add bug fixes due to API changes section, closes #130 (#132) #307
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| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - devel | |
| name: build_deploy | |
| jobs: | |
| build_deploy: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| - name: apt-get update | |
| run: | | |
| apt-get update -y | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install TinyTeX | |
| run: | | |
| install.packages('tinytex') | |
| tinytex::install_tinytex() | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c('remotes', 'BiocManager')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(update = TRUE, ask = FALSE, Ncpus = 2L) | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| install.packages('sessioninfo') | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| # - name: Render book (git) | |
| # run: | | |
| # bookdown::render_book('index.Rmd', 'bookdown::gitbook') | |
| # shell: Rscript {0} | |
| # - name: Render book (pdf) | |
| # run: | | |
| # bookdown::render_book('index.Rmd', 'bookdown::pdf_book') | |
| # shell: Rscript {0} | |
| # - name: Render book (epub) | |
| # run: | | |
| # bookdown::render_book('index.Rmd', 'bookdown::epub_book') | |
| # shell: Rscript {0} | |
| - name: Render book (bs4_book) | |
| run: | | |
| bookdown::render_book('index.Rmd', 'bookdown::bs4_book') | |
| shell: Rscript {0} | |
| - name: Copy docs/ subdirectory to book | |
| run: | | |
| cp -R docs _book/ | |
| # deploy needs rsync? Seems so. | |
| - name: Install deploy dependencies | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' | |
| run: | | |
| apt-get update && apt-get -y install rsync | |
| - name: Deploy 🚀 | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' | |
| uses: JamesIves/[email protected] | |
| with: | |
| ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }} | |
| BRANCH: gh-pages | |
| FOLDER: _book |