Merge branch 'master' into type-elec-struct

.github/workflows/lint.yml

@@ -31,7 +31,7 @@ jobs:
           ruff format --check .
 
       - name: mypy
-        run: mypy ${{ github.event.repository.name }}
+        run: mypy src
 
       - name: pyright
         run: pyright

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.5.0
     hooks:
       - id: ruff
         args: [ --fix, --unsafe-fixes ]

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,

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,

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,

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,

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,

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,

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

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

pyproject.toml

@@ -132,8 +132,8 @@ feff_plot_dos = "pymatgen.cli.feff_plot_dos:main"
 get_environment = "pymatgen.cli.get_environment:main"
 
 [tool.setuptools.packages.find]
-where = ["."]
-include = ["pymatgen.*"]
+where = ["src"]
+include = ["pymatgen"]
 
 [tool.setuptools.package-data]
 "pymatgen.analysis" = ["*.yaml", "*.json", "*.csv"]
@@ -247,9 +247,8 @@ docstring-code-format = true
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
 "tests/**" = ["ANN201", "D", "PLR0124"]
-"tasks.py" = ["D"]
-"pymatgen/analysis/*" = ["D"]
-"pymatgen/io/*" = ["D"]
+"src/pymatgen/analysis/*" = ["D"]
+"src/pymatgen/io/*" = ["D"]
 "dev_scripts/*" = ["D"]
 
 [tool.pytest.ini_options]

setup.py

@@ -15,17 +15,17 @@
     ext_modules=[
         Extension(
             "pymatgen.optimization.linear_assignment",
-            ["pymatgen/optimization/linear_assignment.pyx"],
+            ["src/pymatgen/optimization/linear_assignment.pyx"],
             extra_link_args=extra_link_args,
         ),
         Extension(
             "pymatgen.util.coord_cython",
-            ["pymatgen/util/coord_cython.pyx"],
+            ["src/pymatgen/util/coord_cython.pyx"],
             extra_link_args=extra_link_args,
         ),
         Extension(
             "pymatgen.optimization.neighbors",
-            ["pymatgen/optimization/neighbors.pyx"],
+            ["src/pymatgen/optimization/neighbors.pyx"],
             extra_link_args=extra_link_args,
         ),
     ],

pymatgen/alchemy/filters.py → 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):

pymatgen/alchemy/materials.py → 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):

pymatgen/alchemy/transmuters.py → 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"

pymatgen/analysis/adsorption.py → 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"

pymatgen/analysis/bond_dissociation.py → 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

pymatgen/analysis/bond_valence.py → 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
 

pymatgen/analysis/chemenv/connectivity/connected_components.py → 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
@@ -532,7 +531,6 @@ def show_graph(
                 If not provided, the graph is not saved.
             drawing_type (str): The type of drawing to use. Can be "internal" or "external".
         """
-
         shown_graph = self._connected_subgraph if graph is None else graph
 
         plt.figure()

pymatgen/analysis/chemenv/connectivity/connectivity_finder.py → 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"

pymatgen/analysis/chemenv/connectivity/structure_connectivity.py → 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

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py → 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
@@ -403,7 +402,7 @@ def get_site_coordination_environments_fractions(
     def get_site_ce_fractions_and_neighbors(self, site, full_ce_info=False, strategy_info=False):
         """
         Applies the strategy to the structure_environments object in order to get coordination environments, their
-        fraction, csm, geometry_info, and neighbors
+        fraction, csm, geometry_info, and neighbors.
 
         Args:
             site: Site for which the above information is sought
@@ -458,7 +457,7 @@ def setup_options(self, all_options_dict):
     @abc.abstractmethod
     def __eq__(self, other: object) -> bool:
         """
-        Equality method that should be implemented for any strategy
+        Equality method that should be implemented for any strategy.
 
         Args:
             other: strategy to be compared with the current one
@@ -1122,7 +1121,6 @@ def __init__(
             max_csm:
             symmetry_measure_type:
         """
-
         raise NotImplementedError("TargetedPenaltiedAbundanceChemenvStrategy not yet implemented")
 
         super().__init__(
@@ -1587,6 +1585,7 @@ def get_effective_csm(
         symmetry_measure_type: Type of symmetry measure to be used in the effective CSM.
         max_effective_csm: Max CSM to use for the effective CSM calculation.
         effective_csm_estimator_ratio_function: Ratio function to use to compute effective CSM.
+
     Returns:
         Effective CSM of a given Neighbors set.
     """
@@ -1951,9 +1950,7 @@ def delta_cn_specifics(
         )
 
     def as_dict(self):
-        """
-        MSONable dict.
-        """
+        """MSONable dict."""
         return {
             "@module": type(self).__module__,
             "@class": type(self).__name__,

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py → src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -101,9 +101,7 @@ def as_dict(self):
 
     @classmethod
     def from_dict(cls, dct: dict) -> Self:
-        """
-        Reconstruct ExplicitPermutationsAlgorithm from its JSON-serializable dict representation.
-        """
+        """Reconstruct ExplicitPermutationsAlgorithm from its JSON-serializable dict representation."""
         return cls(dct["permutations"])