Merge branch 'main' into bugfix/416-clipping-warning-images

Author: timtreis

.github/release.yml

@@ -4,6 +4,7 @@ changelog:
       - release-ignore
     authors:
       - pre-commit-ci
+      - pre-commit-ci[bot]
   categories:
     - title: Added
       labels:

.github/workflows/test.yaml

@@ -49,6 +49,7 @@ jobs:
           pip install pytest-cov
       - name: Install dependencies
         run: |
+          pip install numpy
           pip install --pre -e ".[dev,test,pre]"
       - name: Test
         env:

.mypy.ini

@@ -1,6 +1,5 @@
 [mypy]
 python_version = 3.10
-plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False
 warn_redundant_casts = True

.pre-commit-config.yaml

@@ -9,17 +9,17 @@ ci:
   skip: []
 repos:
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.5.3
+    rev: v3.6.2
     hooks:
       - id: prettier
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.9
+    rev: v0.12.11
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.17.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy, types-requests]

src/spatialdata_plot/pl/basic.py

@@ -895,6 +895,7 @@ def show(
                 cs_contents.query(f"cs == '{cs}'").iloc[0, :].values.tolist()
             )
             ax = fig_params.ax if fig_params.axs is None else fig_params.axs[i]
+            assert isinstance(ax, Axes)
 
             wants_images = False
             wants_labels = False

src/spatialdata_plot/pl/render.py

@@ -340,6 +340,8 @@ def _render_shapes(
             vmin = aggregate_with_reduction[0].values if norm.vmin is None else norm.vmin
             vmax = aggregate_with_reduction[1].values if norm.vmax is None else norm.vmax
             if (norm.vmin is not None or norm.vmax is not None) and norm.vmin == norm.vmax:
+                assert norm.vmin is not None
+                assert norm.vmax is not None
                 # value (vmin=vmax) is placed in the middle of the colorbar so that we can distinguish it from over and
                 # under values in case clip=True or clip=False with cmap(under)=cmap(0) & cmap(over)=cmap(1)
                 vmin = norm.vmin - 0.5
@@ -693,6 +695,8 @@ def _render_points(
             vmin = aggregate_with_reduction[0].values if norm.vmin is None else norm.vmin
             vmax = aggregate_with_reduction[1].values if norm.vmax is None else norm.vmax
             if (norm.vmin is not None or norm.vmax is not None) and norm.vmin == norm.vmax:
+                assert norm.vmin is not None
+                assert norm.vmax is not None
                 # value (vmin=vmax) is placed in the middle of the colorbar so that we can distinguish it from over and
                 # under values in case clip=True or clip=False with cmap(under)=cmap(0) & cmap(over)=cmap(1)
                 vmin = norm.vmin - 0.5

src/spatialdata_plot/pl/utils.py

@@ -526,6 +526,8 @@ def _prepare_cmap_norm(
 
     cmap = copy(cmap)
 
+    assert isinstance(cmap, Colormap), f"Invalid type of `cmap`: {type(cmap)}, expected `Colormap`."
+
     if norm is None:
         norm = Normalize(vmin=None, vmax=None, clip=False)
 
@@ -2076,7 +2078,7 @@ def _validate_image_render_params(
         if isinstance(palette, list):
             # case A: single palette for all channels
             if len(palette) == 1:
-                palette_length = len(channel) if channel is not None else len(spatial_element_ch)
+                palette_length = len(channel_list) if channel_list is not None else len(spatial_element_ch)
                 palette = palette * palette_length
             # case B: one palette per channel (either given or derived from channel length)
             channels_to_use = spatial_element_ch if element_params[el]["channel"] is None else channel
@@ -2090,9 +2092,9 @@ def _validate_image_render_params(
 
         if (cmap := param_dict["cmap"]) is not None:
             if len(cmap) == 1:
-                cmap_length = len(channel) if channel is not None else len(spatial_element_ch)
+                cmap_length = len(channel_list) if channel_list is not None else len(spatial_element_ch)
                 cmap = cmap * cmap_length
-            if (channel is not None and len(cmap) != len(channel)) or len(cmap) != len(spatial_element_ch):
+            if (channel_list is not None and len(cmap) != len(channel_list)) or len(cmap) != len(spatial_element_ch):
                 cmap = None
         element_params[el]["cmap"] = cmap
         element_params[el]["norm"] = param_dict["norm"]
@@ -2388,7 +2390,9 @@ def _get_datashader_trans_matrix_of_single_element(
         # no flipping needed
         return tm
     # for a Translation, we need the transposed transformation matrix
-    return tm.T
+    tm_T = tm.T
+    assert isinstance(tm_T, np.ndarray)
+    return tm_T
 
 
 def _get_transformation_matrix_for_datashader(