20210909 styles upgrade

.editorconfig

@@ -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

.github/ISSUE_TEMPLATE.md

@@ -1,11 +1,21 @@
-Please delete this line and the text below before submitting your contribution.
+<details>
+<summary><strong>Instructions</strong></summary>
 
----
+Thanks for contributing! :heart:
 
-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.  
+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.
 
-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 The Carpentries Team at team@carpentries.org.  
+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>

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,9 +1,19 @@
-Please delete this line and the text below before submitting your contribution.
+<details>
+<summary><strong>Instructions</strong></summary>
 
----
+Thanks for contributing! :heart:
 
-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.  
+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!
 
-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 The Carpentries Team at team@carpentries.org.  
+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>

.github/workflows/template.yml

@@ -0,0 +1,184 @@
+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 "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+
+      - name: Set up R
+        if: steps.check-rmd.outputs.count != 0
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+
+      - name: Install needed packages
+        if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
+        run: |
+          source('bin/dependencies.R')
+          install_required_packages(.libPaths()[1])
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
+        run: |
+          source('bin/dependencies.R')
+          deps <- identify_dependencies()
+          create_description(deps)
+          use_bioc_repos()
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$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

.github/workflows/website.yml

@@ -0,0 +1,122 @@
+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: ${{ github.event.pull_request.head.sha }}
+
+      - name: Look for R-markdown files
+        id: check-rmd
+        run: |
+          echo "::set-output name=count::$(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: 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()

.gitignore

@@ -3,10 +3,16 @@
 .DS_Store
 .ipynb_checkpoints
 .sass-cache
+.jekyll-cache/
+.jekyll-metadata
 __pycache__
 _site
 .Rproj.user
 .Rhistory
 .RData
-.jekyll-cache
-
+.bundle/
+.vendor/
+vendor/
+.docker-vendor/
+Gemfile.lock
+.*history