run all notebooks #14
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| # This notebook will run all Python notebooks | |
| # | |
| # The environment variable NOTEBOOKS should contain all notebooks, so if you | |
| # create a new one or notice a missing notebook, please feel free to add it! | |
| name: run all notebooks | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '40 12 * * 1' | |
| jobs: | |
| run_all_notebooks: | |
| runs-on: ubuntu-latest | |
| env: | |
| NOTEBOOKS: | | |
| ( | |
| "examples/core_examples/FileIO_DataStore.ipynb" | |
| "examples/core_examples/hyperbolic_magnitude_test.ipynb" | |
| "examples/core_examples/iterator_test.ipynb" | |
| "examples/core_examples/Run_Pipe.ipynb" | |
| "examples/core_examples/Pipe_Example.ipynb" | |
| "examples/creation_examples/posterior-demo.ipynb" | |
| "examples/creation_examples/degradation-demo.ipynb" | |
| "examples/creation_examples/example_GridSelection_for_HSC.ipynb" | |
| "examples/creation_examples/example_SpecSelection_for_zCOSMOS.ipynb" | |
| "examples/estimation_examples/NZDir.ipynb" | |
| "examples/estimation_examples/test_sampled_summarizers.ipynb" | |
| "examples/goldenspike_examples/goldenspike.ipynb" | |
| ) | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel numpy # For somoclu | |
| pip install . | |
| pip install git+https://github.com/LSSTDESC/rail_bpz@lynn/rail-directory-match | |
| pip install flake8 pytest pytest-cov mockmpi pytest-timeout | |
| pip install -r docs/requirements.txt | |
| pip install -r docs/nbconvert-requirements.txt | |
| pip install jupyter nbconvert nbformat | |
| - name: Core notebooks | |
| shell: bash | |
| run: | | |
| allnotebooks=${{ env.NOTEBOOKS }} | |
| for notebook in ${allnotebooks[*]}; do | |
| if [[ $notebook == *"core_examples"* ]]; then | |
| jupyter nbconvert --to html --execute "$notebook" | |
| fi | |
| done | |
| - name: Creation notebooks | |
| shell: bash | |
| run: | | |
| allnotebooks=${{ env.NOTEBOOKS }} | |
| for notebook in ${allnotebooks[*]}; do | |
| if [[ $notebook == *"creation_examples"* ]]; then | |
| jupyter nbconvert --to html --execute "$notebook" | |
| fi | |
| done | |
| - name: Estimation notebooks | |
| shell: bash | |
| run: | | |
| allnotebooks=${{ env.NOTEBOOKS }} | |
| for notebook in ${allnotebooks[*]}; do | |
| if [[ $notebook =~ "estimation_examples" ]]; then | |
| jupyter nbconvert --to html --execute "$notebook" | |
| fi | |
| done | |
| - name: Goldenspike notebooks | |
| shell: bash | |
| run: | | |
| allnotebooks=${{ env.NOTEBOOKS }} | |
| for notebook in ${allnotebooks[*]}; do | |
| if [[ $notebook =~ "goldenspike_examples" ]]; then | |
| jupyter nbconvert --to html --execute "$notebook" | |
| fi | |
| done | |
| - name: Other notebooks | |
| shell: bash | |
| run: | | |
| allnotebooks=${{ env.NOTEBOOKS }} | |
| for notebook in ${allnotebooks[*]}; do | |
| if [[ ! $notebook =~ "core_examples" && | |
| ! $notebook =~ "creation_examples" && | |
| ! $notebook =~ "estimation_examples" && | |
| ! $notebook =~ "goldenspike_examples" ]]; then | |
| jupyter nbconvert --to html --execute "$notebook" | |
| fi | |
| done |