_ion.py b/tests/core/test_ion.py
index 16037ec35be..f501287ed6d 100644
--- a/tests/core/test_ion.py
+++ b/tests/core/test_ion.py
@@ -4,7 +4,6 @@
 from unittest import TestCase
 
 import pytest
-
 from pymatgen.core import Composition, Element
 from pymatgen.core.ion import Ion
 
diff --git a/tests/core/test_lattice.py b/tests/core/test_lattice.py
index ce5cff053aa..91a84688039 100644
--- a/tests/core/test_lattice.py
+++ b/tests/core/test_lattice.py
@@ -5,11 +5,10 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.core.lattice import Lattice, get_points_in_spheres
 from pymatgen.core.operations import SymmOp
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestLattice(PymatgenTest):
diff --git a/tests/core/test_molecular_orbitals.py b/tests/core/test_molecular_orbitals.py
index 4476c856d17..a1699967585 100644
--- a/tests/core/test_molecular_orbitals.py
+++ b/tests/core/test_molecular_orbitals.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import pytest
-
 from pymatgen.core.molecular_orbitals import MolecularOrbitals
 from pymatgen.util.testing import PymatgenTest
 
diff --git a/tests/core/test_operations.py b/tests/core/test_operations.py
index d2dcc26de42..abd9d4357a6 100644
--- a/tests/core/test_operations.py
+++ b/tests/core/test_operations.py
@@ -2,7 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-
 from pymatgen.core.operations import MagSymmOp, SymmOp
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.util.testing import PymatgenTest
diff --git a/tests/core/test_periodic_table.py b/tests/core/test_periodic_table.py
index 90cfdc11eaf..a0ffe06fead 100644
--- a/tests/core/test_periodic_table.py
+++ b/tests/core/test_periodic_table.py
@@ -8,13 +8,12 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.core import DummySpecies, Element, Species, get_el_sp
 from pymatgen.core.periodic_table import ElementBase, ElementType
 from pymatgen.core.units import Ha_to_eV
 from pymatgen.io.core import ParseError
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestElement(PymatgenTest):
diff --git a/tests/core/test_sites.py b/tests/core/test_sites.py
index a80689d9dfd..ee3911c29eb 100644
--- a/tests/core/test_sites.py
+++ b/tests/core/test_sites.py
@@ -5,11 +5,10 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core import Composition, Element, Lattice, PeriodicSite, Site, Species
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 class TestSite(PymatgenTest):
diff --git a/tests/core/test_spectrum.py b/tests/core/test_spectrum.py
index 86fb7e7266b..9f6fe473eba 100644
--- a/tests/core/test_spectrum.py
+++ b/tests/core/test_spectrum.py
@@ -2,11 +2,10 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-from scipy import stats
-
 from pymatgen.core.spectrum import Spectrum
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
+from scipy import stats
 
 
 class TestSpectrum(PymatgenTest):
diff --git a/tests/core/test_structure.py b/tests/core/test_structure.py
index e1d911ad40c..ded309c74aa 100644
--- a/tests/core/test_structure.py
+++ b/tests/core/test_structure.py
@@ -12,8 +12,6 @@
 import pytest
 from monty.json import MontyDecoder, MontyEncoder
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.core import SETTINGS, Composition, Element, Lattice, Species
 from pymatgen.core.operations import SymmOp
 from pymatgen.core.structure import (
@@ -30,6 +28,7 @@
 from pymatgen.io.cif import CifParser
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
+from pytest import approx
 
 try:
     from ase.atoms import Atoms
diff --git a/tests/core/test_surface.py b/tests/core/test_surface.py
index 8548e13d74e..7c386a2c7e2 100644
--- a/tests/core/test_surface.py
+++ b/tests/core/test_surface.py
@@ -6,10 +6,8 @@
 import unittest
 
 import numpy as np
-from numpy.testing import assert_allclose
-from pytest import approx
-
 import pymatgen
+from numpy.testing import assert_allclose
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import Lattice, Structure
 from pymatgen.core.surface import (
@@ -26,6 +24,7 @@
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.symmetry.groups import SpaceGroup
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 
 class TestSlab(PymatgenTest):
diff --git a/tests/core/test_tensors.py b/tests/core/test_tensors.py
index 28548c3c3ba..0be6d488207 100644
--- a/tests/core/test_tensors.py
+++ b/tests/core/test_tensors.py
@@ -6,12 +6,11 @@
 import pytest
 from monty.serialization import MontyDecoder, loadfn
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core.operations import SymmOp
 from pymatgen.core.tensors import SquareTensor, Tensor, TensorCollection, TensorMapping, itertools, symmetry_reduce
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 
 class TestTensor(PymatgenTest):
diff --git a/tests/core/test_trajectory.py b/tests/core/test_trajectory.py
index 444b476c66b..f767412e7c8 100644
--- a/tests/core/test_trajectory.py
+++ b/tests/core/test_trajectory.py
@@ -6,7 +6,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.core.trajectory import Trajectory
diff --git a/tests/core/test_units.py b/tests/core/test_units.py
index 2abfd5df8f0..f2c2881b189 100644
--- a/tests/core/test_units.py
+++ b/tests/core/test_units.py
@@ -4,8 +4,6 @@
 
 import pytest
 from numpy.testing import assert_array_equal
-from pytest import approx
-
 from pymatgen.core.units import (
     ArrayWithUnit,
     Energy,
@@ -27,6 +25,7 @@
     unitized,
 )
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 
 def test_unit_conversions():
diff --git a/tests/core/test_xcfunc.py b/tests/core/test_xcfunc.py
index 1cc64bbebc8..8eba2c2dcc8 100644
--- a/tests/core/test_xcfunc.py
+++ b/tests/core/test_xcfunc.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import pytest
-
 from pymatgen.core.xcfunc import XcFunc
 from pymatgen.util.testing import PymatgenTest
 
diff --git a/tests/electronic_structure/test_bandstructure.py b/tests/electronic_structure/test_bandstructure.py
index a6d9d9dfc41..0daa57fcab2 100644
--- a/tests/electronic_structure/test_bandstructure.py
+++ b/tests/electronic_structure/test_bandstructure.py
@@ -8,8 +8,6 @@
 import pytest
 from monty.serialization import loadfn
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.electronic_structure.bandstructure import (
     BandStructureSymmLine,
@@ -21,6 +19,7 @@
 from pymatgen.electronic_structure.plotter import BSPlotterProjected
 from pymatgen.io.vasp import BSVasprun
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/bandstructure"
 
