Merge branch 'master' of github.com:materialsproject/pymatgen

Author: Shyue Ping Ong

.gitattributes

@@ -2,5 +2,4 @@
 tests/files/**/* linguist-vendored
 cmd_line/* linguist-vendored
 docs/**/* linguist-generated
-docs_rst/**/* linguist-documentation
 dev_scripts/**/* linguist-vendored

docs/compatibility.md

@@ -335,7 +335,9 @@ def to_snl(self, authors, **kwargs) -> StructureNL:
 
         :param authors: List of authors
         :param **kwargs: All kwargs supported by StructureNL.
-        :return: StructureNL
+
+        Returns:
+            StructureNL
         """
         if self.other_parameters:
             warn("Data in TransformedStructure.other_parameters discarded during type conversion to SNL")

pymatgen/alchemy/materials.py

@@ -846,6 +846,7 @@ def from_dict(cls, d):
 
         Args:
             d (dict): dict representation of the ConnectedComponent object
+
         Returns:
             ConnectedComponent: The connected component representing the links of a given set of environments.
         """

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -37,7 +37,9 @@ def get_structure_connectivity(self, light_structure_environments):
 
         :param light_structure_environments: LightStructureEnvironments with the
         relevant coordination environments in the structure
-        :return: a StructureConnectivity object describing the connectivity of
+
+        Returns:
+            a StructureConnectivity object describing the connectivity of
         the environments in the structure
         """
         logging.info("Setup of structure connectivity graph")

