Merge pull request #104 from dstansby/nptyping

Add numpy and matplotlib to typing checks

Author: samcunliffe

.pre-commit-config.yaml

@@ -25,6 +25,7 @@ repos:
     rev: v1.2.0
     hooks:
      - id: mypy
+       additional_dependencies: [numpy, matplotlib]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.

src/napari_matplotlib/scatter.py

@@ -1,8 +1,8 @@
-from typing import List, Optional, Tuple
+from typing import Any, List, Optional, Tuple
 
 import matplotlib.colors as mcolor
 import napari
-import numpy as np
+import numpy.typing as npt
 from magicgui import magicgui
 from magicgui.widgets import ComboBox
 
@@ -65,7 +65,7 @@ def draw(self) -> None:
         self.axes.set_xlabel(x_axis_name)
         self.axes.set_ylabel(y_axis_name)
 
-    def _get_data(self) -> Tuple[List[np.ndarray], str, str]:
+    def _get_data(self) -> Tuple[List[npt.NDArray[Any]], str, str]:
         """Get the plot data.
 
         This must be implemented on the subclass.
@@ -93,7 +93,7 @@ class ScatterWidget(ScatterBaseWidget):
     n_layers_input = Interval(2, 2)
     input_layer_types = (napari.layers.Image,)
 
-    def _get_data(self) -> Tuple[List[np.ndarray], str, str]:
+    def _get_data(self) -> Tuple[List[npt.NDArray[Any]], str, str]:
         """
         Get the plot data.
 
@@ -191,7 +191,7 @@ def _get_valid_axis_keys(
         else:
             return self.layers[0].features.keys()
 
-    def _get_data(self) -> Tuple[List[np.ndarray], str, str]:
+    def _get_data(self) -> Tuple[List[npt.NDArray[Any]], str, str]:
         """
         Get the plot data.
 

src/napari_matplotlib/slice.py

@@ -1,7 +1,8 @@
-from typing import Dict, Tuple
+from typing import Any, Dict, Tuple
 
 import napari
 import numpy as np
+import numpy.typing as npt
 from qtpy.QtWidgets import QComboBox, QHBoxLayout, QLabel, QSpinBox
 
 from .base import NapariMPLWidget
@@ -87,7 +88,7 @@ def update_slice_selectors(self) -> None:
         for i, dim in enumerate(_dims_sel):
             self.slice_selectors[dim].setRange(0, self.layer.data.shape[i])
 
-    def get_xy(self) -> Tuple[np.ndarray, np.ndarray]:
+    def get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
         """
         Get data for plotting.
         """

src/napari_matplotlib/tests/test_scatter.py

@@ -1,6 +1,7 @@
 from typing import Any, Dict, Tuple
 
 import numpy as np
+import numpy.typing as npt
 
 from napari_matplotlib import FeaturesScatterWidget, ScatterWidget
 
@@ -22,7 +23,7 @@ def test_features_scatter_widget(make_napari_viewer):
 
 
 def make_labels_layer_with_features() -> (
-    Tuple[np.ndarray, Dict[str, Tuple[Any]]]
+    Tuple[npt.NDArray[np.uint16], Dict[str, Any]]
 ):
     label_image = np.zeros((100, 100), dtype=np.uint16)
     for label_value, start_index in enumerate([10, 30, 50], start=1):