diff --git a/tests/electronic_structure/test_boltztrap.py b/tests/electronic_structure/test_boltztrap.py
index 4d1637dd56d..8bdb69a5e19 100644
--- a/tests/electronic_structure/test_boltztrap.py
+++ b/tests/electronic_structure/test_boltztrap.py
@@ -6,12 +6,11 @@
 
 import pytest
 from monty.serialization import loadfn
-from pytest import approx
-
 from pymatgen.electronic_structure.bandstructure import BandStructure
 from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer, BoltztrapRunner
 from pymatgen.electronic_structure.core import OrbitalType, Spin
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 try:
     from ase.io.cube import read_cube
diff --git a/tests/electronic_structure/test_boltztrap2.py b/tests/electronic_structure/test_boltztrap2.py
index 35926215e2e..b8660fbe61d 100644
--- a/tests/electronic_structure/test_boltztrap2.py
+++ b/tests/electronic_structure/test_boltztrap2.py
@@ -5,11 +5,10 @@
 import numpy as np
 import pytest
 from monty.serialization import loadfn
-from pytest import approx
-
 from pymatgen.electronic_structure.core import OrbitalType, Spin
 from pymatgen.io.vasp import Vasprun
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 try:
     from pymatgen.electronic_structure.boltztrap2 import (
diff --git a/tests/electronic_structure/test_cohp.py b/tests/electronic_structure/test_cohp.py
index 2f9f827ba8b..2b44b6eca1b 100644
--- a/tests/electronic_structure/test_cohp.py
+++ b/tests/electronic_structure/test_cohp.py
@@ -5,8 +5,6 @@
 
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.electronic_structure.cohp import (
     Cohp,
     CompleteCohp,
@@ -16,6 +14,7 @@
 )
 from pymatgen.electronic_structure.core import Orbital, Spin
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/cohp"
 
diff --git a/tests/electronic_structure/test_core.py b/tests/electronic_structure/test_core.py
index 2abad986cc4..243d1bef73b 100644
--- a/tests/electronic_structure/test_core.py
+++ b/tests/electronic_structure/test_core.py
@@ -3,7 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.core import Lattice
 from pymatgen.electronic_structure.core import Magmom, Orbital, Spin
 
diff --git a/tests/electronic_structure/test_dos.py b/tests/electronic_structure/test_dos.py
index c69cbcc54ba..e515f0411c4 100644
--- a/tests/electronic_structure/test_dos.py
+++ b/tests/electronic_structure/test_dos.py
@@ -8,12 +8,11 @@
 from monty.io import zopen
 from monty.serialization import loadfn
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core import Element, Structure
 from pymatgen.electronic_structure.core import Orbital, OrbitalType, Spin
 from pymatgen.electronic_structure.dos import DOS, CompleteDos, FermiDos, LobsterCompleteDos
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/dos"
 
diff --git a/tests/electronic_structure/test_plotter.py b/tests/electronic_structure/test_plotter.py
index 9728bc8d5d4..304c7216083 100644
--- a/tests/electronic_structure/test_plotter.py
+++ b/tests/electronic_structure/test_plotter.py
@@ -10,8 +10,6 @@
 import pytest
 from matplotlib import rc
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine
 from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer
@@ -31,6 +29,7 @@
 )
 from pymatgen.io.vasp import Vasprun
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import approx
 
 BAND_TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/bandstructure"
 
diff --git a/tests/entries/test_compatibility.py b/tests/entries/test_compatibility.py
index 850a4234d69..7eeea95e918 100644
--- a/tests/entries/test_compatibility.py
+++ b/tests/entries/test_compatibility.py
@@ -9,11 +9,9 @@
 from typing import TYPE_CHECKING
 from unittest import TestCase
 
+import pymatgen
 import pytest
 from monty.json import MontyDecoder
-from pytest import approx
-
-import pymatgen
 from pymatgen.core import Element, Species
 from pymatgen.core.composition import Composition
 from pymatgen.core.lattice import Lattice
@@ -34,6 +32,7 @@
 )
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry, ConstantEnergyAdjustment
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 if TYPE_CHECKING:
     from pymatgen.util.typing import CompositionLike
diff --git a/tests/entries/test_computed_entries.py b/tests/entries/test_computed_entries.py
index aee3aade715..a7a00c7f88c 100644
--- a/tests/entries/test_computed_entries.py
+++ b/tests/entries/test_computed_entries.py
@@ -7,8 +7,6 @@
 
 import pytest
 from monty.json import MontyDecoder
-from pytest import approx
-
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
 from pymatgen.entries.computed_entries import (
@@ -23,6 +21,7 @@
 )
 from pymatgen.io.vasp.outputs import Vasprun
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_OUT_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/entries"
 
diff --git a/tests/entries/test_correction_calculator.py b/tests/entries/test_correction_calculator.py
index 02d0fb517a8..c5b8f90a657 100644
--- a/tests/entries/test_correction_calculator.py
+++ b/tests/entries/test_correction_calculator.py
@@ -3,7 +3,6 @@
 from unittest import TestCase
 
 import pytest
-
 from pymatgen.entries.correction_calculator import CorrectionCalculator
 from pymatgen.util.testing import TEST_FILES_DIR
 
diff --git a/tests/entries/test_entry_tools.py b/tests/entries/test_entry_tools.py
index 01f4255d8ff..a939dd4106e 100644
--- a/tests/entries/test_entry_tools.py
+++ b/tests/entries/test_entry_tools.py
@@ -4,7 +4,6 @@
 
 import pytest
 from monty.serialization import dumpfn, loadfn
-
 from pymatgen.core import Element
 from pymatgen.entries.computed_entries import ComputedEntry
 from pymatgen.entries.entry_tools import EntrySet, group_entries_by_composition, group_entries_by_structure
diff --git a/tests/entries/test_exp_entries.py b/tests/entries/test_exp_entries.py
index b73be4ad8a4..4ebb14d9d70 100644
--- a/tests/entries/test_exp_entries.py
+++ b/tests/entries/test_exp_entries.py
@@ -4,10 +4,9 @@
 from unittest import TestCase
 
 from monty.json import MontyDecoder
-from pytest import approx
-
 from pymatgen.entries.exp_entries import ExpEntry
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 
 class TestExpEntry(TestCase):
diff --git a/tests/entries/test_mixing_scheme.py b/tests/entries/test_mixing_scheme.py
index 860ab42a0e7..33d71c5a5b8 100644
--- a/tests/entries/test_mixing_scheme.py
+++ b/tests/entries/test_mixing_scheme.py
@@ -108,7 +108,6 @@
 import pytest
 from monty.json import MontyDecoder
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core.lattice import Lattice
diff --git a/tests/ext/test_cod.py b/tests/ext/test_cod.py
index 9a3164d03d0..e2bc6ba9143 100644
--- a/tests/ext/test_cod.py
+++ b/tests/ext/test_cod.py
@@ -6,7 +6,6 @@
 
