Deploy Documentation #1
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| name: Deploy Documentation | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| deploy: | |
| description: "Whether to deploy the website to GitHub Pages" | |
| type: boolean | |
| required: false | |
| default: false | |
| workflow_call: | |
| inputs: | |
| deploy: | |
| description: "Whether to deploy the website to GitHub Pages" | |
| type: boolean | |
| required: false | |
| default: false | |
| # Allow this job to clone the repo and create a page deployment | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| concurrency: | |
| group: "docs-deploy-${{ github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| parameters-component: | |
| name: pipeline_parameters | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: scilus/sf-tractomics | |
| ref: ${{ github.event.pull_request.head.sha || 'main' }} | |
| fetch-depth: 0 # Shallow clones should be disabled for a version bump to work | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: "3.13" | |
| architecture: "x64" | |
| - name: read .nf-core.yml | |
| uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 | |
| id: read_yml | |
| with: | |
| config: ${{ github.workspace }}/.nf-core.yml | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | |
| - name: Fetch pipeline parameters | |
| id: pipeline_params | |
| run: | | |
| nf-core pipelines schema docs -o parameters.md -x markdown | |
| echo '' | cat - parameters.md > temp && mv temp parameters.md | |
| echo '---' | cat - parameters.md > temp && mv temp parameters.md | |
| echo 'description: sf-tractomics parameters' | cat - parameters.md > temp && mv temp parameters.md | |
| echo 'title: Pipeline Parameters' | cat - parameters.md > temp && mv temp parameters.md | |
| echo '---' | cat - parameters.md > temp && mv temp parameters.md | |
| sed -E -i 's/^## (.*)$/### **\1**/' parameters.md | |
| sed -E -i '/^# scilus\/sf-tractomics pipeline parameters$/,/^sf-tractomics is a neuroimaging pipeline to process dMRI data\.$/d' parameters.md | |
| - name: Pack into artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: markdown | |
| path: parameters.md | |
| build: | |
| needs: parameters-component | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout website code | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: scilus/sf-tractomics-documentation | |
| - name: Download pipeline parameters | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: markdown | |
| path: src/content/docs/guides/ | |
| - name: Install, build, and upload the site | |
| uses: withastro/action@v2 | |
| with: | |
| node-version: 22 | |
| package-manager: npm@latest | |
| deploy: | |
| if: ${{ inputs.deploy }} | |
| needs: build | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 | |
| # preview-deploy: | |
| # if: ${{ !inputs.deploy && (github.event_name == 'pull_request' || github.event_name == 'pull_request_target') }} | |
| # needs: build | |
| # runs-on: ubuntu-latest | |
| # environment: | |
| # name: pr-preview-${{ github.event.pull_request.number }} | |
| # url: ${{ steps.preview.outputs.page_url }} | |
| # steps: | |
| # - name: Deploy PR preview to GitHub Pages | |
| # id: preview | |
| # uses: actions/deploy-pages@v4 | |
| # with: | |
| # preview: 'true' | |
| # - name: Comment on PR with preview link | |
| # if: ${{ success() && (github.event_name == 'pull_request' || github.event_name == 'pull_request_target') }} | |
| # env: | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # PREVIEW_URL: ${{ steps.preview.outputs.page_url }} | |
| # run: | | |
| # gh api repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments \ | |
| # -f body="🚀 **Documentation preview deployed!** | |
| # | |
| # You can view the live preview here: | |
| # 👉 [${{ env.PREVIEW_URL }}](${{ env.PREVIEW_URL }}) | |
| # | |
| # _(This preview will be automatically removed when the PR is closed or merged.)_" |