Merge branch 'giovp/get_element_instances' of https://github.com/scverse/spatialdata-plot into giovp/get_element_instances

Author: LucaMarconato

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`.

README.md

@@ -26,8 +26,8 @@ SpatialData’s plotting capabilities allow to quickly visualise all contained m
 
 For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the
 
--   [API documentation][link-api].
--   [Example notebooks][link-notebooks] (section "Visiualizations")
+- [API documentation][link-api].
+- [Example notebooks][link-notebooks] (section "Visiualizations")
 
 ## Installation
 

docs/contributing.md

@@ -82,11 +82,11 @@ out to the developers of the dependency before the package is released to a wide
 
 Many tests will produce plots and check that they are correct by comparing them with a previously saved and serialized version of the same plots. The ground truth images are located in `tests/_images`. Different OS/versions may produce similar but not identical plots (for instance the ticks/padding could vary). To take into account for this please consider the following:
 
--   you should not use locally generated plots as ground truth images, but you should commit images that have been generated by a GitHub Action. The recommended workflow is to go to the ["actions" page for the repo](https://github.com/scverse/spatialdata-plot/actions/workflows/test.yaml), download the artifacts, and upload them as ground truth (after having reviewed them).
--   the ground truth images need to be updated when a new test is passing, or when a test starts producing a slightly different (but consistent) plot.
--   please never replace the ground truth images without having manually reviewed them.
--   if you run the tests locally in macOS or Windows they will likely fail because the ground truth images are generated using Ubuntu. To overcome this you can use `act`, which will generate a Docker reproducing the environment used in the GitHub Action. After the Docker container is generated you can use it within IDEs to run tests and debug code.
--   in the case of PyCharm, it is easier to create a container from a `Dockerfile` instead of using `act`. Please in such case use the `Dockerfile` made availabel in the repository. If you encountering problems with `act` or `docker`, please [get in touch with the developers via Zulip](https://scverse.zulipchat.com/#narrow/channel/443514-spatialdata-dev) and we will help troubleshoot the issue. See also additional details [here](https://github.com/scverse/spatialdata-plot/pull/397).
+- you should not use locally generated plots as ground truth images, but you should commit images that have been generated by a GitHub Action. The recommended workflow is to go to the ["actions" page for the repo](https://github.com/scverse/spatialdata-plot/actions/workflows/test.yaml), download the artifacts, and upload them as ground truth (after having reviewed them).
+- the ground truth images need to be updated when a new test is passing, or when a test starts producing a slightly different (but consistent) plot.
+- please never replace the ground truth images without having manually reviewed them.
+- if you run the tests locally in macOS or Windows they will likely fail because the ground truth images are generated using Ubuntu. To overcome this you can use `act`, which will generate a Docker reproducing the environment used in the GitHub Action. After the Docker container is generated you can use it within IDEs to run tests and debug code.
+- in the case of PyCharm, it is easier to create a container from a `Dockerfile` instead of using `act`. Please in such case use the `Dockerfile` made availabel in the repository. If you encountering problems with `act` or `docker`, please [get in touch with the developers via Zulip](https://scverse.zulipchat.com/#narrow/channel/443514-spatialdata-dev) and we will help troubleshoot the issue. See also additional details [here](https://github.com/scverse/spatialdata-plot/pull/397).
 
 ## Publishing a release
 
@@ -109,11 +109,11 @@ Specify `vX.X.X` as a tag name and create a release. For more information, see [
 
 Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
 
--   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
--   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
--   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
--   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
--   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.
@@ -130,10 +130,10 @@ repository.
 
 #### Hints
 
--   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
-    if you do so can sphinx automatically create a link to the external documentation.
--   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
-    the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+  if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+  the `nitpick_ignore` list in `docs/conf.py`
 
 #### Building the docs locally