Officially support Python 3.12 and test in CI

.github/workflows/release.yml

@@ -29,7 +29,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Build sdist
         run: |
@@ -45,7 +45,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-14, windows-latest]
-        python-version: ["39", "310", "311"]
+        python-version: ["39", "310", "311", "312"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repo
@@ -68,10 +68,10 @@ jobs:
       # For pypi trusted publishing
       id-token: write
     steps:
-      - name: Set up Python 3.11
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Get build artifacts
         uses: actions/download-artifact@v3

.github/workflows/test.yml

@@ -27,16 +27,16 @@ jobs:
       matrix:
         # pytest-split automatically distributes work load so parallel jobs finish in similar time
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.9", "3.12"]
         split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
         # include/exclude is meant to maximize CI coverage of different platforms and python
         # versions while minimizing the total number of jobs. We run all pytest splits with the
         # oldest supported python version (currently 3.9) on windows (seems most likely to surface
-        # errors) and with newest version (currently 3.11) on ubuntu (to get complete and speedy
+        # errors) and with newest version (currently 3.12) on ubuntu (to get complete and speedy
         # coverage on unix). We ignore mac-os, which is assumed to be similar to ubuntu.
         exclude:
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
           - os: ubuntu-latest
             python-version: "3.9"
 

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -209,7 +209,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
             # Definition of the facets
             all_planes_point_indices = [algo.plane_points]
             if algo.other_plane_points is not None:
-                all_planes_point_indices.extend(algo.other_plane_points)
+                all_planes_point_indices += algo.other_plane_points
 
             # Loop on the facets
             explicit_permutations_per_plane = []
@@ -305,7 +305,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
             # Definition of the facets
             all_planes_point_indices = [algo.plane_points]
             if algo.other_plane_points is not None:
-                all_planes_point_indices.extend(algo.other_plane_points)
+                all_planes_point_indices += algo.other_plane_points
 
             # Setup of the permutations to be used for this algorithm
 

dev_scripts/chemenv/plane_multiplicity.py

@@ -12,11 +12,11 @@
 __date__ = "Feb 20, 2016"
 
 if __name__ == "__main__":
-    allcg = AllCoordinationGeometries()
+    all_cg = AllCoordinationGeometries()
 
     cg_symbol = "I:12"
     all_plane_points = []
-    cg = allcg[cg_symbol]
+    cg = all_cg[cg_symbol]
 
     # I:12
     if cg_symbol == "I:12":
@@ -25,7 +25,7 @@
         for edge in edges:
             opposite_edge = [opposite_points[edge[0]], opposite_points[edge[1]]]
             equiv_plane = list(edge)
-            equiv_plane.extend(opposite_edge)
+            equiv_plane += opposite_edge
             equiv_plane.sort()
             all_plane_points.append(tuple(equiv_plane))
         all_plane_points = [tuple(equiv_plane) for equiv_plane in set(all_plane_points)]

pymatgen/alchemy/materials.py

@@ -228,7 +228,7 @@ def __str__(self) -> str:
         for hist in self.history:
             hist.pop("input_structure", None)
             output.append(str(hist))
-        output.extend(("\nOther parameters", "------------", str(self.other_parameters)))
+        output += ("\nOther parameters", "------------", str(self.other_parameters))
         return "\n".join(output)
 
     def set_parameter(self, key: str, value: Any) -> TransformedStructure:

pymatgen/alchemy/transmuters.py

@@ -130,8 +130,8 @@ def append_transformation(self, transformation, extend_collection=False, clear_r
             for x in self.transformed_structures:
                 new = x.append_transformation(transformation, extend_collection, clear_redo=clear_redo)
                 if new is not None:
-                    new_structures.extend(new)
-            self.transformed_structures.extend(new_structures)
+                    new_structures += new
+            self.transformed_structures += new_structures
 
     def extend_transformations(self, transformations):
         """Extends a sequence of transformations to the TransformedStructure.
@@ -142,7 +142,7 @@ def extend_transformations(self, transformations):
         for trafo in transformations:
             self.append_transformation(trafo)
 
-    def apply_filter(self, structure_filter):
+    def apply_filter(self, structure_filter: Callable):
         """Applies a structure_filter to the list of TransformedStructures
         in the transmuter.
 
