fix/ignore some mypy errors, still some left

ADMIN.md

@@ -8,7 +8,7 @@ following assumes you are using miniconda or Anaconda.
 The general procedure to releasing pymatgen comprises the following
 steps:
 
-1. Wait for all unittests to pass on CircleCI.
+1. Make sure all CI checks are green. We don't want to release known bugs.
 2. Update and edit change log.
 3. Release PyPI versions + doc.
 4. Release conda versions.

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -2,6 +2,8 @@
 Connected components.
 """
 
+from __future__ import annotations
+
 import itertools
 import logging
 
@@ -222,7 +224,7 @@ def __init__(
         Returns:
             ConnectedComponent: Instance of this class
         """
-        self._periodicity_vectors = None
+        self._periodicity_vectors: list[list] | None = None
         self._primitive_reduced_connected_subgraph = None
         self._projected = False
         if graph is None:
@@ -420,7 +422,7 @@ def compute_periodicity_all_simple_paths_algorithm(self):
             paths = []
             # TODO: its probably possible to do just a dfs or bfs traversal instead of taking all simple paths!
             test_node_neighbors = my_simple_graph.neighbors(test_node)
-            breaknodeloop = False
+            break_node_loop = False
             for test_node_neighbor in test_node_neighbors:
                 # Special case for two nodes
                 if len(self._connected_subgraph[test_node][test_node_neighbor]) > 1:
@@ -442,7 +444,7 @@ def compute_periodicity_all_simple_paths_algorithm(self):
                     test_node_neighbor,
                     cutoff=len(self._connected_subgraph),
                 ):
-                    path_indices = [nodepath.isite for nodepath in path]
+                    path_indices = [node_path.isite for node_path in path]
                     if path_indices == [test_node.isite, test_node_neighbor.isite]:
                         continue
                     path_indices.append(test_node.isite)
@@ -465,9 +467,9 @@ def compute_periodicity_all_simple_paths_algorithm(self):
                     this_node_cell_img_vectors.extend(this_path_deltas)
                     this_node_cell_img_vectors = get_linearly_independent_vectors(this_node_cell_img_vectors)
                     if len(this_node_cell_img_vectors) == 3:
-                        breaknodeloop = True
+                        break_node_loop = True
                         break
-                if breaknodeloop:
+                if break_node_loop:
                     break
             this_node_cell_img_vectors = get_linearly_independent_vectors(this_node_cell_img_vectors)
             independent_cell_img_vectors = this_node_cell_img_vectors
@@ -504,7 +506,6 @@ def compute_periodicity_cycle_basis(self):
             all_deltas.extend(this_cycle_deltas)
             all_deltas = get_linearly_independent_vectors(all_deltas)
             if len(all_deltas) == 3:
-                self._periodicity_vectors = all_deltas
                 return
         # One has to consider pairs of nodes with parallel edges (these are not considered in the simple graph cycles)
         edges = my_simple_graph.edges()
@@ -603,6 +604,7 @@ def is_0d(self) -> bool:
         """
         if self._periodicity_vectors is None:
             self.compute_periodicity()
+        assert self._periodicity_vectors is not None  # fix mypy arg 1 to len has incompatible type Optional
         return len(self._periodicity_vectors) == 0
 
     @property
@@ -612,6 +614,7 @@ def is_1d(self) -> bool:
         """
         if self._periodicity_vectors is None:
             self.compute_periodicity()
+        assert self._periodicity_vectors is not None  # fix mypy arg 1 to len has incompatible type Optional
         return len(self._periodicity_vectors) == 1
 
     @property
@@ -621,6 +624,7 @@ def is_2d(self) -> bool:
         """
         if self._periodicity_vectors is None:
             self.compute_periodicity()
+        assert self._periodicity_vectors is not None  # fix mypy arg 1 to len has incompatible type Optional
         return len(self._periodicity_vectors) == 2
 
     @property
@@ -630,6 +634,7 @@ def is_3d(self) -> bool:
         """
         if self._periodicity_vectors is None:
             self.compute_periodicity()
+        assert self._periodicity_vectors is not None  # fix mypy arg 1 to len has incompatible type Optional
         return len(self._periodicity_vectors) == 3
 
