run all notebooks #16
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |