Merge branch 'master' into zopen-explicit-mode

Author: DanielYang59

.github/workflows/test.yml

@@ -61,36 +61,34 @@ jobs:
       - name: Check out repo
         uses: actions/checkout@v4
 
-      - name: Set up micromamba
-        uses: mamba-org/setup-micromamba@main
-
       - name: Create mamba environment
-        run: |
-          micromamba create -n pmg python=${{ matrix.config.python }} --yes
+        uses: mamba-org/setup-micromamba@main
+        with:
+          environment-name: pmg
+          create-args: >-
+            python=${{ matrix.config.python }}
 
       - name: Install ubuntu-only conda dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |
           micromamba install -n pmg -c conda-forge bader enumlib \
             openff-toolkit packmol pygraphviz tblite --yes
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
       - name: Install pymatgen and dependencies via uv
         run: |
           micromamba activate pmg
-
-          pip install uv
-
           # TODO1 (use uv over pip) uv install torch is flaky, track #3826
           # TODO2 (pin torch version): DGL library (matgl) doesn't support torch > 2.2.1,
           # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302
           pip install torch==2.2.1
 
           # Install from wheels to test the content
-          uv pip install build
-          python -m build --wheel
-
-          uv pip install dist/*.whl
-          uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
+          uv build --wheel --no-build-logs
+          WHEEL_FILE=$(ls dist/pymatgen*.whl)
+          uv pip install $WHEEL_FILE[${{matrix.config.extras}}] --resolution=${{matrix.config.resolution}}
 
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.8.1
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -36,7 +36,7 @@ repos:
         exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.2
+    rev: v0.16.6
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]
@@ -48,7 +48,7 @@ repos:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.42.0
+    rev: v0.43.0
     hooks:
       - id: markdownlint
         # MD013: line too long
@@ -59,12 +59,12 @@ repos:
         args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.0
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.387
+    rev: v1.1.389
     hooks:
       - id: pyright

README.md

@@ -21,7 +21,7 @@ Pymatgen (Python Materials Genomics) is a robust, open-source Python
 library for materials analysis. These are some of the main features:
 
 1. Highly flexible classes for the representation of `Element`, `Site`, `Molecule` and `Structure` objects.
-2. Extensive input/output support, including support for [VASP](https://cms.mpi.univie.ac.at/vasp), [ABINIT](https://abinit.org), [CIF](https://wikipedia.org/wiki/Crystallographic_Information_File), [Gaussian](https://gaussian.com), [XYZ](https://wikipedia.org/wiki/XYZ_file_format), and many other file formats.
+2. Extensive input/output support, including support for [VASP](https://www.vasp.at/), [ABINIT](https://abinit.github.io/abinit_web/), [CIF](https://wikipedia.org/wiki/Crystallographic_Information_File), [Gaussian](https://gaussian.com), [XYZ](https://wikipedia.org/wiki/XYZ_file_format), and many other file formats.
 3. Powerful analysis tools, including generation of phase diagrams, Pourbaix diagrams, diffusion analyses, reactions, etc.
 4. Electronic structure analyses, such as density of states and band structure.
 5. Integration with the [Materials Project] REST API.

dev_scripts/potcar_scrambler.py

@@ -164,7 +164,7 @@ def generate_fake_potcar_libraries() -> None:
                 zpath(f"{func_dir}/{psp_name}/POTCAR"),
             ]
             if not any(map(os.path.isfile, paths_to_try)):
-                warnings.warn(f"Could not find {psp_name} in {paths_to_try}")
+                warnings.warn(f"Could not find {psp_name} in {paths_to_try}", stacklevel=2)
             for potcar_path in paths_to_try:
                 if os.path.isfile(potcar_path):
                     os.makedirs(rebase_dir, exist_ok=True)

pyproject.toml

@@ -87,8 +87,7 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-# PR4128: netcdf4 1.7.[0/1] yanked, 1.7.1.post[1/2]/1.7.2 cause CI error
-abinit = ["netcdf4>=1.6.5,!=1.7.1.post1,!=1.7.1.post2,!=1.7.2"]
+abinit = ["netcdf4>=1.7.2"]
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
@@ -193,7 +192,6 @@ ignore = [
 
