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CI: Add the "Doctests" workflow to run doctests weekly #2456
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adbb19d
Do not run the full tests in the Tests workflow
seisman 9f4a136
Add a new workflow to run doctests weekly
seisman d4d3aba
Temporarily enable the workflow in PR
seisman 63d28d4
Update the workflow
seisman 952456b
Add the workflow information to maintainers guides
seisman f904987
Merge branch 'main' into workflow-doctests
seisman da5535b
Add rioxarray
seisman d03048f
Merge branch 'main' into workflow-doctests
seisman 8e0acfc
Merge branch 'main' into workflow-doctests
seisman 142add7
Python 3.8 is no longer supported
seisman 5946fd4
Merge branch 'main' into workflow-doctests
seisman f17b57c
Only run on Python 3.11
seisman d1344cd
Doctests don't produce any diff images
seisman 8ac89f2
matrix.numpy-version is not defined and fix a typo
seisman eea0b4a
Disable the workflow in PR and fix a typo
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| # This workflow installs PyGMT and runs all doctests | ||
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| name: Doctests | ||
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| on: | ||
| # push: | ||
| # branches: [ main ] | ||
| # pull_request: | ||
| # Schedule weekly tests on Sunday | ||
| schedule: | ||
| - cron: '0 0 * * 0' | ||
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| jobs: | ||
| test: | ||
| name: ${{ matrix.os }} | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: [ubuntu-latest, macOS-latest, windows-latest] | ||
| timeout-minutes: 30 | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
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| steps: | ||
| # Cancel previous runs that are not completed | ||
| - name: Cancel Previous Runs | ||
| uses: styfle/cancel-workflow-action@0.11.0 | ||
| with: | ||
| access_token: ${{ github.token }} | ||
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| # Checkout current git repository | ||
| - name: Checkout | ||
| uses: actions/checkout@v3.4.0 | ||
| with: | ||
| # fetch all history so that setuptools-scm works | ||
| fetch-depth: 0 | ||
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| # Install Mambaforge with conda-forge dependencies | ||
| - name: Setup Mambaforge | ||
| uses: conda-incubator/setup-miniconda@v2.2.0 | ||
| with: | ||
| activate-environment: pygmt | ||
| python-version: '3.11' | ||
| channels: conda-forge,nodefaults | ||
| channel-priority: strict | ||
| miniforge-version: latest | ||
| miniforge-variant: Mambaforge | ||
| mamba-version: "*" | ||
| run-post: false | ||
| use-mamba: true | ||
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| # Install GMT and other required dependencies from conda-forge | ||
| - name: Install dependencies | ||
| run: | | ||
| mamba install gmt=6.4.0 numpy \ | ||
| pandas xarray netCDF4 packaging \ | ||
| build make 'pytest>=6.0' \ | ||
| pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery \ | ||
| contextily geopandas ipython rioxarray | ||
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| # Show installed pkg information for postmortem diagnostic | ||
| - name: List installed packages | ||
| run: mamba list | ||
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| # Download cached remote files (artifacts) from GitHub | ||
| - name: Download remote data from GitHub | ||
| uses: dawidd6/action-download-artifact@v2.26.0 | ||
| with: | ||
| workflow: cache_data.yaml | ||
| workflow_conclusion: success | ||
| name: gmt-cache | ||
| path: .gmt | ||
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| # Move downloaded files to ~/.gmt directory and list them | ||
| - name: Move and list downloaded remote files | ||
| run: | | ||
| mkdir -p ~/.gmt | ||
| mv .gmt/* ~/.gmt | ||
| # Change modification times of the two files, so GMT won't refresh it | ||
| touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt | ||
| ls -lhR ~/.gmt | ||
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| # Install the package that we want to test | ||
| - name: Install the package | ||
| run: make install | ||
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| # Run the doctests | ||
| - name: Run doctests | ||
| run: make doctest PYTEST_EXTRA="-r P" |
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Off-topic question: Currently, we're documenting what a workflow does in the maintainers' guide, but it's very likely that we may forget to update the guides when we make changes to a workflow.
Perhaps we should only keep a short, one-sentence description for each workflow in the maintainers' guide and put a much longer description in the workflow file.
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Ping @GenericMappingTools/pygmt-maintainers for comments on this.
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Maybe have a README.md under https://github.com/GenericMappingTools/pygmt/tree/v0.9.0/.github/workflows to document, so that people looking at the folder can see what the *.yml files are for? Also fine with including it in the YAML file since that will be more visible.
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I'm inclined to this option because (1) we won't forget to update the workflow descriptions; (2) the workflows are more self-explanatory.
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Ok, so just document things in the YAML files and remove the descriptions from the doc/maintenance.md file. Can do this in another PR once this one is merged.