R docker refactor for lab sessions #57
Workflow file for this run
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| name: CI | |
| # Enable Buildkit and let compose use it to speed up image building | |
| env: | |
| DOCKER_BUILDKIT: 1 | |
| COMPOSE_DOCKER_CLI_BUILD: 1 | |
| CONDA_ENV_NAME: clim-recal | |
| MIN_PYTHON_VERSION: 3.9 | |
| PYTHON_MODULE_FOLDER: /home/jovyan/python/ | |
| COVERAGE_SVG_FOLDER: docs/assets/ | |
| COVERAGE_SVG_FILE_NAME: coverage.svg | |
| # replace below with references to previous config lines | |
| COVERAGE_SVG_PATH: docs/assets/coverage.svg | |
| GH_PAGE_PATH: _gh-page | |
| on: | |
| pull_request: | |
| branches: ['main', 'doc-deploy', 'ruth-notebook-for-workshop', 'r-docker-refactor'] | |
| paths-ignore: ['docs/**'] | |
| push: | |
| branches: ['main', 'doc-deploy', 'ruth-notebook-for-workshop', 'r-docker-refactor'] | |
| concurrency: | |
| group: ${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: write | |
| jobs: | |
| linter: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Code Repository | |
| uses: actions/checkout@main | |
| - name: Set up Python | |
| uses: actions/setup-python@main | |
| with: | |
| python-version: ${{ env.MIN_PYTHON_VERSION }} | |
| - name: Run pre-commit | |
| uses: pre-commit/action@main | |
| - name: Update pre-commit | |
| uses: pre-commit-ci/[email protected] | |
| if: always() | |
| # With no caching at all the entire ci process takes 4m 30s to complete! | |
| pytest: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Code Repository | |
| uses: actions/checkout@main | |
| - name: Build, Test and Save Test Coverage | |
| run: | | |
| docker compose build jupyter | |
| docker compose up jupyter --detach | |
| docker compose exec -u 0 jupyter bash -c "conda run -n ${{ env.CONDA_ENV_NAME }} --cwd python pytest" | |
| export JUPYTER_ID=$(docker compose ps -q jupyter) | |
| echo "jupyter_id=$JUPYTER_ID" >> $GITHUB_ENV | |
| - name: Check accessing saved jupyter_id | |
| run: | | |
| echo ${{ env.jupyter_id }} | |
| - name: Copy test coverage results | |
| run: | | |
| docker cp ${{ env.jupyter_id }}:${{ env.PYTHON_MODULE_FOLDER }}${{ env.COVERAGE_SVG_PATH }} ${{ env.COVERAGE_SVG_FOLDER }} | |
| - name: Archive coverage svg | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage-badge | |
| path: ${{ env.COVERAGE_SVG_PATH }} | |
| - name: Tear down the Stack | |
| run: docker compose down | |
| docs: | |
| needs: [linter, pytest] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download coverage svg | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: coverage-badge | |
| path: ${{ env.GH_PAGE_PATH }}${{ env.COVERAGE_SVG_PATH }} | |
| # Other options for documentation build for future testing outside docker | |
| # - name: Set up conda environment | |
| # uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # activate-environment: environment.yml | |
| # | |
| # From https://github.com/r-lib/actions/tree/v2-branch/setup-r | |
| # - name: Setup R | |
| # uses: r-lib/actions/setup-r@v2 | |
| # Potentially necessary for future interactive documentation builds following uatk-spc | |
| # - name: Install node | |
| # uses: actions/setup-node@v2 | |
| # with: | |
| # node-version: 18.x | |
| # cache: 'npm' | |
| # cache-dependency-path: web/package-lock.json | |
| # | |
| # - name: Build web app | |
| # run: | | |
| # cd web | |
| # npm ci | |
| # npm run build --if-present | |
| # mv dist ../docs/_book/app | |
| - name: Build docker quarto | |
| run: | | |
| # A potentially quicker build option to try in future, requires running in detatched mode | |
| # DOCKER_BUILDKIT=1 docker build --no-cache -f compose/docs/Dockerfile --target builder --tag 'clim-recal-docs' . | |
| docker compose build docs | |
| docker compose up --detach | |
| docker cp $(docker compose ps -q docs):/usr/local/apache2/htdocs/ ${{ env.GH_PAGE_PATH }} | |
| - name: Publish | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ${{ env.GH_PAGE_PATH }} | |
| keep_files: false |