Merge branch 'master' into type-lobsterenv-outputs

.github/workflows/lint.yml

@@ -31,7 +31,7 @@ jobs:
           ruff format --check .
 
       - name: mypy
-        run: mypy ${{ github.event.repository.name }}
+        run: mypy src
 
       - name: pyright
         run: pyright

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.5.0
     hooks:
       - id: ruff
         args: [ --fix, --unsafe-fixes ]

pyproject.toml

@@ -132,8 +132,8 @@ feff_plot_dos = "pymatgen.cli.feff_plot_dos:main"
 get_environment = "pymatgen.cli.get_environment:main"
 
 [tool.setuptools.packages.find]
-where = ["."]
-include = ["pymatgen.*"]
+where = ["src"]
+include = ["pymatgen"]
 
 [tool.setuptools.package-data]
 "pymatgen.analysis" = ["*.yaml", "*.json", "*.csv"]
@@ -247,9 +247,8 @@ docstring-code-format = true
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
 "tests/**" = ["ANN201", "D", "PLR0124"]
-"tasks.py" = ["D"]
-"pymatgen/analysis/*" = ["D"]
-"pymatgen/io/*" = ["D"]
+"src/pymatgen/analysis/*" = ["D"]
+"src/pymatgen/io/*" = ["D"]
 "dev_scripts/*" = ["D"]
 
 [tool.pytest.ini_options]

setup.py

@@ -15,17 +15,17 @@
     ext_modules=[
         Extension(
             "pymatgen.optimization.linear_assignment",
-            ["pymatgen/optimization/linear_assignment.pyx"],
+            ["src/pymatgen/optimization/linear_assignment.pyx"],
             extra_link_args=extra_link_args,
         ),
         Extension(
             "pymatgen.util.coord_cython",
-            ["pymatgen/util/coord_cython.pyx"],
+            ["src/pymatgen/util/coord_cython.pyx"],
             extra_link_args=extra_link_args,
         ),
         Extension(
             "pymatgen.optimization.neighbors",
-            ["pymatgen/optimization/neighbors.pyx"],
+            ["src/pymatgen/optimization/neighbors.pyx"],
             extra_link_args=extra_link_args,
         ),
     ],

pymatgen/analysis/chemenv/connectivity/connected_components.py → src/pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -532,7 +532,6 @@ def show_graph(
                 If not provided, the graph is not saved.
             drawing_type (str): The type of drawing to use. Can be "internal" or "external".
         """
-
         shown_graph = self._connected_subgraph if graph is None else graph
 
         plt.figure()

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py → src/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -403,7 +403,7 @@ def get_site_coordination_environments_fractions(
     def get_site_ce_fractions_and_neighbors(self, site, full_ce_info=False, strategy_info=False):
         """
         Applies the strategy to the structure_environments object in order to get coordination environments, their
-        fraction, csm, geometry_info, and neighbors
+        fraction, csm, geometry_info, and neighbors.
 
         Args:
             site: Site for which the above information is sought
@@ -458,7 +458,7 @@ def setup_options(self, all_options_dict):
     @abc.abstractmethod
     def __eq__(self, other: object) -> bool:
         """
-        Equality method that should be implemented for any strategy
+        Equality method that should be implemented for any strategy.
 
         Args:
             other: strategy to be compared with the current one
@@ -1122,7 +1122,6 @@ def __init__(
             max_csm:
             symmetry_measure_type:
         """
-
         raise NotImplementedError("TargetedPenaltiedAbundanceChemenvStrategy not yet implemented")
 
         super().__init__(
@@ -1587,6 +1586,7 @@ def get_effective_csm(
         symmetry_measure_type: Type of symmetry measure to be used in the effective CSM.
         max_effective_csm: Max CSM to use for the effective CSM calculation.
         effective_csm_estimator_ratio_function: Ratio function to use to compute effective CSM.
+
     Returns:
         Effective CSM of a given Neighbors set.
     """
@@ -1951,9 +1951,7 @@ def delta_cn_specifics(
         )
 
     def as_dict(self):
-        """
-        MSONable dict.
-        """
+        """MSONable dict."""
         return {
             "@module": type(self).__module__,
             "@class": type(self).__name__,

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py → src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -101,9 +101,7 @@ def as_dict(self):
 
     @classmethod
     def from_dict(cls, dct: dict) -> Self:
-        """
-        Reconstruct ExplicitPermutationsAlgorithm from its JSON-serializable dict representation.
-        """
+        """Reconstruct ExplicitPermutationsAlgorithm from its JSON-serializable dict representation."""
         return cls(dct["permutations"])
 
 

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

@@ -86,7 +86,7 @@ def __init__(
         optimization=None,
     ):
         """
-        Constructor for the abstract geometry
+        Constructor for the abstract geometry.
 
