Merge branch gh-pages of carpentries/styles

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

@@ -12,9 +12,9 @@ jobs:
       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]
         include:
-          - os: ubuntu-latest
+          - os: ubuntu-20.04
             os-name: Ubuntu
           - os: macos-latest
             os-name: macOS
@@ -30,12 +30,13 @@ jobs:
       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@main
+        uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7.1'
+          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(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 +120,19 @@ 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

.github/workflows/website.yml

@@ -1,20 +1,26 @@
-name: Build website
+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@main
+        uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7.1'
+          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

@@ -5,6 +5,7 @@
 .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 +2,13 @@
 
 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 '>=2.5.8'
+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 .
 
 
@@ -96,7 +99,7 @@ workshop-check :
 .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.
@@ -115,7 +118,7 @@ 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
 
@@ -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