Remove disallow_any_unimported from mypy, removed related type: ignore comments, addressed some mypy warnings related to Number type used

Author: nmaarnio

eis_toolkit/checks/dataframe.py

@@ -4,7 +4,7 @@
 
 
 @beartype
-def check_columns_valid(df: pd.DataFrame, columns: Sequence[str]) -> bool:  # type: ignore[no-any-unimported]
+def check_columns_valid(df: pd.DataFrame, columns: Sequence[str]) -> bool:
     """
     Check that all specified columns are in the dataframe.
 
@@ -19,7 +19,7 @@ def check_columns_valid(df: pd.DataFrame, columns: Sequence[str]) -> bool:  # ty
 
 
 @beartype
-def check_columns_numeric(df: pd.DataFrame, columns: Sequence[str]) -> bool:  # type: ignore[no-any-unimported]
+def check_columns_numeric(df: pd.DataFrame, columns: Sequence[str]) -> bool:
     """
     Check that all specified columns are numeric.
 

eis_toolkit/checks/parameter.py

@@ -32,7 +32,7 @@ def check_numeric_value_sign(parameter_value: Number) -> bool:
     Returns:
         True if parameter value is positive, False if not
     """
-    if parameter_value > 0:
+    if parameter_value > 0:  # type: ignore
         return True
     else:
         return False

eis_toolkit/checks/raster.py

@@ -6,7 +6,7 @@
 
 
 @beartype
-def check_matching_cell_size(  # type: ignore[no-any-unimported]
+def check_matching_cell_size(
     rasters: Sequence[rasterio.io.DatasetReader],
 ) -> bool:
     """Check if all input rasters have matching cell size.
@@ -26,7 +26,7 @@ def check_matching_cell_size(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def check_matching_pixel_alignment(  # type: ignore[no-any-unimported]
+def check_matching_pixel_alignment(
     rasters: Sequence[rasterio.io.DatasetReader],
 ) -> bool:
     """Check if all input rasters have matching cell size and matching pixel alignment.
@@ -53,7 +53,7 @@ def check_matching_pixel_alignment(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def check_matching_bounds(  # type: ignore[no-any-unimported]
+def check_matching_bounds(
     rasters: Sequence[rasterio.io.DatasetReader],
 ) -> bool:
     """Check if all input rasters have matching bounds.
@@ -73,9 +73,7 @@ def check_matching_bounds(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def check_raster_grids(  # type: ignore[no-any-unimported]
-    rasters: Sequence[rasterio.io.DatasetReader], same_extent: bool = False
-) -> bool:
+def check_raster_grids(rasters: Sequence[rasterio.io.DatasetReader], same_extent: bool = False) -> bool:
     """
     Check all input rasters for matching gridding and optionally matching bounds.
 

eis_toolkit/conversions/csv_to_geodataframe.py

@@ -13,7 +13,7 @@
 )
 
 
-def _csv_to_geodataframe(  # type: ignore[no-any-unimported]
+def _csv_to_geodataframe(
     csv: Path,
     indexes: Sequence[int],
     target_crs: int,
@@ -77,7 +77,7 @@ def _csv_to_geodataframe(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def csv_to_geodataframe(  # type: ignore[no-any-unimported]
+def csv_to_geodataframe(
     csv: Path,
     indexes: Sequence[int],
     target_crs: int,

eis_toolkit/conversions/raster_to_dataframe.py

@@ -7,7 +7,7 @@
 from beartype.typing import Sequence
 
 
-def _raster_to_dataframe(  # type: ignore[no-any-unimported]
+def _raster_to_dataframe(
     raster: rasterio.io.DatasetReader,
     bands: Optional[Sequence[int]],
     add_coordinates: bool,
@@ -31,7 +31,7 @@ def _raster_to_dataframe(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def raster_to_dataframe(  # type: ignore[no-any-unimported]
+def raster_to_dataframe(
     raster: rasterio.io.DatasetReader,
     bands: Optional[Sequence[int]] = None,
     add_coordinates: bool = False,

eis_toolkit/exploratory_analyses/pca.py

@@ -8,9 +8,7 @@
 from eis_toolkit.exceptions import EmptyDataFrameException, InvalidParameterValueException
 
