doc str + var name fixes

materialsproject · Nov 8, 2023 · 1c18213 · 1c18213
1 parent 535f925
commit 1c18213
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diff --git a/dev_scripts/update_pt_data.py b/dev_scripts/update_pt_data.py
@@ -14,27 +14,26 @@
 from monty.serialization import dumpfn, loadfn
 from ruamel import yaml
 
-from pymatgen.core import Element
-from pymatgen.core.periodic_table import get_el_sp
+from pymatgen.core import Element, get_el_sp
 
 
 def test_yaml():
-    with open("periodic_table.yaml") as f:
-        data = yaml.load(f)
+    with open("periodic_table.yaml") as file:
+        data = yaml.load(file)
         print(data)
 
 
 def test_json():
-    with open("periodic_table.json") as f:
-        data = json.load(f)
+    with open("periodic_table.json") as file:
+        data = json.load(file)
         print(data)
 
 
 def parse_oxi_state():
-    with open("periodic_table.yaml") as f:
-        data = yaml.load(f)
-    with open("oxidation_states.txt") as f:
-        oxi_data = f.read()
+    with open("periodic_table.yaml") as file:
+        data = yaml.load(file)
+    with open("oxidation_states.txt") as file:
+        oxi_data = file.read()
     oxi_data = re.sub("[\n\r]", "", oxi_data)
     patt = re.compile("<tr>(.*?)</tr>", re.MULTILINE)
 
@@ -65,8 +64,8 @@ def parse_oxi_state():
             data[el]["Common oxidation states"] = common_oxi
         else:
             print(el)
-    with open("periodic_table2.yaml", "w") as f:
-        yaml.dump(data, f)
+    with open("periodic_table2.yaml", "w") as file:
+        yaml.dump(data, file)
 
 
 def parse_ionic_radii():
@@ -254,7 +253,7 @@ def add_electron_affinities():
     import requests
     from bs4 import BeautifulSoup
 
-    req = requests.get("https://en.wikipedia.org/wiki/Electron_affinity_(data_page)")
+    req = requests.get("https://wikipedia.org/wiki/Electron_affinity_(data_page)")
     soup = BeautifulSoup(req.text, "html.parser")
     for t in soup.find_all("table"):
         if "Hydrogen" in t.text:

diff --git a/pymatgen/alchemy/transmuters.py b/pymatgen/alchemy/transmuters.py
@@ -99,18 +99,15 @@ def append_transformation(self, transformation, extend_collection=False, clear_r
             transformation: Transformation to append
             extend_collection: Whether to use more than one output structure
                 from one-to-many transformations. extend_collection can be a
-                number, which determines the maximum branching for each
-                transformation.
+                number, which determines the maximum branching for each transformation.
             clear_redo (bool): Whether to clear the redo list. By default,
                 this is True, meaning any appends clears the history of
                 undoing. However, when using append_transformation to do a
-                redo, the redo list should not be cleared to allow multiple
-                redos.
+                redo, the redo list should not be cleared to allow multiple redos.
 
         Returns:
-            List of booleans corresponding to initial transformed structures
-            each boolean describes whether the transformation altered the
-            structure
+            list[bool]: corresponding to initial transformed structures each boolean
+                describes whether the transformation altered the structure
         """
         if self.ncores and transformation.use_multiprocessing:
             with Pool(self.ncores) as p:
@@ -369,8 +366,8 @@ def _apply_transformation(inputs):
             collection, and a boolean indicating whether to clear the redo
 
     Returns:
-        List of output structures (the modified initial structure, plus
-        any new structures created by a one-to-many transformation)
+        list[Structure]: the modified initial structure, plus
+            any new structures created by a one-to-many transformation
     """
     ts, transformation, extend_collection, clear_redo = inputs
     new = ts.append_transformation(transformation, extend_collection, clear_redo=clear_redo)

diff --git a/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py b/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py
@@ -42,9 +42,7 @@
     sort_separation,
     sort_separation_tuple,
 )
-from pymatgen.core.lattice import Lattice
-from pymatgen.core.periodic_table import Species
-from pymatgen.core.structure import Structure
+from pymatgen.core import Lattice, Species, Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.due import Doi, due
 

