change ci #157
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| name: Execute notebooks | |
| on: [push] | |
| jobs: | |
| run-notebooks: | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ['3.9', '3.11'] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: python3 -m pip install anoexpress malariagen_data nbformat ipykernel papermill nbconvert | |
| - run: python -m ipykernel install --user --name anoexpress | |
| - run: papermill workflow/notebooks/plot-gene-expression.ipynb ci.ipynb -k anoexpress | |
| - run: papermill workflow/notebooks/plot-families-expression.ipynb ci2.ipynb -k anoexpress | |
| - run: papermill workflow/notebooks/expression-candidates.ipynb ci3.ipynb -k anoexpress | |
| - run: papermill workflow/notebooks/enrichment.ipynb ci4.ipynb -k anoexpress | |
| - run: papermill workflow/notebooks/utility-functions.ipynb ci5.ipynb -k anoexpress |