[pre-commit.ci] pre-commit autoupdate (#356)

Author: LucaMarconato

.pre-commit-config.yaml

@@ -9,25 +9,25 @@ ci:
   skip: []
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.14.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy, types-requests]
         exclude: tests/|docs/
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.8.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -12,169 +12,169 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
--   Transformations of Points and Shapes are now applied before rendering with datashader (#378)
--   Fix bug due to `sc.get.obs_df()` returning a different type (#393)
--   Allowing instance mismatch between shapes and tables (#396)
--   Fix bug when plotting categorical points with datashader (#395)
+- Transformations of Points and Shapes are now applied before rendering with datashader (#378)
+- Fix bug due to `sc.get.obs_df()` returning a different type (#393)
+- Allowing instance mismatch between shapes and tables (#396)
+- Fix bug when plotting categorical points with datashader (#395)
 
 ## [0.2.8] - 2024-11-26
 
 ### Changed
 
--   Support for `xarray.DataTree` (which moved from `datatree.DataTree`) (#380)
+- Support for `xarray.DataTree` (which moved from `datatree.DataTree`) (#380)
 
 ## [0.2.7] - 2024-10-24
 
 ### Added
 
--   The user can now specify `datashader_reduction` to control the rendering behavior (#309)
--   Rendering outlines of shapes with datashader works now (#309)
+- The user can now specify `datashader_reduction` to control the rendering behavior (#309)
+- Rendering outlines of shapes with datashader works now (#309)
 
 ### Fixed
 
--   datashader now uses canvas size = image size which speeds up the rendering (#309)
--   datashader now uses the `linear` as interpolation method for colormaps instead of the default `eq_hist` to make it equivalent to matplotlib (#309)
--   point sizes of datashader now agree with matplotlib also when dpi != 100 (#309)
--   Giving a custom colormap when rendering a multiscale image now works (#586)
+- datashader now uses canvas size = image size which speeds up the rendering (#309)
+- datashader now uses the `linear` as interpolation method for colormaps instead of the default `eq_hist` to make it equivalent to matplotlib (#309)
+- point sizes of datashader now agree with matplotlib also when dpi != 100 (#309)
+- Giving a custom colormap when rendering a multiscale image now works (#586)
 
 ## [0.2.6] - 2024-09-04
 
 ### Changed
 
--   Lowered RMSE-threshold for plot-based tests from 45 to 15 (#344)
--   When subsetting to `groups`, `NA` isn't automatically added to legend (#344)
--   When rendering a single image channel, a colorbar is now shown (#346)
--   Removed `percentiles_for_norm` parameter (#346)
--   Changed `norm` to no longer accept bools, only `mpl.colors.Normalise` or `None` (#346)
+- Lowered RMSE-threshold for plot-based tests from 45 to 15 (#344)
+- When subsetting to `groups`, `NA` isn't automatically added to legend (#344)
+- When rendering a single image channel, a colorbar is now shown (#346)
+- Removed `percentiles_for_norm` parameter (#346)
+- Changed `norm` to no longer accept bools, only `mpl.colors.Normalise` or `None` (#346)
 
 ### Fixed
 
--   Filtering with `groups` now preserves original cmap (#344)
--   Non-selected `groups` are now not shown in `na_color` (#344)
--   Several issues associated with `norm` and `colorbar` (#346)
+- Filtering with `groups` now preserves original cmap (#344)
+- Non-selected `groups` are now not shown in `na_color` (#344)
+- Several issues associated with `norm` and `colorbar` (#346)
 
 ## [0.2.5] - 2024-08-23
 
 ### Changed
 
--   Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
--   Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
--   Removed `preprocessing` (.pp) accessor (#329)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Removed `preprocessing` (.pp) accessor (#329)
 
 ### Fixed
 
--   Minor fixes for several tests as a result of the threshold change (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ## [0.2.4] - 2024-08-07
 
 ### Added
 
--   Added utils function for 0-transparent cmaps (#302)
+- Added utils function for 0-transparent cmaps (#302)
 
