Hide all type-hint-only imports behind if TYPE_CHECKING (#2992)

* remove unnecessary decimal points (.0)

* fix mypy

* ruff enable TCH (flake8-type-checking)

* hide all type-hint-only imports behind if TYPE_CHECKING

remove numpy.typing.ArrayLike re-export from pymatgen/util/typing.py

* shorten import pymatgen.core.(structure.)Structure

* fix mypy

Author: janosh

dev_scripts/chemenv/plane_multiplicity.py

@@ -32,8 +32,7 @@
             equiv_plane.extend(opposite_edge)
             equiv_plane.sort()
             all_plane_points.append(tuple(equiv_plane))
-        all_plane_points = list(set(all_plane_points))
-        all_plane_points = [list(equiv_plane) for equiv_plane in all_plane_points]
+        all_plane_points = [tuple(equiv_plane) for equiv_plane in set(all_plane_points)]
 
     print(f"All plane points ({len(all_plane_points):d}) for {cg_symbol} : ")
     print(all_plane_points)

dev_scripts/chemenv/test_algos.py

@@ -87,7 +87,7 @@
             algos_results.append(min(results[0]))
 
             if not np.isclose(min(results[0]), 0):
-                print("Following is not 0.0 ...")
+                print("Following is not 0 ...")
                 input(results)
         print("   => ", algos_results)
         idx_perm += 1

dev_scripts/chemenv/test_algos_all_geoms.py

@@ -118,7 +118,7 @@
                     algos_results.append(min(results[0]))
 
                     if not min(results[0]) < 1.5:
-                        print("Following is not close to 0.0 ...")
+                        print("Following is not close to 0 ...")
                         input(results)
                 print("   => ", algos_results)
                 i_perm += 1

docs_rst/conf-normal.py

@@ -204,7 +204,7 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements = {
+latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
     # The font size ('10pt', '11pt' or '12pt').

pymatgen/alchemy/filters.py

@@ -6,14 +6,17 @@
 
 import abc
 from collections import defaultdict
+from typing import TYPE_CHECKING
 
 from monty.json import MSONable
 
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core.periodic_table import get_el_sp
-from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
 
 class AbstractStructureFilter(MSONable, metaclass=abc.ABCMeta):
     """

pymatgen/alchemy/materials.py

@@ -10,19 +10,21 @@
 import json
 import os
 import re
-from typing import Any
+from typing import TYPE_CHECKING, Any
 from warnings import warn
 
 from monty.json import MSONable, jsanitize
 
-from pymatgen.alchemy.filters import AbstractStructureFilter
 from pymatgen.core.structure import Structure
 from pymatgen.io.cif import CifParser
 from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.io.vasp.sets import MPRelaxSet, VaspInputSet
-from pymatgen.transformations.transformation_abc import AbstractTransformation
 from pymatgen.util.provenance import StructureNL
 
+if TYPE_CHECKING:
+    from pymatgen.alchemy.filters import AbstractStructureFilter
+    from pymatgen.transformations.transformation_abc import AbstractTransformation
+
 
 class TransformedStructure(MSONable):
     """

pymatgen/analysis/bond_valence.py

@@ -181,7 +181,7 @@ def _calc_site_probabilities(self, site, nn):
         try:
             prob = {k: v / sum(prob.values()) for k, v in prob.items()}
         except ZeroDivisionError:
-            prob = {k: 0.0 for k in prob}
+            prob = {key: 0 for key in prob}
         return prob
 
     def _calc_site_probabilities_unordered(self, site, nn):
@@ -202,7 +202,7 @@ def _calc_site_probabilities_unordered(self, site, nn):
             try:
                 prob[el] = {k: v / sum(prob[el].values()) for k, v in prob[el].items()}
             except ZeroDivisionError:
-                prob[el] = {k: 0.0 for k in prob[el]}
+                prob[el] = {key: 0 for key in prob[el]}
         return prob
 
     def get_valences(self, structure):

pymatgen/analysis/chemenv/utils/defs_utils.py

@@ -4,10 +4,15 @@
 
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import (
     is_anion_cation_bond,
 )
-from pymatgen.core.structure import Structure
+
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
 
