Methods section for metadata and ontologies #148
Workflow file for this run
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| name: Manubot | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| inputs: | |
| BUILD_PDF: | |
| type: boolean | |
| description: generate PDF output | |
| default: true | |
| BUILD_DOCX: | |
| type: boolean | |
| description: generate DOCX output | |
| default: false | |
| BUILD_LATEX: | |
| type: boolean | |
| description: generate LaTeX output | |
| default: false | |
| SPELLCHECK: | |
| type: boolean | |
| description: Check spelling | |
| default: true | |
| MANUBOT_USE_DOCKER: | |
| type: boolean | |
| description: Use Docker to generate PDF | |
| default: true | |
| concurrency: | |
| # only one run per branch at a time | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| manubot: | |
| name: Manubot | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| env: | |
| GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }} | |
| # Set SPELLCHECK to true/false for whether to check spelling in this action. | |
| # For workflow dispatch jobs, this SPELLCHECK setting will be overridden by the user input. | |
| SPELLCHECK: true | |
| defaults: | |
| run: | |
| shell: bash --login {0} | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| with: | |
| # fetch entire commit history to support get_rootstock_commit | |
| fetch-depth: 0 | |
| - name: Set Environment Variables (Workflow Dispatch) | |
| if: github.event_name == 'workflow_dispatch' | |
| run: | | |
| echo "BUILD_PDF=${{ github.event.inputs.BUILD_PDF }}" >> $GITHUB_ENV | |
| echo "BUILD_DOCX=${{ github.event.inputs.BUILD_DOCX }}" >> $GITHUB_ENV | |
| echo "BUILD_LATEX=${{ github.event.inputs.BUILD_LATEX }}" >> $GITHUB_ENV | |
| echo "SPELLCHECK=${{ github.event.inputs.SPELLCHECK }}" >> $GITHUB_ENV | |
| echo "MANUBOT_USE_DOCKER=${{ github.event.inputs.MANUBOT_USE_DOCKER }}" >> $GITHUB_ENV | |
| - name: Set Environment Variables | |
| run: | | |
| TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA} | |
| echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV | |
| echo "TRIGGERING_SHA: $TRIGGERING_SHA" | |
| DEFAULT_BRANCH=${{ github.event.repository.default_branch }} | |
| echo "DEFAULT_BRANCH=${DEFAULT_BRANCH}" >> $GITHUB_ENV | |
| echo "DEFAULT_BRANCH_REF=refs/heads/$DEFAULT_BRANCH" >> $GITHUB_ENV | |
| echo "DEFAULT_BRANCH=$DEFAULT_BRANCH" | |
| - name: Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ci/cache | |
| key: ci-cache-${{ github.ref }} | |
| restore-keys: | | |
| ci-cache-${{ env.DEFAULT_BRANCH_REF }} | |
| - name: Install Environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: manubot | |
| environment-file: build/environment.yml | |
| auto-activate-base: false | |
| miniforge-variant: Mambaforge | |
| miniforge-version: "latest" | |
| use-mamba: true | |
| - name: Install Spellcheck | |
| if: env.SPELLCHECK == 'true' | |
| run: bash ci/install-spellcheck.sh | |
| - name: Build Manuscript | |
| run: bash build/build.sh | |
| - name: Upload Artifacts | |
| uses: actions/upload-artifact@v4 | |
| id: artifact-upload-step | |
| with: | |
| name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }} | |
| path: output | |
| - name: Deploy Manuscript | |
| if: github.ref == env.DEFAULT_BRANCH_REF && github.event_name != 'pull_request' && !github.event.repository.fork | |
| env: | |
| MANUBOT_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }} | |
| CI_BUILD_WEB_URL: https://github.com/${{ github.repository }}/commit/${{ github.sha }}/checks | |
| CI_JOB_WEB_URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| run: bash ci/deploy.sh | |
| - name: Post artifact comment to PR | |
| if: github.event_name == 'pull_request' | |
| uses: peter-evans/create-or-update-comment@v4 | |
| with: | |
| issue-number: ${{ github.event.pull_request.number }} | |
| body: | | |
| **Click the link below to download the manuscript build as a ZIP file.** | |
| This build is associated with commit ${{ env.TRIGGERING_SHA_7 }}. | |
| [Manuscript build](${{ steps.artifact-upload-step.outputs.artifact-url }}) |