 import pytest
 import requests
-
 from pymatgen.ext.cod import COD
 
 if "CI" in os.environ:  # test is slow and flaky, skip in CI. see
diff --git a/tests/ext/test_matproj.py b/tests/ext/test_matproj.py
index ec5ee928620..8489cf438c3 100644
--- a/tests/ext/test_matproj.py
+++ b/tests/ext/test_matproj.py
@@ -7,9 +7,6 @@
 import pytest
 import requests
 from numpy.testing import assert_allclose
-from pytest import approx
-from ruamel.yaml import YAML
-
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixEntry
 from pymatgen.analysis.reaction_calculator import Reaction
@@ -24,6 +21,8 @@
 from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
 from pymatgen.phonon.dos import CompletePhononDos
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
+from ruamel.yaml import YAML
 
 try:
     skip_mprester_tests = requests.get("https://materialsproject.org", timeout=600).status_code != 200
diff --git a/tests/ext/test_optimade.py b/tests/ext/test_optimade.py
index ea351acb8c7..2af457c38af 100644
--- a/tests/ext/test_optimade.py
+++ b/tests/ext/test_optimade.py
@@ -2,7 +2,6 @@
 
 import pytest
 import requests
-
 from pymatgen.ext.optimade import OptimadeRester
 from pymatgen.util.testing import PymatgenTest
 
diff --git a/tests/io/abinit/test_abiobjects.py b/tests/io/abinit/test_abiobjects.py
index 8bbfa3a7441..5dcbff0b26d 100644
--- a/tests/io/abinit/test_abiobjects.py
+++ b/tests/io/abinit/test_abiobjects.py
@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.core.structure import Structure
 from pymatgen.core.units import Ha_to_eV, bohr_to_ang
 from pymatgen.io.abinit.abiobjects import (
@@ -20,6 +18,7 @@
     structure_to_abivars,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 
 class TestLatticeFromAbivars(PymatgenTest):
diff --git a/tests/io/abinit/test_inputs.py b/tests/io/abinit/test_inputs.py
index 6becf8953f8..287bfa68401 100644
--- a/tests/io/abinit/test_inputs.py
+++ b/tests/io/abinit/test_inputs.py
@@ -6,7 +6,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_array_equal
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.abinit.inputs import (
     BasicAbinitInput,
diff --git a/tests/io/abinit/test_netcdf.py b/tests/io/abinit/test_netcdf.py
index cd01b0e4b90..45f3343315c 100644
--- a/tests/io/abinit/test_netcdf.py
+++ b/tests/io/abinit/test_netcdf.py
@@ -3,7 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.abinit import EtsfReader
 from pymatgen.io.abinit.netcdf import AbinitHeader
diff --git a/tests/io/abinit/test_pseudos.py b/tests/io/abinit/test_pseudos.py
index 66b9e22f10e..28a48cfcf1e 100644
--- a/tests/io/abinit/test_pseudos.py
+++ b/tests/io/abinit/test_pseudos.py
@@ -4,10 +4,9 @@
 from collections import defaultdict
 
 import pytest
-from pytest import approx
-
 from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/abinit"
 
diff --git a/tests/io/aims/conftest.py b/tests/io/aims/conftest.py
index 5060ba4b259..177aeb38001 100644
--- a/tests/io/aims/conftest.py
+++ b/tests/io/aims/conftest.py
@@ -3,7 +3,6 @@
 import os
 
 import pytest
-
 from pymatgen.core import SETTINGS
 
 module_dir = os.path.dirname(__file__)
diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py
index d39baafd277..5ded1722eaf 100644
--- a/tests/io/aims/test_aims_inputs.py
+++ b/tests/io/aims/test_aims_inputs.py
@@ -8,7 +8,6 @@
 import pytest
 from monty.json import MontyDecoder, MontyEncoder
 from numpy.testing import assert_allclose
-
 from pymatgen.core import SETTINGS
 from pymatgen.io.aims.inputs import (
     ALLOWED_AIMS_CUBE_TYPES,
diff --git a/tests/io/aims/test_aims_outputs.py b/tests/io/aims/test_aims_outputs.py
index deb0554f658..1d675dad2a3 100644
--- a/tests/io/aims/test_aims_outputs.py
+++ b/tests/io/aims/test_aims_outputs.py
@@ -6,7 +6,6 @@
 
 from monty.json import MontyDecoder, MontyEncoder
 from numpy.testing import assert_allclose
-
 from pymatgen.core import Structure
 from pymatgen.io.aims.outputs import AimsOutput
 
diff --git a/tests/io/aims/test_aims_parsers.py b/tests/io/aims/test_aims_parsers.py
index 1d30799122d..e6cb7d6eb7a 100644
--- a/tests/io/aims/test_aims_parsers.py
+++ b/tests/io/aims/test_aims_parsers.py
@@ -6,7 +6,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.core.tensors import Tensor
 from pymatgen.io.aims.parsers import (
     EV_PER_A3_TO_KBAR,
diff --git a/tests/io/aims/test_sets/test_input_set.py b/tests/io/aims/test_sets/test_input_set.py
index fb7acf5011d..f5d87fe3881 100644
--- a/tests/io/aims/test_sets/test_input_set.py
+++ b/tests/io/aims/test_sets/test_input_set.py
@@ -5,7 +5,6 @@
 from pathlib import Path
 
 import pytest
-
 from pymatgen.core import Structure
 from pymatgen.io.aims.sets import AimsInputSet
 
diff --git a/tests/io/cp2k/test_inputs.py b/tests/io/cp2k/test_inputs.py
index a4b344cda19..9120a789f6d 100644
--- a/tests/io/cp2k/test_inputs.py
+++ b/tests/io/cp2k/test_inputs.py
@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.io.cp2k.inputs import (
     BasisFile,
@@ -23,6 +21,7 @@
     SectionList,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k"
 
diff --git a/tests/io/cp2k/test_outputs.py b/tests/io/cp2k/test_outputs.py
index cd3214af175..fafe2b8be91 100644
--- a/tests/io/cp2k/test_outputs.py
+++ b/tests/io/cp2k/test_outputs.py
@@ -4,10 +4,9 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.io.cp2k.outputs import Cp2kOutput
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k"
 
diff --git a/tests/io/cp2k/test_sets.py b/tests/io/cp2k/test_sets.py
index ecb644a82a3..c986f02db6a 100644
--- a/tests/io/cp2k/test_sets.py
+++ b/tests/io/cp2k/test_sets.py
@@ -1,11 +1,10 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.io.cp2k.sets import SETTINGS, Cp2kValidationError, DftSet, GaussianTypeOrbitalBasisSet, GthPotential
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k"
 
diff --git a/tests/io/exciting/test_inputs.py b/tests/io/exciting/test_inputs.py
index a5a221221b3..02528023893 100644
--- a/tests/io/exciting/test_inputs.py
+++ b/tests/io/exciting/test_inputs.py
@@ -3,7 +3,6 @@
 from xml.etree import ElementTree
 
 from numpy.testing import assert_allclose
-
 from pymatgen.core import Lattice, Structure
 from pymatgen.io.exciting import ExcitingInput
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
diff --git a/tests/io/feff/test_inputs.py b/tests/io/feff/test_inputs.py
index b95bcc536e1..cf06dd92bf9 100644
--- a/tests/io/feff/test_inputs.py
+++ b/tests/io/feff/test_inputs.py
@@ -4,11 +4,10 @@
 from unittest import TestCase
 
