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Update to final version of styles lesson template (#352)
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Update a very large set of changes to the template on this repository: not been updated since 2018.
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tobyhodges authored Apr 18, 2023
1 parent b126ed3 commit 8b5457d
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1 change: 1 addition & 0 deletions .editorconfig
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Expand Up @@ -9,6 +9,7 @@ trim_trailing_whitespace = true
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
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2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -4,7 +4,7 @@
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
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
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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
123 changes: 123 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 ..
- run: make lesson-check-all
if: always()
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -5,6 +5,7 @@
.ipynb_checkpoints
.sass-cache
.jekyll-cache/
.jekyll-metadata
__pycache__
_site
.Rproj.user
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25 changes: 25 additions & 0 deletions 404.md
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---
layout: base
root: .
permalink: 404.html
title: "Page not found"
---

# Oops! We cannot find that page.
{: style="text-align: center;"}

> ## Our apologies!
>
> We cannot seem to find the page you are looking for.
> Try going back to the <a href="javascript:history.back()">previous page</a> or
> navigate to any other page using the navigation bar above
> {%- if site.kind == "lesson" -%} or the schedule below {%- endif -%}.
> If you got here by clicking on a link in the
> {%- if site.kind == "lesson" -%} lesson {%- else -%} workshop {%- endif -%},
> please report this link to the
> {%- if site.kind == "lesson" -%} lesson developers {%- else -%} workshop organizers {%- endif -%}.
{: .caution}

{% if site.kind == "lesson" %}
{% include syllabus.html %}
{% endif%}
3 changes: 2 additions & 1 deletion CODE_OF_CONDUCT.md
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Expand Up @@ -8,4 +8,5 @@ we pledge to follow the [Carpentry Code of Conduct][coc].
Instances of abusive, harassing, or otherwise unacceptable behavior
may be reported by following our [reporting guidelines][coc-reporting].

{% include links.md %}
[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
8 changes: 6 additions & 2 deletions Gemfile
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Expand Up @@ -2,9 +2,13 @@

source 'https://rubygems.org'

git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }

# Synchronize with https://pages.github.com/versions
ruby '>=2.5.8'
ruby '>=2.7.1'

gem 'github-pages', group: :jekyll_plugins

if Gem::Version.new(RUBY_VERSION) >= Gem::Version.new('3.0.0')
gem 'webrick', '>= 1.6.1'
end
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