Merge pull request #932

Author: maxim-belkin

.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

@@ -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 "[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"
+          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
@@ -96,7 +138,8 @@ jobs:
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
         run: |
-          install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
+          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
+          install.packages(packages, repo="https://cran.rstudio.com/")
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -118,14 +161,22 @@ jobs:
           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")')
+          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-latest
+    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: |
@@ -46,10 +52,19 @@ jobs:
         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(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
+          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
+          install.packages(packages, repo="https://cran.rstudio.com/")
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -62,24 +77,45 @@ jobs:
           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")')
+          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 ..
 
-      - 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
 .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%}

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

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, are 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.
 
@@ -94,7 +94,7 @@ and (b) explain what you would take out to make room for it.
 The first encourages contributors to be honest about requirements;
 the second, to think hard about priorities.
 
-We are also not looking for exercises or other material that only run on one platform.
+We are also not looking for exercises or other material that will only run on one platform.
 Our workshops typically contain a mixture of Windows, macOS, and Linux users;
 in order to be usable,
 our lessons must run equally well on all three.
@@ -104,7 +104,7 @@ our lessons must run equally well on all three.
 If you choose to contribute via GitHub, you may want to look at
 [How to Contribute to an Open Source Project on GitHub][how-contribute].
 To manage changes, we follow [GitHub flow][github-flow].
-Each lesson has two maintainers who review issues and pull requests or encourage others to do so.
+Each lesson has at least two maintainers who review issues and pull requests or encourage others to do so.
 The maintainers are community volunteers and have final say over what gets merged into the lesson.
 To use the web interface for contributing to a lesson:
 
@@ -128,12 +128,12 @@ repository for reference while revising.
 
 ## Other Resources
 
-General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
+General discussion of [Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]
 happens on the [discussion mailing list][discuss-list],
 which everyone is welcome to join.
 You can also [reach us by email][email].
 
-[email]: mailto:admin@software-carpentry.org
+[email]: mailto:team@carpentries.org
 [dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/

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