Read the docs #301
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| name: Run tutorials | |
| on: | |
| push: | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | |
| jobs: | |
| installer: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Free space | |
| # HACK fixes 'No space left on device' | |
| # see: https://github.com/orgs/community/discussions/25678#discussioncomment-5242449 | |
| # NOTE we don't use those, we use conda for everything anyway | |
| run: rm -rf /opt/hostedtoolcache | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: | | |
| docs | |
| tests | |
| sparse-checkout-cone-mode: false | |
| lfs: false | |
| # - name: Install conda environment dependencies | |
| # uses: conda-incubator/setup-miniconda@v3 | |
| # with: | |
| # miniforge-version: latest | |
| # miniforge-variant: Miniforge3 | |
| # mamba-version: "*" | |
| # use-mamba: true | |
| # no-implicit-channels: true | |
| # channels: conda-forge,bioconda | |
| # channel-priority: strict | |
| # activate-environment: JupyText | |
| # auto-update-conda: true | |
| # environment-file: tests/conda_tutorials_env.yaml | |
| # | |
| # - name: Setup Jupyter kernel | |
| # run: | | |
| # python -m ipykernel install --user | |
| - name: Install python environment | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' | |
| - name: Run installation tutorial | |
| working-directory: ./docs | |
| # run: ./convert.sh --branch *_install.md | |
| run: | | |
| mkdir -p _test_tutorials | |
| ./convert.sh --version --branch --sralog --patch-only documentation/*.md tutorials/*.md | |
| python extract_bash_code.py -o _test_tutorials documentation/*.md tutorials/*.md | |
| cd _test_tutorials | |
| bash installation.sh | |
| - name: Create V-pipe installation archive | |
| # HACK this acceleraters upload while preserving Unix-specifics (case sensitivity, file attributes). | |
| run: tar --zstd -cvf vpipeinstallation.tar.zst ./docs/_test_tutorials/vp-analysis ./docs/_test_tutorials/*.sh | |
| - name: Keep installation | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: VPipeInstallation | |
| path: vpipeinstallation.tar.zst | |
| compression-level: 0 # no compression | |
| if-no-files-found: error | |
| # - name: Save notebooks | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: JupyterNotebooks-Install | |
| # path: ./docs/*.ipynb | |
| tutorial: | |
| needs: installer | |
| strategy: | |
| max-parallel: 5 | |
| fail-fast: false | |
| matrix: | |
| virus: ["hiv"] #, "sarscov2"] | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Free space | |
| # HACK fixes 'No space left on device' | |
| # see: https://github.com/orgs/community/discussions/25678#discussioncomment-5242449 | |
| # NOTE we don't use those, we use conda for everything anyway | |
| run: rm -rf /opt/hostedtoolcache | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: | | |
| docs | |
| tests | |
| sparse-checkout-cone-mode: false | |
| lfs: false | |
| - name: Reuse installation | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: VPipeInstallation | |
| - name: Extract V-pipe installation archive | |
| run: tar --zstd -xvf vpipeinstallation.tar.zst | |
| # - name: Install conda environment dependencies | |
| # uses: conda-incubator/setup-miniconda@v3 | |
| # with: | |
| # miniforge-version: latest | |
| # miniforge-variant: Miniforge3 | |
| # python-version: "3.11" | |
| # mamba-version: "*" | |
| # use-mamba: true | |
| # no-implicit-channels: true | |
| # channels: conda-forge,bioconda | |
| # channel-priority: strict | |
| # activate-environment: JupyText | |
| # auto-update-conda: true | |
| # environment-file: tests/conda_tutorials_env.yaml | |
| # | |
| # - name: Setup Jupyter kernel | |
| # run: | | |
| # python -m ipykernel install --user | |
| - name: Install python environment | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' | |
| - name: Run analysis tutorial | |
| working-directory: ./docs | |
| #run: ./convert.sh --version --branch --sralog tutorial*_${{ matrix.virus }}.md | |
| run: | | |
| cd _test_tutorials | |
| bash tutorial_${{ matrix.virus }}.sh | |
| - name: Save output | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Tutorial_${{ matrix.virus }} | |
| path: | | |
| ./docs/_test_tutorials/ | |
| !./docs/_test_tutorials/vp-analysis/work*/.snakemake/conda/*/ | |
| !./docs/_test_tutorials/vp-analysis/mini*/pkgs/ | |
| include-hidden-files: true | |
| if-no-files-found: ignore | |
| # - name: Save notebooks | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: JupyterNotebooks-${{ matrix.virus }} | |
| # path: ./docs/*.ipynb | |
| # - name: Publish | |
| # uses: peaceiris/actions-gh-pages@v3 | |
| # with: | |
| # github_token: ${{ secrets.GITHUB_TOKEN }} | |
| # publish_dir: ./docs |