     @staticmethod

pymatgen/analysis/magnetism/analyzer.py

@@ -858,7 +858,7 @@ def _generate_transformations(self, structure: Structure) -> dict[str, MagOrderi
             fm_structure = analyzer.get_ferromagnetic_structure()
             # store magmom as spin property, to be consistent with output from
             # other transformations
-            fm_structure.add_spin_by_site(fm_structure.site_properties["magmom"])
+            fm_structure.add_spin_by_site(fm_structure.site_properties["magmom"])  # type: ignore[arg-type]
             fm_structure.remove_site_property("magmom")
 
             # we now have our first magnetic ordering...

pymatgen/core/operations.py

@@ -111,7 +111,7 @@ def operate(self, point: ArrayLike) -> np.ndarray:
         Returns:
             Coordinates of point after operation.
         """
-        affine_point = np.array([point[0], point[1], point[2], 1])
+        affine_point = np.array([*point, 1])  # type: ignore
         return np.dot(self.affine_matrix, affine_point)[0:3]
 
     def operate_multi(self, points: ArrayLike) -> np.ndarray:
@@ -577,7 +577,7 @@ class or as list or np array-like
         return Magmom.from_global_moment_and_saxis(transformed_moment, magmom.saxis)
 
     @classmethod
-    def from_symmop(cls, symmop, time_reversal) -> MagSymmOp:
+    def from_symmop(cls, symmop: SymmOp, time_reversal) -> MagSymmOp:
         """
         Initialize a MagSymmOp from a SymmOp and time reversal operator.
 
@@ -588,8 +588,8 @@ def from_symmop(cls, symmop, time_reversal) -> MagSymmOp:
         Returns:
             MagSymmOp object
         """
-        magsymmop = cls(symmop.affine_matrix, time_reversal, symmop.tol)
-        return magsymmop
+        mag_symmop = cls(symmop.affine_matrix, time_reversal, symmop.tol)
+        return mag_symmop
 
     @staticmethod
     def from_rotation_and_translation_and_time_reversal(
@@ -611,10 +611,10 @@ def from_rotation_and_translation_and_time_reversal(
         Returns:
             MagSymmOp object
         """
-        symmop = SymmOp.from_rotation_and_translation(
+        symm_op = SymmOp.from_rotation_and_translation(
             rotation_matrix=rotation_matrix, translation_vec=translation_vec, tol=tol
         )
-        return MagSymmOp.from_symmop(symmop, time_reversal)
+        return MagSymmOp.from_symmop(symm_op, time_reversal)
 
     @staticmethod
     def from_xyzt_string(xyzt_string: str) -> MagSymmOp:
@@ -626,12 +626,12 @@ def from_xyzt_string(xyzt_string: str) -> MagSymmOp:
         Returns:
             MagSymmOp object
         """
-        symmop = SymmOp.from_xyz_string(xyzt_string.rsplit(",", 1)[0])
+        symm_op = SymmOp.from_xyz_string(xyzt_string.rsplit(",", 1)[0])
         try:
             time_reversal = int(xyzt_string.rsplit(",", 1)[1])
         except Exception:
             raise Exception("Time reversal operator could not be parsed.")
-        return MagSymmOp.from_symmop(symmop, time_reversal)
+        return MagSymmOp.from_symmop(symm_op, time_reversal)
 
     def as_xyzt_string(self) -> str:
         """

pymatgen/core/structure.py

@@ -309,18 +309,18 @@ def atomic_numbers(self) -> tuple[int, ...]:
             raise AttributeError("atomic_numbers available only for ordered Structures")
 
     @property
-    def site_properties(self) -> dict[str, list]:
+    def site_properties(self) -> dict[str, Sequence]:
         """
         Returns the site properties as a dict of sequences. E.g.,
         {"magmom": (5,-5), "charge": (-4,4)}.
         """
-        props: dict[str, list] = {}
+        props: dict[str, Sequence] = {}
         prop_keys: set[str] = set()
         for site in self:
             prop_keys.update(site.properties)
 