 __author__ = "David Waroquiers"
 __copyright__ = "Copyright 2012, The Materials Project"

pymatgen/analysis/chempot_diagram.py

@@ -27,6 +27,7 @@
 import warnings
 from functools import lru_cache
 from itertools import groupby
+from typing import TYPE_CHECKING
 
 import numpy as np
 import plotly.express as px
@@ -36,10 +37,12 @@
 
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.core.composition import Composition, Element
-from pymatgen.entries.computed_entries import ComputedEntry
 from pymatgen.util.coord import Simplex
 from pymatgen.util.string import htmlify
 
+if TYPE_CHECKING:
+    from pymatgen.entries.computed_entries import ComputedEntry
+
 with open(os.path.join(os.path.dirname(__file__), "..", "util", "plotly_chempot_layouts.json")) as f:
     plotly_layouts = json.load(f)
 

pymatgen/analysis/diffraction/core.py

@@ -6,13 +6,16 @@
 
 import abc
 import collections
+from typing import TYPE_CHECKING
 
 import numpy as np
 
 from pymatgen.core.spectrum import Spectrum
-from pymatgen.core.structure import Structure
 from pymatgen.util.plotting import add_fig_kwargs
 
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
 
 class DiffractionPattern(Spectrum):
     """

pymatgen/analysis/diffraction/neutron.py

@@ -7,6 +7,7 @@
 import json
 import os
 from math import asin, cos, degrees, pi, radians, sin
+from typing import TYPE_CHECKING
 
 import numpy as np
 
@@ -15,9 +16,11 @@
     DiffractionPattern,
     get_unique_families,
 )
-from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
 __author__ = "Yuta Suzuki"
 __copyright__ = "Copyright 2018, The Materials Project"
 __version__ = "0.1"

pymatgen/analysis/diffraction/tem.py

@@ -11,18 +11,20 @@
 from collections import namedtuple
 from fractions import Fraction
 from functools import lru_cache
-from typing import List, Tuple, cast
+from typing import TYPE_CHECKING, List, Tuple, cast
 
 import numpy as np
 import pandas as pd
 import plotly.graph_objs as go
 import scipy.constants as sc
 
 from pymatgen.analysis.diffraction.core import AbstractDiffractionPatternCalculator
-from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.util.string import latexify_spacegroup, unicodeify_spacegroup
 
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
 with open(os.path.join(os.path.dirname(__file__), "atomic_scattering_params.json")) as f:
     ATOMIC_SCATTERING_PARAMS = json.load(f)
 

pymatgen/analysis/diffraction/xrd.py

@@ -7,6 +7,7 @@
 import json
 import os
 from math import asin, cos, degrees, pi, radians, sin
+from typing import TYPE_CHECKING
 
 import numpy as np
 
@@ -15,9 +16,11 @@
     DiffractionPattern,
     get_unique_families,
 )
-from pymatgen.core.structure import Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
 # XRD wavelengths in angstroms
 WAVELENGTHS = {
     "CuKa": 1.54184,

pymatgen/analysis/disorder.py

@@ -6,8 +6,10 @@
 
 import collections
 import itertools
+from typing import TYPE_CHECKING
 
-from pymatgen.core.structure import Structure
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
 
 
 def get_warren_cowley_parameters(structure: Structure, r: float, dr: float) -> dict[tuple, float]:

pymatgen/analysis/elasticity/elastic.py

@@ -8,6 +8,7 @@
 
 import itertools
 import warnings
+from typing import TYPE_CHECKING
 
 import numpy as np
 import sympy as sp
@@ -17,7 +18,6 @@
 
 from pymatgen.analysis.elasticity.strain import Strain
 from pymatgen.analysis.elasticity.stress import Stress
-from pymatgen.core.structure import Structure
 from pymatgen.core.tensors import (
     DEFAULT_QUAD,
     SquareTensor,
@@ -27,6 +27,10 @@
 )
 from pymatgen.core.units import Unit
 