         Args:
             central_site: Coordinates of the central site
@@ -159,7 +159,7 @@ def __init__(
         self.bare_coords = self._bare_coords
 
     def __str__(self):
-        """String representation of the AbstractGeometry
+        """String representation of the AbstractGeometry.
 
         Returns:
             str: String representation of the AbstractGeometry.
@@ -277,12 +277,12 @@ def points_wocs_ctwocc(self, permutation=None):
 
     @property
     def cn(self):
-        """Coordination number"""
+        """Coordination number."""
         return len(self.coords)
 
     @property
     def coordination_number(self):
-        """Coordination number"""
+        """Coordination number."""
         return len(self.coords)
 
 
@@ -453,7 +453,7 @@ def setup_parameters(
 
     def setup_parameter(self, parameter, value):
         """Setup of one specific parameter to the given value. The other parameters are unchanged. See setup_parameters
-        method for the list of possible parameters
+        method for the list of possible parameters.
 
         Args:
             parameter: Parameter to setup/update
@@ -463,7 +463,7 @@ def setup_parameter(self, parameter, value):
 
     def setup_structure(self, structure: Structure):
         """Set up the structure for which the coordination geometries have to be identified. The structure is analyzed
-        with the space group analyzer and a refined structure is used
+        with the space group analyzer and a refined structure is used.
 
         Args:
             structure: A pymatgen Structure.
@@ -502,7 +502,7 @@ def get_structure(self):
 
     def set_structure(self, lattice: Lattice, species, coords, coords_are_cartesian):
         """Set up the pymatgen structure for which the coordination geometries have to be identified starting from the
-        lattice, the species and the coordinates
+        lattice, the species and the coordinates.
 
         Args:
             lattice: The lattice of the structure
@@ -580,7 +580,7 @@ def compute_structure_environments(
         optimization=PRESETS["DEFAULT"]["optimization"],
     ):
         """Compute and returns the StructureEnvironments object containing all the information
-        about the coordination environments in the structure
+        about the coordination environments in the structure.
 
         Args:
             excluded_atoms: Atoms for which the coordination geometries does not have to be identified
@@ -1123,7 +1123,7 @@ def setup_random_structure(self, coordination):
         self.setup_random_indices_local_geometry(coordination)
 
     def setup_random_indices_local_geometry(self, coordination):
-        """Set up random indices for the local geometry, for testing purposes
+        """Set up random indices for the local geometry, for testing purposes.
 
         Args:
             coordination: coordination of the local geometry.
@@ -1133,7 +1133,7 @@ def setup_random_indices_local_geometry(self, coordination):
         np.random.shuffle(self.indices)
 
     def setup_ordered_indices_local_geometry(self, coordination):
-        """Set up ordered indices for the local geometry, for testing purposes
+        """Set up ordered indices for the local geometry, for testing purposes.
 
         Args:
             coordination: coordination of the local geometry.
@@ -1142,7 +1142,7 @@ def setup_ordered_indices_local_geometry(self, coordination):
         self.indices = list(range(1, coordination + 1))
 
     def setup_explicit_indices_local_geometry(self, explicit_indices):
-        """Set up explicit indices for the local geometry, for testing purposes
+        """Set up explicit indices for the local geometry, for testing purposes.
 
         Args:
             explicit_indices: explicit indices for the neighbors (set of numbers
@@ -1428,7 +1428,7 @@ def coordination_geometry_symmetry_measures_standard(
     ):
         """Get the symmetry measures for a set of permutations (whose setup depends on the coordination geometry)
         for the coordination geometry "coordination_geometry". Standard implementation looking for the symmetry
-        measures of each permutation
+        measures of each permutation.
 
         Args:
             coordination_geometry: The coordination geometry to be investigated
@@ -2032,7 +2032,7 @@ def coordination_geometry_symmetry_measures_fallback_random(
     ):
         """Get the symmetry measures for a random set of permutations for the coordination geometry
         "coordination_geometry". Fallback implementation for the plane separation algorithms measures
-        of each permutation
+        of each permutation.
 
         Args:
             coordination_geometry: The coordination geometry to be investigated