Initial commit

.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

.github/FUNDING.yml

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

.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
+[email protected] 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 [email protected].
+
+You may delete these instructions from your comment.
+
+\- The Carpentries
+</details>

.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
+[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.
+
+\- The Carpentries
+</details>

.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 }}
+    strategy:
+      fail-fast: false
+      matrix:
+        lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git]
+        os: [ubuntu-20.04, macos-latest, windows-latest]
+        include:
+          - os: ubuntu-20.04
+            os-name: Ubuntu
+          - 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
+    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: actions/setup-ruby@v1
+        with:
+          ruby-version: '2.7'
+
+      - 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: ${{ matrix.lesson }}
+          path: lesson
+          fetch-depth: 0
+
+      - name: Determine the proper reference to use
+        id: styles-ref
+        run: |
+          if [[ -n "${{ github.event.pull_request.number }}" ]]; then
+            echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
+          else
+            echo "::set-output name=ref::gh-pages"
+          fi
+
+      - name: Sync lesson with carpentries/styles
+        working-directory: lesson
+        run: |
+          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 config --local remote.styles.tagOpt --no-tags
+          git fetch styles ${{ steps.styles-ref.outputs.ref }}:styles-ref
+          git merge -s recursive -Xtheirs --no-commit styles-ref
+          git commit -m "Sync lesson with carpentries/styles"
+
+      - name: Look for R-markdown files
+        id: check-rmd
+        working-directory: lesson
+        run: |
+          echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+
+      - name: Set up R
+        if: steps.check-rmd.outputs.count != 0
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+
+      - name: Install needed packages
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          install.packages(setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages())))
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
+        run: |
+          source('bin/dependencies.R')
+          deps <- identify_dependencies()
+          create_description(deps)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$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

.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: actions/setup-ruby@v1
+        with:
+          ruby-version: '2.7'
+
+      - 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: ${{ github.event.pull_request.head.sha }}
+
+      - name: Look for R-markdown files
+        id: check-rmd
+        run: |
+          echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+
+      - name: Set up R
+        if: steps.check-rmd.outputs.count != 0
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+
+      - name: Cache R packages
+        if: 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 needed packages
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          install.packages(setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.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)
+          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
+          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 "[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()

.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

.mailmap

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+Abigail Cabunoc Mayes <[email protected]>
+Abigail Cabunoc Mayes <[email protected]> <[email protected]>
+Amy Brown <[email protected]> <[email protected]>
+Andrew Walker <[email protected]> <[email protected]>
+Andy Boughton <[email protected]> <[email protected]>
+Ben Jolly <[email protected]>
+Erin Becker <[email protected]>
+Evan P. Williamson <[email protected]>
+François Michonneau <[email protected]>
+François Michonneau <[email protected]> <[email protected]>
+Greg Wilson <[email protected]> <[email protected]>
+James Allen <[email protected]> <[email protected]>
+Jonah Duckles <[email protected]> <[email protected]>
+Jonathan Cooper <[email protected]> <[email protected]>
+Lauren Michael <[email protected]>
+Leighton Pritchard <[email protected]>
+Lex Nederbragt <[email protected]> <[email protected]>
+Maneesha Sane <[email protected]>
+Marianna Foos <[email protected]>
+Maxim Belkin <[email protected]> <[email protected]>
+Mike Jackson <[email protected]> <[email protected]>
+Neal Davis <[email protected]> <[email protected]>
+Pauline Barmby <[email protected]>
+Philipp Von Bieberstein <[email protected]>
+Raniere Silva <[email protected]> <[email protected]>
+Raniere Silva <[email protected]> <[email protected]>
+Rémi Emonet <[email protected]> <[email protected]>
+Rémi Emonet <[email protected]> <[email protected]>
+Sarah Stevens <[email protected]> <[email protected]>
+Timothée Poisot <[email protected]> <[email protected]>
+Yashasvi Girdhar <[email protected]>