STY: Sync Carpentries lesson template

.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/workflows/template.yml

@@ -0,0 +1,136 @@
+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
+
+      - 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

@@ -0,0 +1,114 @@
+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
+
+      - 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: |
+          # 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 ..
+
+      - run: make lesson-check-all
+        if: always()

.gitignore

@@ -4,6 +4,7 @@
 .ipynb_checkpoints
 .sass-cache
 .jekyll-cache/
+.jekyll-metadata
 __pycache__
 _site
 .Rproj.user

404.md

@@ -0,0 +1,25 @@
+---
+layout: base
+root: .
+permalink: 404.html
+title: "Page not found"
+---
+
+# Oops! We can't find that page.
+{: style="text-align: center;"}
+
+> ## Our apologies!
+>
+> We can't seem to find the page you're 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%}

Gemfile

@@ -2,9 +2,9 @@
 
 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

Makefile

@@ -96,10 +96,10 @@ workshop-check :
 ## III. Commands specific to lesson websites
 ## =================================================
 
-.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme install-rmd-deps
 
 # RMarkdown files
-RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
+RMD_SRC = $(wildcard _episodes_rmd/*.Rmd)
 RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
 
 # Lesson source files in the order they appear in the navigation menu.
@@ -118,14 +118,19 @@ HTML_DST = \
   ${DST}/conduct/index.html \
   ${DST}/setup/index.html \
   $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
-  ${DST}/reference/index.html \
+  ${DST}/reference.html \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
   ${DST}/license/index.html
 
+## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson
+install-rmd-deps:
+	@${SHELL} bin/install_r_deps.sh
+
 ## * lesson-md        : convert Rmarkdown files to markdown
 lesson-md : ${RMD_DST}
 
-_episodes/%.md: _episodes_rmd/%.Rmd
+_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps
+	@mkdir -p _episodes
 	@bin/knit_lessons.sh $< $@
 
 # * lesson-check     : validate lesson Markdown

bin/boilerplate/CONTRIBUTING.md

@@ -70,7 +70,7 @@ There are many ways to contribute,
 from writing new exercises and improving existing ones
 to updating or filling in the documentation
 and submitting [bug reports][issues]
-about things that don't work, aren't clear, or are missing.
+about things that do not work, aren not clear, or are missing.
 If you are looking for ideas, please see the 'Issues' tab for
 a list of issues associated with this repository,
 or you may also look at the issues for [Data Carpentry][dc-issues], 
@@ -79,7 +79,7 @@ or you may also look at the issues for [Data Carpentry][dc-issues],
 Comments on issues and reviews of pull requests are just as welcome:
 we are smarter together than we are on our own.
 Reviews from novices and newcomers are particularly valuable:
-it's easy for people who have been using these lessons for a while
+it is easy for people who have been using these lessons for a while
 to forget how impenetrable some of this material can be,
 so fresh eyes are always welcome.
 
@@ -137,7 +137,7 @@ You can also [reach us by email][email].
 [dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/
-[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
+[discuss-list]: https://carpentries.topicbox.com/groups/discuss
 [github]: https://github.com
 [github-flow]: https://guides.github.com/introduction/flow/
 [github-join]: https://github.com/join

bin/boilerplate/_config.yml

@@ -7,6 +7,7 @@
 # dc: Data Carpentry
 # lc: Library Carpentry
 # cp: Carpentries (to use for instructor traning for instance)
+# incubator: Carpentries Incubator
 carpentry: "swc"
 
 # Overall title for pages.