     # Single rules
     "B023",    # Function definition does not bind loop variable
-    "B028",    # No explicit stacklevel keyword argument found
     "B904",    # Within an except clause, raise exceptions with ...
     "C408",    # unnecessary-collection-call
     "D105",    # Missing docstring in magic method

src/pymatgen/alchemy/materials.py

@@ -362,7 +362,7 @@ def to_snl(self, authors: list[str], **kwargs) -> StructureNL:
             StructureNL: The generated StructureNL object.
         """
         if self.other_parameters:
-            warn("Data in TransformedStructure.other_parameters discarded during type conversion to SNL")
+            warn("Data in TransformedStructure.other_parameters discarded during type conversion to SNL", stacklevel=2)
         history = []
         for hist in self.history:
             snl_metadata = hist.pop("_snl", {})

src/pymatgen/analysis/bond_dissociation.py

@@ -107,7 +107,8 @@ def __init__(
         if multibreak:
             warnings.warn(
                 "Breaking pairs of ring bonds. WARNING: Structure changes much more likely, meaning dissociation values"
-                " are less reliable! This is a bad idea!"
+                " are less reliable! This is a bad idea!",
+                stacklevel=2,
             )
             self.bond_pairs = []
             for ii, bond in enumerate(self.ring_bonds, start=1):
@@ -164,7 +165,8 @@ def fragment_and_process(self, bonds):
                         warnings.warn(
                             f"Missing ring opening fragment resulting from the breakage of {specie[bonds[0][0]]} "
                             f"{specie[bonds[0][1]]} bond {bonds[0][0]} {bonds[0][1]} which would yield a "
-                            f"molecule with this SMILES string: {smiles}"
+                            f"molecule with this SMILES string: {smiles}",
+                            stacklevel=2,
                         )
                     elif len(good_entries) == 1:
                         # If we have only one good entry, format it and add it to the list that will eventually return
@@ -212,14 +214,14 @@ def fragment_and_process(self, bonds):
                     smiles = pb_mol.write("smi").split()[0]
                     for charge in self.expected_charges:
                         if charge not in frag1_charges_found:
-                            warnings.warn(f"Missing {charge=} for fragment {smiles}")
+                            warnings.warn(f"Missing {charge=} for fragment {smiles}", stacklevel=2)
                 if len(frag2_charges_found) < len(self.expected_charges):
                     bb = BabelMolAdaptor(fragments[1].molecule)
                     pb_mol = bb.pybel_mol
                     smiles = pb_mol.write("smi").split()[0]
                     for charge in self.expected_charges:
                         if charge not in frag2_charges_found:
-                            warnings.warn(f"Missing {charge=} for fragment {smiles}")
+                            warnings.warn(f"Missing {charge=} for fragment {smiles}", stacklevel=2)
                 # Now we attempt to pair fragments with the right total charge, starting with only fragments with no
                 # structural change:
                 for frag1 in frag1_entries[0]:  # 0 -> no structural change

src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -218,7 +218,9 @@ def points_wcs_csc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wcs_csc
-        return np.concatenate((self._points_wcs_csc[:1], self._points_wocs_csc.take(permutation, axis=0)))
+        return np.concatenate(
+            (self._points_wcs_csc[:1], self._points_wocs_csc.take(np.array(permutation, dtype=np.intp), axis=0))
+        )
 
     def points_wocs_csc(self, permutation=None):
         """
@@ -227,7 +229,7 @@ def points_wocs_csc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wocs_csc
-        return self._points_wocs_csc.take(permutation, axis=0)
+        return self._points_wocs_csc.take(np.array(permutation, dtype=np.intp), axis=0)
 
     def points_wcs_ctwcc(self, permutation=None):
         """
@@ -239,7 +241,7 @@ def points_wcs_ctwcc(self, permutation=None):
         return np.concatenate(
             (
                 self._points_wcs_ctwcc[:1],
-                self._points_wocs_ctwcc.take(permutation, axis=0),
+                self._points_wocs_ctwcc.take(np.array(permutation, dtype=np.intp), axis=0),
             )
         )
 
@@ -250,7 +252,7 @@ def points_wocs_ctwcc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wocs_ctwcc
-        return self._points_wocs_ctwcc.take(permutation, axis=0)
+        return self._points_wocs_ctwcc.take(np.array(permutation, dtype=np.intp), axis=0)
 
     def points_wcs_ctwocc(self, permutation=None):
         """
@@ -262,7 +264,7 @@ def points_wcs_ctwocc(self, permutation=None):
         return np.concatenate(
             (
                 self._points_wcs_ctwocc[:1],
-                self._points_wocs_ctwocc.take(permutation, axis=0),
+                self._points_wocs_ctwocc.take(np.array(permutation, dtype=np.intp), axis=0),
             )
         )
 