 ### Fixed
 
--   Took RNG out of categorical label test (#306)
--   Performance bug when plotting shapes (#298)
--   scale parameter was ignored for single-scale images (#301)
--   Changes to support for dask-expr (#283)
--   Added error handling for non-existent elements (#305)
--   Specifying vmin and vmax properly clips image data (#307)
--   import bug `get_cmap()` (8fd969c)
+- Took RNG out of categorical label test (#306)
+- Performance bug when plotting shapes (#298)
+- scale parameter was ignored for single-scale images (#301)
+- Changes to support for dask-expr (#283)
+- Added error handling for non-existent elements (#305)
+- Specifying vmin and vmax properly clips image data (#307)
+- import bug `get_cmap()` (8fd969c)
 
 ## [0.2.3] - 2024-07-03
 
 ### Added
 
--   Datashader support for points and shapes (#244)
+- Datashader support for points and shapes (#244)
 
 ### Changed
 
--   All parameters are now provided for a single element (#272)
+- All parameters are now provided for a single element (#272)
 
 ### Fixed
 
--   Fix color assignment for NaN values (#257)
--   Zorder of rendering now strictly follows the order of the render_x calls (#244)
+- Fix color assignment for NaN values (#257)
+- Zorder of rendering now strictly follows the order of the render_x calls (#244)
 
 ## [0.2.2] - 2024-05-02
 
 ### Fixed
 
--   Fixed `fill_alpha` ignoring `alpha` channel from custom cmap (#236)
--   Fix channel str support (#221)
+- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap (#236)
+- Fix channel str support (#221)
 
 ## [0.2.1] - 2024-03-26
 
 ### Minor
 
--   Adjusted GitHub worklows
+- Adjusted GitHub worklows
 
 ## [0.2.0] - 2024-03-24
 
 ### Added
 
--   Support for plotting multiple tables @melonora
+- Support for plotting multiple tables @melonora
 
 ### Fixed
 
--   Several bugfixes, especially for colors and palettes @melonora
+- Several bugfixes, especially for colors and palettes @melonora
 
 ## [0.1.0] - 2024-01-17
 
 ### Added
 
--   Multiscale image handling: user can specify a scale, else the best scale is selected automatically given the figure size and dpi (#164)
--   Large images are automatically rasterized to speed up performance (#164)
--   Added better error message for mismatch in cs and ax number (#185)
--   Beter test coverage for correct plotting of elements after transformation (#198)
--   Can now stack render commands (#190, #192)
--   The `color` argument in render_shapes/points now accepts actual colors as well (#199)
--   Input arguments are now evaulated for their types in basic.py (#199)
+- Multiscale image handling: user can specify a scale, else the best scale is selected automatically given the figure size and dpi (#164)
+- Large images are automatically rasterized to speed up performance (#164)
+- Added better error message for mismatch in cs and ax number (#185)
+- Beter test coverage for correct plotting of elements after transformation (#198)
+- Can now stack render commands (#190, #192)
+- The `color` argument in render_shapes/points now accepts actual colors as well (#199)
+- Input arguments are now evaulated for their types in basic.py (#199)
 
 ### Fixed
 
--   Now dropping index when plotting shapes after spatial query (#177)
--   Points are now being correctly rotated (#198)
--   User can now pass Colormap objects to the cmap argument in render_images. When only one cmap is given for 3 channels, it is now applied to each channel (#188, #194)
+- Now dropping index when plotting shapes after spatial query (#177)
+- Points are now being correctly rotated (#198)
+- User can now pass Colormap objects to the cmap argument in render_images. When only one cmap is given for 3 channels, it is now applied to each channel (#188, #194)
 
 ## [0.0.6] - 2023-11-06
 
 ### Added
 
--   Pushed `get_extent` functionality upstream to `spatialdata` (#162)
+- Pushed `get_extent` functionality upstream to `spatialdata` (#162)
 
 ## [0.0.5] - 2023-10-02
 
 ### Added
 
--   Can now scale shapes (#152)
--   Can now plot columns from GeoDataFrame (#149)
+- Can now scale shapes (#152)
+- Can now plot columns from GeoDataFrame (#149)
 
