Add plot_ma for DGE results #535
Workflow file for this run
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| name: Test tutorials | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| 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} | |
| env: | |
| NOTEBOOK_PATH: docs/tutorials/notebooks | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| notebook: [ | |
| "augur.ipynb", | |
| "cinemaot.ipynb", | |
| "dialogue.ipynb", | |
| "differential_gene_expression.ipynb", | |
| "distances.ipynb", | |
| "distance_tests.ipynb", | |
| "enrichment.ipynb", | |
| "guide_rna_assignment.ipynb", | |
| "milo.ipynb", | |
| "perturbation_efficacy.ipynb", | |
| "sccoda.ipynb", | |
| # "perturbation_space.ipynb", seems to run OOM as of Jax implementation | |
| # "tasccoda.ipynb", a pain to get running because of the required QT dependency. The QT action leads to a dead kernel | |
| # also no use cases yet | |
| ] | |
| steps: | |
| - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 | |
| with: | |
| filter: blob:none | |
| fetch-depth: 0 | |
| submodules: "true" | |
| persist-credentials: false | |
| - name: Cache pertpy's metadata folder | |
| uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | |
| with: | |
| path: cache | |
| key: ${{ runner.os }}-pertpy-cache-${{ hashFiles('src/pertpy/metadata/**') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pertpy-cache | |
| - name: Cache data aka datasets folder | |
| uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | |
| with: | |
| path: data | |
| key: ${{ runner.os }}-pertpy-data | |
| restore-keys: | | |
| ${{ runner.os }}-pertpy-data | |
| - name: Set up Python | |
| uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 | |
| with: | |
| python-version: "3.14" | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@d3c5be51b12e724e68f33216ca3c148b66d5f0b6 # v2 | |
| with: | |
| r-version: "4.5.3" | |
| use-public-rspm: true | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@d3c5be51b12e724e68f33216ca3c148b66d5f0b6 # v2 | |
| with: | |
| packages: | | |
| any::statmod | |
| bioc::edgeR | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: pyproject.toml | |
| - name: Install dependencies | |
| run: | | |
| uv pip install --system rpy2 decoupler muon | |
| uv pip install --system ".[dev,test,all]" | |
| uv pip install --system nbconvert ipykernel | |
| - name: Run ${{ matrix.notebook }} Notebook | |
| run: jupyter nbconvert --to notebook --execute ${{ env.NOTEBOOK_PATH }}/${{ matrix.notebook }} |