Update styles 2021-04-14

.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 "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 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/links.md

@@ -12,7 +12,7 @@
 [cran-stringr]: https://cran.r-project.org/package=stringr
 [dc-lessons]: http://www.datacarpentry.org/lessons/
 [email]: mailto:team@carpentries.org
-[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

@@ -210,6 +210,20 @@ 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 +301,11 @@ span.fold-unfold {
 }
 
 
+p.image-with-shadow img,
+img.image-with-shadow {
+  box-shadow: 0 6px 24px 0 #888;
+}
+
 //----------------------------------------
 // Life cycle box
 //----------------------------------------

bin/dependencies.R

@@ -5,19 +5,20 @@ install_required_packages <- function(lib = NULL, repos = getOption("repos", def
   }
 
   message("lib paths: ", paste(lib, collapse = ", "))
-  missing_pkgs <- setdiff(
-    c("rprojroot", "desc", "remotes", "renv"),
-    rownames(installed.packages(lib.loc = lib))
-  )
+  required_pkgs <- c("rprojroot", "desc", "remotes", "renv")
+  installed_pkgs <- rownames(installed.packages(lib.loc = lib))
+  missing_pkgs <- setdiff(required_pkgs, installed_pkgs)
+
   # The default installation of R will have "@CRAN@" as the default repository, which directs contrib.url() to either
   # force the user to choose a mirror if interactive or fail if not. Since we are not interactve, we need to force the
   # mirror here.
   if ("@CRAN@" %in% repos) {
     repos <- c(CRAN = "https://cran.rstudio.com/")
   }
 
-  install.packages(missing_pkgs, lib = lib, repos = repos)
-
+  if (length(missing_pkgs) != 0) {
+    install.packages(missing_pkgs, lib = lib, repos = repos)
+  }
 }
 
 find_root <- function() {

bin/lesson_check.py

@@ -113,7 +113,10 @@ def main():
     if life_cycle == "pre-alpha":
         args.permissive = True
     check_source_rmd(args.reporter, args.source_dir, args.parser)
-    args.references = read_references(args.reporter, args.reference_path)
+
+    args.references = {}
+    if not using_remote_theme(args.source_dir):
+        args.references = read_references(args.reporter, args.reference_path)
 
     docs = read_all_markdown(args.source_dir, args.parser)
     check_fileset(args.source_dir, args.reporter, list(docs.keys()))
@@ -167,6 +170,10 @@ def parse_args():
 
     return args
 
+def using_remote_theme(source_dir):
+    config_file = os.path.join(source_dir, '_config.yml')
+    config = load_yaml(config_file)
+    return 'remote_theme' in config
 
 def check_config(reporter, source_dir):
     """Check configuration file."""
@@ -188,6 +195,8 @@ def check_config(reporter, source_dir):
         reporter.check(defaults in config.get('defaults', []),
                    'configuration',
                    '"root" not set to "." in configuration')
+    if 'life_cycle' not in config:
+        config['life_cycle'] = None
     return config['life_cycle']
 
 def check_source_rmd(reporter, source_dir, parser):
@@ -390,7 +399,8 @@ def check_codeblock_classes(self):
 
         for node in self.find_all(self.doc, {'type': 'codeblock'}):
             cls = self.get_val(node, 'attr', 'class')
-            self.reporter.check(cls in KNOWN_CODEBLOCKS or cls.startswith('language-'),
+            self.reporter.check(cls is not None and (cls in KNOWN_CODEBLOCKS or
+                cls.startswith('language-')),
                                 (self.filename, self.get_loc(node)),
                                 'Unknown or missing code block type {0}',
                                 cls)
@@ -490,7 +500,8 @@ def check(self):
         """Run extra tests."""
 
         super().check()
-        self.check_reference_inclusion()
+        if not using_remote_theme():
+            self.check_reference_inclusion()
 
     def check_metadata(self):
         super().check_metadata()

bin/markdown_ast.rb

@@ -5,9 +5,10 @@
 require "bundler/inline"
 
 require 'kramdown'
+require 'kramdown-parser-gfm'
 require 'json'
 
 markdown = $stdin.read
-doc = Kramdown::Document.new(markdown)
+doc = Kramdown::Document.new(markdown, input: 'GFM', hard_wrap: false)
 tree = doc.to_hash_a_s_t
 puts JSON.pretty_generate(tree)

bin/util.py

@@ -115,7 +115,7 @@ def read_markdown(parser, path):
              for (i, line) in enumerate(body.split('\n'))]
 
     # Parse Markdown.
-    cmd = 'ruby {0}'.format(parser)
+    cmd = 'bundle exec ruby {0}'.format(parser)
     p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE,
               close_fds=True, universal_newlines=True, encoding='utf-8')
     stdout_data, stderr_data = p.communicate(body)

bin/workshop_check.py

@@ -17,7 +17,7 @@
 
 # Defaults.
 CARPENTRIES = ("dc", "swc", "lc", "cp")
-DEFAULT_CONTACT_EMAIL = 'admin@software-carpentry.org'
+DEFAULT_CONTACT_EMAIL = 'team@carpentries.org'
 
 USAGE = 'Usage: "workshop_check.py path/to/root/directory"'