@@ -196,11 +196,11 @@ def append_transformed_structures(self, trafo_structs_or_transmuter):
                 transmuter.
         """
         if isinstance(trafo_structs_or_transmuter, self.__class__):
-            self.transformed_structures.extend(trafo_structs_or_transmuter.transformed_structures)
+            self.transformed_structures += trafo_structs_or_transmuter.transformed_structures
         else:
             for ts in trafo_structs_or_transmuter:
                 assert isinstance(ts, TransformedStructure)
-            self.transformed_structures.extend(trafo_structs_or_transmuter)
+            self.transformed_structures += trafo_structs_or_transmuter
 
     @classmethod
     def from_structures(cls, structures, transformations=None, extend_collection=0) -> Self:
@@ -373,7 +373,7 @@ def _apply_transformation(inputs):
     """
     ts, transformation, extend_collection, clear_redo = inputs
     new = ts.append_transformation(transformation, extend_collection, clear_redo=clear_redo)
-    o = [ts]
+    out = [ts]
     if new:
-        o.extend(new)
-    return o
+        out += new
+    return out

pymatgen/io/vasp/outputs.py

@@ -1480,7 +1480,7 @@ def _parse_calculation(self, elem):
         return istep
 
     @staticmethod
-    def _parse_dos(elem):
+    def _parse_dos(elem) -> tuple[Dos, Dos, list[dict]]:
         efermi = float(elem.find("i").text)
         energies = None
         tdensities = {}
@@ -1500,22 +1500,18 @@ def _parse_dos(elem):
             orbs.pop(0)
             lm = any("x" in s for s in orbs)
             for s in partial.find("array").find("set").findall("set"):
-                pdos = defaultdict(dict)
+                pdos: dict[Orbital | OrbitalType, dict[Spin, np.ndarray]] = defaultdict(dict)
 
                 for ss in s.findall("set"):
                     spin = Spin.up if ss.attrib["comment"] == "spin 1" else Spin.down
                     data = np.array(_parse_vasp_array(ss))
-                    _nrow, ncol = data.shape
-                    for j in range(1, ncol):
-                        orb = Orbital(j - 1) if lm else OrbitalType(j - 1)
-                        pdos[orb][spin] = data[:, j]
+                    _n_row, n_col = data.shape
+                    for col_idx in range(1, n_col):
+                        orb = Orbital(col_idx - 1) if lm else OrbitalType(col_idx - 1)
+                        pdos[orb][spin] = data[:, col_idx]  # type: ignore[index]
                 pdoss.append(pdos)
         elem.clear()
-        return (
-            Dos(efermi, energies, tdensities),
-            Dos(efermi, energies, idensities),
-            pdoss,
-        )
+        return Dos(efermi, energies, tdensities), Dos(efermi, energies, idensities), pdoss
 
     @staticmethod
     def _parse_eigen(elem):

setup.py

@@ -48,10 +48,11 @@
     ],
     extras_require={
         "ase": ["ase>=3.3"],
-        "tblite": ["tblite[ase]>=0.3.0"],
+        # don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175
+        "tblite": ["tblite[ase]>=0.3.0; python_version<'3.12'"],
         "vis": ["vtk>=6.0.0"],
         "abinit": ["netcdf4"],
-        "relaxation": ["matgl", "chgnet"],
+        "relaxation": ["matgl", "chgnet>=0.3.0"],
         "electronic_structure": ["fdint>=2.0.2"],
         "dev": [
             "mypy",
@@ -74,7 +75,7 @@
             # caused CI failure due to ModuleNotFoundError: No module named 'packaging'
             # "BoltzTraP2>=22.3.2; platform_system!='Windows'",
             "chemview>=0.6",
-            "chgnet",
+            "chgnet>=0.3.0",
             "f90nml>=1.1.2",
             "galore>=0.6.1",
             "h5py>=3.8.0",
@@ -83,7 +84,8 @@
             "netCDF4>=1.5.8",
             "phonopy>=2.4.2",
             "seekpath>=1.9.4",
-            "tblite[ase]>=0.3.0; platform_system=='Linux'",
+            # don't depend on tblite above 3.11 since unsupported https://github.com/tblite/tblite/issues/175
+            "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
             # "hiphive>=0.6",
             # "openbabel>=3.1.1; platform_system=='Linux'",
         ],
@@ -159,6 +161,7 @@
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Programming Language :: Python :: 3",
         "Topic :: Scientific/Engineering :: Chemistry",
         "Topic :: Scientific/Engineering :: Information Analysis",

