Refactor to only require pymatgen-core, and fix docs building (#224)

* Update imports to match latest ``pymatgen``, and update minimum version

* Fix docs building issue

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: kavanase

.github/workflows/testing.yml

@@ -34,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
@@ -59,7 +59,7 @@ jobs:
         run: pytest --nbmake ./docs/source/content
 
       - uses: codecov/codecov-action@v4
-        if: matrix.python-version == '3.10'
+        if: matrix.python-version == '3.13'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
@@ -79,7 +79,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.13"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -88,10 +88,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e .[docs]
       - name: Build
-        if: github.ref == 'refs/heads/develop'
-        # This line below is wrong and needs to be updated
         run: jupyter-book build --path-output docs docs/source
-        # Develop branch only
       - name: Deploy
         if: github.ref == 'refs/heads/main'
         uses: peaceiris/actions-gh-pages@v4

pymatgen/analysis/defects/ccd.py

@@ -184,7 +184,7 @@ def _parse_vasprun(vasprun: Vasprun) -> tuple[float, Structure]:
             energy_struct[-1],
             lambda x, y: get_dQ(x[1], y[1]),
         )
-        energies, structures = list(zip(*sorted_list))
+        energies, structures = list(zip(*sorted_list, strict=False))
 
         if not np.allclose(unsorted_e, energies, atol=1e-99):  # pragma: no cover
             msg = "The vaspruns should already be in order."
@@ -347,7 +347,8 @@ def read_wswqs(
                 msg,
             )
         self.wswqs = [
-            {"Q": d, "wswq": WSWQ.from_file(f)} for d, f in zip(distortions, wswq_files)
+            {"Q": d, "wswq": WSWQ.from_file(f)}
+            for d, f in zip(distortions, wswq_files, strict=False)
         ]
 
     def get_elph_me(self, defect_state: tuple) -> npt.ArrayLike:
@@ -574,7 +575,7 @@ def get_dQ(ground: Structure, excited: Structure) -> float:
         np.sum(
             [
                 x[0].distance(x[1]) ** 2 * x[0].specie.atomic_mass
-                for x in zip(ground, excited)
+                for x in zip(ground, excited, strict=False)
             ],
         ),
     )
@@ -631,7 +632,12 @@ def _get_wswq_slope(distortions: list[float], wswqs: list[WSWQ]) -> npt.NDArray:
             Since there is always ambiguity in the phase, we require that the output
             is always positive.
     """
-    yy = np.stack([np.abs(ww.data) * np.sign(qq) for qq, ww in zip(distortions, wswqs)])
+    yy = np.stack(
+        [
+            np.abs(ww.data) * np.sign(qq)
+            for qq, ww in zip(distortions, wswqs, strict=False)
+        ]
+    )
     _, *oldshape = yy.shape
     return np.polyfit(distortions, yy.reshape(yy.shape[0], -1), deg=1)[0].reshape(
         *oldshape,

pymatgen/analysis/defects/core.py

@@ -11,18 +11,19 @@
 import numpy as np
 from monty.json import MSONable
 from pymatgen.analysis.defects.supercells import get_sc_fromstruct
-from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core import Element, PeriodicSite, Species
 from pymatgen.core.periodic_table import DummySpecies
+from pymatgen.core.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
 from .utils import get_plane_spacing
 
 if TYPE_CHECKING:
+    from typing import Self
+
     from numpy.typing import ArrayLike
     from pymatgen.core import Structure
     from pymatgen.symmetry.structure import SymmetrizedStructure
-    from typing_extensions import Self
 
 # TODO Possible redesign idea: ``DefectSite`` class defined with a defect object.
 # This makes some of the accounting logic a bit harder since we will probably

pymatgen/analysis/defects/corrections/freysoldt.py

@@ -162,6 +162,7 @@ def get_freysoldt_correction(
         list_bulk_plnr_avg_esp,
         list_defect_plnr_avg_esp,
         [0, 1, 2],
+        strict=False,
     ):
         alignment_corr, md = perform_pot_corr(
             axis_grid=x,

pymatgen/analysis/defects/finder.py

@@ -124,7 +124,10 @@ def get_native_defect_position(
             (in fractional coordinates)
         """
         distored_sites, distortions = list(
-            zip(*self.get_most_distorted_sites(defect_structure, base_structure)),
+            zip(
+                *self.get_most_distorted_sites(defect_structure, base_structure),
+                strict=False,
+            ),
         )
         positions = [defect_structure[isite].frac_coords for isite in distored_sites]
         return get_weighted_average_position(
@@ -370,7 +373,7 @@ def get_weighted_average_position(
         raise ValueError(msg)
 
     # TODO: can be replaced with the zip(..., strict=True) syntax in Python 3.10
-    pos_weights = list(zip(frac_positions, weights))
+    pos_weights = list(zip(frac_positions, weights, strict=False))
     pos_weights.sort(key=lambda x: x[1], reverse=True)
 
