Merge pull request datacarpentry#149 from datacarpentry/update-styles…

…-v9.5.2

Update to styles v9.5.2
I'll go ahead and merge this, thanks for updating

.gitignore

@@ -5,3 +5,7 @@
 .sass-cache
 __pycache__
 _site
+.Rproj.user
+.Rhistory
+.RData
+

CODE_OF_CONDUCT.md

@@ -0,0 +1,11 @@
+---
+layout: page
+title: "Contributor Code of Conduct"
+---
+As contributors and maintainers of this project,
+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 %}

LICENSE.md

@@ -1,7 +1,7 @@
 ---
 layout: page
 title: "Licenses"
-permalink: /license/
+root: .
 ---
 ## Instructional Material
 
@@ -71,17 +71,14 @@ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
 LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-<<<<<<< HEAD
-=======
 
 ## Trademark
 
 "Software Carpentry" and "Data Carpentry" and their respective logos
-are registered trademarks of [NumFOCUS][numfocus].
+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
-[mit-license]: http://opensource.org/licenses/mit-license.html
-[numfocus]: http://numfocus.org/
-[osi]: http://opensource.org
-
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[ci]: http://communityin.org/
+[osi]: https://opensource.org

Makefile

@@ -4,6 +4,7 @@
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
 JEKYLL=jekyll
+JEKYLL_VERSION=3.7.3
 PARSER=bin/markdown_ast.rb
 DST=_site
 
@@ -16,6 +17,10 @@ all : commands
 commands :
 	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
 
+## docker-serve     : use docker to build the site
+docker-serve :
+	docker run --rm -it -v ${PWD}:/srv/jekyll -p 127.0.0.1:4000:4000 jekyll/jekyll:${JEKYLL_VERSION} make serve
+
 ## serve            : run a local server.
 serve : lesson-md
 	${JEKYLL} serve
@@ -63,21 +68,21 @@ RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
 # Lesson source files in the order they appear in the navigation menu.
 MARKDOWN_SRC = \
   index.md \
-  CONDUCT.md \
+  CODE_OF_CONDUCT.md \
   setup.md \
-  $(wildcard _episodes/*.md) \
+  $(sort $(wildcard _episodes/*.md)) \
   reference.md \
-  $(wildcard _extras/*.md) \
+  $(sort $(wildcard _extras/*.md)) \
   LICENSE.md
 
 # Generated lesson files in the order they appear in the navigation menu.
 HTML_DST = \
   ${DST}/index.html \
   ${DST}/conduct/index.html \
   ${DST}/setup/index.html \
-  $(patsubst _episodes/%.md,${DST}/%/index.html,$(wildcard _episodes/*.md)) \
+  $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
   ${DST}/reference/index.html \
-  $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
+  $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
   ${DST}/license/index.html
 
 ## lesson-md        : convert Rmarkdown files to markdown
@@ -88,20 +93,16 @@ ${RMD_DST} : ${RMD_SRC}
 	@bin/knit_lessons.sh ${RMD_SRC}
 
 ## lesson-check     : validate lesson Markdown.
-lesson-check :
+lesson-check : lesson-fixme
 	@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 :
-	@bin/lesson_check.py -s . -p ${PARSER} -l -w
-
-## lesson-figures   : re-generate inclusion displaying all figures.
-lesson-figures :
-	@bin/extract_figures.py -p ${PARSER} ${MARKDOWN_SRC} > _includes/all_figures.html
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
 
 ## unittest         : run unit tests on checking tools.
 unittest :
-	python bin/test_lesson_check.py
+	@bin/test_lesson_check.py
 
 ## lesson-files     : show expected names of generated files for debugging.
 lesson-files :

_config.yml

@@ -2,16 +2,16 @@
 # Values for this lesson.
 #------------------------------------------------------------
 
-# Which carpentry is this ("swc", "dc", or "lc")?
+# Which carpentry is this ("swc", "dc", "lc", or "cp")?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor traning for instance)
 carpentry: "dc"
 
 # Overall title for pages.
 title: "Shell Genomics"
 
-# Contact.  This *must* include the protocol: if it's an email
-# address, it must look like "mailto:lessons@software-carpentry.org",
-# or if it's a URL, "https://gitter.im/username/ProjectName".
-contact: "mailto:lessons@datacarpentry.org"
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
@@ -22,21 +22,28 @@ kind: "lesson"
 
 # Magic to make URLs resolve both locally and on GitHub.
 # See https://help.github.com/articles/repository-metadata-on-github-pages/.
+# Please don't change it: <USERNAME>/<PROJECT> is correct.
 repository: <USERNAME>/<PROJECT>
 
