Merge https://github.com/carpentries/styles into update-styles-2021-0…

…4-20

.github/workflows/template.yml

@@ -33,9 +33,10 @@ jobs:
       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 +45,7 @@ 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: |
@@ -96,7 +97,8 @@ jobs:
       - 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())))
+          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

.github/workflows/website.yml

@@ -17,9 +17,10 @@ jobs:
         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
@@ -28,7 +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: |
@@ -62,7 +63,8 @@ jobs:
       - 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())))
+          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
@@ -97,6 +99,11 @@ jobs:
       - 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
@@ -105,7 +112,7 @@ jobs:
           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 commit --allow-empty -m "[Github Actions] render website (via ${{ github.sha }})"
           git push origin gh-pages
           # return
           cd ..

CODE_OF_CONDUCT.md

@@ -7,4 +7,5 @@ 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

@@ -8,3 +8,7 @@ git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
 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

Makefile

@@ -3,7 +3,7 @@
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=bundle config --local set path .vendor/bundle && bundle install && bundle update && bundle exec jekyll
+JEKYLL=bundle config set --local path .vendor/bundle && bundle install && bundle update && bundle exec jekyll
 PARSER=bin/markdown_ast.rb
 DST=_site
 
@@ -12,7 +12,7 @@ DST=_site
 PYTHON3_EXE := $(shell which python3 2>/dev/null)
 ifneq (, $(PYTHON3_EXE))
   ifeq (,$(findstring Microsoft/WindowsApps/python3,$(subst \,/,$(PYTHON3_EXE))))
-    PYTHON := python3
+    PYTHON := $(PYTHON3_EXE)
   endif
 endif
 
@@ -21,25 +21,25 @@ ifeq (,$(PYTHON))
   ifneq (, $(PYTHON_EXE))
     PYTHON_VERSION_FULL := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
     PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION_FULL})
-    ifneq (3, ${PYTHON_VERSION_MAJOR})
-      $(error "Your system does not appear to have Python 3 installed.")
+    ifeq (3, ${PYTHON_VERSION_MAJOR})
+      PYTHON := $(PYTHON_EXE)
+    else
+      PYTHON_NOTE = "Your system does not appear to have Python 3 installed."
     endif
-    PYTHON := python
   else
-      $(error "Your system does not appear to have any Python installed.")
+      PYTHON_NOTE = "Your system does not appear to have any Python installed."
   endif
 endif
 
 
-# Controls
-.PHONY : commands clean files
-
 # Default target
 .DEFAULT_GOAL := commands
 
 ## I. Commands for both workshop and lesson websites
 ## =================================================
 
+.PHONY: site docker-serve repo-check clean clean-rmd
+
 ## * serve            : render website and run a local server
 serve : lesson-md
 	${JEKYLL} serve
@@ -50,8 +50,8 @@ site : lesson-md
 
 ## * docker-serve     : use Docker to serve the site
 docker-serve :
-	docker pull carpentries/lesson-docker:latest
-	docker run --rm -it \
+	@docker pull carpentries/lesson-docker:latest
+	@docker run --rm -it \
 		-v $${PWD}:/home/rstudio \
 		-p 4000:4000 \
 		-p 8787:8787 \
@@ -60,14 +60,17 @@ docker-serve :
 		carpentries/lesson-docker:latest
 
 ## * repo-check       : check repository settings
-repo-check :
+repo-check : python
 	@${PYTHON} bin/repo_check.py -s .
 
 ## * clean            : clean up junk files
 clean :
 	@rm -rf ${DST}
 	@rm -rf .sass-cache
 	@rm -rf bin/__pycache__
+	@rm -rf .vendor
+	@rm -rf .bundle
+	@rm -f Gemfile.lock
 	@find . -name .DS_Store -exec rm {} \;
 	@find . -name '*~' -exec rm {} \;
 	@find . -name '*.pyc' -exec rm {} \;
@@ -85,7 +88,7 @@ clean-rmd :
 .PHONY : workshop-check
 
 ## * workshop-check   : check workshop homepage
-workshop-check :
+workshop-check : python
 	@${PYTHON} bin/workshop_check.py .
 