tests/io/vasp/test_outputs.py

@@ -21,7 +21,7 @@
 from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine
 from pymatgen.electronic_structure.core import Magmom, Orbital, OrbitalType, Spin
 from pymatgen.entries.compatibility import MaterialsProjectCompatibility
-from pymatgen.io.vasp.inputs import Kpoints, Poscar, Potcar
+from pymatgen.io.vasp.inputs import Incar, Kpoints, Poscar, Potcar
 from pymatgen.io.vasp.outputs import (
     WSWQ,
     BSVasprun,
@@ -251,8 +251,8 @@ def test_standard(self):
         assert len(trajectory) == len(vasp_run.ionic_steps)
         assert "forces" in trajectory[0].site_properties
 
-        for i, step in enumerate(vasp_run.ionic_steps):
-            assert vasp_run.structures[i] == step["structure"]
+        for idx, step in enumerate(vasp_run.ionic_steps):
+            assert vasp_run.structures[idx] == step["structure"]
 
         assert all(
             vasp_run.structures[idx] == vasp_run.ionic_steps[idx]["structure"]
@@ -263,27 +263,27 @@ def test_standard(self):
 
         assert vasp_run.atomic_symbols == ["Li"] + 4 * ["Fe"] + 4 * ["P"] + 16 * ["O"]
         assert vasp_run.final_structure.reduced_formula == "LiFe4(PO4)4"
-        assert vasp_run.incar is not None, "Incar cannot be read"
-        assert vasp_run.kpoints is not None, "Kpoints cannot be read"
-        assert vasp_run.eigenvalues is not None, "Eigenvalues cannot be read"
+        assert isinstance(vasp_run.incar, Incar), f"{vasp_run.incar=}"
+        assert isinstance(vasp_run.kpoints, Kpoints), f"{vasp_run.kpoints=}"
+        assert isinstance(vasp_run.eigenvalues, Eigenval), f"{vasp_run.eigenvalues=}"
         assert vasp_run.final_energy == approx(-269.38319884, abs=1e-7)
         assert vasp_run.tdos.get_gap() == approx(2.0589, abs=1e-4)
         expected = (2.539, 4.0906, 1.5516, False)
         assert vasp_run.eigenvalue_band_properties == approx(expected)
-        assert not vasp_run.is_hubbard
+        assert vasp_run.is_hubbard is False
         assert vasp_run.potcar_symbols == [
             "PAW_PBE Li 17Jan2003",
             "PAW_PBE Fe 06Sep2000",
             "PAW_PBE Fe 06Sep2000",
             "PAW_PBE P 17Jan2003",
             "PAW_PBE O 08Apr2002",
         ]
-        assert vasp_run.kpoints is not None, "Kpoints cannot be read"
-        assert vasp_run.actual_kpoints is not None, "Actual kpoints cannot be read"
-        assert vasp_run.actual_kpoints_weights is not None, "Actual kpoints weights cannot be read"
+        assert isinstance(vasp_run.kpoints, Kpoints), f"{vasp_run.kpoints=}"
+        assert isinstance(vasp_run.actual_kpoints, list), f"{vasp_run.actual_kpoints=}"
+        assert isinstance(vasp_run.actual_kpoints_weights, list), f"{vasp_run.actual_kpoints_weights=}"
         for atom_doses in vasp_run.pdos:
             for orbital_dos in atom_doses:
-                assert orbital_dos is not None, "Partial Dos cannot be read"
+                assert isinstance(orbital_dos, Orbital), f"{orbital_dos=}"
 
         # test skipping ionic steps.
         vasprun_skip = Vasprun(filepath, 3, parse_potcar_file=False)