Disable disallow_any_generics for mypy (#316)

examples/polar_cap/simons_5_1.py

@@ -1,3 +1,5 @@
+import typing
+
 import matplotlib.pyplot as plt
 import numpy as np
 import numpy.typing as npt
@@ -47,7 +49,7 @@ def main() -> None:
 
 
 def _helper(  # noqa: PLR0913
-    ax: npt.NDArray,
+    ax: npt.NDArray[typing.Any],
     slepian: sleplet.slepian.SlepianPolarCap,
     resolution: int,
     x: npt.NDArray[np.float_],

examples/polar_cap/simons_5_3.py

@@ -1,3 +1,5 @@
+import typing
+
 import matplotlib.pyplot as plt
 import numpy as np
 import numpy.typing as npt
@@ -28,7 +30,9 @@ def main() -> None:
     plt.close()
 
 
-def _create_plot(ax: npt.NDArray, position: tuple[int, int], theta_max: int) -> None:
+def _create_plot(
+    ax: npt.NDArray[typing.Any], position: tuple[int, int], theta_max: int
+) -> None:
     """Create the plot."""
     print(f"theta_max={theta_max}")
     slepian = sleplet.slepian.SlepianPolarCap(L, np.deg2rad(theta_max))

pyproject.toml

@@ -58,6 +58,7 @@ optional-dependencies = {dev = [
     "build",
     "mypy",
     "pre-commit",
+    "pytest",
     "ruff",
     "tox",
     "twine",
@@ -102,7 +103,6 @@ paths.source = [
 ]
 
 [tool.mypy]
-disallow_any_generics = false
 disallow_subclassing_any = false
 disallow_untyped_decorators = false
 explicit_package_bases = true

src/sleplet/_data/setup_pooch.py

@@ -16,7 +16,7 @@
 _POOCH.load_registry_from_doi()
 
 
-def find_on_pooch_then_local(filename: str) -> os.PathLike | None:
+def find_on_pooch_then_local(filename: str) -> os.PathLike[str] | None:
     """Find a file on POOCH first and if not look in data folder."""
     if filename in _POOCH.registry:
         msg = f"Found {filename} at https://doi.org/{_ZENODO_DATA_DOI}"

src/sleplet/_mask_methods.py

@@ -1,5 +1,6 @@
 import logging
 import os
+import typing
 
 import numpy as np
 import numpy.typing as npt
@@ -114,7 +115,7 @@ def create_default_region() -> "sleplet.slepian.region.Region":
 
 
 def create_mesh_region(
-    mesh_config: dict,
+    mesh_config: dict[str, typing.Any],
     vertices: npt.NDArray[np.float_],
 ) -> npt.NDArray[np.bool_]:
     """Create a boolean region for the given mesh."""

src/sleplet/_mesh_methods.py

@@ -1,5 +1,6 @@
 import logging
 import pathlib
+import typing
 
 import igl
 import numpy as np
@@ -40,7 +41,7 @@ def average_functions_on_vertices_to_faces(
 
 
 def create_mesh_region(
-    mesh_config: dict,
+    mesh_config: dict[str, typing.Any],
     vertices: npt.NDArray[np.float_],
 ) -> npt.NDArray[np.bool_]:
     """Create a boolean region for the given mesh."""
@@ -54,7 +55,7 @@ def create_mesh_region(
     )
 
 
-def extract_mesh_config(mesh_name: str) -> dict:
+def extract_mesh_config(mesh_name: str) -> dict[str, float | int | str]:
     """Read in the given mesh region settings file."""
     with pathlib.Path.open(
         _data_path / f"meshes_regions_{mesh_name}.toml",
@@ -110,7 +111,9 @@ def mesh_eigendecomposition(
     return eigenvalues, eigenvectors, number_basis_functions
 
 
-def read_mesh(mesh_config: dict) -> tuple[npt.NDArray[np.float_], npt.NDArray[np.int_]]:
+def read_mesh(
+    mesh_config: dict[str, float | int | str]
+) -> tuple[npt.NDArray[np.float_], npt.NDArray[np.int_]]:
     """Read in the given mesh."""
     vertices, faces = igl.read_triangle_mesh(
         str(_data_path / f"meshes_polygons_{mesh_config['FILENAME']}"),

src/sleplet/_plotly_methods.py

@@ -1,3 +1,5 @@
+import typing
+
 import plotly.graph_objs as go
 
 _axis = {
@@ -30,7 +32,7 @@ def create_camera(  # noqa: PLR0913
 def create_layout(
     camera: go.layout.scene.Camera,
     *,
-    annotations: list[dict] | None = None,
+    annotations: list[dict[str, float | int]] | None = None,
 ) -> go.Layout:
     """Create the default plotly layout."""
     return go.Layout(
@@ -65,7 +67,7 @@ def create_colour_bar(
     bar_len: float = 0.94,
     bar_pos: float = 0.97,
     font_size: int = 38,
-) -> dict:
+) -> dict[str, typing.Any]:
     """Create the default plotly colour bar."""
     return {
         "x": bar_pos,