@@ -273,7 +275,7 @@ def points_wocs_ctwocc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wocs_ctwocc
-        return self._points_wocs_ctwocc.take(permutation, axis=0)
+        return self._points_wocs_ctwocc.take(np.array(permutation, dtype=np.intp), axis=0)
 
     @property
     def cn(self):
@@ -1976,6 +1978,7 @@ def _cg_csm_separation_plane_optim2(
         stop_search = False
         # TODO: do not do that several times ... also keep in memory
         if sepplane.ordered_plane:
+            separation_indices = [arr.astype(np.intp) for arr in separation_indices]
             inp = self.local_geometry.coords.take(separation_indices[1], axis=0)
             if sepplane.ordered_point_groups[0]:
                 pp_s0 = self.local_geometry.coords.take(separation_indices[0], axis=0)
@@ -2051,10 +2054,7 @@ def coordination_geometry_symmetry_measures_fallback_random(
             The symmetry measures for the given coordination geometry for each permutation investigated.
         """
         if "NRANDOM" in kwargs:
-            warnings.warn(
-                "NRANDOM is deprecated, use n_random instead",
-                category=DeprecationWarning,
-            )
+            warnings.warn("NRANDOM is deprecated, use n_random instead", category=DeprecationWarning, stacklevel=2)
             n_random = kwargs.pop("NRANDOM")
         permutations_symmetry_measures = [None] * n_random
         permutations = []

src/pymatgen/analysis/chempot_diagram.py

@@ -391,7 +391,7 @@ def _get_3d_plot(
         if formulas_to_draw:
             for formula in formulas_to_draw:
                 if formula not in domain_simplexes:
-                    warnings.warn(f"Specified formula to draw, {formula}, not found!")
+                    warnings.warn(f"Specified formula to draw, {formula}, not found!", stacklevel=2)
 
         if draw_formula_lines:
             data.extend(self._get_3d_formula_lines(draw_domains, formula_colors))

src/pymatgen/analysis/elasticity/elastic.py

@@ -63,7 +63,7 @@ def __new__(cls, input_array, check_rank=None, tol: float = 1e-4) -> Self:
         if obj.rank % 2 != 0:
             raise ValueError("ElasticTensor must have even rank")
         if not obj.is_voigt_symmetric(tol):
-            warnings.warn("Input elastic tensor does not satisfy standard Voigt symmetries")
+            warnings.warn("Input elastic tensor does not satisfy standard Voigt symmetries", stacklevel=2)
         return obj.view(cls)
 
     @property
@@ -476,7 +476,8 @@ def from_pseudoinverse(cls, strains, stresses) -> Self:
         # convert the stress/strain to Nx6 arrays of voigt notation
         warnings.warn(
             "Pseudo-inverse fitting of Strain/Stress lists may yield "
-            "questionable results from vasp data, use with caution."
+            "questionable results from vasp data, use with caution.",
+            stacklevel=2,
         )
         stresses = np.array([Stress(stress).voigt for stress in stresses])
         with warnings.catch_warnings():
@@ -505,7 +506,9 @@ def from_independent_strains(cls, strains, stresses, eq_stress=None, vasp=False,
         if not set(strain_states) <= set(ss_dict):
             raise ValueError(f"Missing independent strain states: {set(strain_states) - set(ss_dict)}")
         if len(set(ss_dict) - set(strain_states)) > 0:
-            warnings.warn("Extra strain states in strain-stress pairs are neglected in independent strain fitting")
+            warnings.warn(
+                "Extra strain states in strain-stress pairs are neglected in independent strain fitting", stacklevel=2
+            )
         c_ij = np.zeros((6, 6))
         for ii in range(6):
             strains = ss_dict[strain_states[ii]]["strains"]
@@ -916,7 +919,7 @@ def find_eq_stress(strains, stresses, tol: float = 1e-10):
             )
         eq_stress = eq_stress[0]
     else:
-        warnings.warn("No eq state found, returning zero voigt stress")
+        warnings.warn("No eq state found, returning zero voigt stress", stacklevel=2)
         eq_stress = Stress(np.zeros((3, 3)))
     return eq_stress
 

src/pymatgen/analysis/ewald.py

@@ -288,7 +288,7 @@ def get_site_energy(self, site_index):
             self._initialized = True
 
