Run notebooks in CI #1
Workflow file for this run
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| name: Test | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u). | |
| shell: bash -euo pipefail {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| notebook: [ | |
| "docs/tutorials/notebooks/augur.ipynb", | |
| ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| filter: blob:none | |
| fetch-depth: 0 | |
| - name: Cache .pertpy_cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: cache | |
| key: ${{ runner.os }}-pertpy-cache-${{ hashFiles('pertpy/metadata/**') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pertpy-cache | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.13" | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.4.3" | |
| - name: Cache R packages | |
| id: r-cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ hashFiles('**/pertpy/tools/_milo.py') }} | |
| restore-keys: ${{ runner.os }}-r- | |
| - name: Install R dependencies | |
| if: steps.r-cache.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir -p ${{ env.R_LIBS_USER }} | |
| Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); BiocManager::install('edgeR', lib='${{ env.R_LIBS_USER }}')" | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: pyproject.toml | |
| - name: Install dependencies | |
| run: | | |
| uv pip install --system rpy2 | |
| uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]" | |
| - name: Run ${{ matrix.notebook }} Notebook | |
| run: jupyter nbconvert --to notebook --execute ${{ matrix.notebook }} |