Merge branch 'main' into giovp/get_element_instances

Author: LucaMarconato

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
-  "checkout": "v0.3.0",
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "spatialdata-plot",
@@ -13,7 +13,8 @@
       "project_repo": "https://github.com/scverse/spatialdata-plot",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,

.github/workflows/test.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.9", "3.10"]
+        python: ["3.10", "3.12"]
         os: [ubuntu-latest]
 
     env:
@@ -49,25 +49,19 @@ jobs:
           pip install pytest-cov
       - name: Install dependencies
         run: |
-          pip install --pre -e ".[dev,test]"
+          pip install --pre -e ".[dev,test,pre]"
       - name: Test
         env:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
           pytest -v --cov --color=yes --cov-report=xml
-      # - name: Generate GH action "groundtruth" figures as artifacts, uncomment if needed
-      #   if: always()
-      #   uses: actions/upload-artifact@v3
-      #   with:
-      #       name: groundtruth-figures
-      #       path: /home/runner/work/spatialdata-plot/spatialdata-plot/tests/_images/*
       - name: Archive figures generated during testing
         if: always()
         uses: actions/upload-artifact@v3
         with:
-          name: plotting-results
+          name: visual_test_results_${{ matrix.os }}-python${{ matrix.python }}
           path: /home/runner/work/spatialdata-plot/spatialdata-plot/tests/figures/*
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

.mypy.ini

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.9
+python_version = 3.10
 plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False
@@ -25,4 +25,4 @@ no_warn_no_return = True
 
 show_error_codes = True
 show_column_numbers = True
-error_summary = True
+error_summary = True

.pre-commit-config.yaml

@@ -2,32 +2,32 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 ci:
   skip: []
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    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: v1.10.1
+    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: v0.5.0
+    rev: v0.8.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -8,24 +8,99 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [0.2.4] - tbd
+## [0.2.9] - tbd
+
+### 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)
+
+## [0.2.8] - 2024-11-26
+
+### Changed
+
+-   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)
+
+### 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)
+
+## [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)
+
+### 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)
+
+## [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)
+
+### Fixed
+
+-   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)
+
+### 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)
 
 ## [0.2.3] - 2024-07-03
 
+### Added
+
+-   Datashader support for points and shapes (#244)
+
 ### Changed
 
--   All parameters are now provided for a single element. If element in pl.render is None then this value will be broadcasted
+-   All parameters are now provided for a single element (#272)
 
 ### Fixed
 
 -   Fix color assignment for NaN values (#257)
--   Fix channel str support #221
+-   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
+-   Fixed `fill_alpha` ignoring `alpha` channel from custom cmap (#236)
 -   Fix channel str support (#221)
 
 ## [0.2.1] - 2024-03-26

README.md

@@ -31,7 +31,7 @@ For more information on the `spatialdata-plot` library, please refer to the [doc
 
 ## Installation
 
-You need to have Python 3.9 or newer installed on your system. If you don't have
+You need to have Python 3.10 or newer installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 There are several alternative options to install spatialdata-plot:

docs/conf.py

@@ -1,5 +1,5 @@
 # Configuration file for the Sphinx documentation builder.
-#
+
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -37,10 +37,10 @@
 
 html_context = {
     "display_github": True,  # Integrate GitHub
-    "github_user": "scverse",  # Username
-    "github_repo": project_name,  # Repo name
-    "github_version": "main",  # Version
-    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
+    "github_user": "scverse",
+    "github_repo": "https://github.com/scverse/spatialdata-plot",
+    "github_version": "main",
+    "conf_py_path": "/docs/",
 }
 
 # -- General configuration ---------------------------------------------------

docs/contributing.md

@@ -51,7 +51,7 @@ and [prettier][prettier-editors].
 ## Writing tests
 
 ```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
+Remember to first install the package with `pip install -e '.[dev,test]'`
 ```
 
 This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
@@ -78,6 +78,16 @@ out to the developers of the dependency before the package is released to a wide
 
 [scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
 
+### Testing the correctness of the plots
+
+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).
+
 ## Publishing a release
 
 ### Updating the version number
@@ -93,7 +103,7 @@ Before making a release, you need to update the version number in the `pyproject
 > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
 
 Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
 
 ## Writing documentation
 
@@ -157,3 +167,4 @@ open _build/html/index.html
 [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
 [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 [pypi]: https://pypi.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository