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timtreisclaude
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Merge main into feature/outline_color_for_labels to resolve conflicts
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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‎.cruft.json‎

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
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"checkout": "v0.4.0",
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"commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
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"checkout": "v0.7.0",
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"context": {
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"cookiecutter": {
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"project_name": "spatialdata-plot",
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"author_full_name": "scverse",
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"author_email": "scverse",
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"github_user": "scverse",
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"project_repo": "https://github.com/scverse/spatialdata-plot",
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"github_repo": "spatialdata-plot",
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"license": "BSD 3-Clause License",
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"ide_integration": false,
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"_copy_without_render": [
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".github/workflows/build.yaml",
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".github/workflows/test.yaml",
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"docs/_templates/autosummary/**.rst"
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],
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"_exclude_on_template_update": [
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"CHANGELOG.md",
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"LICENSE",
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"README.md",
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"docs/api.md",
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"docs/index.md",
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"docs/notebooks/example.ipynb",
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"docs/references.bib",
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"docs/references.md",
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"src/**",
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"tests/**"
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],
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"_render_devdocs": false,
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"_jinja2_env_vars": {
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"lstrip_blocks": true,
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"trim_blocks": true
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},
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"_template": "https://github.com/scverse/cookiecutter-scverse"
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"_template": "https://github.com/scverse/cookiecutter-scverse",
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"_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
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}
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},
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"directory": null

‎.editorconfig‎

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trim_trailing_whitespace = true
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insert_final_newline = true
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[*.{yml,yaml}]
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indent_size = 2
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[.cruft.json]
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[{*.{yml,yaml,toml},.cruft.json}]
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indent_size = 2
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[Makefile]

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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name: Bug report
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description: Report something that is broken or incorrect
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type: Bug
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body:
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- type: markdown
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attributes:
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value: |
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**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
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detailing how to provide the necessary information for us to reproduce your bug. In brief:
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* Please provide exact steps how to reproduce the bug in a clean Python environment.
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* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
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* Replicate problems on public datasets or share data subsets when full sharing isn't possible.
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- type: textarea
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id: report
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attributes:
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label: Report
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: versions
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attributes:
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label: Versions
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description: |
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Which version of packages.
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Please install `session-info2`, run the following command in a notebook,
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click the "Copy as Markdown" button, then paste the results into the text box below.
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```python
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In[1]: import session_info2; session_info2.session_info(dependencies=True)
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```
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Alternatively, run this in a console:
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```python
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>>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
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```
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render: python

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: false
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contact_links:
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- name: Scverse Community Forum
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url: https://discourse.scverse.org/
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about: If you have questions about "How to do X", please ask them here.

‎.github/ISSUE_TEMPLATE/feature_request.yml‎

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name: Feature request
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description: Propose a new feature for spatialdata-plot
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type: Enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
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validations:
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required: true

‎.github/workflows/build.yaml‎

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name: Check Build
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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package:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Build package
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run: uv build
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- name: Check package
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run: uvx twine check --strict dist/*.whl

‎.github/workflows/release.yaml‎

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release:
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types: [published]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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package_and_release:
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build:
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags/v')
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.12
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uses: actions/setup-python@v5
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- uses: actions/checkout@v5
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with:
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python-version: "3.12"
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cache: pip
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- name: Install build dependencies
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run: python -m pip install --upgrade pip wheel twine build
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Build package
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run: python -m build
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run: uv build
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- name: Check package
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run: twine check --strict dist/*.whl
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- name: Install hatch
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run: pip install hatch
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- name: Build project for distribution
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run: hatch build
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- name: Publish a Python distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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run: uvx twine check --strict dist/*
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- name: Upload build artifacts
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uses: actions/upload-artifact@v4
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with:
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password: ${{ secrets.PYPI_API_TOKEN }}
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name: dist
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path: dist/
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publish:
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needs: build
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runs-on: ubuntu-latest
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permissions:
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id-token: write # for PyPI trusted publishing
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environment:
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name: pypi
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url: https://pypi.org/p/spatialdata-plot
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steps:
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- name: Download build artifacts
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uses: actions/download-artifact@v4
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with:
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name: dist
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path: dist/
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/test.yaml‎

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on:
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push:
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branches: [main]
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tags: ["v*"] # Push events to matching v*, i.e. v1.0, v20.15.10
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tags: ["v*"]
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pull_request:
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branches: ["*"]
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branches: [main]
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schedule:
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- cron: "0 5 1,15 * *"
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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MPLBACKEND: agg
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test:
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# Dynamically extract the test matrix from hatch so pyproject.toml is the single source of truth.
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# See [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml.
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get-environments:
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runs-on: ubuntu-latest
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outputs:
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envs: ${{ steps.get-envs.outputs.envs }}
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steps:
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- uses: actions/checkout@v5
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Get test environments
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id: get-envs
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run: |
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ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
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| map(
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select(.key | startswith("hatch-test"))
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| {
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name: .key,
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label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
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python: .value.python
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}
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)')
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echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
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test:
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needs: get-environments
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permissions:
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id-token: write # for codecov OIDC
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strategy:
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matrix:
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env: ["dev-py311", "dev-py313"]
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os: [ubuntu-latest]
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env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
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# Configure pytest-xdist
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env:
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OMP_NUM_THREADS: "1"
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OPENBLAS_NUM_THREADS: "1"
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MKL_NUM_THREADS: "1"
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NUMEXPR_MAX_THREADS: "1"
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MPLBACKEND: "agg"
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DISPLAY: ":42"
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PYTEST_ADDOPTS: "-n auto --dist=load --durations=10"
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name: ${{ matrix.env.label }}
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runs-on: ${{ matrix.os }}
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continue-on-error: ${{ contains(matrix.env.name, 'pre') }}
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- uses: actions/checkout@v4
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# Cache rattler's shared package cache (speeds up downloads)
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- name: Restore rattler cache
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uses: actions/cache@v4
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- uses: actions/checkout@v5
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with:
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path: ~/.cache/rattler
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key: rattler-${{ runner.os }}-${{ matrix.env }}-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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rattler-${{ runner.os }}-${{ matrix.env }}-
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rattler-${{ runner.os }}-
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# Install pixi and the requested environment
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- uses: prefix-dev/setup-pixi@v0.9.0
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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with:
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environments: ${{ matrix.env }}
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# We're not comitting the pixi-lock file
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locked: false
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cache: false
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activate-environment: ${{ matrix.env }}
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- name: Show versions
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run: |
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python --version
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pixi --version
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python-version: ${{ matrix.env.python }}
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- name: Ensure figure directory exists
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run: mkdir -p tests/figures
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- name: Create hatch environment
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run: uvx hatch env create ${{ matrix.env.name }}
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MPLBACKEND: agg
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DISPLAY: ":42"
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run: >-
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uvx hatch run ${{ matrix.env.name }}:${{
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matrix.env.name == 'hatch-test.py3.14-stable' && 'run-cov' || 'run'
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}} -v --color=yes ${{
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matrix.env.name == 'hatch-test.py3.14-stable' && ' ' || '-n auto'
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}}
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- name: Generate coverage report
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if: matrix.env.name == 'hatch-test.py3.14-stable'
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pytest -v --cov --color=yes --cov-report=xml
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- name: Archive figures generated during testing
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test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
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uvx hatch run ${{ matrix.env.name }}:cov-report
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- name: Archive visual test figures
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name: visual_test_results_${{ matrix.env }}
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path: /home/runner/work/spatialdata-plot/spatialdata-plot/tests/figures/*
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name: visual_test_results_${{ matrix.env.name }}
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path: tests/figures/*
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- name: Upload coverage
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if: matrix.env.name == 'hatch-test.py3.14-stable'
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uses: codecov/codecov-action@v5
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with:
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fail_ci_if_error: true
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use_oidc: true
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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# Single required check for branch protection.
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# See https://github.com/re-actors/alls-green#why
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check:
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name: Tests pass in all hatch environments
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if: always()
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needs:
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- get-environments
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- test
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runs-on: ubuntu-latest
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steps:
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- uses: re-actors/alls-green@release/v1
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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jobs: ${{ toJSON(needs) }}

‎.gitignore‎

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# Compiled files
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.venv/
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__pycache__/
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.mypy_cache/
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.ruff_cache/
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.*cache/
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# Distribution / packaging
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/*.egg-info/
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# Tests and coverage
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/.pytest_cache/
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/data/
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*failed-diff.png
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# test
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tests/figures/
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