DOC: Update introduction and preprocessing lessons #204
Workflow file for this run
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name: Test template | |
on: | |
push: | |
branches: gh-pages | |
pull_request: | |
jobs: | |
check-template: | |
name: ${{ matrix.lesson-name }} (${{ matrix.os-name }}) | |
if: github.repository == 'carpentries/styles' | |
runs-on: ${{ matrix.os }} | |
continue-on-error: ${{ matrix.experimental }} | |
strategy: | |
fail-fast: false | |
matrix: | |
lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git] | |
os: [ubuntu-20.04, macos-latest, windows-latest] | |
experimental: [false] | |
include: | |
- os: ubuntu-20.04 | |
os-name: Linux | |
- os: macos-latest | |
os-name: macOS | |
- os: windows-latest | |
os-name: Windows | |
- lesson: swcarpentry/shell-novice | |
lesson-name: (SWC) Shell novice | |
- lesson: datacarpentry/r-intro-geospatial | |
lesson-name: (DC) R Intro Geospatial | |
- lesson: librarycarpentry/lc-git | |
lesson-name: (LC) Intro to Git | |
- lesson: datacarpentry/astronomy-python | |
lesson-name: (DC) Foundations of Astronomical Data Science | |
experimental: true | |
os: ubuntu-20.04 | |
os-name: Linux | |
- lesson: carpentries/lesson-example | |
lesson-name: (CP) Lesson Example | |
experimental: false | |
os: ubuntu-20.04 | |
os-name: Linux | |
defaults: | |
run: | |
shell: bash # forces 'Git for Windows' on Windows | |
env: | |
RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest' | |
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@v4 | |
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: | | |
if [[ $RUNNER_OS == macOS || $RUNNER_OS == Linux ]]; then | |
python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests | |
elif [[ $RUNNER_OS == Windows ]]; then | |
python -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests | |
fi | |
- name: Checkout the ${{ matrix.lesson }} lesson | |
uses: actions/checkout@master | |
with: | |
repository: ${{ matrix.lesson }} | |
path: lesson | |
fetch-depth: 0 | |
- name: Sync lesson with carpentries/styles | |
working-directory: lesson | |
run: | | |
echo "::group::Fetch Styles" | |
if [[ -n "${{ github.event.pull_request.number }}" ]] | |
then | |
ref="refs/pull/${{ github.event.pull_request.number }}/head" | |
else | |
ref="gh-pages" | |
fi | |
git config --global user.email "[email protected]" | |
git config --global user.name "The Carpentries Bot" | |
git remote add styles https://github.com/carpentries/styles.git | |
git fetch styles $ref:styles-ref | |
echo "::endgroup::" | |
echo "::group::Synchronize Styles" | |
# Sync up only if necessary | |
if [[ $(git rev-list --count HEAD..styles-ref) != 0 ]] | |
then | |
# The merge command below might fail for lessons that use remote theme | |
# https://github.com/carpentries/carpentries-theme | |
echo "Testing merge using recursive strategy, accepting upstream changes without committing" | |
if ! git merge -s recursive -Xtheirs --no-commit styles-ref | |
then | |
# Remove "deleted by us, unmerged" files from the staging area. | |
# these are the files that were removed from the lesson | |
# but are still present in the carpentries/styles repo | |
echo "Removing previously deleted files" | |
git rm $(git diff --name-only --diff-filter=DU) | |
# If there are still "unmerged" files, | |
# let's raise an error and look into this more closely | |
if [[ -n $(git diff --name-only --diff-filter=U) ]] | |
then | |
echo "There were unmerged files in ${{ matrix.lesson-name }}:" | |
echo "$(git diff --compact-summary --diff-filter=U)" | |
exit 1 | |
fi | |
fi | |
echo "Committing changes" | |
git commit -m "Sync lesson with carpentries/styles" | |
fi | |
echo "::endgroup::" | |
- name: Look for R-markdown files | |
id: check-rmd | |
working-directory: lesson | |
run: | | |
echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT | |
- name: Set up R | |
if: steps.check-rmd.outputs.count != 0 | |
uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
install-r: false | |
r-version: 'release' | |
- name: Install needed packages | |
if: steps.check-rmd.outputs.count != 0 | |
run: | | |
packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages())) | |
install.packages(packages, repo="https://cran.rstudio.com/") | |
shell: Rscript {0} | |
- name: Query dependencies | |
if: steps.check-rmd.outputs.count != 0 | |
working-directory: lesson | |
run: | | |
source('bin/dependencies.R') | |
deps <- identify_dependencies() | |
create_description(deps) | |
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
shell: Rscript {0} | |
- name: Cache R packages | |
if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0 | |
uses: actions/cache@v1 | |
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 stringi from source | |
if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0 | |
run: install.packages('stringi', repos='https://cloud.r-project.org') | |
shell: Rscript {0} | |
- name: Install system dependencies for R packages | |
if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0 | |
working-directory: lesson | |
run: | | |
while read -r cmd | |
do | |
eval sudo $cmd | |
done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")') | |
- run: make site | |
working-directory: lesson | |
- run: make lesson-check-all | |
working-directory: lesson |