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Merge pull request #161 from zkamvar/znk-update-styles
Update Styles
2 parents 13e0f2c + bb48666 commit 22a821f

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‎.editorconfig

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indent_size = 2
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indent_style = space
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max_line_length = 100 # Please keep this in sync with bin/lesson_check.py!
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trim_trailing_whitespace = false # keep trailing spaces in markdown - 2+ spaces are translated to a hard break (<br/>)
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[*.r]
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max_line_length = 80

‎.github/FUNDING.yml

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github: [carpentries, swcarpentry, datacarpentry, librarycarpentry]
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custom: ["https://carpentries.wedid.it"]

‎.github/ISSUE_TEMPLATE.md

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Please delete the text below before submitting your contribution.
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<details>
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<summary><strong>Instructions</strong></summary>
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---
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Thanks for contributing! :heart:
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Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.
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If this contribution is for instructor training, please email the link to this contribution to
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checkout@carpentries.org so we can record your progress. You've completed your contribution
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step for instructor checkout by submitting this contribution!
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7-
Please keep in mind that lesson maintainers are volunteers and it may be some time before they can 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 Kate Hertweck (k8hertweck@gmail.com).
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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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---
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Keep in mind that **lesson maintainers are volunteers** and it may take them some time to
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respond to your contribution. Although not all contributions can be incorporated into the lesson
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materials, we appreciate your time and effort to improve the curriculum. If you have any questions
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about the lesson maintenance process or would like to volunteer your time as a contribution
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reviewer, please contact The Carpentries Team at team@carpentries.org.
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You may delete these instructions from your comment.
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\- The Carpentries
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</details>

‎.github/PULL_REQUEST_TEMPLATE.md

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Please delete the text below before submitting your contribution.
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<details>
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<summary><strong>Instructions</strong></summary>
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3-
---
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Thanks for contributing! :heart:
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Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.
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If this contribution is for instructor training, please email the link to this contribution to
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checkout@carpentries.org so we can record your progress. You've completed your contribution
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step for instructor checkout by submitting this contribution!
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7-
Please keep in mind that lesson maintainers are volunteers and it may be some time before they can 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 Kate Hertweck (k8hertweck@gmail.com).
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Keep in mind that **lesson maintainers are volunteers** and it may take them some time to
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respond to your contribution. Although not all contributions can be incorporated into the lesson
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materials, we appreciate your time and effort to improve the curriculum. If you have any questions
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about the lesson maintenance process or would like to volunteer your time as a contribution
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reviewer, please contact The Carpentries Team at team@carpentries.org.
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---
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You may delete these instructions from your comment.
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\- The Carpentries
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</details>

‎.github/workflows/template.yml

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name: Test template
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on:
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push:
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branches: gh-pages
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pull_request:
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jobs:
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check-template:
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name: ${{ matrix.lesson-name }} (${{ matrix.os-name }})
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if: github.repository == 'carpentries/styles'
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git]
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os: [ubuntu-20.04, macos-latest, windows-latest]
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include:
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- os: ubuntu-20.04
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os-name: Ubuntu
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- os: macos-latest
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os-name: macOS
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- os: windows-latest
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os-name: Windows
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- lesson: swcarpentry/shell-novice
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lesson-name: (SWC) Shell novice
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- lesson: datacarpentry/r-intro-geospatial
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lesson-name: (DC) R Intro Geospatial
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- lesson: librarycarpentry/lc-git
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lesson-name: (LC) Intro to Git
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defaults:
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run:
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shell: bash # forces 'Git for Windows' on Windows
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env:
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RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest'
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steps:
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- name: Set up Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: '2.7'
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bundler-cache: true
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install GitHub Pages, Bundler, and kramdown gems
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run: |
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gem install github-pages bundler kramdown kramdown-parser-gfm
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- name: Install Python modules
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run: |
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if [[ $RUNNER_OS == macOS || $RUNNER_OS == Linux ]]; then
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python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
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elif [[ $RUNNER_OS == Windows ]]; then
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python -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
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fi
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- name: Checkout the ${{ matrix.lesson }} lesson
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uses: actions/checkout@master
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with:
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repository: ${{ matrix.lesson }}
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path: lesson
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fetch-depth: 0
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- name: Determine the proper reference to use
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id: styles-ref
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run: |
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if [[ -n "${{ github.event.pull_request.number }}" ]]; then
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echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
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else
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echo "::set-output name=ref::gh-pages"
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fi
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- name: Sync lesson with carpentries/styles
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working-directory: lesson
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run: |
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git config --global user.email "team@carpentries.org"
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git config --global user.name "The Carpentries Bot"
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git remote add styles https://github.com/carpentries/styles.git
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git config --local remote.styles.tagOpt --no-tags
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git fetch styles ${{ steps.styles-ref.outputs.ref }}:styles-ref
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git merge -s recursive -Xtheirs --no-commit styles-ref
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git commit -m "Sync lesson with carpentries/styles"
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- name: Look for R-markdown files
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id: check-rmd
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working-directory: lesson
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run: |
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echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
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- name: Set up R
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if: steps.check-rmd.outputs.count != 0
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uses: r-lib/actions/setup-r@master
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with:
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r-version: 'release'
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- name: Install needed packages
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if: steps.check-rmd.outputs.count != 0
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run: |
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packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
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install.packages(packages, repo="https://cran.rstudio.com/")
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shell: Rscript {0}
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- name: Query dependencies
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if: steps.check-rmd.outputs.count != 0
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working-directory: lesson
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run: |
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source('bin/dependencies.R')
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deps <- identify_dependencies()
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create_description(deps)
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0
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uses: actions/cache@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install stringi from source
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if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0
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run: install.packages('stringi', repos='https://cloud.r-project.org')
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shell: Rscript {0}
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- name: Install system dependencies for R packages
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if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0
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working-directory: lesson
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run: |
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
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- run: make site
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working-directory: lesson