 ### Fixed
 
--   Multipolygons are now handled correctly (#93)
--   Legend order is now deterministic (#143)
--   Images no longer normalised by default (#150)
--   Filtering of shapes and points using the `groups` argument is now possible, coloring by palette and cmap arguments works for shapes and points (#153)
--   Colorbar no longer autoscales to [0, 1] (#155)
--   Plotting shapes after a spatial query is now possible (#163)
+- Multipolygons are now handled correctly (#93)
+- Legend order is now deterministic (#143)
+- Images no longer normalised by default (#150)
+- Filtering of shapes and points using the `groups` argument is now possible, coloring by palette and cmap arguments works for shapes and points (#153)
+- Colorbar no longer autoscales to [0, 1] (#155)
+- Plotting shapes after a spatial query is now possible (#163)
 
 ## [0.0.4] - 2023-08-11
 
 ### Fixed
 
--   Multi-scale images/labels are now correctly substituted and the action is logged (#131).
--   Empty geometries among the shapes can be handeled (#133).
--   `outline_width` parameter in render_shapes is now a float that actually determines the line width (#139).
+- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
+- Empty geometries among the shapes can be handeled (#133).
+- `outline_width` parameter in render_shapes is now a float that actually determines the line width (#139).
 
 ## [0.0.2] - 2023-06-25
 
 ### Fixed
 
--   Multiple bugfixes of which I didn't keep track of.
+- Multiple bugfixes of which I didn't keep track of.
 
 ## [0.0.1] - 2023-04-04
 
 ### Added
 
--   Initial release of `spatialdata-plot` with support for `images`, `labels`, `points` and `shapes`.
+- Initial release of `spatialdata-plot` with support for `images`, `labels`, `points` and `shapes`.

src/spatialdata_plot/pl/basic.py

@@ -272,7 +272,7 @@ def render_shapes(
             scale=scale,
             table_name=table_name,
             method=method,
-            ds_reduction=kwargs.get("datashader_reduction", None),
+            ds_reduction=kwargs.get("datashader_reduction"),
         )
 
         sdata = self._copy()
@@ -296,7 +296,7 @@ def render_shapes(
                 palette=param_values["palette"],
                 outline_alpha=param_values["outline_alpha"],
                 fill_alpha=param_values["fill_alpha"],
-                transfunc=kwargs.get("transfunc", None),
+                transfunc=kwargs.get("transfunc"),
                 table_name=param_values["table_name"],
                 zorder=n_steps,
                 method=param_values["method"],
@@ -403,7 +403,7 @@ def render_points(
             norm=norm,
             size=size,
             table_name=table_name,
-            ds_reduction=kwargs.get("datashader_reduction", None),
+            ds_reduction=kwargs.get("datashader_reduction"),
         )
 
         if method is not None:
@@ -430,7 +430,7 @@ def render_points(
                 cmap_params=cmap_params,
                 palette=param_values["palette"],
                 alpha=param_values["alpha"],
-                transfunc=kwargs.get("transfunc", None),
+                transfunc=kwargs.get("transfunc"),
                 size=param_values["size"],
                 table_name=param_values["table_name"],
                 zorder=n_steps,
@@ -675,7 +675,7 @@ def render_labels(
                 palette=param_values["palette"],
                 outline_alpha=param_values["outline_alpha"],
                 fill_alpha=param_values["fill_alpha"],
-                transfunc=kwargs.get("transfunc", None),
+                transfunc=kwargs.get("transfunc"),
                 scale=param_values["scale"],
                 table_name=param_values["table_name"],
                 zorder=n_steps,

src/spatialdata_plot/pl/render.py

@@ -717,8 +717,10 @@ def _render_images(
             extent=extent,
         )
 
-    channels = img.coords["c"].values if render_params.channel is None else render_params.channel
+    channels = img.coords["c"].values.tolist() if render_params.channel is None else render_params.channel
 
+    # the channel parameter has been previously validated, so when not None, render_params.channel is a list
+    assert isinstance(channels, list)
     n_channels = len(channels)
 
     # True if user gave n cmaps for n channels