Merge remote-tracking branch 'styles/gh-pages' into gh-pages

.all-contributorsrc

@@ -0,0 +1,14 @@
+{
+  "files": [
+    "README.md",
+    "_includes/authors.html"
+  ],
+  "projectName": "test-module",
+  "projectOwner": "hsf-training",
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "skipCi": true,
+  "contributors": [
+  ],
+  "contributorsPerLine": 7
+}

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,12 +3,13 @@
 
 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
-step for instructor checkout by submitting this contribution!
-
 Keep in mind that **lesson maintainers are volunteers** and it may take them some time to
-respond to your contribution. Although not all contributions can be incorporated into the lesson
+respond to your contribution.
+
+To ensure that someone gets notified, you can also click on "Request a review" and add
+the suggested person.
+
+Although not all contributions can be incorporated into the lesson
 materials, we appreciate your time and effort to improve the curriculum. If you have any questions
 about the lesson maintenance process or would like to volunteer your time as a contribution
 reviewer, please contact the HSF training convenors.

.github/workflows/template.yml

@@ -1,26 +1,41 @@
-name: Template
+name: Test template
 on:
   push:
     branches: gh-pages
   pull_request:
 jobs:
   check-template:
-    name: Test lesson template
-    if: github.repository == 'carpentries/styles'
+    name: ${{ matrix.lesson-name }} (${{ matrix.os-name }})
+    if: github.repository == 'hsf-training/hsf-styles'
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git]
         os: [ubuntu-latest, macos-latest, windows-latest]
+        include:
+          - os: ubuntu-latest
+            os-name: Ubuntu
+          - os: macos-latest
+            os-name: macOS
+          - os: windows-latest
+            os-name: Windows
+          - lesson: swcarpentry/shell-novice
+            lesson-name: (SWC) Shell novice
+          - lesson: datacarpentry/r-intro-geospatial
+            lesson-name: (DC) R Intro Geospatial
+          - lesson: librarycarpentry/lc-git
+            lesson-name: (LC) Intro to Git
     defaults:
       run:
         shell: bash # forces 'Git for Windows' on Windows
+    env:
+      RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/bionic/latest'
     steps:
       - name: Set up Ruby
-        uses: actions/setup-ruby@main
+        uses: actions/setup-ruby@v1
         with:
-          ruby-version: '2.7.1'
+          ruby-version: '2.7'
 
       - name: Set up Python
         uses: actions/setup-python@v2
@@ -46,6 +61,26 @@ jobs:
           path: lesson
           fetch-depth: 0
 
+      - name: Determine the proper reference to use
+        id: styles-ref
+        run: |
+          if [[ -n "${{ github.event.pull_request.number }}" ]]; then
+            echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
+          else
+            echo "::set-output name=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"
+
       - name: Look for R-markdown files
         id: check-rmd
         working-directory: lesson
@@ -61,7 +96,7 @@ jobs:
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
         run: |
-          install.packages(c('remotes', 'rprojroot', 'renv', 'desc'))
+          install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -89,36 +124,8 @@ jobs:
         run: |
           while read -r cmd
           do
-            eval $cmd
+            eval sudo $cmd
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
 
-      - name: Install R lessons package dependencies
-        if: steps.check-rmd.outputs.count != 0
-        working-directory: lesson
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          file.remove("DESCRIPTION")
-        shell: Rscript {0}
-
-      - name: Determine the proper reference to use
-        id: styles-ref
-        run: |
-          if [[ -n "${{ github.event.pull_request.number }}" ]]; then
-            echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
-          else
-            echo "::set-output name=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"
-
       - run: make site
         working-directory: lesson

.github/workflows/website.yml

@@ -0,0 +1,85 @@
+name: Website
+on:
+  push:
+    branches: gh-pages
+  pull_request: []
+jobs:
+  build-website:
+    if: ${{ !endsWith(github.repository, '/hsf-styles') }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Set up Ruby
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: '2.7'
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Install GitHub Pages, Bundler, and kramdown gems
+        run: |
+          gem install github-pages bundler kramdown
+
+      - name: Install Python modules
+        run: |
+          python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
+
+      - name: Checkout the lesson
+        uses: actions/checkout@master
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Look for R-markdown files
+        id: check-rmd
+        run: |
+          echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+
+      - name: Set up R
+        if: steps.check-rmd.outputs.count != 0
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+
+      - name: Install needed packages
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          source('bin/dependencies.R')
+          deps <- identify_dependencies()
+          create_description(deps)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$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")')
+
+      - 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

@@ -2,10 +2,10 @@
 
 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 '>=2.5.5'
 
 gem 'github-pages', group: :jekyll_plugins
 

Makefile

@@ -32,7 +32,7 @@ endif
 
 
 # Controls
-.PHONY : commands clean files install-rmd-deps
+.PHONY : commands clean files
 
 # Default target
 .DEFAULT_GOAL := commands
@@ -93,10 +93,10 @@ workshop-check :
 ## III. Commands specific to lesson websites
 ## =================================================
 
-.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+.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.
@@ -115,18 +115,18 @@ 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
 
 ## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson
 install-rmd-deps:
-	Rscript -e 'source("bin/dependencies.R"); install_dependencies(identify_dependencies())'
+	@${SHELL} bin/install_r_deps.sh
 
 ## * lesson-md        : convert Rmarkdown files to markdown
 lesson-md : ${RMD_DST}
 
-_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-dependencies
+_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps
 	@mkdir -p _episodes
 	@bin/knit_lessons.sh $< $@
 

_includes/authors.html

@@ -0,0 +1,11 @@
+<h2>Authors</h2>
+The following people contributed to the content of this lesson:
+<div class="author-table">
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+<!-- markdownlint-enable -->
+<!-- prettier-ignore-end -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+</div>
+Note that this list does not include the contributors to the framework.

_includes/lesson_footer.html

@@ -48,7 +48,7 @@
 	/
 	<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a>
 	/
-	<a href="mailto:{{ site.email }}">Contact</a>
+	<a href="mailto:{{ site.email }}">Contact (public mailing list)</a>
     </div>
   </div>
   <div class="row">

_includes/workshop_footer.html

@@ -21,7 +21,7 @@ <h4>
     </div>
     <div class="col-md-6" align="right">
       <h4>
-	<a href="mailto:{{ site.email }}">Contact The Carpentries</a>
+	<a href="mailto:{{ site.email }}">Contact (public mailing list)</a>
       </h4>
     </div>
   </div>

_layouts/lesson.html

@@ -6,3 +6,8 @@
   {{ content }}
 </article>
 {% include syllabus.html %}
+{% if site.show_authors %}
+<article>
+{% include authors.html %}
+</article>
+{% endif %}