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root = true | ||
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[*] | ||
charset = utf-8 | ||
insert_final_newline = true | ||
trim_trailing_whitespace = true | ||
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[*.md] | ||
indent_size = 2 | ||
indent_style = space | ||
max_line_length = 100 # Please keep this in sync with bin/lesson_check.py! | ||
trim_trailing_whitespace = false # keep trailing spaces in markdown - 2+ spaces are translated to a hard break (<br/>) | ||
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[*.r] | ||
max_line_length = 80 | ||
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[*.py] | ||
indent_size = 4 | ||
indent_style = space | ||
max_line_length = 79 | ||
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[*.sh] | ||
end_of_line = lf | ||
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[Makefile] | ||
indent_style = tab |
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<details> | ||
<summary><strong>Instructions</strong></summary> | ||
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Thanks for contributing! :heart: | ||
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If this contribution is for instructor training, please email the link to this contribution to | ||
[email protected] so we can record your progress. You've completed your contribution | ||
step for instructor checkout by submitting this contribution! | ||
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If this issue is about a specific episode within a lesson, please provide its link or filename. | ||
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Keep in mind that **lesson maintainers are volunteers** and it may take them some time to | ||
respond to your contribution. Although not all contributions can be incorporated into the lesson | ||
materials, we appreciate your time and effort to improve the curriculum. If you have any questions | ||
about the lesson maintenance process or would like to volunteer your time as a contribution | ||
reviewer, please contact The Carpentries Team at [email protected]. | ||
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You may delete these instructions from your comment. | ||
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\- The Carpentries | ||
</details> |
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<details> | ||
<summary><strong>Instructions</strong></summary> | ||
|
||
Thanks for contributing! :heart: | ||
|
||
If this contribution is for instructor training, please email the link to this contribution to | ||
[email protected] so we can record your progress. You've completed your contribution | ||
step for instructor checkout by submitting this contribution! | ||
|
||
Keep in mind that **lesson maintainers are volunteers** and it may take them some time to | ||
respond to your contribution. Although not all contributions can be incorporated into the lesson | ||
materials, we appreciate your time and effort to improve the curriculum. If you have any questions | ||
about the lesson maintenance process or would like to volunteer your time as a contribution | ||
reviewer, please contact The Carpentries Team at [email protected]. | ||
|
||
You may delete these instructions from your comment. | ||
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||
\- The Carpentries | ||
</details> |
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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 | ||
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- name: Set up Python | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: '3.x' | ||
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- 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: ${{ matrix.lesson }} | ||
path: lesson | ||
fetch-depth: 0 | ||
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- name: Sync lesson with carpentries/styles | ||
working-directory: lesson | ||
run: | | ||
echo "::group::Fetch Styles" | ||
if [[ -n "${{ 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[@]})" >> $GITHUB_OUTPUT | ||
- name: Set up R | ||
if: steps.check-rmd.outputs.count != 0 | ||
uses: r-lib/actions/setup-r@v2 | ||
with: | ||
use-public-rspm: true | ||
install-r: false | ||
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- name: Install needed packages | ||
if: steps.check-rmd.outputs.count != 0 | ||
working-directory: lesson | ||
run: | | ||
source('bin/dependencies.R') | ||
install_required_packages(.libPaths()[1]) | ||
shell: Rscript {0} | ||
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- name: Query dependencies | ||
if: steps.check-rmd.outputs.count != 0 | ||
working-directory: lesson | ||
run: | | ||
source('bin/dependencies.R') | ||
deps <- identify_dependencies() | ||
create_description(deps) | ||
use_bioc_repos() | ||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
shell: Rscript {0} | ||
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- name: Restore Package Cache | ||
if: runner.os != 'Windows' && 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- | ||
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- 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} | ||
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- 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 || echo "Nothing to update" | ||
done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")') | ||
- run: make site | ||
working-directory: lesson | ||
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- run: make lesson-check-all | ||
working-directory: lesson |
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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: '3.0' | ||
bundler-cache: true | ||
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- name: Set up Python | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: '3.x' | ||
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- 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: ${{ github.event.pull_request.head.sha }} | ||
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- name: Look for R-markdown files | ||
id: check-rmd | ||
run: | | ||
echo "count=$(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 | ||
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- 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- | ||
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- name: Install needed packages | ||
if: steps.check-rmd.outputs.count != 0 | ||
run: | | ||
source('bin/dependencies.R') | ||
install_required_packages() | ||
shell: Rscript {0} | ||
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- 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} | ||
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- 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 | ||
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- 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 | ||
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- 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 "[email protected]" | ||
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 .. | ||
# waiting for https://github.com/carpentries/styles/issues/551 | ||
# to be addressed | ||
# - run: make lesson-check-all | ||
# if: always() |
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*.pyc | ||
*~ | ||
.DS_Store | ||
.ipynb_checkpoints | ||
.sass-cache | ||
.jekyll-cache/ | ||
.jekyll-metadata | ||
__pycache__ | ||
_site | ||
.Rproj.user | ||
.Rhistory | ||
.RData | ||
.bundle/ | ||
.vendor/ | ||
vendor/ | ||
.docker-vendor/ | ||
Gemfile.lock | ||
.*history |
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