update to final version of styles

Author: tobyhodges

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,7 +4,7 @@
 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
+instructor.training@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

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/check_transition_variables.html

@@ -0,0 +1,22 @@
+{% assign date = include.need_transition_date %}
+
+{% if date == "true" %}
+{% unless site.transition_date_prebeta %}
+<div class="alert alert-danger">
+  you need to specify the variable <code>transition_date_prebeta</code>
+  in <code>_config.yml</code>.
+</div>
+{% endunless %}
+{% unless site.transition_date_beta %}
+<div class="alert alert-danger">
+  you need to specify the variable <code>transition_date_beta</code>
+  in <code>_config.yml</code>.
+</div>
+{% endunless %}
+{% unless site.transition_date_prerelease %}
+<div class="alert alert-danger">
+  you need to specify the variable <code>transition_date_prerelease</code>
+  in <code>_config.yml</code>.
+</div>
+{% endunless %}
+{% endif %}

_includes/javascript.html

@@ -5,14 +5,27 @@
 <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');
+  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>

_includes/lesson_footer.html

@@ -28,13 +28,16 @@
 	{% endif %}
     </div>
     <div class="col-md-6 help-links" align="right">
-	{% if page.source %}
-	{% if page.source == "Rmd" %}
-	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Edit on GitHub</a>
-	{% endif %}
-	{% else %}
-	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit on GitHub</a>
-	{% endif %}
+    {% if site.life_cycle == 'transition-step-2' %}
+    {% assign edit_url = "https://carpentries.github.io/workbench/contributor/beta.html?id=" | append: repo_url %}
+    {% else %}
+    {% assign edit_url = repo_url %}
+    {% endif %}
+    {% if page.source == "Rmd" %}
+    <a href="{{edit_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Edit on GitHub</a>
+    {% else %}
+    <a href="{{edit_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit on GitHub</a>
+    {% endif %}
 	/
 	<a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md" data-checker-ignore>Contributing</a>
 	/

_includes/life_cycle.html

@@ -28,7 +28,66 @@
 {% elsif site.life_cycle == "stable" %}
 
 {% comment %}
-We don't do anything special for now
+We do not do anything special for lessons in stable
 {% endcomment %}
 
+
+{% comment %}
+Below we cover the 2 phases of lesson transition towards the Carpentries Workbench:
+Variables needed:
+  - transition_date_prebeta: the date of the prebeta stage
+  - transition_date_beta: the date of the beta stage
+  - transition_date_prerelease: the date of the prerelease stage
+
+- transition-step-1: We notify that there is a snapshot of the lesson available for testing, and that it will supersede this version.
+- transition-step-2 We indicate that this version of the lesson is a snapshot and a new version of the lesson is avaiable and will supersede this version at a given date.
+{% endcomment %}
+
+{% elsif site.life_cycle == "transition-step-1" %}
+{% include check_transition_variables.html need_transition_date = 'true' %}
+
+<div id="life-cycle" class="alert alert-warning life-cycle panel-body">
+  A snapshot of this lesson from {{ site.transition_date_prebeta }} is being tested on
+  <a href='https://carpentries.github.io/workbench'>The Carpentries Workbench</a>:
+  <a href="https://preview.carpentries.org/{{ repo_name }}">https://preview.carpentries.org/{{ repo_name }}</a>.
+  <br>
+  <b>The Workbench version of this lesson will become default on {{ site.transition_date_prerelease }}</b>.
+  <button type="button" style="border: true; position: absolute; top: 10px; right: 27px; color: #383838;" class="close" data-dismiss="alert" aria-label="Close">
+    <span aria-hidden="true" style='font-size:34pt'>&times;</span>
+  </button>
+</div>
+
+{% elsif site.life_cycle == "transition-step-2" %}
+{% include check_transition_variables.html need_transition_date = 'true' %}
+
+<div id="life-cycle" class="alert alert-danger alert-dismissible life-cycle panel-body" role="alert">
+  This lesson is a <b>snapshot from {{ site.transition_date_beta }}</b>.
+  A newer version is being tested on <a href='https://carpentries.github.io/workbench'>The Carpentries Workbench</a>:
+  <a href="https://preview.carpentries.org/{{ repo_name }}">https://preview.carpentries.org/{{ repo_name }}</a>.
+  <br>
+  <b>The Workbench version of this lesson will become default on {{ site.transition_date_prerelease }}</b>.
+  <button type="button" style="border: true; position: absolute; top: 10px; right: 27px; color: #383838;" class="close" data-dismiss="alert" aria-label="Close">
+    <span aria-hidden="true" style='font-size:34pt'>&times;</span>
+  </button>
+</div>
+
+{% endif %}
+
+
+
+{% comment %}
+For Carpentries Lab lessons we add a banner about the review status
+{% 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 %}

_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 %}
@@ -80,20 +84,26 @@
             {% 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>
 	{% endif %}
 
 	{% comment %} Always show license. {% endcomment %}
         <li><a href="{{ relative_root_path }}{% link LICENSE.md %}">License</a></li>
-	{% if page.source %}
-	{% if page.source == "Rmd" %}
-	<li><a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
-	{% endif %}
+        {% if site.life_cycle == 'transition-step-2' %}
+        {% assign edit_url = "https://carpentries.github.io/workbench/contributor/beta.html?id=" | append: repo_url %}
+        {% else %}
+        {% assign edit_url = repo_url %}
+        {% endif %}
+
+        {% if page.source == "Rmd" %}
+	<li><a href="{{edit_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
 	{% else %}
-	<li><a href="{{repo_url}}/edit/{{ default_branch}}/{{page.path}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
+	<li><a href="{{edit_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
 	{% endif %}
       </ul>
       <form class="navbar-form navbar-right" role="search" id="search" onsubmit="google_search(); return false;">