Improved typing and removed unused ignores

as per mypy directives

.pre-commit-config.yaml

@@ -120,7 +120,7 @@ repos:
     hooks:
       - id: mypy
         exclude: "docs|benchmark/|.*/tests?/.*"
-        additional_dependencies: [types-all, types-attrs]
+        additional_dependencies: [types-attrs, types-tabulate]
 
   - repo: https://github.com/econchick/interrogate
     rev: 1.5.0

glotaran/model/model.py

@@ -60,7 +60,9 @@ def __init__(self, error: str):
 
 
 def _load_item_from_dict(
-    item_type: type[Item], value: Item | dict[str, Any], extra: dict[str, Any] | None = None
+    item_type: type[Item],
+    value: Item | dict[str, Any],
+    extra: dict[str, Any] | None = None,
 ) -> Item:
     """Load an item from a dictionary.
 
@@ -136,7 +138,7 @@ def _load_global_items_from_dict(
 
 
 def _load_dataset_groups(
-    dataset_groups: dict[str, DatasetGroupModel | Any]
+    dataset_groups: dict[str, DatasetGroupModel | Any],
 ) -> dict[str, DatasetGroupModel]:
     """Add the default dataset group if not present.
 
@@ -340,7 +342,9 @@ def get_dataset_groups(self) -> dict[str, DatasetGroup]:
             groups[group].dataset_models[dataset_model.label] = dataset_model
         return groups
 
-    def iterate_items(self) -> Generator[tuple[str, dict[str, Item] | list[Item]], None, None]:
+    def iterate_items(
+        self,
+    ) -> Generator[tuple[str, dict[str, Item] | list[Item]], None, None]:
         """Iterate items.
 
         Yields
@@ -387,10 +391,7 @@ def generate_parameters(self) -> Parameters:
         .. # noqa: D414
         """
         return Parameters(
-            {
-                label: Parameter(label=label, value=0)  # type:ignore[call-arg]
-                for label in self.get_parameter_labels()
-            }
+            {label: Parameter(label=label, value=0) for label in self.get_parameter_labels()}
         )
 
     def get_issues(self, *, parameters: Parameters | None = None) -> list[ItemIssue]:

glotaran/optimization/data_provider.py

@@ -67,7 +67,7 @@ def __init__(self, scheme: Scheme, dataset_group: DatasetGroup):
             )
             self.add_model_weight(scheme.model, label, model_dimension, global_dimension)
 
-            self._data[label] = self.get_from_dataset(  # type:ignore[assignment]
+            self._data[label] = self.get_from_dataset(
                 dataset, "data", model_dimension, global_dimension
             )
             if self._weight[label] is not None:
@@ -585,7 +585,7 @@ def align_dataset_indices(self, aligned_global_axes: dict[str, ArrayLike]) -> li
 
     @staticmethod
     def align_groups(
-        aligned_global_axes: dict[str, ArrayLike]
+        aligned_global_axes: dict[str, ArrayLike],
     ) -> tuple[ArrayLike, dict[str, list[str]]]:
         """Align the groups in a dataset group.
 
@@ -622,7 +622,10 @@ def align_groups(
         for i, group_label in enumerate(aligned_group_labels):
             if group_label not in group_definitions:
                 group_definitions[group_label] = list(
-                    filter(lambda label: label != "", aligned_groups.isel({"global": i}).data)
+                    filter(
+                        lambda label: label != "",
+                        aligned_groups.isel({"global": i}).data,
+                    )
                 )
         return aligned_group_labels, group_definitions
 

glotaran/optimization/estimation_provider.py

@@ -353,7 +353,10 @@ def get_result(
                 ).clp_labels
                 clps[label] = xr.DataArray(
                     np.array(self._clps[label]).reshape((len(global_clp_labels), len(clp_labels))),
-                    coords={"global_clp_label": global_clp_labels, "clp_label": clp_labels},
+                    coords={
+                        "global_clp_label": global_clp_labels,
+                        "clp_label": clp_labels,
+                    },
                     dims=["global_clp_label", "clp_label"],
                 )
 
@@ -397,8 +400,8 @@ def calculate_estimation(self, dataset_model: DatasetModel):
             The dataset model.
         """
         label = dataset_model.label
-        self._clps[label].clear()  # type:ignore[union-attr]
-        self._residuals[label].clear()  # type:ignore[union-attr]
+        self._clps[label].clear()
+        self._residuals[label].clear()
 
         global_axis = self._data_provider.get_global_axis(label)
         data = self._data_provider.get_data(label)
@@ -411,14 +414,19 @@ def calculate_estimation(self, dataset_model: DatasetModel):
             )
             clp_labels.append(self._matrix_provider.get_matrix_container(label).clp_labels)
             clp = self.retrieve_clps(
-                clp_labels[index], matrix_container.clp_labels, reduced_clps, global_index_value
+                clp_labels[index],
+                matrix_container.clp_labels,
+                reduced_clps,
+                global_index_value,
             )
 
-            self._clps[label].append(clp)  # type:ignore[union-attr]
-            self._residuals[label].append(residual)  # type:ignore[union-attr]
+            self._clps[label].append(clp)
+            self._residuals[label].append(residual)
 
         self._clp_penalty += self.calculate_clp_penalties(
-            clp_labels, self._clps[label], global_axis  # type:ignore[arg-type]
+            clp_labels,
+            self._clps[label],
+            global_axis,
         )
 
 
@@ -445,12 +453,8 @@ def __init__(
         super().__init__(dataset_group)
         self._data_provider = data_provider
         self._matrix_provider = matrix_provider
-        self._clps: list[ArrayLike] = [
-            None  # type:ignore[list-item]
-        ] * self._data_provider.aligned_global_axis.size
-        self._residuals: list[ArrayLike] = [
-            None  # type:ignore[list-item]
-        ] * self._data_provider.aligned_global_axis.size
+        self._clps: list[ArrayLike] = [None] * self._data_provider.aligned_global_axis.size
+        self._residuals: list[ArrayLike] = [None] * self._data_provider.aligned_global_axis.size
 
     def estimate(self):
         """Calculate the estimation."""

glotaran/optimization/matrix_provider.py

@@ -195,7 +195,7 @@ def calculate_dataset_matrix(
                 clp_labels, matrix = MatrixProvider.combine_megacomplex_matrices(
                     matrix, this_matrix, clp_labels, this_clp_labels
                 )
-        return MatrixContainer(clp_labels, matrix)  # type:ignore[arg-type]
+        return MatrixContainer(clp_labels, matrix)
 
     @staticmethod
     def combine_megacomplex_matrices(
@@ -718,7 +718,8 @@ def calculate_aligned_matrices(self):
             ]
 
             group_matrix = self.align_matrices(
-                matrix_containers, matrix_scales  # type:ignore[arg-type]
+                matrix_containers,
+                matrix_scales,  # type:ignore[arg-type]
             )
 
             self._aligned_full_clp_labels[i] = full_clp_labels[group_label]