added 2-factor design #640
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| name: Build and Deploy GitHub Pages | |
| # Build site for commits pushed to all branches | |
| # Deploy only if on default branch | |
| on: | |
| push: | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| fetch-depth: 0 # Fetch all history for all branches and tags | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9.x' # same as macOS | |
| cache: pip | |
| - name: Install dependencies | |
| run: pip install -r requirements.txt | |
| # - name: Debug - Show biotips file status | |
| # run: | | |
| # echo 'Biotips submodule directory listing:' | |
| # ls -lh docs/workshops/biotips/ || echo 'biotips dir missing' | |
| # echo | |
| # echo 'File type:' | |
| # file docs/workshops/biotips/setup-cannon.md || echo 'setup-cannon.md missing' | |
| # echo | |
| # echo 'First 20 lines:' | |
| # head -20 docs/workshops/biotips/setup-cannon.md || echo 'setup-cannon.md missing' | |
| - name: Build site | |
| run: mkdocs build | |
| - name: Patch jupyter HTML with metadata # Adds title and description to HTML rendered from jupyter notebooks | |
| run: python scripts/add_jupyter_meta.py | |
| - name: Upload site/ | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: site | |
| link-checker: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| permissions: | |
| actions: read | |
| steps: | |
| # Cache lychee external URL results for 30 days | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Download site | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: github-pages | |
| - name: Extract artifact | |
| run: tar -xf artifact.tar && rm artifact.tar | |
| # https://github.com/lycheeverse/lychee-action#utilising-the-cache-feature | |
| - name: Restore lychee cache | |
| id: restore-cache | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: .lycheecache | |
| key: cache-lychee-${{ github.sha }} | |
| restore-keys: cache-lychee- | |
| - name: Run lychee | |
| uses: lycheeverse/[email protected] | |
| with: | |
| args: "--base . --cache --config .github/workflows/lychee.toml -- 'site/**/*.html' 'site/**/*.css'" | |
| fail: true | |
| - name: Save lychee cache | |
| uses: actions/cache/save@v3 | |
| if: always() | |
| with: | |
| path: .lycheecache | |
| key: ${{ steps.restore-cache.outputs.cache-primary-key }} | |
| deploy: | |
| if: github.ref == format('refs/heads/{0}', github.event.repository.default_branch) | |
| runs-on: ubuntu-latest | |
| needs: build | |
| permissions: | |
| pages: write | |
| id-token: write | |
| actions: read | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |