Sync lesson style with carpentries/styles

Conflicts:
	_includes/javascript.html
	aio.md

Author: maxim-belkin

.github/workflows/template.yml

@@ -137,9 +137,10 @@ jobs:
 
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
         run: |
-          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
-          install.packages(packages, repo="https://cran.rstudio.com/")
+          source('bin/dependencies.R')
+          install_required_packages(.libPaths()[1])
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -149,13 +150,14 @@ jobs:
           source('bin/dependencies.R')
           deps <- identify_dependencies()
           create_description(deps)
+          use_bioc_repos()
           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
+      - name: Restore Package Cache
         if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -172,7 +174,7 @@ jobs:
         run: |
           while read -r cmd
           do
-            eval sudo $cmd
+            eval sudo $cmd || echo "Nothing to update"
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - run: make site

.github/workflows/website.yml

@@ -52,9 +52,9 @@ jobs:
         with:
           r-version: 'release'
 
-      - name: Cache R packages
+      - name: Restore R Cache
         if: steps.check-rmd.outputs.count != 0
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -63,8 +63,8 @@ jobs:
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
         run: |
-          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
-          install.packages(packages, repo="https://cran.rstudio.com/")
+          source('bin/dependencies.R')
+          install_required_packages()
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -73,6 +73,7 @@ jobs:
           source('bin/dependencies.R')
           deps <- identify_dependencies()
           create_description(deps)
+          use_bioc_repos()
           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}
@@ -83,7 +84,7 @@ jobs:
         run: |
           while read -r cmd
           do
-            eval sudo $cmd
+            eval sudo $cmd || echo "Nothing to update"
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - name: Render the markdown and confirm that the site can be built

404.md

@@ -5,12 +5,12 @@ permalink: 404.html
 title: "Page not found"
 ---
 
-# Oops! We can't find that page.
+# Oops! We cannot find that page.
 {: style="text-align: center;"}
 
 > ## Our apologies!
 >
-> We can't seem to find the page you're looking for.
+> We cannot seem to find the page you are 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 -%}.

LICENSE.md

@@ -23,13 +23,15 @@ license terms.
 
 Under the following terms:
 
-* **Attribution**---You must give appropriate credit (mentioning that
-  your work is derived from work that is Copyright © Software
-  Carpentry and, where practical, linking to
-  http://software-carpentry.org/), provide a [link to the
-  license][cc-by-human], and indicate if changes were made. You may do
-  so in any reasonable manner, but not in any way that suggests the
-  licensor endorses you or your use.
+* **Attribution**---You must give appropriate credit by:
+  - mentioning that your work is derived from work that is
+    Copyright © Software Carpentry, Data Carpentry, Library Carpentry,
+    or The Carpentries.
+  - where practical, linking to the respective lesson program website
+    (https://software-carpentry.org/, https://datacarpentry.org, https://librarycarpentry.org, or
+    https://carpentries.org), provide a [link to the license][cc-by-human]
+  - and indicate if changes were made. You may do so in any reasonable manner, but not in any way
+    that suggests the licensor endorses you or your use.
 
 **No additional restrictions**---You may not apply legal terms or
 technological measures that legally restrict others from doing
@@ -73,8 +75,8 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 ## Trademark
 
-"Software Carpentry" and "Data Carpentry" and their respective logos
-are registered trademarks of [Community Initiatives][CI].
+"The Carpentries", "Software Carpentry" and "Data Carpentry" and their respective logos are
+registered trademarks of [Community Initiatives][CI].
 
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
 [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode

Makefile

@@ -7,6 +7,9 @@ JEKYLL=bundle config set --local path .vendor/bundle && bundle install && bundle
 PARSER=bin/markdown_ast.rb
 DST=_site
 
+# Find Docker
+DOCKER := $(shell which docker 2>/dev/null)
+
 # Check Python 3 is installed and determine if it's called via python3 or python
 # (https://stackoverflow.com/a/4933395)
 PYTHON3_EXE := $(shell which python3 2>/dev/null)
@@ -41,23 +44,27 @@ endif
 .PHONY: site docker-serve repo-check clean clean-rmd
 
 ## * serve            : render website and run a local server
-serve : lesson-md
+serve : lesson-md index.md
 	${JEKYLL} serve
 
 ## * site             : build website but do not run a server
-site : lesson-md
+site : lesson-md index.md
 	${JEKYLL} build
 
 ## * docker-serve     : use Docker to serve the site
 docker-serve :
-	@docker pull carpentries/lesson-docker:latest
-	@docker run --rm -it \
+ifeq (, $(DOCKER))
+	$(error Your system does not appear to have Docker installed)
+else
+	@$(DOCKER) pull carpentries/lesson-docker:latest
+	@$(DOCKER) run --rm -it \
 		-v $${PWD}:/home/rstudio \
 		-p 4000:4000 \
 		-p 8787:8787 \
 		-e USERID=$$(id -u) \
 		-e GROUPID=$$(id -g) \
 		carpentries/lesson-docker:latest
+endif
 
 ## * repo-check       : check repository settings
 repo-check : python
@@ -172,3 +179,10 @@ ifeq (, $(PYTHON))
 else
 	@:
 endif
+
+index.md :
+ifeq (, $(wildcard index.md))
+	$(error index.md not found)
+else
+	@:
+endif

_includes/base_path.html

@@ -7,7 +7,7 @@
 'site.url' is set to 'http://localhost:4000' and
 'site.baseurl' is empty.
 
-In both of the above cases we set 'relative_root_path' to 'site.url + site.baseurl'.
+In both of the above cases we set 'relative_root_path' to 'site.baseurl'.
 
 When we build a website locally with `jekyll build`,
 both 'site.url' and 'site.baseurl' are empty.
@@ -25,7 +25,7 @@
 {%- endcomment -%}
 
 {% if site.url %}
-  {% assign relative_root_path = site.url | append: site.baseurl %}
+  {% assign relative_root_path = site.baseurl %}
 {% else %}
   {% assign last_char = page.url | slice: -1 %}
   {% if last_char == "/" %}

_includes/javascript.html

@@ -4,11 +4,52 @@
 <script src="{{ relative_root_path }}/assets/js/jquery.min.js"></script>
 <script src="{{ relative_root_path }}/assets/js/bootstrap.min.js"></script>
 <script src="{{ relative_root_path }}/assets/js/lesson.js"></script>
+
+{% if site.kind == "lesson" %}
+<!-- Matomo -->
 <script>
-  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-  })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
-  ga('create', 'UA-37305346-2', 'auto');
-  ga('send', 'pageview');
-</script>
+  var _paq = window._paq = window._paq || [];
+  /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+  _paq.push(["setDocumentTitle", document.domain + "/" + document.title]);
+  _paq.push(["setDomains", ["*.lessons.carpentries.org","*.datacarpentry.github.io","*.datacarpentry.org","*.librarycarpentry.github.io","*.librarycarpentry.org","*.swcarpentry.github.io"]]);
+  _paq.push(["setDoNotTrack", true]);
+  _paq.push(["disableCookies"]);
+  _paq.push(['trackPageView']);
+  _paq.push(['enableLinkTracking']);
+  (function() {
+    var u="https://carpentries.matomo.cloud/";
+    _paq.push(['setTrackerUrl', u+'matomo.php']);
+    _paq.push(['setSiteId', '1']);
+    var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
+    g.async=true; g.src='//cdn.matomo.cloud/carpentries.matomo.cloud/matomo.js'; s.parentNode.insertBefore(g,s);
+  })();
+</script>
+<!-- End Matomo Code -->
+{% endif %}
+
+{% if page.math %}
+<script src="{{ relative_root_path }}/assets/js/katex.min.js"></script>
+<script>
+options={
+  delimiters: [
+    {left: "$$", right: "$$", display: true},
+    {left: "$", right: "$", display: false},
+    {left: "\\(", right: "\\)", display: false},
+    {left: "\\[", right: "\\]", display: true}
+  ],
+  output: "mathml"
+}
+</script>
+<script src="{{ relative_root_path }}/assets/js/katex-auto-render.min.js" onload="renderMathInElement(document.body, options)"></script>
+{% endif %}
+
+{%- comment -%}
+AnchorJS: A JavaScript utility for adding deep anchor links
+https://github.com/bryanbraun/anchorjs
+https://cdn.jsdelivr.net/npm/anchor-js/anchor.min.js
+{%- endcomment -%}
+
+<script src="{{ relative_root_path }}/assets/js/anchor.min.js"></script>
+<script>
+    anchors.add();
+</script>

_includes/life_cycle.html

@@ -28,7 +28,19 @@
 {% elsif site.life_cycle == "stable" %}
 
 {% comment %}
-We don't do anything special for now
+We do not do anything special unless this is a Carpentries Lab lesson
 {% endcomment %}
 
+{% if site.carpentry == "lab" %}
+{% if site.doi contains "zenodo" %}{% assign listing=" on Zenodo" %}
+{% elsif site.doi contains "jose" %}{% assign listing=" in JOSE" %}
+{% else %}{% assign listing="none" %}
+{% endif %}
+
+<div class="panel panel-default life-cycle">
+  <div id="life-cycle" class="panel-body published">
+    This lesson has passed peer-review! {% if site.doi != "" %}<a href="{{ site.doi }}">See the publication{{ listing }}.</a>{% endif %}
+  </div>
+</div>
+{% endif %}
 {% endif %}

_includes/manual_episode_order.html

@@ -3,7 +3,7 @@
     GitHub Pages switches to Jekyll that supports it
     without any major hackery. Note, some logic will
     be required even when this transition happens
-    but it won't be as involved as what we have to do
+    but it will not be as involved as what we have to do
     in this file.
 
     To order lesson episodes or extras manually

_includes/navbar.html

@@ -32,6 +32,10 @@
       <a href="{{ site.carpentries_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/cp-logo-blue.svg %}" alt="The Carpentries logo" />
       </a>
+      {% elsif site.carpentry == "lab" %}
+      <a href="{{ relative_root_path }}{% link index.md %}" class="pull-left">
+        <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/carpentrieslab.svg %}" alt="The Carpentries Lab" />
+      </a>
       {% endif %}
 
       {% comment %} Always show link to home page. {% endcomment %}
@@ -80,7 +84,9 @@
             {% else %}
               {% assign extra = lesson_extra %}
             {% endif %}
-            <li><a href="{{ relative_root_path }}{{ extra.url }}">{{ extra.title }}</a></li>
+            {% unless extra.exclude %}
+              <li><a href="{{ relative_root_path }}{{ extra.url }}">{{ extra.title }}</a></li>
+            {% endunless %}
             {% endfor %}
           </ul>
         </li>