 
-def _compute_pca(  # type: ignore[no-any-unimported]
-    data: pd.DataFrame, number_of_components: int
-) -> Tuple[pd.DataFrame, np.ndarray]:
+def _compute_pca(data: pd.DataFrame, number_of_components: int) -> Tuple[pd.DataFrame, np.ndarray]:
 
     feature_matrix = data.loc[:, data.columns].values
     standardized_data = StandardScaler().fit_transform(feature_matrix)
@@ -26,9 +24,7 @@ def _compute_pca(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def compute_pca(  # type: ignore[no-any-unimported]
-    data: pd.DataFrame, number_of_components: int
-) -> Tuple[pd.DataFrame, np.ndarray]:
+def compute_pca(data: pd.DataFrame, number_of_components: int) -> Tuple[pd.DataFrame, np.ndarray]:
     """
     Compute the principal components for the input data.
 

eis_toolkit/exploratory_analyses/plot_pca.py

@@ -7,7 +7,7 @@
 
 
 @beartype
-def plot_pca(  # type: ignore[no-any-unimported]
+def plot_pca(
     pca_df: pd.DataFrame, explained_variances: np.ndarray, color_feat: Optional[pd.Series] = None, save_path: str = ""
 ) -> Figure:
     """Plot a scatter matrix of different principal component combinations.

eis_toolkit/raster_processing/clipping.py

@@ -11,9 +11,7 @@
 
 
 # The core clipping functionality. Used internally by clip.
-def _clip_raster(  # type: ignore[no-any-unimported] # noqa: E261
-    raster: rasterio.io.DatasetReader, geometries: Sequence
-) -> Tuple[np.ndarray, dict]:
+def _clip_raster(raster: rasterio.io.DatasetReader, geometries: Sequence) -> Tuple[np.ndarray, dict]:
     out_image, out_transform = mask(dataset=raster, shapes=geometries, crop=True, all_touched=True)
     out_meta = raster.meta.copy()
     out_meta.update(
@@ -24,9 +22,7 @@ def _clip_raster(  # type: ignore[no-any-unimported] # noqa: E261
 
 
 @beartype
-def clip_raster(  # type: ignore[no-any-unimported] # noqa: E261,E262
-    raster: rasterio.io.DatasetReader, geodataframe: geopandas.GeoDataFrame
-) -> Tuple[np.ndarray, dict]:
+def clip_raster(raster: rasterio.io.DatasetReader, geodataframe: geopandas.GeoDataFrame) -> Tuple[np.ndarray, dict]:
     """Clips a raster with polygon geometries.
 
     Args:

eis_toolkit/raster_processing/extract_values_from_raster.py

@@ -10,7 +10,7 @@
 from eis_toolkit.exceptions import NonMatchinParameterLengthsException
 
 
-def _extract_values_from_raster(  # type: ignore[no-any-unimported]
+def _extract_values_from_raster(
     raster_list: Sequence[rasterio.io.DatasetReader],
     geodataframe: gpd.GeoDataFrame,
     raster_column_names: Optional[Sequence[str]],
@@ -43,7 +43,7 @@ def _extract_values_from_raster(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def extract_values_from_raster(  # type: ignore[no-any-unimported]
+def extract_values_from_raster(
     raster_list: Sequence[rasterio.io.DatasetReader],
     geodataframe: gpd.GeoDataFrame,
     raster_column_names: Optional[Sequence[str]] = None,

eis_toolkit/raster_processing/reprojecting.py

@@ -8,7 +8,7 @@
 
 
 # Core reprojecting functionality used internally by reproject_raster and reproject_and_write_raster
-def _reproject_raster(  # type: ignore[no-any-unimported]
+def _reproject_raster(
     raster: rasterio.io.DatasetReader, target_crs: int, resampling_method: warp.Resampling
 ) -> Tuple[np.ndarray, dict]:
 
@@ -53,7 +53,7 @@ def _reproject_raster(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def reproject_raster(  # type: ignore[no-any-unimported]
+def reproject_raster(
     raster: rasterio.io.DatasetReader, target_crs: int, resampling_method: warp.Resampling = warp.Resampling.nearest
 ) -> Tuple[np.ndarray, dict]:
     """Reprojects raster to match given coordinate reference system (EPSG).

