fix typo in first vignette #295
Workflow file for this run
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| on: | |
| push: | |
| branches: | |
| - "master" | |
| pull_request: | |
| branches: | |
| - "*" | |
| name: vignette | |
| env: | |
| cache-version: "cache-v2" | |
| jobs: | |
| check-permissions: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| has_permission: ${{ steps.check_permissions.outputs.has_permission }} | |
| steps: | |
| - name: Check if actor has permission | |
| id: check_permissions | |
| run: | | |
| # Define allowed actors | |
| ALLOWED_ACTORS=("zktuong" "Jiawei-Yu10") # Replace these with the actual GitHub usernames | |
| if [[ " ${ALLOWED_ACTORS[@]} " =~ " ${GITHUB_ACTOR} " ]]; then | |
| echo "has_permission=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "has_permission=false" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Debug permissions output | |
| run: | | |
| echo "Has permission: ${{ steps.check_permissions.outputs.has_permission }}" | |
| vignette: | |
| needs: | |
| - check-permissions | |
| if: needs.check-permissions.outputs.has_permission == 'true' | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest } | |
| runs-on: ${{ matrix.config.os }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup R and Bioconductor | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| id: install-r | |
| with: | |
| bioc-version: devel | |
| - name: Install ubuntu dependencies | |
| if: ${{ matrix.config.os == 'ubuntu-latest' }} | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y libgsl-dev | |
| - name: Install macos dependencies | |
| if: ${{ matrix.config.os == 'macos-latest' }} | |
| run: | | |
| brew install gsl | |
| - name: Get R version | |
| id: R | |
| run: | | |
| R --version > VERSION | |
| echo "version=$(head -1 VERSION | awk '{print $3}')" >> $GITHUB_OUTPUT | |
| shell: bash -l {0} | |
| - name: Get Bioconductor version | |
| id: BIOC | |
| run: | | |
| echo "version=$R_BIOC_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash -l {0} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ steps.BIOC.outputs.version}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ steps.BIOC.outputs.version}}-r-${{ steps.R.outputs.version}}- | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: pkgdown | |
| - name: Install scRepertoire from github | |
| run: | | |
| Rscript -e 'remotes::install_github("ncborcherding/scRepertoire")' | |
| shell: bash -l {0} | |
| # - name: Install specific version of pillar to avoid weird error message | |
| # run: | | |
| # Rscript -e 'remotes::install_github("r-lib/[email protected]")' | |
| # shell: bash -l {0} | |
| - name: Install package | |
| run: R CMD INSTALL . | |
| - name: Configure git | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| - name: Build and publish vignette | |
| if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }} | |
| run: | | |
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' | |
| shell: bash -l {0} | |
| # If events is a PR, set subdir to 'preview/pr<pr_number>' | |
| - name: "[PR] Set documentation subdirectory" | |
| if: github.event_name == 'pull_request' | |
| run: | | |
| echo "PKGDOWN_DEV_MODE=unreleased" >> $GITHUB_ENV | |
| echo "subdir=preview/pr${{ github.event.number }}" >> $GITHUB_ENV | |
| - name: Deploy pkgdown site | |
| id: deploy | |
| shell: Rscript {0} | |
| run: | | |
| subdir <- "${{ env.subdir }}" | |
| pkg <- pkgdown::as_pkgdown(".") | |
| # Deploy pkgdown site to branch | |
| pkgdown::deploy_to_branch(subdir = if (nzchar(subdir)) subdir, clean = nzchar(subdir)) | |
| # Report deployed site URL | |
| deployed_url <- file.path(pkg$meta$url, subdir) | |
| cat(sprintf('url=%s', deployed_url), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE) | |
| - name: Notify pkgdown deployment | |
| if: github.event_name == 'pull_request' | |
| uses: hasura/[email protected] | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| repository: ${{ github.repository }} | |
| number: ${{ github.event.number }} | |
| id: pkgdown-deploy | |
| append: false | |
| message: > | |
| :book: ${{ steps.deploy.outputs.url }} | |
| Preview documentation for this PR (at commit ${{ github.event.pull_request.head.sha }}) |