docs: change fig to canvas to reflect new API (#91) #115
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| # Workflow for deploying static content to GitHub Pages with PR previews | |
| name: Deploy Documentation | |
| on: | |
| # Runs on pushes targeting the default branch | |
| push: | |
| branches: ["main"] | |
| # Runs on pull requests for preview builds | |
| pull_request: | |
| branches: ["main"] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| inputs: | |
| pr_number: | |
| description: 'PR number to build preview for (leave empty for current branch)' | |
| required: false | |
| type: string | |
| # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages | |
| permissions: | |
| contents: write | |
| pages: write | |
| id-token: write | |
| pull-requests: write | |
| # Allow only one concurrent deployment per branch/PR | |
| concurrency: | |
| group: "pages-${{ github.ref }}" | |
| cancel-in-progress: false | |
| jobs: | |
| # Build job - runs for both main branch and PRs | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.12' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt install pandoc | |
| pip install -r requirements.txt | |
| pip install ipykernel rdkit cairosvg pymzml | |
| pip install . | |
| - name: Build Documentation | |
| run: sphinx-build -b html ./docs ./_build | |
| - name: Copy binder files | |
| run: cp -r ./.binder ./_build | |
| - name: Upload build artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: documentation-${{ github.sha }} | |
| path: _build/ | |
| retention-days: 30 | |
| # Deploy to main GitHub Pages (only for main branch) | |
| deploy-main: | |
| if: github.ref == 'refs/heads/main' && github.event_name == 'push' | |
| needs: build | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Download build artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: documentation-${{ github.sha }} | |
| path: _build/ | |
| - name: Setup Pages | |
| uses: actions/configure-pages@v5 | |
| - name: Upload to GitHub Pages | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: _build/ | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 | |
| # Deploy PR preview using subdirectories in gh_pages | |
| deploy-preview: | |
| if: github.event_name == 'pull_request' || (github.event_name == 'workflow_dispatch' && github.event.inputs.pr_number != '') | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout gh_pages branch | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: gh_pages | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Download build artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: documentation-${{ github.sha }} | |
| path: _temp_build/ | |
| - name: Get PR number | |
| id: pr_info | |
| run: | | |
| if [ "${{ github.event_name }}" == "pull_request" ]; then | |
| echo "pr_number=${{ github.event.number }}" >> $GITHUB_OUTPUT | |
| else | |
| echo "pr_number=${{ github.event.inputs.pr_number }}" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Deploy PR preview to subdirectory | |
| run: | | |
| PR_NUMBER="${{ steps.pr_info.outputs.pr_number }}" | |
| PR_DIR="pr-${PR_NUMBER}" | |
| # Remove existing PR directory if it exists | |
| rm -rf "$PR_DIR" | |
| # Create PR directory and copy files | |
| mkdir -p "$PR_DIR" | |
| cp -r _temp_build/* "$PR_DIR/" | |
| # Clean up temp directory | |
| rm -rf _temp_build | |
| # Configure git | |
| git config user.name "github-actions[bot]" | |
| git config user.email "github-actions[bot]@users.noreply.github.com" | |
| # Add and commit changes | |
| git add "$PR_DIR" | |
| git commit -m "Deploy PR #${PR_NUMBER} preview [skip ci]" || echo "No changes to commit" | |
| # Push to gh_pages | |
| git push origin gh_pages | |
| - name: Comment on PR with preview link | |
| if: github.event_name == 'pull_request' || github.event.inputs.pr_number != '' | |
| uses: actions/github-script@v7 | |
| with: | |
| script: | | |
| const prNumber = "${{ steps.pr_info.outputs.pr_number }}"; | |
| const repoOwner = context.repo.owner; | |
| const repoName = context.repo.repo; | |
| const previewUrl = `https://${repoOwner}.github.io/${repoName}/pr-${prNumber}/`; | |
| // Check if we already commented | |
| const comments = await github.rest.issues.listComments({ | |
| owner: repoOwner, | |
| repo: repoName, | |
| issue_number: prNumber, | |
| }); | |
| const botComment = comments.data.find(comment => | |
| comment.user.login === 'github-actions[bot]' && | |
| comment.body.includes('📖 Documentation Preview') | |
| ); | |
| const commentBody = `📖 **Documentation Preview** | |
| The documentation for this PR has been built and is available at: | |
| 🔗 **[View Preview](${previewUrl})** | |
| This preview will be updated automatically when you push new commits to this PR. | |
| --- | |
| *Preview built from commit: \`${context.sha.substring(0, 7)}\`*`; | |
| if (botComment) { | |
| // Update existing comment | |
| await github.rest.issues.updateComment({ | |
| owner: repoOwner, | |
| repo: repoName, | |
| comment_id: botComment.id, | |
| body: commentBody | |
| }); | |
| } else { | |
| // Create new comment | |
| await github.rest.issues.createComment({ | |
| owner: repoOwner, | |
| repo: repoName, | |
| issue_number: prNumber, | |
| body: commentBody | |
| }); | |
| } | |
| # Cleanup old PR preview branches | |
| cleanup-previews: | |
| if: github.event_name == 'pull_request' && github.event.action == 'closed' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| fetch-depth: 0 | |
| - name: Delete PR preview directory | |
| run: | | |
| PR_NUMBER="${{ github.event.number }}" | |
| PR_DIR="pr-${PR_NUMBER}" | |
| # Checkout gh_pages branch | |
| git checkout gh_pages | |
| # Remove PR directory if it exists | |
| if [ -d "$PR_DIR" ]; then | |
| rm -rf "$PR_DIR" | |
| git add "$PR_DIR" | |
| git commit -m "Remove PR #${PR_NUMBER} preview [skip ci]" | |
| git push origin gh_pages | |
| echo "Deleted preview directory: $PR_DIR" | |
| else | |
| echo "Preview directory $PR_DIR not found" | |
| fi | |
| - name: Comment cleanup notification | |
| uses: actions/github-script@v7 | |
| with: | |
| script: | | |
| const prNumber = context.payload.number; | |
| await github.rest.issues.createComment({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: prNumber, | |
| body: `🧹 **Preview Cleanup** | |
| The documentation preview for this PR has been cleaned up and is no longer available.` | |
| }); |