         if self._charged:
-            warn("Per atom energies for charged structures not supported in EwaldSummation")
+            warn("Per atom energies for charged structures not supported in EwaldSummation", stacklevel=2)
         return np.sum(self._recip[:, site_index]) + np.sum(self._real[:, site_index]) + self._point[site_index]
 
     def _calc_ewald_terms(self):

src/pymatgen/analysis/gb/grain.py

@@ -8,4 +8,5 @@
     "Grain boundary analysis has been moved to pymatgen.core.interface."
     "This stub is retained for backwards compatibility and will be removed Dec 31 2024.",
     DeprecationWarning,
+    stacklevel=2,
 )

src/pymatgen/analysis/graphs.py

@@ -383,7 +383,7 @@ def add_edge(
         # edges if appropriate
         if to_jimage is None:
             # assume we want the closest site
-            warnings.warn("Please specify to_jimage to be unambiguous, trying to automatically detect.")
+            warnings.warn("Please specify to_jimage to be unambiguous, trying to automatically detect.", stacklevel=2)
             dist, to_jimage = self.structure[from_index].distance_and_image(self.structure[to_index])
             if dist == 0:
                 # this will happen when from_index == to_index,
@@ -417,7 +417,7 @@ def add_edge(
         # this is a convention to avoid duplicate hops
         if to_index == from_index:
             if to_jimage == (0, 0, 0):
-                warnings.warn("Tried to create a bond to itself, this doesn't make sense so was ignored.")
+                warnings.warn("Tried to create a bond to itself, this doesn't make sense so was ignored.", stacklevel=2)
                 return
 
             # ensure that the first non-zero jimage index is positive
@@ -439,7 +439,8 @@ def add_edge(
                     if warn_duplicates:
                         warnings.warn(
                             "Trying to add an edge that already exists from "
-                            f"site {from_index} to site {to_index} in {to_jimage}."
+                            f"site {from_index} to site {to_index} in {to_jimage}.",
+                            stacklevel=2,
                         )
                     return
 
@@ -1826,7 +1827,9 @@ def add_edge(
         # between two sites
         existing_edge_data = self.graph.get_edge_data(from_index, to_index)
         if existing_edge_data and warn_duplicates:
-            warnings.warn(f"Trying to add an edge that already exists from site {from_index} to site {to_index}.")
+            warnings.warn(
+                f"Trying to add an edge that already exists from site {from_index} to site {to_index}.", stacklevel=2
+            )
             return
 
         # generic container for additional edge properties,

src/pymatgen/analysis/interface_reactions.py

@@ -484,8 +484,10 @@ def _get_entry_energy(pd: PhaseDiagram, composition: Composition):
 
         if not candidate:
             warnings.warn(
-                f"The reactant {composition.reduced_formula} has no matching entry with negative formation"
-                " energy, instead convex hull energy for this composition will be used for reaction energy calculation."
+                f"The reactant {composition.reduced_formula} has no matching entry "
+                "with negative formation energy, instead convex hull energy for "
+                "this composition will be used for reaction energy calculation.",
+                stacklevel=2,
             )
             return pd.get_hull_energy(composition)
         min_entry_energy = min(candidate)
@@ -545,8 +547,9 @@ def get_chempot_correction(cls, element: str, temp: float, pres: float):  # code
             The correction of chemical potential in eV/atom of the gas
             phase at given temperature and pressure.
         """
-        if element not in ["O", "N", "Cl", "F", "H"]:
-            warnings.warn(f"{element=} not one of valid options: ['O', 'N', 'Cl', 'F', 'H']")
+        valid_elements = {"O", "N", "Cl", "F", "H"}
+        if element not in valid_elements:
+            warnings.warn(f"{element=} not one of valid options: {valid_elements}", stacklevel=2)
             return 0
 
         std_temp = 298.15

src/pymatgen/analysis/local_env.py

@@ -4025,7 +4025,8 @@ def get_nn_data(self, structure: Structure, n: int, length=None):
                     warnings.warn(
                         "CrystalNN: cannot locate an appropriate radius, "
                         "covalent or atomic radii will be used, this can lead "
-                        "to non-optimal results."
+                        "to non-optimal results.",
+                        stacklevel=2,
                     )
                     diameter = _get_default_radius(structure[n]) + _get_default_radius(entry["site"])
 
@@ -4231,7 +4232,8 @@ def _get_radius(site):
     else:
         warnings.warn(
             "No oxidation states specified on sites! For better results, set "
-            "the site oxidation states in the structure."
+            "the site oxidation states in the structure.",
+            stacklevel=2,
         )
     return 0