remove duplicated section #8
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| # Github action that renders R markdown when PR is opened | |
| # All R markdown is run in container/rmd.Dockerfile | |
| on: | |
| pull_request: | |
| types: [opened, reopened, edited] | |
| push: | |
| workflow_dispatch: | |
| name: render-notebooks | |
| jobs: | |
| render-rmarkdown: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Check if Dockerfile changed | |
| id: dockerfile-check | |
| run: | | |
| if git diff --name-only HEAD^ HEAD | grep -q 'container/rmd.Dockerfile'; then | |
| echo "dockerfile_changed=true" >> $GITHUB_ENV | |
| else | |
| echo "dockerfile_changed=false" >> $GITHUB_ENV | |
| fi | |
| - name: Extract metadata (tags, labels) for Rmd Docker | |
| id: meta_rmd | |
| uses: docker/[email protected] | |
| with: | |
| images: bcgsc/long-pog-rmd | |
| - name: Build and push Docker image | |
| if: env.dockerfile_changed == 'true' | |
| uses: docker/build-push-action@v5 | |
| with: | |
| file: container/rmd.Dockerfile | |
| context: . | |
| push: true | |
| tags: ${{ steps.meta_rmd.outputs.tags }} | |
| labels: ${{ steps.meta_rmd.outputs.labels }} | |
| - name: Check for changed R Markdown files | |
| id: check_rmd_files | |
| run: | | |
| CHANGED_RMD_FILES=$(git diff --name-only HEAD^ HEAD -- '*.Rmd' '*.rmd') | |
| if [ -n "$CHANGED_RMD_FILES" ]; then | |
| echo "Changed R Markdown files:" | |
| echo "$CHANGED_RMD_FILES" | |
| echo "::set-output name=has_changed::true" | |
| echo "$CHANGED_RMD_FILES" > changed_rmd_files.txt | |
| else | |
| echo "No changed R Markdown files found." | |
| echo "::set-output name=has_changed::false" | |
| - name: Run Docker container to compile changed R Markdown files | |
| if: steps.check_rmd_files.outputs.has_changed == 'true' | |
| uses: addnab/docker-run-action@v3 | |
| with: | |
| image: ${{ steps.meta_rmd.outputs.tags }} | |
| options: | | |
| -v ${{ github.workspace }}:/workspace \ | |
| -v /tmp/cache:/root/.cache \ | |
| --rm -u root | |
| run: | | |
| CHANGED_RMD_FILES=$(cat changed_rmd_files.txt) | |
| for RMD in $CHANGED_RMD_FILES; do | |
| Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f, output_format = "all")' /workspace/$RMD | |
| done | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| render_jupyter: | |
| runs-on: ubuntu-latest | |
| needs: render-rmarkdown | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Check if Dockerfile changed | |
| id: dockerfile-check | |
| run: | | |
| if git diff --name-only HEAD^ HEAD | grep -q 'container/jupyter.Dockerfile'; then | |
| echo "dockerfile_changed=true" >> $GITHUB_ENV | |
| else | |
| echo "dockerfile_changed=false" >> $GITHUB_ENV | |
| fi | |
| - name: Extract metadata (tags, labels) for Jupyter Docker | |
| id: meta_jupyter | |
| uses: docker/[email protected] | |
| with: | |
| images: bcgsc/long-pog-jupyter | |
| - name: Build and push Docker image | |
| if: env.dockerfile_changed == 'true' | |
| uses: docker/build-push-action@v5 | |
| with: | |
| file: container/jupyter.Dockerfile | |
| context: . | |
| push: true | |
| tags: ${{ steps.meta_jupyter.outputs.tags }} | |
| labels: ${{ steps.meta_jupyter.outputs.labels }} | |
| - name: Check for changed Jupyter Notebook files | |
| id: check_ipynb_files | |
| run: | | |
| CHANGED_IPYNB_FILES=$(git diff --name-only HEAD^ HEAD -- '*.ipynb') | |
| if [ -n "$CHANGED_IPYNB_FILES" ]; then | |
| echo "Changed Jupyter Notebook files:" | |
| echo "$CHANGED_IPYNB_FILES" | |
| echo "::set-output name=has_changed::true" | |
| echo "$CHANGED_IPYNB_FILES" > changed_ipynb_files.txt | |
| else | |
| echo "No changed Jupyter Notebook files found." | |
| echo "::set-output name=has_changed::false" | |
| - name: Run Docker container to compile changed Jupyter Notebooks | |
| if: steps.check_ipynb_files.outputs.has_changed == 'true' | |
| uses: addnab/docker-run-action@v3 | |
| with: | |
| image: ${{ steps.meta_jupyter.outputs.tags }} | |
| options: | | |
| -v ${{ github.workspace }}:/workspace \ | |
| -v /tmp/cache:/root/.cache \ | |
| --rm -u root | |
| run: | | |
| CHANGED_IPYNB_FILES=$(cat changed_ipynb_files.txt) | |
| for NOTEBOOK in $CHANGED_IPYNB_FILES; do | |
| jupyter nbconvert --to html --execute /workspace/$NOTEBOOK | |
| jupyter nbconvert --to markdown --execute /workspace/$NOTEBOOK | |
| done | |
| - uses: stefanzweifel/git-auto-commit-action@v5 |