diff --git a/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py b/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py
@@ -425,11 +425,11 @@ def rotateCoords(coords, R):
     Returns:
         List of rotated points.
     """
-    newlist = []
+    new_coords = []
     for pp in coords:
         rpp = matrixTimesVector(R, pp)
-        newlist.append(rpp)
-    return newlist
+        new_coords.append(rpp)
+    return new_coords
 
 
 def rotateCoordsOpt(coords, R):
@@ -461,10 +461,10 @@ def changebasis(uu, vv, nn, pps):
         MM[ii, 1] = vv[ii]
         MM[ii, 2] = nn[ii]
     PP = np.linalg.inv(MM)
-    newpps = []
+    new_pps = []
     for pp in pps:
-        newpps.append(matrixTimesVector(PP, pp))
-    return newpps
+        new_pps.append(matrixTimesVector(PP, pp))
+    return new_pps
 
 
 def collinear(p1, p2, p3=None, tolerance=0.25):

diff --git a/pymatgen/analysis/chemenv/utils/math_utils.py b/pymatgen/analysis/chemenv/utils/math_utils.py
@@ -81,9 +81,9 @@ def divisors(n):
     """
     factors = _factor_generator(n)
     _divisors = []
-    listexponents = [[k**x for x in range(factors[k] + 1)] for k in list(factors)]
-    listfactors = _cartesian_product(listexponents)
-    for f in listfactors:
+    exponents = [[k**x for x in range(factors[k] + 1)] for k in list(factors)]
+    factors = _cartesian_product(exponents)
+    for f in factors:
         _divisors.append(reduce(lambda x, y: x * y, f, 1))
     _divisors.sort()
     return _divisors

diff --git a/pymatgen/analysis/chempot_diagram.py b/pymatgen/analysis/chempot_diagram.py
@@ -648,7 +648,7 @@ def simple_pca(data: np.ndarray, k: int = 2) -> tuple[np.ndarray, np.ndarray, np
         k: Number of principal components returned
 
     Returns:
-        Tuple of projected data, eigenvalues, eigenvectors
+        tuple: projected data, eigenvalues, eigenvectors
     """
     data = data - np.mean(data.T, axis=1)  # centering the data
     cov = np.cov(data.T)  # calculating covariance matrix

diff --git a/pymatgen/analysis/costdb_elements.csv b/pymatgen/analysis/costdb_elements.csv
@@ -1,21 +1,21 @@
 Ag,780.88,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 Pd,23036.01,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
-C,24,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-Cl,1.5,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-F,1900,pure F,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-Ir,42000,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-K,1000,pure K,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-Na,250,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-O,3,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-P,300,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-Pa,280000,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-Sc,14000,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-Xe,1200,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+C,24,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Cl,1.5,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+F,1900,pure F,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Ir,42000,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+K,1000,pure K,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Na,250,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+O,3,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+P,300,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Pa,280000,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Sc,14000,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Xe,1200,,|@misc{wikipedia, title = "Wikipedia", month = "September", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
 Al,2.46035592,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 As,0.641103496,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 Au,45386.51194,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 B,0.871045362,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
-Ba,0.2605,,|@misc{wikipedia, title = "Wikipedia", month = "August", year = "2019", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Ba,0.2605,,|@misc{wikipedia, title = "Wikipedia", month = "August", year = "2019", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
 Be,447.978784,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 Bi,25.3090376,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 Br,1.39001291,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
@@ -77,7 +77,7 @@ Yb,1599.892734,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "Septembe
 Zn,2.33910182,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 Zr,2.64995324,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
 He,15.9,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "June", year = "2020", url = "http://www.wolframalpha.org"}|
-H,1.4,,|@misc{wikipedia, title = "Wikipedia", month = "June", year = "2020", url = "https://en.wikipedia.org/wiki/Hydrogen_economy#Costs"}|
+H,1.4,,|@misc{wikipedia, title = "Wikipedia", month = "June", year = "2020", url = "https://wikipedia.org/wiki/Hydrogen_economy#Costs"}|
 Ar,19.56,,|@misc{internet_search, title = "Aqua-Calc", month = "June", year = "2020", url = "https://www.aqua-calc.com/calculate/materials-price/substance/argon"}|
 Ne,660000,,|@misc{internet_search, title = "Pomona College", month = "June", year = "2020", url = "http://www.chemistry.pomona.edu/chemistry/periodic_table/elements/neptunium/the%20facts.htm"}|
 Kr,330,,|@misc{internet_search, title = "Chemicool", month = "June", year = "2020", url = "https://www.chemicool.com/elements/krypton.html"}|