eis_toolkit/raster_processing/resampling.py

@@ -12,7 +12,7 @@
 
 
 # The core resampling functionality. Used internally by resample.
-def _resample(  # type: ignore[no-any-unimported]
+def _resample(
     raster: rasterio.io.DatasetReader,
     resampling_method: Resampling,
     upscale_factor: Number,
@@ -44,7 +44,7 @@ def _resample(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def resample(  # type: ignore[no-any-unimported]
+def resample(
     raster: rasterio.io.DatasetReader,
     upscale_factor: Number,
     upscale_factor_y: Optional[Number] = None,

eis_toolkit/raster_processing/snapping.py

@@ -10,9 +10,7 @@
 
 
 # The core snapping functionality. Used internally by snap.
-def _snap(  # type: ignore[no-any-unimported]
-    raster: rasterio.DatasetReader, snap_raster: rasterio.DatasetReader
-) -> Tuple[np.ndarray, dict]:
+def _snap(raster: rasterio.DatasetReader, snap_raster: rasterio.DatasetReader) -> Tuple[np.ndarray, dict]:
     raster_bounds = raster.bounds
     snap_bounds = snap_raster.bounds
     raster_pixel_size_x = raster.transform.a
@@ -66,9 +64,7 @@ def _snap(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def snap_with_raster(  # type: ignore[no-any-unimported]
-    raster: rasterio.DatasetReader, snap_raster: rasterio.DatasetReader
-) -> Tuple[np.ndarray, dict]:
+def snap_with_raster(raster: rasterio.DatasetReader, snap_raster: rasterio.DatasetReader) -> Tuple[np.ndarray, dict]:
     """Snaps/aligns raster to given snap raster.
 
     Raster is snapped from its left-bottom corner to nearest snap raster grid corner in left-bottom direction.

eis_toolkit/raster_processing/unifying.py

@@ -8,7 +8,7 @@
 from eis_toolkit.exceptions import InvalidParameterValueException
 
 
-def _unify_raster_grids(  # type: ignore[no-any-unimported]
+def _unify_raster_grids(
     base_raster: rasterio.io.DatasetReader,
     rasters_to_unify: Sequence[rasterio.io.DatasetReader],
     resampling_method: Resampling,
@@ -85,7 +85,7 @@ def _unify_raster_grids(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def unify_raster_grids(  # type: ignore[no-any-unimported]
+def unify_raster_grids(
     base_raster: rasterio.io.DatasetReader,
     rasters_to_unify: Sequence[rasterio.io.DatasetReader],
     resampling_method: Resampling = Resampling.nearest,

eis_toolkit/raster_processing/windowing.py

@@ -10,7 +10,7 @@
 from eis_toolkit.exceptions import CoordinatesOutOfBoundsException, InvalidParameterValueException
 
 
-def _extract_window(  # type: ignore[no-any-unimported]
+def _extract_window(
     raster: rasterio.io.DatasetReader,
     center_coords: Tuple[Number, Number],
     height: int,
@@ -79,7 +79,7 @@ def _extract_window(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def extract_window(  # type: ignore[no-any-unimported]
+def extract_window(
     raster: rasterio.io.DatasetReader,
     center_coords: Tuple[Number, Number],
     height: int,

eis_toolkit/utilities/miscellaneous.py

@@ -26,7 +26,7 @@ def replace_values(
         Raster data with replaced values.
     """
     out_data = data.copy()
-    return np.where(np.isin(out_data, values_to_replace), replace_value, out_data)
+    return np.where(np.isin(out_data, values_to_replace), replace_value, out_data)  # type: ignore
 
 
 @beartype

eis_toolkit/utilities/nodata.py

@@ -31,7 +31,9 @@ def set_nodata_raster_meta(raster_meta: Dict, nodata_value: Number) -> Dict:
 
 @beartype
 def replace_raster_nodata_each_band(
-    raster_data: np.ndarray, nodata_per_band: Dict[int, Union[Number, Sequence[Number]]], new_nodata: Number = -9999
+    raster_data: np.ndarray,
+    nodata_per_band: Dict[int, Union[Number, Sequence[Number]]],
+    new_nodata: Number = -9999,  # type: ignore
 ) -> np.ndarray:
     """
     Replace old nodata values with a new nodata value in a raster for each band separately.
@@ -72,7 +74,7 @@ def nodata_to_nan(data: np.ndarray, nodata_value: Number) -> np.ndarray:
     Returns:
         Input array where specified nodata has been converted to np.nan.
     """
-    return np.where(np.isin(data, nodata_value), np.nan, data)
+    return np.where(np.isin(data, nodata_value), np.nan, data)  # type: ignore
 
