Update ci_scheduled.yml #2
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| name: Scheduled Notebook Execution | ||
| on: | ||
| workflow_call: | ||
| inputs: | ||
| python-version: | ||
| required: true | ||
| type: string | ||
| secrets: | ||
| CASJOBS_USERID: | ||
| description: 'CASJOBS user ID' | ||
| required: false | ||
| CASJOBS_PW: | ||
| description: 'CASJOBS password' | ||
| required: false | ||
| #permissions: write-all | ||
| jobs: | ||
| gather-notebooks: | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ steps.set-matrix.outputs.matrix }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - id: set-matrix | ||
| run: echo "matrix=$(find notebooks -name "*.ipynb" | jq -cnR '[inputs | select(length>0)]')" >> $GITHUB_OUTPUT | ||
| tests: | ||
| needs: gather-notebooks | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| notebooks: ${{ fromJson(needs.gather-notebooks.outputs.matrix) }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| #- run: | | ||
| # pip install -r ${${{ matrix.notebooks }}%/*}/requirements.txt | ||
| - uses: actions/checkout@v4 | ||
| - name: Set up Python ${{ inputs.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ inputs.python-version }} | ||
| #- name: Add conda to system path | ||
| # run: | | ||
| # # $CONDA is an environment variable pointing to the root of the miniconda directory | ||
| # echo $CONDA/bin >> $GITHUB_PATH | ||
| - name: Install dependencies | ||
| run: | | ||
| # pip install wheel | ||
| export PYDEVD_DISABLE_FILE_VALIDATION=1 | ||
| export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True | ||
| # python -m pip install --upgrade pip | ||
| echo "Path to req's: $(dirname ${{ matrix.notebooks }})/requirements.txt" | ||
| ls $(dirname ${{ matrix.notebooks }}) | ||
| echo --- | ||
| if [ -f $(dirname "${{ matrix.notebooks }}")/pre-install.sh ]; then | ||
| chmod +x $(dirname "${{ matrix.notebooks }}")/pre-install.sh | ||
| ./$(dirname "${{ matrix.notebooks }}")/pre-install.sh | ||
| fi | ||
| if [ -f $(dirname "${{ matrix.notebooks }}")/pre-requirements.sh ]; then | ||
| chmod +x $(dirname "${{ matrix.notebooks }}")/pre-requirements.sh | ||
| ./$(dirname "${{ matrix.notebooks }}")/pre-requirements.sh | ||
| fi | ||
| if [ -f $(dirname "${{ matrix.notebooks }}")/pre-requirements.txt ]; then | ||
| pip install -r $(dirname "${{ matrix.notebooks }}")/pre-requirements.txt | ||
| fi | ||
| if [ -f pre-requirements.txt ]; then | ||
| pip install -r pre-requirements.txt | ||
| fi | ||
| pip install -r $(dirname ${{ matrix.notebooks }})/requirements.txt | ||
| pip install pytest | ||
| pip install nbval | ||
| pip install nbconvert | ||
| if [ "${GITHUB_REPOSITORY}" == "spacetelescope/hst_notebooks" ]; then | ||
| source /usr/share/miniconda/etc/profile.d/conda.sh | ||
| conda create --yes -n hstcal -c conda-forge hstcal | ||
| fi | ||
| - name: Execute notebooks | ||
| run: | | ||
| if [ "${GITHUB_REPOSITORY}" == "spacetelescope/hst_notebooks" ]; then | ||
| source /usr/share/miniconda/etc/profile.d/conda.sh | ||
| conda init | ||
| conda activate hstcal | ||
| fi | ||
| jupyter nbconvert --template classic --to html --execute "${{ matrix.notebooks }}" | ||
| - name: Validate notebooks | ||
| run: | | ||
| if [ "${GITHUB_REPOSITORY}" == "spacetelescope/hst_notebooks" ]; then | ||
| source /usr/share/miniconda/etc/profile.d/conda.sh | ||
| conda init | ||
| conda activate hstcal | ||
| fi | ||
| git checkout gh-storage | ||
| pytest --nbval "${{ matrix.notebooks }}" | ||