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core import Molecule, Structure
 from pymatgen.io.feff.inputs import Atoms, Header, Paths, Potential, Tags
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 FEFF_TEST_DIR = f"{TEST_FILES_DIR}/io/feff"
 
diff --git a/tests/io/feff/test_sets.py b/tests/io/feff/test_sets.py
index e57e560996c..059d2422550 100644
--- a/tests/io/feff/test_sets.py
+++ b/tests/io/feff/test_sets.py
@@ -5,7 +5,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.core.structure import Lattice, Molecule, Structure
 from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags
 from pymatgen.io.feff.sets import FEFFDictSet, MPELNESSet, MPEXAFSSet, MPXANESSet
diff --git a/tests/io/lammps/test_data.py b/tests/io/lammps/test_data.py
index d2fb6541926..e88732fb033 100644
--- a/tests/io/lammps/test_data.py
+++ b/tests/io/lammps/test_data.py
@@ -10,12 +10,11 @@
 import pytest
 from monty.json import MontyDecoder, MontyEncoder
 from numpy.testing import assert_allclose
-from pytest import approx
-from ruamel.yaml import YAML
-
 from pymatgen.core import Element, Lattice, Molecule, Structure
 from pymatgen.io.lammps.data import CombinedData, ForceField, LammpsBox, LammpsData, Topology, lattice_2_lmpbox
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
+from ruamel.yaml import YAML
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/lammps"
 
diff --git a/tests/io/lammps/test_inputs.py b/tests/io/lammps/test_inputs.py
index d56765fdad3..a3abdcceb16 100644
--- a/tests/io/lammps/test_inputs.py
+++ b/tests/io/lammps/test_inputs.py
@@ -6,7 +6,6 @@
 
 import pandas as pd
 import pytest
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.io.lammps.data import LammpsData
diff --git a/tests/io/lammps/test_outputs.py b/tests/io/lammps/test_outputs.py
index 6d5e83c3089..e982cf21f18 100644
--- a/tests/io/lammps/test_outputs.py
+++ b/tests/io/lammps/test_outputs.py
@@ -7,7 +7,6 @@
 import numpy as np
 import pandas as pd
 from numpy.testing import assert_allclose
-
 from pymatgen.io.lammps.outputs import LammpsDump, parse_lammps_dumps, parse_lammps_log
 from pymatgen.util.testing import TEST_FILES_DIR
 
diff --git a/tests/io/lobster/test_inputs.py b/tests/io/lobster/test_inputs.py
index 6675eaf70c8..98343d785d0 100644
--- a/tests/io/lobster/test_inputs.py
+++ b/tests/io/lobster/test_inputs.py
@@ -7,8 +7,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.core.structure import Structure
 from pymatgen.electronic_structure.cohp import IcohpCollection
 from pymatgen.electronic_structure.core import Orbital, Spin
@@ -32,6 +30,7 @@
 from pymatgen.io.vasp import Vasprun
 from pymatgen.io.vasp.inputs import Incar, Kpoints, Potcar
 from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/cohp"
 
diff --git a/tests/io/lobster/test_lobsterenv.py b/tests/io/lobster/test_lobsterenv.py
index 713c4b17eff..a97f2d5ecdd 100644
--- a/tests/io/lobster/test_lobsterenv.py
+++ b/tests/io/lobster/test_lobsterenv.py
@@ -5,8 +5,6 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.graphs import StructureGraph
 from pymatgen.core import Element
 from pymatgen.core.structure import Structure
@@ -15,6 +13,7 @@
 from pymatgen.io.lobster import Charge, Icohplist
 from pymatgen.io.lobster.lobsterenv import LobsterNeighbors
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 __author__ = "Janine George"
 __copyright__ = "Copyright 2021, The Materials Project"
diff --git a/tests/io/pwmat/test_inputs.py b/tests/io/pwmat/test_inputs.py
index 1343ef6832a..8ee41de8552 100644
--- a/tests/io/pwmat/test_inputs.py
+++ b/tests/io/pwmat/test_inputs.py
@@ -3,7 +3,6 @@
 import pytest
 from monty.io import zopen
 from numpy.testing import assert_allclose
-
 from pymatgen.core import Composition, Structure
 from pymatgen.io.pwmat.inputs import (
     ACExtractor,
diff --git a/tests/io/qchem/test_inputs.py b/tests/io/qchem/test_inputs.py
index 6a49daba428..c5c0515fa57 100644
--- a/tests/io/qchem/test_inputs.py
+++ b/tests/io/qchem/test_inputs.py
@@ -5,7 +5,6 @@
 
 import pytest
 from monty.serialization import loadfn
-
 from pymatgen.core.structure import Molecule
 from pymatgen.io.qchem.inputs import QCInput
 from pymatgen.io.qchem.sets import OptSet
diff --git a/tests/io/qchem/test_outputs.py b/tests/io/qchem/test_outputs.py
index bd900253583..31e54f67b3f 100644
--- a/tests/io/qchem/test_outputs.py
+++ b/tests/io/qchem/test_outputs.py
@@ -7,8 +7,6 @@
 import pytest
 from monty.serialization import dumpfn, loadfn
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core.structure import Molecule
 from pymatgen.io.qchem.outputs import (
     QCOutput,
@@ -18,6 +16,7 @@
     orbital_coeffs_parser,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 try:
     from openbabel import openbabel
diff --git a/tests/io/qchem/test_sets.py b/tests/io/qchem/test_sets.py
index 041003d4428..aa2037dac17 100644
--- a/tests/io/qchem/test_sets.py
+++ b/tests/io/qchem/test_sets.py
@@ -3,7 +3,6 @@
 import os
 
 import pytest
-
 from pymatgen.io.qchem.sets import (
     ForceSet,
     FreqSet,
diff --git a/tests/io/qchem/test_utils.py b/tests/io/qchem/test_utils.py
index 394ab8c142b..260dd803462 100644
--- a/tests/io/qchem/test_utils.py
+++ b/tests/io/qchem/test_utils.py
@@ -5,7 +5,6 @@
 
 import pytest
 from monty.io import zopen
-
 from pymatgen.io.qchem.utils import lower_and_check_unique, process_parsed_hess
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
diff --git a/tests/io/test_adf.py b/tests/io/test_adf.py
index d3b6785320f..702fbc87d72 100644
--- a/tests/io/test_adf.py
+++ b/tests/io/test_adf.py
@@ -1,10 +1,9 @@
 from __future__ import annotations
 
-from pytest import approx
-
 from pymatgen.core.structure import Molecule
 from pymatgen.io.adf import AdfInput, AdfKey, AdfOutput, AdfTask
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 __author__ = "Xin Chen, chenxin13@mails.tsinghua.edu.cn"
 
diff --git a/tests/io/test_ase.py b/tests/io/test_ase.py
index daf7b0c77bd..5ed59b6afff 100644
--- a/tests/io/test_ase.py
+++ b/tests/io/test_ase.py
@@ -3,7 +3,6 @@
 import numpy as np
 import pytest
 from monty.json import MontyDecoder, jsanitize
-
 from pymatgen.core import Composition, Lattice, Molecule, Structure
 from pymatgen.core.structure import StructureError
 from pymatgen.io.ase import AseAtomsAdaptor, MSONAtoms
diff --git a/tests/io/test_atat.py b/tests/io/test_atat.py
index a9562f92511..6cf13574495 100644
--- a/tests/io/test_atat.py
+++ b/tests/io/test_atat.py
@@ -1,11 +1,10 @@
 from __future__ import annotations
 
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.atat import Mcsqs
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/atat/mcsqs"
 
diff --git a/tests/io/test_babel.py b/tests/io/test_babel.py
index e1724176ec4..589330d94c5 100644
--- a/tests/io/test_babel.py
+++ b/tests/io/test_babel.py
@@ -4,14 +4,13 @@
 from unittest import TestCase
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.analysis.molecule_matcher import MoleculeMatcher
 from pymatgen.core.structure import Molecule
 from pymatgen.io.babel import BabelMolAdaptor
 from pymatgen.io.xyz import XYZ
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 pybel = pytest.importorskip("openbabel.pybel")
 
diff --git a/tests/io/test_cif.py b/tests/io/test_cif.py
index f536a4f4021..8abc5127813 100644
--- a/tests/io/test_cif.py
+++ b/tests/io/test_cif.py
@@ -2,14 +2,13 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import Composition, DummySpecies, Element, Lattice, Species, Structure
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.io.cif import CifBlock, CifParser, CifWriter
 from pymatgen.symmetry.structure import SymmetrizedStructure
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
+from pytest import approx
 
 try:
     import pybtex
diff --git a/tests/io/test_core.py b/tests/io/test_core.py
index f3f08b46185..7c457339249 100644
--- a/tests/io/test_core.py
+++ b/tests/io/test_core.py
@@ -6,7 +6,6 @@
 
 import pytest
 from monty.serialization import MontyDecoder
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.cif import CifParser, CifWriter
 from pymatgen.io.core import InputFile, InputSet
diff --git a/tests/io/test_gaussian.py b/tests/io/test_gaussian.py
index 7dc76b78b1b..fc694fa7f97 100644
--- a/tests/io/test_gaussian.py
+++ b/tests/io/test_gaussian.py
@@ -3,12 +3,11 @@
 from unittest import TestCase
 
 import pytest
-from pytest import approx
-
 from pymatgen.core.structure import Molecule
 from pymatgen.electronic_structure.core import Spin
 from pymatgen.io.gaussian import GaussianInput, GaussianOutput
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/gaussian"
 
diff --git a/tests/io/test_jarvis.py b/tests/io/test_jarvis.py
index 75c3c78eb82..00a6b4f88f0 100644
--- a/tests/io/test_jarvis.py
+++ b/tests/io/test_jarvis.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import pytest
-
 from pymatgen.core import Structure
 from pymatgen.io.jarvis import Atoms, JarvisAtomsAdaptor
 from pymatgen.util.testing import VASP_IN_DIR
diff --git a/tests/io/test_lmto.py b/tests/io/test_lmto.py
index 393a0b06bae..d398bd431b3 100644
--- a/tests/io/test_lmto.py
+++ b/tests/io/test_lmto.py
@@ -4,7 +4,6 @@
 
 import numpy as np
 from numpy.testing import assert_array_equal
-
 from pymatgen.core.structure import Structure
 from pymatgen.core.units import Ry_to_eV
 from pymatgen.electronic_structure.core import Spin
diff --git a/tests/io/test_nwchem.py b/tests/io/test_nwchem.py
index a81dc751ec0..5f4a13c8b5a 100644
--- a/tests/io/test_nwchem.py
+++ b/tests/io/test_nwchem.py
@@ -4,11 +4,10 @@
 from unittest import TestCase
 
 import pytest
-from pytest import approx
-
 from pymatgen.core.structure import Molecule
 from pymatgen.io.nwchem import NwInput, NwInputError, NwOutput, NwTask
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/nwchem"
 
diff --git a/tests/io/test_openff.py b/tests/io/test_openff.py
index 2152b3e955e..41057daeb0b 100644
--- a/tests/io/test_openff.py
+++ b/tests/io/test_openff.py
@@ -5,7 +5,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.analysis.local_env import OpenBabelNN
 from pymatgen.core import Molecule
diff --git a/tests/io/test_packmol.py b/tests/io/test_packmol.py
index 15d3c86b547..e82f627e310 100644
--- a/tests/io/test_packmol.py
+++ b/tests/io/test_packmol.py
@@ -6,7 +6,6 @@
 from subprocess import TimeoutExpired
 
 import pytest
-
 from pymatgen.analysis.molecule_matcher import MoleculeMatcher
 from pymatgen.core import Molecule
 from pymatgen.io.packmol import PackmolBoxGen
diff --git a/tests/io/test_phonopy.py b/tests/io/test_phonopy.py
index f12cce1f0a0..c3bc2e18187 100644
--- a/tests/io/test_phonopy.py
+++ b/tests/io/test_phonopy.py
@@ -7,8 +7,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.core import Element
 from pymatgen.io.phonopy import (
     CompletePhononDos,
@@ -29,6 +27,7 @@
     get_thermal_displacement_matrices,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 try:
     from phonopy import Phonopy
diff --git a/tests/io/test_pwscf.py b/tests/io/test_pwscf.py
index 6666b3c7938..7137f7f97a8 100644
--- a/tests/io/test_pwscf.py
+++ b/tests/io/test_pwscf.py
@@ -3,10 +3,9 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.io.pwscf import PWInput, PWInputError, PWOutput
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/pwscf"
 