+# Email address, no mailto:
+email: "team@carpentries.org"
+
 # Sites.
 amy_site: "https://amy.software-carpentry.org/workshops"
+carpentries_github: "https://github.com/carpentries"
+carpentries_pages: "https://carpentries.github.io"
+carpentries_site: "https://carpentries.org/"
 dc_site: "http://datacarpentry.org"
+example_repo: "https://github.com/carpentries/lesson-example"
+example_site: "https://carpentries.github.io/lesson-example"
+lc_site: "https://librarycarpentry.github.io/"
 swc_github: "https://github.com/swcarpentry"
-swc_site: "https://software-carpentry.org"
 swc_pages: "https://swcarpentry.github.io"
-lc_site: "http://librarycarpentry.github.io/"
+swc_site: "https://software-carpentry.org"
 template_repo: "https://github.com/carpentries/styles"
-example_repo: "https://github.com/carpentries/lesson-example"
-example_site: "https://carpentries.github.io/lesson-example"
+training_site: "https://carpentries.github.io/instructor-training"
 workshop_repo: "https://github.com/carpentries/workshop-template"
 workshop_site: "https://carpentries.github.io/workshop-template"
-training_site: "https://carpentries.github.io/instructor-training"
 
 # Surveys.
 pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
@@ -50,24 +57,34 @@ start_time: 0
 collections:
   episodes:
     output: true
-    permalink: /:path/
+    permalink: /:path/index.html
   extras:
     output: true
+    permalink: /:path/index.html
 
 # Set the default layout for things in the episodes collection.
 defaults:
   - values:
-      root: ..
+      root: .
+      layout: page
   - scope:
       path: ""
       type: episodes
     values:
+      root: ..
       layout: episode
+  - scope:
+      path: ""
+      type: extras
+    values:
+      root: ..
+      layout: page
 
 # Files and directories that are not to be copied.
 exclude:
   - Makefile
-  - bin
+  - bin/
+  - .Rproj.user/
 
-# Turn off built-in syntax highlighting.
-highlighter: false
+# Turn on built-in syntax highlighting.
+highlighter: rouge

_includes/carpentries.html

@@ -29,10 +29,10 @@
 <br/>
 <div class="row">
   <div class="col-md-2" align="center">
-    <a href="{{ site.lc_site }}"><img src="{{ page.root }}/assets/img/lc-icon-black.svg" alt="Library Carpentry logo" /></a>
+    <a href="{{ site.lc_site }}"><img src="{{ page.root }}/assets/img/lc-icon-black.png" alt="Library Carpentry logo" /></a>
   </div>
   <div class="col-md-8">
-    Library Carpentry is made by librarians to help librarians
+    <a href="{{ site.lc_site }}">Library Carpentry</a> is made by librarians to help librarians
     automate repetitive, boring, error-prone tasks;
     create, maintain and analyse sustainable and reusable data;
     work effectively with IT and systems colleagues;

_includes/episode_navbar.html

@@ -2,22 +2,22 @@
   Navigation bar for an episode.
 {% endcomment %}
 <div class="row">
-  <div class="col-md-1">
-    <h3>
+  <div class="col-xs-1">
+    <h3 class="text-left">
       {% if page.previous.url %}
       <a href="{{ page.root }}{{ page.previous.url }}"><span class="glyphicon glyphicon-menu-left" aria-hidden="true"></span><span class="sr-only">previous episode</span></a>
       {% else %}
       <a href="{{ page.root }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
       {% endif %}
     </h3>
   </div>
-  <div class="col-md-10">
+  <div class="col-xs-10">
     {% if include.episode_navbar_title %}
     <h3 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a></h3>
     {% endif %}
   </div>
-  <div class="col-md-1">
-    <h3>
+  <div class="col-xs-1">
+    <h3 class="text-right">
       {% if page.next.url %}
       <a href="{{ page.root }}{{ page.next.url }}"><span class="glyphicon glyphicon-menu-right" aria-hidden="true"></span><span class="sr-only">next episode</span></a>
       {% else %}

