PDF vignette from R Markdown #1
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| name: PDF vignette from R Markdown | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| create-vignette: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| ## A small set of pandoc and tinytex versions. | |
| ## TinyTex versions selected to match the release date of the pandoc version | |
| ## Note that TinyTex version years do not perfectly map to TexLive release years! | |
| - { pandoc: '2.8', tinytex: '2020.10', tlmgr-repo: 'https://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2020/tlnet-final'} | |
| - { pandoc: '2.10', tinytex: '2020.10', tlmgr-repo: 'https://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2020/tlnet-final'} | |
| - { pandoc: '2.12', tinytex: '2021.03', tlmgr-repo: 'https://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2020/tlnet-final'} | |
| - { pandoc: '2.14', tinytex: '2021.05', tlmgr-repo: 'https://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2021/tlnet-final'} | |
| - { pandoc: '2.17', tinytex: '2022.01', tlmgr-repo: 'https://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2021/tlnet-final'} | |
| - { pandoc: 'default', tinytex: '' , tlmgr-repo: 'https://mirror.ctan.org/systems/texlive/tlnet'} | |
| name: "Pandoc: ${{ matrix.config.pandoc }}, TinyTex: ${{ matrix.config.tinytex }}" | |
| steps: | |
| - name: Install ghostscript | |
| run: sudo apt-get update && sudo apt-get -y -qq install ghostscript libavfilter-dev libmagick++-dev | |
| - name: Setup R and Bioconductor | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| with: | |
| bioc-version: devel | |
| - name: Install Pandoc | |
| if: ${{ matrix.config.pandoc != 'default' }} | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| with: | |
| pandoc-version: ${{ matrix.config.pandoc }} | |
| - name: Install Pandoc | |
| if: ${{ matrix.config.pandoc == 'default' }} | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install TinyTex | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| env: | |
| TINYTEX_VERSION: ${{ matrix.config.tinytex }} | |
| - name: Install Latex Packages | |
| run: | | |
| tlmgr option repository ${{ matrix.config.tlmgr-repo }} | |
| tlmgr update --self | |
| tlmgr install \ | |
| pdfcrop titling bera titlesec fancyhdr silence \ | |
| enumitem parskip nowidow parnotes preprint soul \ | |
| placeins ragged2e footmisc marginfix changepage \ | |
| caption xstring mathtools everysel bera | |
| shell: bash | |
| - name: Checkout BiocStyle repository | |
| uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| magick | |
| - name: Install this BiocStyle | |
| run: R CMD INSTALL ../BiocStyle | |
| shell: bash | |
| - name: Build PDF from RMD | |
| run: rmarkdown::render("AuthoringRmdVignettes.Rmd", output_format = "BiocStyle::pdf_document", quiet = TRUE) | |
| working-directory: vignettes | |
| shell: Rscript {0} | |
| - name: Upload PDF vignette | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: pandoc-v${{ matrix.config.pandoc }}-vignette | |
| if-no-files-found: error | |
| path: | | |
| vignettes/*.pdf | |
| - name: Build, Install, Check | |
| uses: grimbough/bioc-actions/build-install-check@devel | |