diff --git a/tests/io/test_res.py b/tests/io/test_res.py
index 5617ad86492..2e05ee5769a 100644
--- a/tests/io/test_res.py
+++ b/tests/io/test_res.py
@@ -1,11 +1,10 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.core import Structure
 from pymatgen.io.res import AirssProvider, ResParseError, ResWriter
 from pymatgen.util.testing import TEST_FILES_DIR
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/res"
 
diff --git a/tests/io/test_shengbte.py b/tests/io/test_shengbte.py
index 67779c458a1..60bc58b2a4a 100644
--- a/tests/io/test_shengbte.py
+++ b/tests/io/test_shengbte.py
@@ -4,7 +4,6 @@
 
 import pytest
 from numpy.testing import assert_array_equal
-
 from pymatgen.io.shengbte import Control
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
diff --git a/tests/io/test_template_input.py b/tests/io/test_template_input.py
index 3be8ae45374..313fa8fc540 100644
--- a/tests/io/test_template_input.py
+++ b/tests/io/test_template_input.py
@@ -3,7 +3,6 @@
 import os
 
 import pytest
-
 from pymatgen.io.template import TemplateInputGen
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
diff --git a/tests/io/test_wannier90.py b/tests/io/test_wannier90.py
index ca4704dfe72..32757970eeb 100644
--- a/tests/io/test_wannier90.py
+++ b/tests/io/test_wannier90.py
@@ -5,10 +5,9 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.io.wannier90 import Unk
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/wannier90"
 
diff --git a/tests/io/test_xcrysden.py b/tests/io/test_xcrysden.py
index 3a13a2cf7b5..88db940bcf8 100644
--- a/tests/io/test_xcrysden.py
+++ b/tests/io/test_xcrysden.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.core.structure import Structure
 from pymatgen.io.xcrysden import XSF
 from pymatgen.util.testing import PymatgenTest
diff --git a/tests/io/test_xyz.py b/tests/io/test_xyz.py
index 2314eefdc8e..77e3c582efa 100644
--- a/tests/io/test_xyz.py
+++ b/tests/io/test_xyz.py
@@ -4,12 +4,11 @@
 
 import pandas as pd
 import pytest
-from pytest import approx
-
 from pymatgen.core import Structure
 from pymatgen.core.structure import Molecule
 from pymatgen.io.xyz import XYZ
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
+from pytest import approx
 
 
 class TestXYZ(TestCase):
diff --git a/tests/io/test_zeopp.py b/tests/io/test_zeopp.py
index 2f38d24086c..3656530cb4e 100644
--- a/tests/io/test_zeopp.py
+++ b/tests/io/test_zeopp.py
@@ -4,8 +4,6 @@
 from unittest import TestCase
 
 import pytest
-from pytest import approx
-
 from pymatgen.analysis.bond_valence import BVAnalyzer
 from pymatgen.core import Molecule, Species, Structure
 from pymatgen.io.zeopp import (
@@ -16,6 +14,7 @@
     get_voronoi_nodes,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
+from pytest import approx
 
 try:
     import zeo
diff --git a/tests/io/vasp/test_inputs.py b/tests/io/vasp/test_inputs.py
index cfd2769ff5e..aba859bea1f 100644
--- a/tests/io/vasp/test_inputs.py
+++ b/tests/io/vasp/test_inputs.py
@@ -15,8 +15,6 @@
 from monty.io import zopen
 from monty.serialization import loadfn
 from numpy.testing import assert_allclose
-from pytest import MonkeyPatch, approx
-
 from pymatgen.core import SETTINGS
 from pymatgen.core.composition import Composition
 from pymatgen.core.structure import Structure
@@ -36,6 +34,7 @@
     _gen_potcar_summary_stats,
 )
 from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import MonkeyPatch, approx
 
 # make sure _gen_potcar_summary_stats runs and works with all tests in this file
 _summ_stats = _gen_potcar_summary_stats(append=False, vasp_psp_dir=str(FAKE_POTCAR_DIR), summary_stats_filename=None)
diff --git a/tests/io/vasp/test_optics.py b/tests/io/vasp/test_optics.py
index 3a2caf7a94a..3e660a58797 100644
--- a/tests/io/vasp/test_optics.py
+++ b/tests/io/vasp/test_optics.py
@@ -4,7 +4,6 @@
 import pytest
 import scipy.special
 from numpy.testing import assert_allclose
-
 from pymatgen.io.vasp.optics import DielectricFunctionCalculator, delta_func, delta_methfessel_paxton, step_func
 from pymatgen.io.vasp.outputs import Vasprun
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
diff --git a/tests/io/vasp/test_outputs.py b/tests/io/vasp/test_outputs.py
index a5faadac3ca..fb2a9697842 100644
--- a/tests/io/vasp/test_outputs.py
+++ b/tests/io/vasp/test_outputs.py
@@ -13,8 +13,6 @@
 import pytest
 from monty.io import zopen
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core import Element
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
@@ -42,6 +40,7 @@
 )
 from pymatgen.io.wannier90 import Unk
 from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import approx
 
 try:
     import h5py
diff --git a/tests/io/vasp/test_sets.py b/tests/io/vasp/test_sets.py
index ceb2d8e5424..9f1a0c40bbb 100644
--- a/tests/io/vasp/test_sets.py
+++ b/tests/io/vasp/test_sets.py
@@ -10,8 +10,6 @@
 from monty.json import MontyDecoder
 from monty.serialization import loadfn
 from numpy.testing import assert_allclose
-from pytest import MonkeyPatch, approx, mark
-
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import SETTINGS, Lattice, Species, Structure
 from pymatgen.core.composition import Composition
@@ -55,6 +53,7 @@
 )
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import MonkeyPatch, approx, mark
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/vasp"
 
diff --git a/tests/io/xtb/test_outputs.py b/tests/io/xtb/test_outputs.py
index c4d3fe69777..dd1afc090af 100644
--- a/tests/io/xtb/test_outputs.py
+++ b/tests/io/xtb/test_outputs.py
@@ -2,12 +2,11 @@
 
