run in a container #280
Workflow file for this run
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| name: CI with dynamic parallel matrix | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| packages: write | |
| env: | |
| TIMEOUT: '-1' # nbconvert timeout | |
| EXTRA_ARGS: '' # Extra arguments for nbconvert | |
| PYTHON_VER: '3.11' | |
| jobs: | |
| setup: | |
| container: | |
| image: julia:1.9.3 | |
| env: | |
| JULIA_CPU_TARGET: 'generic;haswell,clone_all' | |
| JULIA_NUM_THREADS: 'auto' | |
| JULIA_CONDAPKG_BACKEND: 'Null' | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VER }} | |
| - name: Cache Julia deps | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.julia/artifacts | |
| ~/.julia/compiled | |
| ~/.julia/packages | |
| key: ${{ runner.os }}-juliacontainer-${{ hashFiles('Manifest.toml')}} | |
| restore-keys: | | |
| ${{ runner.os }}-juliacontainer- | |
| - name: Install Julia packages | |
| env: | |
| PYTHON: ${{ env.pythonLocation }}/python | |
| JULIA_PYTHONCALL_EXE: ${{ env.pythonLocation }}/python | |
| run: | | |
| julia --project="" --color=yes -e 'using Pkg; Pkg.add(["IJulia"])' | |
| julia --project=@. --color=yes -e 'using Pkg; Pkg.instantiate(); Pkg.precompile(); Pkg.gc()' | |
| - name: List notebooks as a JSON array | |
| id: set-matrix | |
| working-directory: docs | |
| run: echo "matrix=$(python -c 'import glob, json; print(json.dumps(glob.glob("**/*.ipynb", recursive=True)))')" >> "$GITHUB_OUTPUT" | |
| execute: | |
| needs: setup | |
| strategy: | |
| max-parallel: 20 | |
| fail-fast: false | |
| matrix: | |
| # Notebooks need to be executed | |
| notebook: ${{ fromJSON(needs.setup.outputs.matrix) }} | |
| runs-on: ubuntu-latest | |
| container: | |
| image: julia:1.9.3 | |
| env: | |
| JULIA_CPU_TARGET: 'generic;haswell,clone_all' | |
| JULIA_NUM_THREADS: 'auto' | |
| JULIA_CONDAPKG_BACKEND: 'Null' | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Get notebook path | |
| id: file | |
| run: echo "name=docs/${{ matrix.notebook }}" >> "$GITHUB_OUTPUT" | |
| - name: Restore notebook if present | |
| uses: actions/cache/restore@v3 | |
| id: cache | |
| with: | |
| path: ${{ steps.file.outputs.name }} | |
| key: ${{ runner.os }}-notebook-${{ hashFiles(steps.file.outputs.name, 'requirements.txt', 'Project.toml', 'Manifest.toml', 'src/**', '.github/Dockerfile') }} | |
| - name: Setup Python | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VER }} | |
| - name: Install Python deps | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| run: | | |
| python -m pip install --no-cache-dir nbconvert | |
| python -m pip install --no-cache-dir -r requirements.txt | |
| - name: Cache Julia deps | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.julia/artifacts | |
| ~/.julia/compiled | |
| ~/.julia/packages | |
| key: ${{ runner.os }}-juliacontainer-${{ hashFiles('Manifest.toml')}} | |
| restore-keys: | | |
| ${{ runner.os }}-juliacontainer- | |
| - name: Install Julia packages | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| env: | |
| PYTHON: ${{ env.pythonLocation }}/python | |
| JULIA_PYTHONCALL_EXE: ${{ env.pythonLocation }}/python | |
| run: | | |
| julia --project="" --color=yes -e 'using Pkg; Pkg.add(["IJulia"]); import IJulia; IJulia.installkernel("Julia", "--project=@.")' | |
| julia --project=@. --color=yes -e 'using Pkg; Pkg.instantiate(); Pkg.precompile(); Pkg.gc()' | |
| - name: Execute Notebook | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| run: > | |
| jupyter nbconvert --to notebook --execute --inplace ${{ env.EXTRA_ARGS }} | |
| --ExecutePreprocessor.timeout=${{ env.TIMEOUT }} | |
| --ExecutePreprocessor.kernel_name=julia-1.$(julia -e 'print(VERSION.minor)') | |
| docs/${{ matrix.notebook }} | |
| - name: Cache notebook | |
| uses: actions/cache/save@v3 | |
| if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| with: | |
| path: ${{ steps.file.outputs.name }} | |
| key: ${{ steps.cache.outputs.cache-primary-key }} | |
| - name: Upload Notebook | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: notebooks | |
| path: docs*/${{ matrix.notebook }} # keep folder structure | |
| retention-days: 1 | |
| jupyter-book: | |
| needs: execute | |
| runs-on: ubuntu-latest | |
| # store success output flag for the ci job | |
| outputs: | |
| success: ${{ steps.setoutput.outputs.success }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Download notebooks | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: notebooks | |
| path: out/ | |
| - name: Display structure of downloaded files | |
| run: ls -R | |
| working-directory: out | |
| - name: Copy back built notebooks | |
| run: cp --verbose -rf out/docs/* docs/ | |
| - name: Setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: jupyterbook.yml | |
| init-shell: bash | |
| cache-environment: true | |
| post-cleanup: all | |
| - name: Build website | |
| shell: micromamba-shell {0} | |
| run: jupyter-book build docs/ | |
| - name: Upload pages artifact | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| uses: actions/upload-pages-artifact@v2 | |
| with: | |
| path: docs/_build/html | |
| - name: Set output flag | |
| id: setoutput | |
| run: echo "success=true" >> $GITHUB_OUTPUT | |
| # CI conclusion for GitHub status check | |
| # https://brunoscheufler.com/blog/2022-04-09-the-required-github-status-check-that-wasnt | |
| CI: | |
| needs: jupyter-book | |
| if: always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| # pass step only when output of previous jupyter-book job is set | |
| # in case at least one of the execution fails, jupyter-book is skipped | |
| # and the output will not be set, which will then cause the ci job to fail | |
| - run: | | |
| passed="${{ needs.jupyter-book.outputs.success }}" | |
| if [[ $passed == "true" ]]; then | |
| echo "Tests passed" | |
| exit 0 | |
| else | |
| echo "Tests failed" | |
| exit 1 | |
| fi | |
| # Deployment job | |
| deploy: | |
| name: Deploy to GitHub pages | |
| needs: jupyter-book | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| # Grant GITHUB_TOKEN the permissions required to make a Pages deployment | |
| permissions: | |
| pages: write # to deploy to Pages | |
| id-token: write # to verify the deployment originates from an appropriate source | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v2 |