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ggrimes authored Oct 3, 2023
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26 changes: 26 additions & 0 deletions .editorconfig
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root = true

[*]
charset = utf-8
insert_final_newline = true
trim_trailing_whitespace = true

[*.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/>)

[*.r]
max_line_length = 80

[*.py]
indent_size = 4
indent_style = space
max_line_length = 79

[*.sh]
end_of_line = lf

[Makefile]
indent_style = tab
21 changes: 21 additions & 0 deletions .github/ISSUE_TEMPLATE.md
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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
checkout@carpentries.org so we can record your progress. You've completed your contribution
step for instructor checkout by submitting this contribution!

If this issue is about a specific episode within a lesson, please provide its link or filename.

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 team@carpentries.org.

You may delete these instructions from your comment.

\- The Carpentries
</details>
19 changes: 19 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
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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
instructor.training@carpentries.org 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 team@carpentries.org.

You may delete these instructions from your comment.

\- The Carpentries
</details>
185 changes: 185 additions & 0 deletions .github/workflows/template.yml
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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@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: |
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 "team@carpentries.org"
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

- 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}

- 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}

- 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-

- 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 || echo "Nothing to update"
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
125 changes: 125 additions & 0 deletions .github/workflows/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 ..
# waiting for https://github.com/carpentries/styles/issues/551
# to be addressed
# - run: make lesson-check-all
# if: always()
18 changes: 18 additions & 0 deletions .gitignore
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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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