add check to only recompile notebooks that have changed #3
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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: Run Docker container to compile changed R Markdown files | ||
| uses: addnab/docker-run-action@v3 | ||
| with: | ||
| image: ${{ steps.meta_rmd.outputs.tags }} | ||
| options: -v ${{ github.workspace }}:/workspace --rm -u root | ||
| run: | | ||
| CHANGED_RMD_FILES=$(git diff --name-only HEAD^ HEAD -- '*.Rmd' '*.rmd') | ||
| if [ -n "$CHANGED_RMD_FILES" ]; then | ||
| echo "Changed R Markdown files:" | ||
| echo "$CHANGED_RMD_FILES" | ||
| 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 | ||
| else | ||
| echo "No changed R Markdown files found. Skipping execution." | ||
| fi | ||
| - name: Run Docker container to compile assets | ||
| uses: addnab/docker-run-action@v3 | ||
| with: | ||
| image: ${{ steps.meta_rmd.outputs.tags }} | ||
| options: -v ${{ github.workspace }}:/workspace --rm -u root | ||
| run: | | ||
| RMD_FILES=$( find /workspace -name "*Rmd" -o -name "*rmd" ) | ||
| if [ -n "$RMD_FILES" ]; then | ||
| echo $RMD_FILES | ||
| for RMD in $RMD_FILES | ||
| do | ||
| Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f, output_format = "all")' $RMD | ||
| done | ||
| else | ||
| echo "No R markdown found. Skipping execution." | ||
| fi | ||
| #Checkout again to avoid race condition with parallel-running Jupyter rendering script. | ||
| - uses: actions/checkout@v4 | ||
| - 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: Run Docker container to compile JupyterNotebook | ||
| uses: addnab/docker-run-action@v3 | ||
| with: | ||
| image: ${{ steps.meta_jupyter.outputs.tags }} | ||
| options: -v ${{ github.workspace }}:/workspace --rm -u root | ||
| run: | | ||
| changed_notebooks=$(git diff --name-only HEAD^ HEAD -- '*.ipynb') | ||
| if [ -n "$changed_notebooks" ]; then | ||
| echo "Changed notebooks:" | ||
| echo "$changed_notebooks" | ||
| for notebook in $changed_notebooks; do | ||
| jupyter nbconvert --to html --execute /workspace/$notebook | ||
| jupyter nbconvert --to markdown --execute /workspace/$notebook | ||
| done | ||
| else | ||
| echo "No changed Jupyter notebooks found. Skipping execution." | ||
| fi | ||
| - uses: stefanzweifel/git-auto-commit-action@v5 | ||