-        for k in prop_keys:
-            props[k] = [site.properties.get(k, None) for site in self]
+        for key in prop_keys:
+            props[key] = [site.properties.get(key) for site in self]
         return props
 
     def __contains__(self, site: object) -> bool:

pymatgen/core/trajectory.py

@@ -12,7 +12,7 @@
 import warnings
 from fnmatch import fnmatch
 from pathlib import Path
-from typing import Any, Dict, List, Tuple, Union
+from typing import Any, Dict, List, Sequence, Tuple, Union
 
 import numpy as np
 from monty.io import zopen
@@ -34,7 +34,7 @@
 
 Vector3D = Tuple[float, float, float]
 Matrix3D = Tuple[Vector3D, Vector3D, Vector3D]
-SitePropsType = Union[List[Dict[Any, List[Any]]], Dict[Any, List[Any]]]
+SitePropsType = Union[List[Dict[Any, Sequence[Any]]], Dict[Any, Sequence[Any]]]
 
 
 class Trajectory(MSONable):
@@ -445,7 +445,7 @@ def from_structures(
             lattice,
             species,  # type: ignore
             frac_coords,
-            site_properties=site_properties,
+            site_properties=site_properties,  # type: ignore
             constant_lattice=constant_lattice,
             **kwargs,
         )
@@ -503,7 +503,9 @@ def _combine_lattice(lat1: np.ndarray, lat2: np.ndarray, len1: int, len2: int) -
         return lat, constant_lat
 
     @staticmethod
-    def _combine_site_props(prop1: SitePropsType | None, prop2: SitePropsType | None, len1: int, len2: int):
+    def _combine_site_props(
+        prop1: SitePropsType | None, prop2: SitePropsType | None, len1: int, len2: int
+    ) -> SitePropsType | None:
         """
         Combine site properties.
 
@@ -515,7 +517,7 @@ def _combine_site_props(prop1: SitePropsType | None, prop2: SitePropsType | None
         if prop1 is None and prop2 is None:
             return None
 
-        if isinstance(prop1, dict) and isinstance(prop2, dict) and prop1 == prop2:
+        if isinstance(prop1, dict) and prop1 == prop2:
             return prop1
 
         # general case

pymatgen/io/lammps/data.py

@@ -845,7 +845,7 @@ def from_structure(cls, structure: Structure, ff_elements=None, atom_style="char
             velos = np.array(s.site_properties["velocities"])
             rot = SymmOp.from_rotation_and_translation(symm_op.rotation_matrix)
             rot_velos = rot.operate_multi(velos)
-            site_properties.update({"velocities": rot_velos})
+            site_properties.update({"velocities": rot_velos})  # type: ignore
         boxed_s = Structure(
             box.to_lattice(),
             s.species,

pymatgen/symmetry/analyzer.py

@@ -757,9 +757,9 @@ def get_conventional_standard_structure(self, international_monoclinic=True, kee
                 ],
             ]
 
-            def is_all_acute_or_obtuse(m) -> bool:
-                recp_angles = np.array(Lattice(m).reciprocal_lattice.angles)
-                return np.all(recp_angles <= 90) or np.all(recp_angles > 90)
+            def is_all_acute_or_obtuse(matrix) -> bool:
+                recp_angles = np.array(Lattice(matrix).reciprocal_lattice.angles)
+                return all(recp_angles <= 90) or all(recp_angles > 90)
 
             if is_all_acute_or_obtuse(test_matrix):
                 transf = np.eye(3)

pymatgen/util/coord.py

@@ -67,7 +67,8 @@ def is_coord_subset(subset, superset, atol=1e-8) -> bool:
     Doesn't use periodic boundary conditions
 
     Args:
-        subset, superset: List of coords
+        subset: List of coords
+        superset: List of coords
 
     Returns:
         True if all of subset is in superset.
@@ -76,7 +77,7 @@ def is_coord_subset(subset, superset, atol=1e-8) -> bool:
     c2 = np.array(superset)
     is_close = np.all(np.abs(c1[:, None, :] - c2[None, :, :]) < atol, axis=-1)
     any_close = np.any(is_close, axis=-1)
-    return np.all(any_close)
+    return all(any_close)
 
 
 def coord_list_mapping(subset, superset, atol=1e-8):