Merge branch 'master' into type-core-remain2-struct-unit-tracj

materialsproject · May 16, 2024 · 43096cf · 43096cf
2 parents f448ec7 + bb68c78
commit 43096cf
Show file tree

Hide file tree

Showing 116 changed files with 1,045 additions and 1,057 deletions.
diff --git a/docs/_config.yml b/docs/_config.yml
diff --git a/docs/index.md b/docs/index.md
diff --git a/docs/pymatgen.md b/docs/pymatgen.md
diff --git a/examples/README.md b/examples/README.md
@@ -0,0 +1,7 @@
+All examples are housed at [matgenb]. Please consult this resource first.
+
+If there are questions that cannot be found in the examples, you may use the [pymatgen MatSci forum] or [GitHub discussion].
+
+[matgenb]: https://matgenb.materialsvirtuallab.org/
+[pymatgen MatSci forum]: https://matsci.org/pymatgen
+[github discussion]: https://github.com/materialsproject/pymatgen/discussions
diff --git a/examples/aims_io/FHI-aims-example.ipynb b/examples/aims_io/FHI-aims-example.ipynb
diff --git a/pymatgen/alchemy/materials.py b/pymatgen/alchemy/materials.py
@@ -8,7 +8,7 @@
 import datetime
 import json
 import re
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 from warnings import warn
 
 from monty.json import MSONable, jsanitize
@@ -22,15 +22,15 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Any
 
     from typing_extensions import Self
 
     from pymatgen.alchemy.filters import AbstractStructureFilter
 
 
 class TransformedStructure(MSONable):
-    """Container object for new structures that include history of
-    transformations.
+    """Container for new structures that include history of transformations.
 
     Each transformed structure is made up of a sequence of structures with
     associated transformation history.

diff --git a/pymatgen/alchemy/transmuters.py b/pymatgen/alchemy/transmuters.py
@@ -12,13 +12,14 @@
 import os
 import re
 from multiprocessing import Pool
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
 
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.io.vasp.sets import MPRelaxSet, VaspInputSet
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Callable
 
     from typing_extensions import Self
 

diff --git a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py b/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py
@@ -1265,7 +1265,7 @@ def from_dict(cls, dct: dict) -> Self:
 
 
 class NbSetWeight(MSONable, abc.ABC):
-    """Abstract object for neighbors sets weights estimations."""
+    """Abstract base class for neighbor set weight estimations."""
 
     @abc.abstractmethod
     def as_dict(self):
@@ -1282,7 +1282,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
 
 
@@ -1313,7 +1313,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.aw(nb_set=nb_set)
 
@@ -1534,7 +1534,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         fda_list = self.fda(nb_set=nb_set)
         return self.eval(fda_list=fda_list)
@@ -1680,7 +1680,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         effective_csm = get_effective_csm(
             nb_set=nb_set,
@@ -1791,7 +1791,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         effcsm = get_effective_csm(
             nb_set=nb_set,
@@ -2006,7 +2006,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.cn_weights[len(nb_set)]
 
@@ -2186,7 +2186,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.area_weight(
             nb_set=nb_set,
@@ -2379,7 +2379,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.weight_rf.eval(nb_set.distance_plateau())
 
@@ -2446,7 +2446,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.weight_rf.eval(nb_set.angle_plateau())
 
@@ -2509,7 +2509,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         cn = cn_map[0]
         isite = nb_set.isite
@@ -2590,7 +2590,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         cn = cn_map[0]
         isite = nb_set.isite