_includes/favicons.html

@@ -0,0 +1,33 @@
+{% assign favicon_url = site.baseurl | append: '/assets/favicons/' | append: site.carpentry | prepend: site.url %}
+
+{% if site.carpentry == 'swc' %}
+{% assign carpentry = 'Software Carpentry' %}
+{% elsif site.carpentry == 'dc' %}
+{% assign carpentry = 'Data Carpentry' %}
+{% elsif site.carpentry == 'lc' %}
+{% assign carpentry = 'Library Carpentry' %}
+{% elsif site.carpentry == 'cp' %}
+{% assign carpentry = 'The Carpentries' %}
+{% endif %}
+
+    <!-- Favicons for everyone -->
+    <link rel="apple-touch-icon-precomposed" sizes="57x57" href="{{ favicon_url }}/apple-touch-icon-57x57.png" />
+    <link rel="apple-touch-icon-precomposed" sizes="114x114" href="{{ favicon_url }}/apple-touch-icon-114x114.png" />
+    <link rel="apple-touch-icon-precomposed" sizes="72x72" href="{{ favicon_url }}/apple-touch-icon-72x72.png" />
+    <link rel="apple-touch-icon-precomposed" sizes="144x144" href="{{ favicon_url }}/apple-touch-icon-144x144.png" />
+    <link rel="apple-touch-icon-precomposed" sizes="60x60" href="{{ favicon_url }}/apple-touch-icon-60x60.png" />
+    <link rel="apple-touch-icon-precomposed" sizes="120x120" href="{{ favicon_url }}/apple-touch-icon-120x120.png" />
+    <link rel="apple-touch-icon-precomposed" sizes="76x76" href="{{ favicon_url }}/apple-touch-icon-76x76.png" />
+    <link rel="apple-touch-icon-precomposed" sizes="152x152" href="{{ favicon_url }}/apple-touch-icon-152x152.png" />
+    <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-196x196.png" sizes="196x196" />
+    <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-96x96.png" sizes="96x96" />
+    <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-32x32.png" sizes="32x32" />
+    <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-16x16.png" sizes="16x16" />
+    <link rel="icon" type="image/png" href="{{ favicon_url }}/favicon-128.png" sizes="128x128" />
+    <meta name="application-name" content="{{ carpentry }} - {{ site.title }}"/>
+    <meta name="msapplication-TileColor" content="#FFFFFF" />
+    <meta name="msapplication-TileImage" content="{{ favicon_url }}/mstile-144x144.png" />
+    <meta name="msapplication-square70x70logo" content="{{ favicon_url }}/mstile-70x70.png" />
+    <meta name="msapplication-square150x150logo" content="{{ favicon_url }}/mstile-150x150.png" />
+    <meta name="msapplication-wide310x150logo" content="{{ favicon_url }}/mstile-310x150.png" />
+    <meta name="msapplication-square310x310logo" content="{{ favicon_url }}/mstile-310x310.png" />

_includes/lc/intro.html

@@ -14,6 +14,6 @@
     Library Carpentry introduces you to the fundamentals of computing
     and provides you with a platform for further self-directed learning.
     For more information on what we teach and why, please see our paper
-    "<a href="http://doi.org/10.18352/lq.10176">Library Carpentry: software skills training for library professionals</a>".
+    "<a href="https://doi.org/10.18352/lq.10176">Library Carpentry: software skills training for library professionals</a>".
   </em>
 </p>

_includes/lc/syllabys.html → _includes/lc/syllabus.html

@@ -8,7 +8,7 @@ <h3 id="syllabus-python">Data Intro</h3>
       <li>Plain text formats</li>
       <li>Naming files</li>
       <li>Regular expressions</li>
-      <li><a href="http://data-lessons.github.io/library-data-intro/reference/">Reference...</a></li>
+      <li><a href="https://data-lessons.github.io/library-data-intro/reference/">Reference...</a></li>
     </ul>
   </div>
   <div class="col-md-6">
@@ -19,7 +19,7 @@ <h3 id="syllabus-shell">The Unix Shell</h3>
       <li>Counting and sorting contents in files</li>
       <li>Pipes and redirection</li>
       <li>Mining or searching in files</li>
-      <li><a href="http://data-lessons.github.io/library-shell/reference/">Reference...</a></li>
+      <li><a href="https://data-lessons.github.io/library-shell/reference/">Reference...</a></li>
     </ul>
   </div>
 
@@ -35,7 +35,7 @@ <h3 id="syllabus-git">Version Control with Git</h3>
       <li>Viewing state changes with <code>status</code></li>
       <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
       <li>Where to host work, and why</li>
-      <li><a href="http://data-lessons.github.io/library-git/reference">Reference...</a></li>
+      <li><a href="https://data-lessons.github.io/library-git/reference">Reference...</a></li>
     </ul>
   </div>
   <div class="col-md-6">
@@ -46,7 +46,7 @@ <h3 id="syllabus-r">Open Refine</h3>
         <li>Importing data</li>
         <li>Basic functions</li>
         <li>Advanced Functions</li>
-        <li><a href="http://data-lessons.github.io/library-openrefine/reference">Reference...</a></li>
+        <li><a href="https://data-lessons.github.io/library-openrefine/reference">Reference...</a></li>
       </ul>
     </div>
   </div>
@@ -62,7 +62,7 @@ <h3 id="syllabus-sql">SQL Intro</h3>
       <li>Filtering with <code>where</code></li>
       <li>Combining values using aggregation</li>
       <li>Combining information from multiple tables using <code>join</code></li>
-      <li><a href="http://data-lessons.github.io//library-sql/reference/">Reference...</a></li>
+      <li><a href="https://data-lessons.github.io//library-sql/reference/">Reference...</a></li>
     </ul>
   </div>
 </div>