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website.yml
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name: Website
on:
push:
branches:
- gh-pages
- main
pull_request: []
jobs:
build-website:
if: ${{ !endsWith(github.repository, '/styles') }}
runs-on: ubuntu-20.04
env:
RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
defaults:
run:
shell: bash
steps:
- name: Set up Ruby
uses: ruby/setup-ruby@v1
with:
ruby-version: '2.7'
bundler-cache: true
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.x'
- name: Install GitHub Pages, Bundler, and kramdown gems
run: |
gem install github-pages bundler kramdown kramdown-parser-gfm
- name: Install Python modules
run: |
python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
- name: Checkout the lesson
uses: actions/checkout@master
with:
fetch-depth: 0
ref: ${{ github.event.pull_request.head.sha }}
- name: Look for R-markdown files
id: check-rmd
run: |
echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT
- name: Set up R
if: steps.check-rmd.outputs.count != 0
uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
install-r: false
- name: Restore R Cache
if: steps.check-rmd.outputs.count != 0
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
- name: Install needed packages
if: steps.check-rmd.outputs.count != 0
run: |
source('bin/dependencies.R')
install_required_packages()
shell: Rscript {0}
- name: Query dependencies
if: steps.check-rmd.outputs.count != 0
run: |
source('bin/dependencies.R')
deps <- identify_dependencies()
create_description(deps)
use_bioc_repos()
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Install system dependencies for R packages
if: steps.check-rmd.outputs.count != 0
run: |
while read -r cmd
do
eval sudo $cmd || echo "Nothing to update"
done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
- name: Render the markdown and confirm that the site can be built
run: make site
- name: Checkout github pages
if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
uses: actions/checkout@master
with:
ref: gh-pages
path: gh-pages
- name: Commit and Push
if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
run: |
# clean up gh-pages
cd gh-pages
git rm -rf . # remove all previous files
git restore --staged . # remove things from the stage
cd ..
# copy everything into gh-pages site
cp -r `ls -A | grep -v 'gh-pages' | grep -v '.git' | grep -v '.bundle/' | grep -v '_site'` gh-pages
# move into gh-pages, add, commit, and push
cd gh-pages
# setup git
git config --local user.email "actions@github.com"
git config --local user.name "GitHub Actions"
git add -A .
git commit --allow-empty -m "[Github Actions] render website (via ${{ github.sha }})"
git push origin gh-pages
# return
cd ..
- run: make lesson-check-all
if: always()