Update scRNA tutorial #240
Workflow file for this run
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| name: Execute notebooks | |
| on: | |
| pull_request: | |
| branches: [main] | |
| paths: | |
| - ".github/workflows/execute-nbs.yaml" | |
| - "docs/**" | |
| - "environment.yml" | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| runnbs: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write # Allow GH actions to push changes to repo | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| ref: ${{ github.head_ref }} | |
| filter: blob:none | |
| fetch-depth: 0 | |
| - name: Cache conda | |
| uses: actions/cache@v2 | |
| env: | |
| # Increase this value to reset cache if env file has not changed | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} | |
| - name: Cache notebooks | |
| uses: actions/cache@v2 | |
| env: | |
| # Increase this value to reset cache if env file has not changed | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: .jupyter_cache | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: tutorials | |
| channel-priority: strict | |
| environment-file: environment.yml | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| use-mamba: true | |
| use-only-tar-bz2: true # This needs to be set for caching to work properly! | |
| - name: execute notebooks | |
| run: | | |
| mkdir -p .jupyter_cache | |
| # set kernel to "python3" (just in case someone used a custom conda env kernel locally) | |
| for f in docs/notebooks/*.ipynb ; do | |
| jupytext --to notebook --set-kernel python3 $f | |
| done | |
| # First remove all notebooks from the project, then add all again. | |
| # This does not remove them from the cache. This step is required since a notebook could be in the cache, but not in the PR. | |
| jcache notebook clear --force | |
| jcache notebook add docs/notebooks/*.ipynb | |
| jcache project execute --timeout 1800 | |
| - name: output logs | |
| run: | | |
| jcache notebook list | |
| for f in docs/notebooks/*.ipynb ; do | |
| jcache notebook info --tb $f | |
| done | |
| # write changed outputs back to the ipynb files | |
| # will fail if there was an execution error | |
| - name: merge notebooks | |
| run: | | |
| for f in docs/notebooks/*.ipynb ; do | |
| jcache notebook merge $f $f | |
| done | |
| - uses: stefanzweifel/git-auto-commit-action@v4 | |
| with: | |
| commit_message: Render notebooks |