Request to add BiocAsia (#40) #81
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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: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- name: Check out repo | |
uses: actions/checkout@v3 | |
# No need to install pandoc in this docker container | |
# - name: Set up pandoc | |
# uses: r-lib/actions/setup-pandoc@v2 | |
- name: Update apt-get | |
run: | | |
sudo apt-get update | |
- name: Install TinyTeX | |
uses: r-lib/actions/setup-tinytex@v2 | |
- name: Install dependencies | |
run: | | |
install.packages(c('remotes', 'BiocManager')) | |
local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 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} | |
# 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 |