diff --git a/pymatgen/analysis/dimensionality.py b/pymatgen/analysis/dimensionality.py
@@ -32,9 +32,8 @@
 from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
 from pymatgen.analysis.local_env import JmolNN
 from pymatgen.analysis.structure_analyzer import get_max_bond_lengths
+from pymatgen.core import Molecule, Species, Structure
 from pymatgen.core.lattice import get_integer_index
-from pymatgen.core.periodic_table import Species
-from pymatgen.core.structure import Molecule, Structure
 from pymatgen.core.surface import SlabGenerator
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 

diff --git a/pymatgen/analysis/local_env.py b/pymatgen/analysis/local_env.py
@@ -26,9 +26,7 @@
 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.periodic_table import Element, Species
-from pymatgen.core.sites import PeriodicSite, Site
-from pymatgen.core.structure import IStructure, PeriodicNeighbor, Structure
+from pymatgen.core import Element, IStructure, PeriodicNeighbor, PeriodicSite, Site, Species, Structure
 
 try:
     from openbabel import openbabel
@@ -1929,7 +1927,7 @@ def solid_angle(center, coords):
     r_norm = [np.linalg.norm(i) for i in r]
 
     # Compute the solid angle for each tetrahedron that makes up the facet
-    #  Following: https://en.wikipedia.org/wiki/Solid_angle#Tetrahedron
+    #  Following: https://wikipedia.org/wiki/Solid_angle#Tetrahedron
     angle = 0
     for i in range(1, len(r) - 1):
         j = i + 1

diff --git a/pymatgen/analysis/molecule_matcher.py b/pymatgen/analysis/molecule_matcher.py
@@ -810,7 +810,7 @@ def kabsch(P: np.ndarray, Q: np.ndarray):
         P and Q, centered around the their centroid.
 
         For more info see:
-        - http://en.wikipedia.org/wiki/Kabsch_algorithm and
+        - http://wikipedia.org/wiki/Kabsch_algorithm and
         - https://cnx.org/contents/HV-RsdwL@23/Molecular-Distance-Measures
 
         Args:

diff --git a/pymatgen/analysis/phase_diagram.py b/pymatgen/analysis/phase_diagram.py
@@ -2028,8 +2028,7 @@ class PhaseDiagramError(Exception):
 
 
 def get_facets(qhull_data: ArrayLike, joggle: bool = False) -> ConvexHull:
-    """
-    Get the simplex facets for the Convex hull.
+    """Get the simplex facets for the Convex hull.
 
     Args:
         qhull_data (np.ndarray): The data from which to construct the convex
@@ -2039,7 +2038,7 @@ def get_facets(qhull_data: ArrayLike, joggle: bool = False) -> ConvexHull:
             errors.
 
     Returns:
-        List of simplices of the Convex Hull.
+        scipy.spatial.ConvexHull: with list of simplices of the convex hull.
     """
     if joggle:
         return ConvexHull(qhull_data, qhull_options="QJ i").simplices

diff --git a/pymatgen/analysis/pourbaix_diagram.py b/pymatgen/analysis/pourbaix_diagram.py
@@ -26,9 +26,8 @@
 
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.analysis.reaction_calculator import Reaction, ReactionError
-from pymatgen.core.composition import Composition
+from pymatgen.core import Composition, Element
 from pymatgen.core.ion import Ion
-from pymatgen.core.periodic_table import Element
 from pymatgen.entries.compatibility import MU_H2O
 from pymatgen.entries.computed_entries import ComputedEntry
 from pymatgen.util.coord import Simplex

diff --git a/pymatgen/analysis/structure_prediction/substitution_probability.py b/pymatgen/analysis/structure_prediction/substitution_probability.py
@@ -16,7 +16,7 @@
 
 from monty.design_patterns import cached_class
 
-from pymatgen.core.periodic_table import Species, get_el_sp
+from pymatgen.core import Species, get_el_sp
 from pymatgen.util.due import Doi, due
 
 __author__ = "Will Richards, Geoffroy Hautier"

diff --git a/pymatgen/apps/battery/insertion_battery.py b/pymatgen/apps/battery/insertion_battery.py
@@ -12,8 +12,7 @@
 
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.apps.battery.battery_abc import AbstractElectrode, AbstractVoltagePair
-from pymatgen.core.composition import Composition
-from pymatgen.core.periodic_table import Element
+from pymatgen.core import Composition, Element
 from pymatgen.core.units import Charge, Time
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 

diff --git a/pymatgen/command_line/mcsqs_caller.py b/pymatgen/command_line/mcsqs_caller.py
@@ -68,7 +68,7 @@ def run_mcsqs(
         tol (int or float): Tolerance for matching correlations (default: 1e-3).
 