 
@@ -128,18 +131,18 @@ lesson-md : ${RMD_DST}
 
 _episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps
 	@mkdir -p _episodes
-	@bin/knit_lessons.sh $< $@
+	@$(SHELL) bin/knit_lessons.sh $< $@
 
 ## * lesson-check     : validate lesson Markdown
-lesson-check : lesson-fixme
+lesson-check : python lesson-fixme
 	@${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
 
 ## * lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace
-lesson-check-all :
+lesson-check-all : python
 	@${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
 
 ## * unittest         : run unit tests on checking tools
-unittest :
+unittest : python
 	@${PYTHON} bin/test_lesson_check.py
 
 ## * lesson-files     : show expected names of generated files for debugging
@@ -157,6 +160,15 @@ lesson-fixme :
 ## IV. Auxililary (plumbing) commands
 ## =================================================
 
+.PHONY : commands python
+
 ## * commands         : show all commands.
 commands :
 	@sed -n -e '/^##/s|^##[[:space:]]*||p' $(MAKEFILE_LIST)
+
+python :
+ifeq (, $(PYTHON))
+	$(error $(PYTHON_NOTE))
+else
+	@:
+endif

_includes/base_path.html

@@ -1,27 +1,41 @@
-{% comment %}
-This is adapted from: https://ricostacruz.com/til/relative-paths-in-jekyll
+{%- comment -%}
+When the website is built by GitHub Pages,
+'site.url' is set to 'https://username.github.io'
+'site.baseurl' is set to '/lesson-name'
 
-`page.url` gives the URL of the current page with a leading /:
+When we start a local server using `jekyll serve`,
+'site.url' is set to 'http://localhost:4000' and
+'site.baseurl' is empty.
 
-- when the URL ends with the extension (e.g., /foo/bar.html) then we can get
-  the depth by counting the number of / and remove - 1
-- when the URL ends with a / (e.g. /foo/bar/) then the number / gives the depth
-  directly
-{% endcomment %}
+In both of the above cases we set 'relative_root_path' to 'site.url + site.baseurl'.
 
-{% assign relative_root_path = '' %}
+When we build a website locally with `jekyll build`,
+both 'site.url' and 'site.baseurl' are empty.
+This case is handled by the last 'else' in the code below.
+The logic there follows the (adapted) instructions found at:
+    https://ricostacruz.com/til/relative-paths-in-jekyll
 
-{% assign last_char = page.url | slice: -1 %}
+    `page.url` gives the URL of the current page with a leading /:
 
-{% if last_char == "/"}
-{% assign offset = 0 %}
-{% else %}
-{% assign offset = 1 %}
-{% endif %}
+    - when the URL ends with an extension (e.g., /foo/bar.html),
+      we can get the 'depth' of the page by counting the number of
+      forward slashes ('/') and subtracting 1
+    - when the URL ends with a forward slash (e.g. /foo/bar/),
+      we can get the depth of the page by counting the number of /
+{%- endcomment -%}
 
-{% assign depth = page.url | split: '/' | size | minus: offset %}
-{% if    depth <= 1 %}{% assign relative_root_path = '.' %}
-{% elsif depth == 2 %}{% assign relative_root_path = '..' %}
-{% elsif depth == 3 %}{% assign relative_root_path = '../..' %}
-{% elsif depth == 4 %}{% assign relative_root_path = '../../..' %}
+{% if site.url %}
+  {% assign relative_root_path = site.url | append: site.baseurl %}
+{% else %}
+  {% assign last_char = page.url | slice: -1 %}
+  {% if last_char == "/" %}
+    {% assign offset = 0 %}
+  {% else %}
+    {% assign offset = 1 %}
+  {% endif %}
+  {% assign depth = page.url | split: '/' | size | minus: offset %}
+  {% if    depth <= 1 %}{% assign relative_root_path = '.' %}
+  {% elsif depth == 2 %}{% assign relative_root_path = '..' %}
+  {% else %}{% capture relative_root_path %}..{% for i in (3..depth) %}/..{% endfor %}{% endcapture %}
+  {% endif %}
 {% endif %}