 import os
 
-from pytest import approx
-
 from pymatgen.core.structure import Molecule
 from pymatgen.io.qchem.outputs import check_for_structure_changes
 from pymatgen.io.xtb.outputs import CRESTOutput
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 try:
     from openbabel import openbabel
diff --git a/tests/optimization/test_linear_assignment.py b/tests/optimization/test_linear_assignment.py
index 961a5032b6d..163a1ac3132 100644
--- a/tests/optimization/test_linear_assignment.py
+++ b/tests/optimization/test_linear_assignment.py
@@ -4,9 +4,8 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.optimization.linear_assignment import LinearAssignment
+from pytest import approx
 
 
 class TestLinearAssignment(TestCase):
diff --git a/tests/optimization/test_neighbors.py b/tests/optimization/test_neighbors.py
index a6374c1f929..8d66dcd9b91 100644
--- a/tests/optimization/test_neighbors.py
+++ b/tests/optimization/test_neighbors.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.optimization.neighbors import find_points_in_spheres
 from pymatgen.util.testing import PymatgenTest
diff --git a/tests/phonon/test_bandstructure.py b/tests/phonon/test_bandstructure.py
index 7f449792544..6f46c3dca38 100644
--- a/tests/phonon/test_bandstructure.py
+++ b/tests/phonon/test_bandstructure.py
@@ -4,11 +4,10 @@
 import json
 
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.electronic_structure.bandstructure import Kpoint
 from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/bandstructure"
 
diff --git a/tests/phonon/test_dos.py b/tests/phonon/test_dos.py
index 0fecb44d6fd..013cfa7e8b3 100644
--- a/tests/phonon/test_dos.py
+++ b/tests/phonon/test_dos.py
@@ -5,11 +5,10 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.core import Element
 from pymatgen.phonon.dos import CompletePhononDos, PhononDos
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/phonon/dos"
 
diff --git a/tests/phonon/test_gruneisen.py b/tests/phonon/test_gruneisen.py
index 5b84acbc33f..321702140af 100644
--- a/tests/phonon/test_gruneisen.py
+++ b/tests/phonon/test_gruneisen.py
@@ -2,12 +2,11 @@
 
 import matplotlib.pyplot as plt
 import pytest
-from pytest import approx
-
 from pymatgen.io.phonopy import get_gruneisen_ph_bs_symm_line, get_gruneisenparameter
 from pymatgen.phonon.gruneisen import GruneisenParameter
 from pymatgen.phonon.plotter import GruneisenPhononBandStructureSymmLine, GruneisenPhononBSPlotter, GruneisenPlotter
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 try:
     import phonopy
diff --git a/tests/phonon/test_ir_spectra.py b/tests/phonon/test_ir_spectra.py
index 7a7eb40f4ce..11bae39d9f7 100644
--- a/tests/phonon/test_ir_spectra.py
+++ b/tests/phonon/test_ir_spectra.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from monty.serialization import loadfn
-
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
 
diff --git a/tests/phonon/test_plotter.py b/tests/phonon/test_plotter.py
index 01e657e7eaf..2e0c762804b 100644
--- a/tests/phonon/test_plotter.py
+++ b/tests/phonon/test_plotter.py
@@ -6,7 +6,6 @@
 import matplotlib.pyplot as plt
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.phonon import CompletePhononDos, PhononBandStructureSymmLine
 from pymatgen.phonon.plotter import PhononBSPlotter, PhononDosPlotter, ThermoPlotter
 from pymatgen.util.testing import TEST_FILES_DIR
diff --git a/tests/phonon/test_thermal_displacements.py b/tests/phonon/test_thermal_displacements.py
index 725c197263f..315680e28d8 100644
--- a/tests/phonon/test_thermal_displacements.py
+++ b/tests/phonon/test_thermal_displacements.py
@@ -2,11 +2,10 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-from pytest import approx
-
 from pymatgen.core.structure import Structure
 from pymatgen.phonon.thermal_displacements import ThermalDisplacementMatrices
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/phonon/thermal_displacement_matrices"
 
diff --git a/tests/symmetry/test_analyzer.py b/tests/symmetry/test_analyzer.py
index a1a19edc4ba..cd0d702f307 100644
--- a/tests/symmetry/test_analyzer.py
+++ b/tests/symmetry/test_analyzer.py
@@ -5,8 +5,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx, raises
-
 from pymatgen.core import Lattice, Molecule, PeriodicSite, Site, Species, Structure
 from pymatgen.io.vasp.outputs import Vasprun
 from pymatgen.symmetry.analyzer import (
@@ -18,6 +16,7 @@
 )
 from pymatgen.symmetry.structure import SymmetrizedStructure
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
+from pytest import approx, raises
 
 TEST_DIR = f"{TEST_FILES_DIR}/symmetry/analyzer"
 
diff --git a/tests/symmetry/test_groups.py b/tests/symmetry/test_groups.py
index 273a6a6d6c3..cee6793d2e7 100644
--- a/tests/symmetry/test_groups.py
+++ b/tests/symmetry/test_groups.py
@@ -2,11 +2,10 @@
 
 import numpy as np
 import pytest
-from pytest import approx
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.operations import SymmOp
 from pymatgen.symmetry.groups import SYMM_DATA, PointGroup, SpaceGroup
+from pytest import approx
 
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Virtual Lab"
diff --git a/tests/symmetry/test_kpath_hin.py b/tests/symmetry/test_kpath_hin.py
index 61d71fd9dd3..63dab783ac2 100644
--- a/tests/symmetry/test_kpath_hin.py
+++ b/tests/symmetry/test_kpath_hin.py
@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import pytest
-from pytest import approx
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.kpath import KPathSeek
 from pymatgen.util.testing import PymatgenTest
+from pytest import approx
 
 try:
     from seekpath import get_path
diff --git a/tests/symmetry/test_kpath_lm.py b/tests/symmetry/test_kpath_lm.py
index dbc8187e6a9..e72ff7ef9d7 100644
--- a/tests/symmetry/test_kpath_lm.py
+++ b/tests/symmetry/test_kpath_lm.py
@@ -1,14 +1,13 @@
 from __future__ import annotations
 
 import numpy as np
-from pytest import approx
-
 from pymatgen.analysis.magnetism.analyzer import CollinearMagneticStructureAnalyzer
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.symmetry.kpath import KPathLatimerMunro
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 
 class TestKPathLatimerMunro(PymatgenTest):
diff --git a/tests/symmetry/test_kpath_sc.py b/tests/symmetry/test_kpath_sc.py
index d88c97f79dd..2dd37d0d77e 100644
--- a/tests/symmetry/test_kpath_sc.py
+++ b/tests/symmetry/test_kpath_sc.py
@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import numpy as np
-from pytest import approx
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.kpath import KPathSetyawanCurtarolo
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
+from pytest import approx
 
