relocate dunder methods to top for core.trajectory

fix `core.operations` add types for site, mypy errors to fix remove no_type_check decorator move dunder methods to the top fix mypy errors remove debug tag improve `spectrum` finish `core.tensors` finish `xcfunc` fix hash of `SymmOp` finish `core.trajectory` Add types for `core.molecular_orbitals/operations/sites/spectrum/tensor/xcfunc` (materialsproject#3829) * fix `core.molecular_orbitals` * fix `core.operations` * add types for site, mypy errors to fix * remove no_type_check decorator * move dunder methods to the top * fix mypy errors * remove debug tag * improve `spectrum` * finish `core.tensors` * finish `xcfunc` * fix hash of `SymmOp` * add a missing type * Revert "fix hash of `SymmOp`" This reverts commit bf2a953. * fix some types in operations * "TEST": remove one unused var, relocate another * final tweak types * avoid hard-code class name * format tweaks * type tweak * fix unit test * replace all `[0:x]` with `[:x]` Guard `TYPE_CHECKING` only imports (materialsproject#3827) * flake8 --select=TYP001 * fix type import * format docstring to google style * fix more unguarded typecheck imports * format more docs to Google format * trigger CI (better var names) --------- Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com> move structures out of util dir (materialsproject#3831) Add matgenb in the aux link section. Because apparently it is not "discoverable". Fixes materialsproject#3811. More updates. Move AIMS notebooks to matgenb. Add README in examples folder that point to proper resources. Improve type annotations and comments for `io.cif` (materialsproject#3820) * remove duplicate warning * type and docstring tweaks * add some types for io.cif * add comments and types * temp save of some formatting * revert functional change * revert unrelated changes * fix unit test * remove update that does nothing * relocate `sub_space_group` and `space_groups` to their usage * add more types * pre-commit auto-fixes * breaking: make parse_magmom/oxi_stats private * remove merge header * fix unit test * add more types * fix mypy errors * add a few spaces * remove if name ==main * simplify "check to see if" in comments * final tweaks * revise docstring * replace deprecated abc.abstractproperty * add missing doc strings and standardize existing * breaking: fix typo in method name orthongonalize_structure * revert accidental change in test_composition.py --------- Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
DanielYang59 · May 16, 2024 · 1683c18 · 1683c18
1 parent 51180fc
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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