Merge pull request #80 from datacarpentry/updates/styles/2023-04

updates/styles/2023 04

Author: tobyhodges

.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/PULL_REQUEST_TEMPLATE.md

@@ -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

.github/workflows/template.yml

@@ -8,14 +8,16 @@ jobs:
     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-latest, macos-latest, windows-latest]
+        os: [ubuntu-20.04, macos-latest, windows-latest]
+        experimental: [false]
         include:
-          - os: ubuntu-latest
-            os-name: Ubuntu
+          - os: ubuntu-20.04
+            os-name: Linux
           - os: macos-latest
             os-name: macOS
           - os: windows-latest
@@ -26,16 +28,27 @@ jobs:
             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__/bionic/latest'
+      RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest'
     steps:
       - name: Set up Ruby
-        uses: actions/setup-ruby@v1
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: '2.7'
+          bundler-cache: true
 
       - name: Set up Python
         uses: actions/setup-python@v2
@@ -44,7 +57,7 @@ jobs:
 
       - name: Install GitHub Pages, Bundler, and kramdown gems
         run: |
-          gem install github-pages bundler kramdown
+          gem install github-pages bundler kramdown kramdown-parser-gfm
 
       - name: Install Python modules
         run: |
@@ -61,25 +74,54 @@ jobs:
           path: lesson
           fetch-depth: 0
 
-      - name: Determine the proper reference to use
-        id: styles-ref
+      - name: Sync lesson with carpentries/styles
+        working-directory: lesson
         run: |
-          if [[ -n "${{ github.event.pull_request.number }}" ]]; then
-            echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
+          echo "::group::Fetch Styles"
+          if [[ -n "${{ github.event.pull_request.number }}" ]]
+          then
+            ref="refs/pull/${{ github.event.pull_request.number }}/head"
           else
-            echo "::set-output name=ref::gh-pages"
+            ref="gh-pages"
           fi
 
-      - name: Sync lesson with carpentries/styles
-        working-directory: lesson
-        run: |
           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 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"
+          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
@@ -96,8 +138,10 @@ jobs:
 
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
         run: |
-          install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
+          source('bin/dependencies.R')
+          install_required_packages(.libPaths()[1])
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -107,26 +151,35 @@ jobs:
           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: Cache R packages
+      - name: Restore Package Cache
         if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0
-        uses: actions/cache@v1
+        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
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
+            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

@@ -1,20 +1,26 @@
 name: Website
 on:
   push:
-    branches: gh-pages
+    branches:
+      - gh-pages
+      - main
   pull_request: []
 jobs:
   build-website:
-    if: github.repository != 'carpentries/styles' && (github.repository_owner == 'swcarpentry' || github.repository_owner == 'datacarpentry' || github.repository_owner == 'librarycarpentry' || github.repository_owner == 'carpentries')
-    runs-on: ubuntu-18.04
+    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
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: '2.7'
+          bundler-cache: true
 
       - name: Set up Python
         uses: actions/setup-python@v2
@@ -23,7 +29,7 @@ jobs:
 
       - name: Install GitHub Pages, Bundler, and kramdown gems
         run: |
-          gem install github-pages bundler kramdown
+          gem install github-pages bundler kramdown kramdown-parser-gfm
 
       - name: Install Python modules
         run: |
@@ -47,10 +53,19 @@ jobs:
           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: |
-          install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
+          source('bin/dependencies.R')
+          install_required_packages()
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -59,28 +74,50 @@ jobs:
           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: 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 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", "18.04"), sep = "\n")')
+            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 site
-      - run: make lesson-check
-        if: always()
       - run: make lesson-check-all
         if: always()

.gitignore

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

404.md

@@ -0,0 +1,25 @@
+---
+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%}

CODE_OF_CONDUCT.md

@@ -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

Gemfile

@@ -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 '>=2.7.1'
 
 gem 'github-pages', group: :jekyll_plugins
+
+if Gem::Version.new(RUBY_VERSION) >= Gem::Version.new('3.0.0')
+    gem 'webrick', '>= 1.6.1'
+end