     Returns:
-        Tuple of Pymatgen structure SQS of the input structure, the mcsqs objective function,
+        tuple: Pymatgen structure SQS of the input structure, the mcsqs objective function,
             list of all SQS structures, and the directory where calculations are run
     """
     num_atoms = len(structure)
@@ -166,7 +166,7 @@ def _parse_sqs_path(path) -> Sqs:
         path: directory to perform parsing.
 
     Returns:
-        Tuple of Pymatgen structure SQS of the input structure, the mcsqs objective function,
+        tuple: Pymatgen structure SQS of the input structure, the mcsqs objective function,
             list of all SQS structures, and the directory where calculations are run
     """
     path = Path(path)
@@ -225,7 +225,14 @@ def _parse_clusters(filename):
         path: directory to perform parsing.
 
     Returns:
-        List of dicts
+        list[dict]: List of cluster dictionaries with keys:
+            multiplicity: int
+            longest_pair_length: float
+            num_points_in_cluster: int
+            coordinates: list[dict] of points with keys:
+                coordinates: list[float]
+                num_possible_species: int
+                cluster_function: float
     """
     with open(filename) as f:
         lines = f.readlines()

diff --git a/pymatgen/core/operations.py b/pymatgen/core/operations.py
@@ -27,7 +27,7 @@
 class SymmOp(MSONable):
     """A symmetry operation in Cartesian space. Consists of a rotation plus a
     translation. Implementation is as an affine transformation matrix of rank 4
-    for efficiency. Read: http://en.wikipedia.org/wiki/Affine_transformation.
+    for efficiency. Read: http://wikipedia.org/wiki/Affine_transformation.
 
     Attributes:
         affine_matrix (np.ndarray): A 4x4 array representing the symmetry operation.

diff --git a/pymatgen/core/periodic_table.py b/pymatgen/core/periodic_table.py
@@ -55,7 +55,7 @@ def __init__(self, symbol: SpeciesLike):
             symbol (str): Element symbol.
             long_name (str): Long name for element. E.g., "Hydrogen".
             atomic_radius_calculated (float): Calculated atomic radius for the element. This is the empirical value.
-                Data is obtained from http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).
+                Data is obtained from http://wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).
             van_der_waals_radius (float): Van der Waals radius for the element. This is the empirical value determined
                 from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental
                 data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å.

diff --git a/pymatgen/util/coord.py b/pymatgen/util/coord.py
@@ -348,7 +348,7 @@ def get_angle(v1: ArrayLike, v2: ArrayLike, units: Literal["degrees", "radians"]
 
 
 class Simplex(MSONable):
-    """A generalized simplex object. See http://en.wikipedia.org/wiki/Simplex.
+    """A generalized simplex object. See http://wikipedia.org/wiki/Simplex.
 
     Attributes:
         space_dim (int): Dimension of the space. Usually, this is 1 more than the simplex_dim.
@@ -409,7 +409,7 @@ def in_simplex(self, point, tolerance=1e-8):
         simplex from this origin by subtracting all other vertices from the
         origin. We then project the point into this coordinate system and
         determine the linear decomposition coefficients in this coordinate
-        system. If the coeffs satisfy that all coeffs >= 0, the composition
+        system. If the coeffs satisfy all(coeffs >= 0), the composition
         is in the facet.
 
         Args:

diff --git a/tests/files/costdb_1.csv b/tests/files/costdb_1.csv
@@ -1,2 +1,2 @@
-O,1,,|@misc{wikipedia, title = "Wikipedia", month = "August", year = "2013", url = "http://en.wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
-Ag,3,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|
+O,1,,|@misc{wikipedia, title = "Wikipedia", month = "August", year = "2013", url = "http://wikipedia.org/wiki/Prices_of_elements_and_their_compounds"}|
+Ag,3,,|@misc{wolfram_alpha, title = "Wolfram Alpha", month = "September", year = "2013", url = "http://www.wolframalpha.org"}|