     # initial guess at the center with zero weight

pymatgen/analysis/defects/generators.py

@@ -388,7 +388,9 @@ def generate(  # type: ignore[override]
             raise ValueError(msg)
         cand_sites_mul_and_equiv_fpos = [*self._get_candidate_sites(structure)]
         for species in insert_species:
-            cand_sites, multiplicity, equiv_fpos = zip(*cand_sites_mul_and_equiv_fpos)
+            cand_sites, multiplicity, equiv_fpos = zip(
+                *cand_sites_mul_and_equiv_fpos, strict=False
+            )
 
             yield from super().generate(
                 structure,
@@ -490,7 +492,9 @@ def generate(  # type: ignore[override]
             raise ValueError(msg)
         cand_sites_mul_and_equiv_fpos = [*self._get_candidate_sites(chgcar)]
         for species in insert_species:
-            cand_sites, multiplicity, equiv_fpos = zip(*cand_sites_mul_and_equiv_fpos)
+            cand_sites, multiplicity, equiv_fpos = zip(
+                *cand_sites_mul_and_equiv_fpos, strict=False
+            )
             if self.max_insertions is not None:
                 cand_sites = cand_sites[: self.max_insertions]
                 multiplicity = multiplicity[: self.max_insertions]

pymatgen/analysis/defects/plotting/thermo.py

@@ -59,7 +59,7 @@ def _plot_line(
     Returns:
         None, modifies the fig object in place.
     """
-    x_pos, y_pos = tuple(zip(*pts))
+    x_pos, y_pos = tuple(zip(*pts, strict=False))
     trace_ = go.Scatter(
         x=x_pos,
         y=y_pos,
@@ -108,13 +108,13 @@ def _label_slopes(fig: go.Figure) -> None:
         fig: A plotly figure object.
     """
     for data_ in filter(lambda x: x.meta.get("formation_energy_plot", False), fig.data):
-        transitions_arr_ = np.array(tuple(zip(data_.x, data_.y)))
+        transitions_arr_ = np.array(tuple(zip(data_.x, data_.y, strict=False)))
         diff_arr = transitions_arr_[1:] - transitions_arr_[:-1]
         slopes = tuple(
             int(slope) for slope in np.round(diff_arr[:, 1] / diff_arr[:, 0])
         )
         pos = (transitions_arr_[:-1] + transitions_arr_[1:]) / 2.0
-        x_pos, y_pos = tuple(zip(*pos))
+        x_pos, y_pos = tuple(zip(*pos, strict=False))
         fig.add_trace(
             go.Scatter(
                 x=x_pos,
@@ -203,6 +203,7 @@ def get_plot_data(
         grouped_feds,
         get_line_style_and_color_sequence(PLOTLY_COLORS, PLOTLY_STYLES),
         x_annos_,
+        strict=False,
     ):
         if chempot is None:
             cation_el_ = fed.chempot_diagram.elements[0]

pymatgen/analysis/defects/recombination.py

@@ -7,13 +7,16 @@
 
 import itertools
 import logging
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
 
 import numpy as np
 from scipy.interpolate import PchipInterpolator
 
 from .constants import AMU2KG, ANGS2M, EV2J, HBAR_EV, HBAR_J, KB, LOOKUP_TABLE
 
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
 _logger = logging.getLogger(__name__)
 
 try:

pymatgen/analysis/defects/supercells.py

@@ -8,8 +8,8 @@
 
 import numpy as np
 from monty.dev import deprecated
-from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core import Lattice
+from pymatgen.core.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.util.coord_cython import pbc_shortest_vectors
 
 # from ase.build import find_optimal_cell_shape, get_deviation_from_optimal_cell_shape

pymatgen/analysis/defects/thermo.py

@@ -7,7 +7,7 @@
 from dataclasses import dataclass, field
 from itertools import chain, groupby
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 from matplotlib import pyplot as plt
@@ -20,18 +20,18 @@
 from pymatgen.analysis.defects.supercells import get_closest_sc_mat
 from pymatgen.analysis.defects.utils import get_zfile, group_docs
 from pymatgen.analysis.phase_diagram import PhaseDiagram
-from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core import Composition, Element
+from pymatgen.core.entries import ComputedEntry
+from pymatgen.core.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.electronic_structure.dos import FermiDos
-from pymatgen.entries.computed_entries import ComputedEntry
 from pymatgen.io.vasp import Locpot, Vasprun, VolumetricData
 from pyrho.charge_density import get_volumetric_like_sc
 from scipy.constants import value as _cd
 from scipy.optimize import bisect
 from scipy.spatial import ConvexHull
 
 if TYPE_CHECKING:
-    from collections.abc import Generator, Sequence
+    from collections.abc import Callable, Generator, Sequence
 
     from matplotlib.axes import Axes
     from numpy.typing import ArrayLike, NDArray
@@ -523,7 +523,7 @@ def _vbm_formation_energy(self, defect_entry: DefectEntry, chempots: dict) -> fl
     def chempot_limits(self) -> list[dict[Element, float]]:
         """Return the chemical potential limits in dictionary format."""
         return [
-            dict(zip(self.chempot_diagram.elements, vertex))
+            dict(zip(self.chempot_diagram.elements, vertex, strict=False))
             for vertex in self._chempot_limits_arr
         ]
 
@@ -535,7 +535,9 @@ def competing_phases(self) -> list[dict[str, ComputedEntry]]:
         res = []
         for pt in self._chempot_limits_arr:
             competing_phases = {}
-            for hp_ent, hp in zip(cd._hyperplane_entries, cd._hyperplanes):
+            for hp_ent, hp in zip(
+                cd._hyperplane_entries, cd._hyperplanes, strict=False
+            ):
                 if hp_ent.composition.reduced_formula == bulk_formula:
                     continue
                 if _is_on_hyperplane(pt, hp):