 
 @beartype
@@ -86,7 +88,7 @@ def nan_to_nodata(data: np.ndarray, nodata_value: Number) -> np.ndarray:
     Returns:
         Input array where np.nan has been converted to specified nodata.
     """
-    return np.where(np.isnan(data), nodata_value, data)
+    return np.where(np.isnan(data), nodata_value, data)  # type: ignore
 
 
 @beartype

eis_toolkit/validation/calculate_base_metrics.py

@@ -11,7 +11,7 @@
 from eis_toolkit.exceptions import NonMatchingCrsException, NotApplicableGeometryTypeException
 
 
-def _calculate_base_metrics(  # type: ignore[no-any-unimported]
+def _calculate_base_metrics(
     raster: rasterio.io.DatasetReader,
     deposits: geopandas.GeoDataFrame,
     band: int,
@@ -71,7 +71,7 @@ def _calculate_base_metrics(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def calculate_base_metrics(  # type: ignore[no-any-unimported]
+def calculate_base_metrics(
     raster: rasterio.io.DatasetReader,
     deposits: geopandas.GeoDataFrame,
     band: int = 1,

eis_toolkit/validation/get_pa_intersection.py

@@ -7,7 +7,7 @@
 from eis_toolkit.exceptions import InvalidParameterValueException
 
 
-def _get_pa_intersection(  # type: ignore[no-any-unimported]
+def _get_pa_intersection(
     true_positive_rate_values: np.ndarray, proportion_of_area_values: np.ndarray, threshold_values: np.ndarray
 ) -> Point:
     true_positive_area_curve = LineString(np.column_stack((threshold_values, true_positive_rate_values)))

eis_toolkit/validation/plot_prediction_area_curves.py

@@ -7,7 +7,7 @@
 from eis_toolkit.validation.get_pa_intersection import get_pa_intersection
 
 
-def _plot_prediction_area_curves(  # type: ignore[no-any-unimported]
+def _plot_prediction_area_curves(
     true_positive_rate_values: np.ndarray, proportion_of_area_values: np.ndarray, threshold_values: np.ndarray
 ) -> matplotlib.figure.Figure:
     intersection = get_pa_intersection(true_positive_rate_values, proportion_of_area_values, threshold_values)
@@ -39,7 +39,7 @@ def _plot_prediction_area_curves(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def plot_prediction_area_curves(  # type: ignore[no-any-unimported]
+def plot_prediction_area_curves(
     true_positive_rate_values: np.ndarray, proportion_of_area_values: np.ndarray, threshold_values: np.ndarray
 ) -> matplotlib.figure.Figure:
     """Plot prediction-area (P-A) plot.

eis_toolkit/validation/plot_rate_curve.py

@@ -7,9 +7,7 @@
 from eis_toolkit.validation.calculate_auc import calculate_auc
 
 
-def _plot_rate_curve(  # type: ignore[no-any-unimported]
-    x_values: np.ndarray, y_values: np.ndarray, label: str, xlab: str
-) -> matplotlib.figure.Figure:
+def _plot_rate_curve(x_values: np.ndarray, y_values: np.ndarray, label: str, xlab: str) -> matplotlib.figure.Figure:
     fig = plt.figure(figsize=(10, 7))
     plt.plot(x_values, y_values, label=label)
     plt.xlim(-0.01, 1)
@@ -27,7 +25,7 @@ def _plot_rate_curve(  # type: ignore[no-any-unimported]
 
 
 @beartype
-def plot_rate_curve(  # type: ignore[no-any-unimported]
+def plot_rate_curve(
     x_values: np.ndarray,
     y_values: np.ndarray,
     plot_type: str = "success_rate",

eis_toolkit/vector_processing/reproject_vector.py

@@ -5,9 +5,7 @@
 
 
 @beartype
-def reproject_vector(  # type: ignore[no-any-unimported]
-    geodataframe: geopandas.GeoDataFrame, target_crs: int
-) -> geopandas.GeoDataFrame:
+def reproject_vector(geodataframe: geopandas.GeoDataFrame, target_crs: int) -> geopandas.GeoDataFrame:
     """Reprojects vector data to match given coordinate reference system (EPSG).
 
     Args:

mypy.ini

@@ -3,7 +3,6 @@ check_untyped_defs = True
 disallow_untyped_defs = True
 disallow_incomplete_defs = True
 disallow_untyped_decorators = True
-disallow_any_unimported = True
 warn_return_any = True
 warn_unused_ignores = True
 no_implicit_optional = True