 TEST_DIR = f"{TEST_FILES_DIR}/symmetry/space_group_structs"
 
diff --git a/tests/symmetry/test_kpaths.py b/tests/symmetry/test_kpaths.py
index 2c907e87135..f13ae4b7a9b 100644
--- a/tests/symmetry/test_kpaths.py
+++ b/tests/symmetry/test_kpaths.py
@@ -4,7 +4,6 @@
 
 import pytest
 from monty.serialization import loadfn
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.symmetry.bandstructure import HighSymmKpath
diff --git a/tests/symmetry/test_maggroups.py b/tests/symmetry/test_maggroups.py
index 72f184d553f..cc4d529b87c 100644
--- a/tests/symmetry/test_maggroups.py
+++ b/tests/symmetry/test_maggroups.py
@@ -2,7 +2,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.symmetry.groups import SpaceGroup
 from pymatgen.symmetry.maggroups import MagneticSpaceGroup
diff --git a/tests/symmetry/test_settings.py b/tests/symmetry/test_settings.py
index 24db5b2b6dc..a6a8ff3e80a 100644
--- a/tests/symmetry/test_settings.py
+++ b/tests/symmetry/test_settings.py
@@ -4,7 +4,6 @@
 
 import numpy as np
 from numpy.testing import assert_allclose
-
 from pymatgen.symmetry.settings import JonesFaithfulTransformation, Lattice, SymmOp
 
 __author__ = "Matthew Horton"
diff --git a/tests/symmetry/test_site_symmetries.py b/tests/symmetry/test_site_symmetries.py
index 21972990e8b..c5696b31f46 100644
--- a/tests/symmetry/test_site_symmetries.py
+++ b/tests/symmetry/test_site_symmetries.py
@@ -4,7 +4,6 @@
 import json
 
 from monty.json import MontyDecoder
-
 from pymatgen.symmetry import site_symmetries as ss
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 225664313dc..1893d0a5738 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -4,7 +4,6 @@
 from typing import TYPE_CHECKING
 
 import pytest
-
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
 
 if TYPE_CHECKING:
diff --git a/tests/transformations/test_advanced_transformations.py b/tests/transformations/test_advanced_transformations.py
index 5dcc3fae6d4..ea0feed09b8 100644
--- a/tests/transformations/test_advanced_transformations.py
+++ b/tests/transformations/test_advanced_transformations.py
@@ -7,8 +7,6 @@
 import pytest
 from monty.serialization import loadfn
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.analysis.energy_models import IsingModel, SymmetryModel
 from pymatgen.analysis.gb.grain import GrainBoundaryGenerator
 from pymatgen.core import Lattice, Molecule, Species, Structure
@@ -41,6 +39,7 @@
     SubstitutionTransformation,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, PymatgenTest
+from pytest import approx
 
 try:
     import hiphive
diff --git a/tests/transformations/test_site_transformations.py b/tests/transformations/test_site_transformations.py
index 3b30670fad3..cddc9bfb53f 100644
--- a/tests/transformations/test_site_transformations.py
+++ b/tests/transformations/test_site_transformations.py
@@ -6,7 +6,6 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.transformations.site_transformations import (
     AddSitePropertyTransformation,
diff --git a/tests/transformations/test_standard_transformations.py b/tests/transformations/test_standard_transformations.py
index 331ed94b9c9..029fad0f8e7 100644
--- a/tests/transformations/test_standard_transformations.py
+++ b/tests/transformations/test_standard_transformations.py
@@ -9,8 +9,6 @@
 import numpy as np
 import pytest
 from monty.json import MontyDecoder
-from pytest import approx
-
 from pymatgen.core import Element, PeriodicSite
 from pymatgen.core.lattice import Lattice
 from pymatgen.symmetry.structure import SymmetrizedStructure
@@ -36,6 +34,7 @@
     SupercellTransformation,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
+from pytest import approx
 
 enumlib_present = which("enum.x") and which("makestr.x")
 
diff --git a/tests/util/test_coord.py b/tests/util/test_coord.py
index 15cfab9d7dc..433831f3c5d 100644
--- a/tests/util/test_coord.py
+++ b/tests/util/test_coord.py
@@ -6,10 +6,9 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
-from pytest import approx
-
 from pymatgen.core.lattice import Lattice
 from pymatgen.util import coord
+from pytest import approx
 
 
 class TestCoordUtils:
diff --git a/tests/util/test_num.py b/tests/util/test_num.py
index e391ba92412..8891e37ca0f 100644
--- a/tests/util/test_num.py
+++ b/tests/util/test_num.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import pytest
-
 from pymatgen.util.num import round_to_sigfigs
 
 
diff --git a/tests/util/test_plotting.py b/tests/util/test_plotting.py
index ae0b6eca76b..85d91b457e8 100644
--- a/tests/util/test_plotting.py
+++ b/tests/util/test_plotting.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import matplotlib.pyplot as plt
-
 from pymatgen.util.plotting import periodic_table_heatmap, van_arkel_triangle
 from pymatgen.util.testing import PymatgenTest
 
diff --git a/tests/util/test_provenance.py b/tests/util/test_provenance.py
index 12ebbb2b13b..9019ee50ebd 100644
--- a/tests/util/test_provenance.py
+++ b/tests/util/test_provenance.py
@@ -7,7 +7,6 @@
 
 import numpy as np
 import pytest
-
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.util.provenance import Author, HistoryNode, StructureNL
 
diff --git a/tests/util/test_string.py b/tests/util/test_string.py
index 5c04a1d51ea..1bb0785cef3 100644
--- a/tests/util/test_string.py
+++ b/tests/util/test_string.py
@@ -2,7 +2,6 @@
 
 import numpy as np
 import pytest
-
 from pymatgen.core import Structure
 from pymatgen.util.string import (
     Stringify,
diff --git a/tests/util/test_typing.py b/tests/util/test_typing.py
index ec04deffbb7..7790c437cd4 100644
--- a/tests/util/test_typing.py
+++ b/tests/util/test_typing.py
@@ -10,7 +10,6 @@
 from typing import TYPE_CHECKING, get_args
 
 import pytest
-
 from pymatgen.core import Composition, DummySpecies, Element, Species
 from pymatgen.entries import Entry
 from pymatgen.util.typing import CompositionLike, EntryLike, PathLike, PbcLike, SpeciesLike
diff --git a/tests/vis/test_plotters.py b/tests/vis/test_plotters.py
index ca0594b4c2d..ab9c95ad547 100644
--- a/tests/vis/test_plotters.py
+++ b/tests/vis/test_plotters.py
@@ -6,7 +6,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from monty.json import MontyDecoder
-
 from pymatgen.analysis.xas.spectrum import XAS
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 from pymatgen.vis.plotters import SpectrumPlotter