src/sleplet/_scripts/plotting_on_sphere.py

@@ -302,7 +302,7 @@ def _translation_helper(
     alpha_pi_frac: float,
     beta_pi_frac: float,
     shannon: int | None,
-) -> tuple[npt.NDArray[np.complex_ | np.float_], str, dict]:
+) -> tuple[npt.NDArray[np.complex_ | np.float_], str, dict[str, float | int]]:
     """Perform the translation specific steps."""
     msg = f"angles: (alpha, beta) = ({alpha_pi_frac}, {beta_pi_frac})"
     _logger.info(msg)

src/sleplet/_slepian_arbitrary_methods.py

@@ -10,14 +10,14 @@
 
 
 def clean_evals_and_evecs(
-    eigendecomposition: tuple,
+    eigendecomposition: tuple[npt.NDArray[np.complex_], npt.NDArray[np.complex_]],
 ) -> tuple[npt.NDArray[np.float_], npt.NDArray[np.complex_]]:
     """Need eigenvalues and eigenvectors to be in a certain format."""
     # access values
-    eigenvalues, eigenvectors = eigendecomposition
+    eigenvalues_complex, eigenvectors = eigendecomposition
 
     # eigenvalues should be real
-    eigenvalues = eigenvalues.real
+    eigenvalues = eigenvalues_complex.real
 
     # Sort eigenvalues and eigenvectors in descending order of eigenvalues
     idx = eigenvalues.argsort()[::-1]

src/sleplet/_string_methods.py

@@ -1,8 +1,13 @@
 import fractions
 import re
+import typing
 
 import numpy as np
 
+if typing.TYPE_CHECKING:
+    import sleplet.functions.coefficients
+    import sleplet.meshes.mesh_coefficients
+
 
 def _get_angle_num_dem(angle_fraction: float) -> tuple[int, int]:
     """Get numerator and denominator for a given decimal."""
@@ -84,7 +89,10 @@ def _convert_camel_case_to_snake_case(name: str) -> str:
 
 
 def convert_classes_list_to_snake_case(
-    classes: list,
+    classes: list[
+        type["sleplet.functions.coefficients.Coefficients"]
+        | type["sleplet.meshes.mesh_coefficients.MeshCoefficients"]
+    ],
     *,
     word_to_remove: str = "",
 ) -> list[str]:

src/sleplet/meshes/mesh_slepian.py

@@ -161,7 +161,7 @@ def _integral(self: typing_extensions.Self, i: int, j: int) -> float:
 
     @staticmethod
     def _clean_evals_and_evecs(
-        eigendecomposition: tuple,
+        eigendecomposition: tuple[npt.NDArray[np.float_], npt.NDArray[np.float_]],
     ) -> tuple[npt.NDArray[np.float_], npt.NDArray[np.float_]]:
         """Need eigenvalues and eigenvectors to be in a certain format."""
         # access values

src/sleplet/plotting/_create_plot_sphere.py

@@ -33,7 +33,7 @@ class PlotSphere:
     _: dataclasses.KW_ONLY
     amplitude: float | None = None
     """Whether to customise the amplitude range of the colour bar."""
-    annotations: list[dict] = pydantic.Field(default_factory=list)
+    annotations: list[dict[str, float | int]] = pydantic.Field(default_factory=list)
     """Whether to display any annotations on the surface plot or not."""
     normalise: bool = True
     """Whether to normalise the plot or not."""

src/sleplet/slepian/slepian_limit_lat_lon.py

@@ -205,14 +205,14 @@ def _slepian_matrix(
 
     @staticmethod
     def _clean_evals_and_evecs(
-        eigendecomposition: tuple,
+        eigendecomposition: tuple[npt.NDArray[np.complex_], npt.NDArray[np.complex_]],
     ) -> tuple[npt.NDArray[np.float_], npt.NDArray[np.complex_]]:
         """Need eigenvalues and eigenvectors to be in a certain format."""
         # access values
-        eigenvalues, eigenvectors = eigendecomposition
+        eigenvalues_complex, eigenvectors = eigendecomposition
 
         # eigenvalues should be real
-        eigenvalues = eigenvalues.real
+        eigenvalues = eigenvalues_complex.real
 
         # Sort eigenvalues and eigenvectors in descending order of eigenvalues
         idx = eigenvalues.argsort()[::-1]