pymatgen/analysis/chemenv/connectivity/connectivity_finder.py

@@ -152,7 +152,9 @@ def __init__(
     def __str__(self):
         """
         String representation of the AbstractGeometry
-        :return: String representation of the AbstractGeometry.
+
+        Returns:
+            String representation of the AbstractGeometry.
         """
         outs = [f"\nAbstract Geometry with {len(self.coords)} points :"]
         for pp in self.coords:
@@ -284,7 +286,8 @@ def symmetry_measure(points_distorted, points_perfect):
         has to be computed with respect to the model polyhedron described by the list of points
         "points_perfect".
     :param points_perfect: List of "perfect" points describing a given model polyhedron.
-    :return: The continuous symmetry measure of the distorted polyhedron with respect to the perfect polyhedron.
+    Returns:
+        The continuous symmetry measure of the distorted polyhedron with respect to the perfect polyhedron.
     """
     # When there is only one point, the symmetry measure is 0.0 by definition
     if len(points_distorted) == 1:
@@ -315,7 +318,8 @@ def find_rotation(points_distorted, points_perfect):
     :param points_distorted: List of points describing a given (distorted) polyhedron for which the rotation that
         aligns these points in a least-square sense to the set of perfect points "points_perfect"
     :param points_perfect: List of "perfect" points describing a given model polyhedron.
-    :return: The rotation matrix.
+    Returns:
+        The rotation matrix.
     """
     H = np.matmul(points_distorted.T, points_perfect)
     U, S, Vt = svd(H)
@@ -330,7 +334,9 @@ def find_scaling_factor(points_distorted, points_perfect, rot):
                              to be obtained.
     :param points_perfect: List of "perfect" points describing a given model polyhedron.
     :param rot: The rotation matrix
-    :return: The scaling factor between the two structures and the rotated set of (distorted) points.
+
+    Returns:
+        The scaling factor between the two structures and the rotated set of (distorted) points.
     """
     rotated_coords = np.matmul(rot, points_distorted.T).T
     num = np.tensordot(rotated_coords, points_perfect)
@@ -469,7 +475,8 @@ def get_structure(self):
         """
         Returns the pymatgen Structure that has been setup for the identification of geometries (the initial one
         might have been refined/symmetrized using the SpaceGroupAnalyzer).
-        :return: The pymatgen Structure that has been setup for the identification of geometries (the initial one
+        Returns:
+            The pymatgen Structure that has been setup for the identification of geometries (the initial one
         might have been refined/symmetrized using the SpaceGroupAnalyzer).
         """
         return self.structure
@@ -583,7 +590,9 @@ def compute_structure_environments(
         :param recompute: whether to recompute the sites already computed (when initial_structure_environments
             is not None)
         :param optimization: optimization algorithm
-        :return: The StructureEnvironments object containing all the information about the coordination
+
+        Returns:
+            The StructureEnvironments object containing all the information about the coordination
             environments in the structure.
         """
         time_init = time.process_time()
@@ -1121,7 +1130,8 @@ def setup_explicit_indices_local_geometry(self, explicit_indices):
     def get_coordination_symmetry_measures(self, only_minimum=True, all_csms=True, optimization=None):
         """
         Returns the continuous symmetry measures of the current local geometry in a dictionary.
-        :return: the continuous symmetry measures of the current local geometry in a dictionary.
+        Returns:
+            the continuous symmetry measures of the current local geometry in a dictionary.
         """
         test_geometries = self.allcg.get_implemented_geometries(len(self.local_geometry.coords))
         if len(self.local_geometry.coords) == 1:
@@ -1249,7 +1259,8 @@ def get_coordination_symmetry_measures_optim(
     ):
         """
         Returns the continuous symmetry measures of the current local geometry in a dictionary.
-        :return: the continuous symmetry measures of the current local geometry in a dictionary.
+        Returns:
+            the continuous symmetry measures of the current local geometry in a dictionary.
         """
         cn = len(self.local_geometry.coords)
         test_geometries = self.allcg.get_implemented_geometries(cn)
@@ -1309,7 +1320,9 @@ def coordination_geometry_symmetry_measures(
         the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination
          geometry, different methods are called.
         :param coordination_geometry: Coordination geometry for which the symmetry measures are looked for
-        :return: the symmetry measures of a given coordination_geometry for a set of permutations
+
+        Returns:
+            the symmetry measures of a given coordination_geometry for a set of permutations
         :raise: NotImplementedError if the permutation_setup does not exists.
         """
         if tested_permutations:
@@ -1353,7 +1366,9 @@ def coordination_geometry_symmetry_measures_sepplane_optim(
         the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination
          geometry, different methods are called.
         :param coordination_geometry: Coordination geometry for which the symmetry measures are looked for
-        :return: the symmetry measures of a given coordination_geometry for a set of permutations
+
+        Returns:
+            the symmetry measures of a given coordination_geometry for a set of permutations
         :raise: NotImplementedError if the permutation_setup does not exists.
         """
         csms = []
@@ -1387,7 +1402,9 @@ def coordination_geometry_symmetry_measures_standard(
         for the coordination geometry "coordination_geometry". Standard implementation looking for the symmetry
         measures of each permutation
         :param coordination_geometry: The coordination geometry to be investigated
-        :return: The symmetry measures for the given coordination geometry for each permutation investigated.
+
+        Returns:
+            The symmetry measures for the given coordination geometry for each permutation investigated.
         """
         # permutations_symmetry_measures = np.zeros(len(algo.permutations),
         #                                           np.float_)
@@ -1464,7 +1481,9 @@ def coordination_geometry_symmetry_measures_separation_plane(
         Returns the symmetry measures of the given coordination geometry "coordination_geometry" using separation
         facets to reduce the complexity of the system. Caller to the refined 2POINTS, 3POINTS and other ...
         :param coordination_geometry: The coordination geometry to be investigated
-        :return: The symmetry measures for the given coordination geometry for each plane and permutation investigated.
+
+        Returns:
+            The symmetry measures for the given coordination geometry for each plane and permutation investigated.
         """
         permutations = []
         permutations_symmetry_measures = []
@@ -1988,7 +2007,9 @@ def coordination_geometry_symmetry_measures_fallback_random(
         of each permutation
         :param coordination_geometry: The coordination geometry to be investigated
         :param NRANDOM: Number of random permutations to be tested
-        :return: The symmetry measures for the given coordination geometry for each permutation investigated.
+
+        Returns:
+            The symmetry measures for the given coordination geometry for each permutation investigated.
         """
         permutations_symmetry_measures = [None] * NRANDOM
         permutations = []