‎.github/workflows/website.yml

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name: Website
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on:
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push:
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branches:
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- gh-pages
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- main
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pull_request: []
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jobs:
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build-website:
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if: ${{ !endsWith(github.repository, '/styles') }}
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runs-on: ubuntu-20.04
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env:
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RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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defaults:
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run:
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shell: bash
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steps:
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- name: Set up Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: '2.7'
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bundler-cache: true
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install GitHub Pages, Bundler, and kramdown gems
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run: |
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gem install github-pages bundler kramdown kramdown-parser-gfm
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- name: Install Python modules
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run: |
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python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
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- name: Checkout the lesson
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uses: actions/checkout@master
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with:
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fetch-depth: 0
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ref: ${{ github.event.pull_request.head.sha }}
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- name: Look for R-markdown files
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id: check-rmd
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run: |
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echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
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- name: Set up R
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if: steps.check-rmd.outputs.count != 0
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uses: r-lib/actions/setup-r@master
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with:
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r-version: 'release'
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- name: Cache R packages
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if: steps.check-rmd.outputs.count != 0
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uses: actions/cache@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install needed packages
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if: steps.check-rmd.outputs.count != 0
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run: |
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packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
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install.packages(packages, repo="https://cran.rstudio.com/")
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shell: Rscript {0}
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- name: Query dependencies
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if: steps.check-rmd.outputs.count != 0
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run: |
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source('bin/dependencies.R')
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deps <- identify_dependencies()
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create_description(deps)
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Install system dependencies for R packages
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if: steps.check-rmd.outputs.count != 0
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run: |
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
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- name: Render the markdown and confirm that the site can be built
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run: make site
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- name: Checkout github pages
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if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
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uses: actions/checkout@master
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with:
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ref: gh-pages
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path: gh-pages
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- name: Commit and Push
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if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
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run: |
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# clean up gh-pages
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cd gh-pages
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git rm -rf . # remove all previous files
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git restore --staged . # remove things from the stage
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cd ..
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# copy everything into gh-pages site
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cp -r `ls -A | grep -v 'gh-pages' | grep -v '.git' | grep -v '.bundle/' | grep -v '_site'` gh-pages
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# move into gh-pages, add, commit, and push
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cd gh-pages
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# setup git
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git config --local user.email "actions@github.com"
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git config --local user.name "GitHub Actions"
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git add -A .
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git commit --allow-empty -m "[Github Actions] render website (via ${{ github.sha }})"
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git push origin gh-pages
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# return
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cd ..
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- run: make lesson-check-all
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if: always()

‎.gitignore

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.DS_Store
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.ipynb_checkpoints
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.sass-cache
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.jekyll-cache/
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.jekyll-metadata
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__pycache__
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_site
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.Rproj.user
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.Rhistory
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.RData
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.bundle/
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.vendor/
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vendor/
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.docker-vendor/
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Gemfile.lock
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.*history

‎404.md

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---
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layout: base
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root: .
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permalink: 404.html
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title: "Page not found"
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---
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# Oops! We can't find that page.
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{: style="text-align: center;"}
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> ## Our apologies!
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>
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> We can't seem to find the page you're looking for.
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> Try going back to the <a href="javascript:history.back()">previous page</a> or
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> navigate to any other page using the navigation bar above
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> {%- if site.kind == "lesson" -%} or the schedule below {%- endif -%}.
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> If you got here by clicking on a link in the
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> {%- if site.kind == "lesson" -%} lesson {%- else -%} workshop {%- endif -%},
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> please report this link to the
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> {%- if site.kind == "lesson" -%} lesson developers {%- else -%} workshop organizers {%- endif -%}.
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{: .caution}
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{% if site.kind == "lesson" %}
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{% include syllabus.html %}
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{% endif%}

‎Gemfile

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# frozen_string_literal: true
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source 'https://rubygems.org'
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git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
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# Synchronize with https://pages.github.com/versions
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ruby '>=2.7.1'
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gem 'github-pages', group: :jekyll_plugins
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if Gem::Version.new(RUBY_VERSION) >= Gem::Version.new('3.0.0')
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gem 'webrick', '>= 1.6.1'
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end

‎LICENSE.md

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---
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## Instructional Material
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All Software Carpentry and Data Carpentry instructional material is
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All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is
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made available under the [Creative Commons Attribution
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license][cc-by-human]. The following is a human-readable summary of
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(and not a substitute for) the [full legal text of the CC BY 4.0

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