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
+
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"
 __credits__ = "Maarten de Jong, Ian Winter, Shyam Dwaraknath, Mark Asta, Anubhav Jain"
@@ -308,7 +312,7 @@ def snyder_ac(self, structure):
             0.38483
             * avg_mass
             * ((self.long_v(structure) + 2.0 * self.trans_v(structure)) / 3.0) ** 3.0
-            / (300.0 * num_density ** (-2.0 / 3.0) * nsites ** (1.0 / 3.0))
+            / (300.0 * num_density ** (-2.0 / 3.0) * nsites ** (1 / 3))
         )
 
     @raise_error_if_unphysical
@@ -329,7 +333,7 @@ def snyder_opt(self, structure):
             * (self.long_v(structure) + 2.0 * self.trans_v(structure))
             / 3.0
             / num_density ** (-2.0 / 3.0)
-            * (1 - nsites ** (-1.0 / 3.0))
+            * (1 - nsites ** (-1 / 3))
         )
 
     @raise_error_if_unphysical
@@ -391,8 +395,8 @@ def debye_temperature(self, structure):
         """
         v0 = structure.volume * 1e-30 / structure.num_sites
         vl, vt = self.long_v(structure), self.trans_v(structure)
-        vm = 3 ** (1.0 / 3.0) * (1 / vl**3 + 2 / vt**3) ** (-1.0 / 3.0)
-        td = 1.05457e-34 / 1.38065e-23 * vm * (6 * np.pi**2 / v0) ** (1.0 / 3.0)
+        vm = 3 ** (1 / 3) * (1 / vl**3 + 2 / vt**3) ** (-1 / 3)
+        td = 1.05457e-34 / 1.38065e-23 * vm * (6 * np.pi**2 / v0) ** (1 / 3)
         return td
 
     @property

pymatgen/analysis/elasticity/strain.py

@@ -8,15 +8,18 @@
 
 import collections
 import itertools
-from typing import Literal
+from typing import TYPE_CHECKING, Literal
 
 import numpy as np
 import scipy
 
 from pymatgen.core.lattice import Lattice
-from pymatgen.core.structure import Structure
 from pymatgen.core.tensors import SquareTensor, symmetry_reduce
-from pymatgen.util.typing import ArrayLike
+
+if TYPE_CHECKING:
+    from numpy.typing import ArrayLike
+
+    from pymatgen.core.structure import Structure
 
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"

pymatgen/analysis/elasticity/stress.py

@@ -55,7 +55,7 @@ def dev_principal_invariants(self):
     @property
     def von_mises(self):
         """
-        Returns the von mises stress
+        Returns the von Mises stress
         """
         if not self.is_symmetric():
             raise ValueError(
@@ -68,7 +68,7 @@ def mean_stress(self):
         """
         Returns the mean stress
         """
-        return 1.0 / 3.0 * self.trace()
+        return 1 / 3 * self.trace()
 
     @property
     def deviator_stress(self):

pymatgen/analysis/elasticity/tests/test_stress.py

@@ -19,7 +19,7 @@ def setUp(self):
     def test_properties(self):
         # mean_stress
         assert self.rand_stress.mean_stress == pytest.approx(
-            1.0 / 3.0 * (self.rand_stress[0, 0] + self.rand_stress[1, 1] + self.rand_stress[2, 2])
+            (self.rand_stress[0, 0] + self.rand_stress[1, 1] + self.rand_stress[2, 2]) / 3
         )
         assert self.symm_stress.mean_stress == pytest.approx(3.66)
         # deviator_stress
@@ -29,11 +29,7 @@ def test_properties(self):
         )
         self.assertArrayAlmostEqual(
             self.non_symm.deviator_stress,
-            [
-                [-0.2666666667, 0.2, 0.3],
-                [0.4, 0.133333333, 0.6],
-                [0.2, 0.5, 0.133333333],
-            ],
+            [[-0.2666666667, 0.2, 0.3], [0.4, 0.133333333, 0.6], [0.2, 0.5, 0.133333333]],
         )
         # deviator_principal_invariants
         self.assertArrayAlmostEqual(self.symm_stress.dev_principal_invariants, [0, 44.2563, 111.953628])