_includes/links.md

@@ -12,7 +12,7 @@
 [cran-stringr]: https://cran.r-project.org/package=stringr
 [dc-lessons]: http://www.datacarpentry.org/lessons/
 [email]: mailto:[email protected]
-[github-importer]: https://import.github.com/
+[github-importer]: https://import2.github.com/
 [importer]: https://github.com/new/import
 [jekyll-collection]: https://jekyllrb.com/docs/collections/
 [jekyll-install]: https://jekyllrb.com/docs/installation/

assets/css/lesson.scss

@@ -64,16 +64,32 @@ div.error::before  { background-color: #ffebe6; content: "Error"; }
 div.warning:before { background-color: #f8f4e8; content:" Warning"; }
 div.output::before { background-color: #efefef; content: "Output"; }
 
-div.language-bash::before   { content: "Bash"; }
-div.language-c::before      { content: "C"; }
-div.language-cmake::before  { content: "CMake"; }
-div.language-cpp::before    { content: "C++"; }
-div.language-html::before   { content: "HTML"; }
-div.language-make::before   { content: "Make"; }
-div.language-matlab::before { content: "MATLAB"; }
-div.language-python::before { content: "Python"; }
-div.language-r::before      { content: "R"; }
-div.language-sql::before    { content: "SQL"; }
+div.language-basic::before    { content: "Basic"; }
+div.language-bash::before     { content: "Bash"; }
+div.language-c::before        { content: "C"; }
+div.language-chapel::before   { content: "Chapel"; }
+div.language-cmake::before    { content: "CMake"; }
+div.language-cpp::before      { content: "C++"; }
+div.language-cuda::before     { content: "Cuda"; }
+div.language-d::before        { content: "D"; }
+div.language-fortran::before  { content: "Fortran"; }
+div.language-go::before       { content: "Go"; }
+div.language-html::before     { content: "HTML"; }
+div.language-java::before     { content: "Java"; }
+div.language-julia::before    { content: "Julia"; }
+div.language-kotlin::before   { content: "Kotlin"; }
+div.language-lua::before      { content: "Lua"; }
+div.language-make::before     { content: "Make"; }
+div.language-matlab::before   { content: "MATLAB"; }
+div.language-opencl::before   { content: "OpenCL"; }
+div.language-perl::before     { content: "Perl"; }
+div.language-python::before   { content: "Python"; }
+div.language-r::before        { content: "R"; }
+div.language-ruby::before     { content: "Ruby"; }
+div.language-rust::before     { content: "Rust"; }
+div.language-scala::before    { content: "Scala"; }
+div.language-sql::before      { content: "SQL"; }
+div.language-vulkan::before   { content: "Vulkan"; }
 
 // Tab panels are used on Setup pages to show instructions for different Operating Systems
 .tab-pane {
@@ -210,6 +226,20 @@ a code {
   color: #006cad;
 }
 
+a:link {
+  color: #196EBD;
+}
+
+a:active,
+a:hover {
+  outline: 0;
+  text-decoration: underline;
+}
+
+a:visited {
+  color: #1AA4DA;
+}
+
 code {
   white-space: nowrap;
   padding: 2px 5px;
@@ -287,6 +317,11 @@ span.fold-unfold {
 }
 
 
+p.image-with-shadow img,
+img.image-with-shadow {
+  box-shadow: 0 6px 24px 0 #888;
+}
+
 //----------------------------------------
 // Life cycle box
 //----------------------------------------