Merge branch 'master' into kpoints-encoding

.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

dev_scripts/potcar_scrambler.py

@@ -124,7 +124,7 @@ def scramble_single_potcar(self, potcar: PotcarSingle) -> str:
         return scrambled_potcar_str
 
     def to_file(self, filename: str) -> None:
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod
@@ -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

@@ -193,7 +193,6 @@ 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

@@ -2051,10 +2051,7 @@ 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
 

src/pymatgen/analysis/magnetism/analyzer.py

@@ -43,7 +43,7 @@
 try:
     DEFAULT_MAGMOMS = loadfn(f"{MODULE_DIR}/default_magmoms.yaml")
 except (FileNotFoundError, MarkedYAMLError):
-    warnings.warn("Could not load default_magmoms.yaml, falling back to VASPIncarBase.yaml")
+    warnings.warn("Could not load default_magmoms.yaml, falling back to VASPIncarBase.yaml", stacklevel=2)
     DEFAULT_MAGMOMS = loadfn(f"{MODULE_DIR}/../../io/vasp/VASPIncarBase.yaml")["INCAR"]["MAGMOM"]
 
 
@@ -159,7 +159,7 @@ def __init__(
             try:
                 structure = trans.apply_transformation(structure)
             except ValueError:
-                warnings.warn(f"Could not assign valences for {structure.reduced_formula}")
+                warnings.warn(f"Could not assign valences for {structure.reduced_formula}", stacklevel=2)
 
         # Check if structure has magnetic moments
         # on site properties or species spin properties,
@@ -186,7 +186,8 @@ def __init__(
             if None in structure.site_properties["magmom"]:
                 warnings.warn(
                     "Be careful with mixing types in your magmom site properties. "
-                    "Any 'None' magmoms have been replaced with zero."
+                    "Any 'None' magmoms have been replaced with zero.",
+                    stacklevel=2,
                 )
             magmoms = [m or 0 for m in structure.site_properties["magmom"]]
         elif has_spin:
@@ -207,7 +208,8 @@ def __init__(
                 "This class is not designed to be used with "
                 "non-collinear structures. If your structure is "
                 "only slightly non-collinear (e.g. canted) may still "
-                "give useful results, but use with caution."
+                "give useful results, but use with caution.",
+                stacklevel=2,
             )
 
         # this is for collinear structures only, make sure magmoms are all floats
@@ -313,8 +315,8 @@ def _round_magmoms(magmoms: ArrayLike, round_magmoms_mode: float) -> np.ndarray:
 
             except Exception as exc:
                 # TODO: typically a singular matrix warning, investigate this
-                warnings.warn("Failed to round magmoms intelligently, falling back to simple rounding.")
-                warnings.warn(str(exc))
+                warnings.warn("Failed to round magmoms intelligently, falling back to simple rounding.", stacklevel=2)
+                warnings.warn(str(exc), stacklevel=2)
 
             # and finally round roughly to the number of significant figures in our kde width
             n_decimals = len(str(round_magmoms_mode).split(".")[1]) + 1
@@ -483,7 +485,7 @@ def ordering(self) -> Ordering:
                 (in which case a warning is issued).
         """
         if not self.is_collinear:
-            warnings.warn("Detecting ordering in non-collinear structures not yet implemented.")
+            warnings.warn("Detecting ordering in non-collinear structures not yet implemented.", stacklevel=2)
             return Ordering.Unknown
 
         if "magmom" not in self.structure.site_properties:

src/pymatgen/analysis/magnetism/jahnteller.py

@@ -286,7 +286,7 @@ def is_jahn_teller_active(
             )
             active = analysis["active"]
         except Exception as exc:
-            warnings.warn(f"Error analyzing {structure.reduced_formula}: {exc}")
+            warnings.warn(f"Error analyzing {structure.reduced_formula}: {exc}", stacklevel=2)
 
         return active
 
@@ -330,7 +330,7 @@ def tag_structure(
                         structure.add_site_property("possible_jt_active", jt_sites)
             return structure
         except Exception as exc:
-            warnings.warn(f"Error analyzing {structure.reduced_formula}: {exc}")
+            warnings.warn(f"Error analyzing {structure.reduced_formula}: {exc}", stacklevel=2)
             return structure
 
     @staticmethod
@@ -380,7 +380,7 @@ def get_magnitude_of_effect_from_species(self, species: str | Species, spin_stat
                 spin_config = self.spin_configs[motif][d_electrons][spin_state]
                 magnitude = JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config(motif, spin_config)
         else:
-            warnings.warn("No data for this species.")
+            warnings.warn("No data for this species.", stacklevel=2)
 
         return magnitude