merge styles v9.5.2

Author: fmichonneau

Diff for: .gitignore

@@ -6,3 +6,6 @@
 __pycache__
 _site
 .Rproj.user
+.Rhistory
+.RData
+

Diff for: CONDUCT.md renamed to CODE_OF_CONDUCT.md

@@ -1,7 +1,6 @@
 ---
 layout: page
 title: "Contributor Code of Conduct"
-permalink: /conduct/
 ---
 As contributors and maintainers of this project,
 we pledge to follow the [Carpentry Code of Conduct][coc].

Diff for: 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
@@ -63,7 +68,7 @@ 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 \
   $(sort $(wildcard _episodes/*.md)) \
   reference.md \

Diff for: _includes/lesson_footer.html

@@ -44,8 +44,8 @@
   </div>
   <div class="row">
     <div class="col-md-12" align="center">
-      Using <a href="https://github.com/swcarpentry/styles/">The Carpentries style</a> 
-      version <a href="https://github.com/swcarpentry/styles/releases/tag/v9.5.0">9.5.0</a>.
+      Using <a href="https://github.com/carpentries/styles/">The Carpentries style</a>
+      version <a href="https://github.com/carpentries/styles/releases/tag/v9.5.2">9.5.2</a>.
     </div>
   </div>
 </footer>

Diff for: _includes/links.md

@@ -9,14 +9,16 @@
 [cran-checkpoint]: https://cran.r-project.org/package=checkpoint
 [cran-knitr]: https://cran.r-project.org/package=knitr
 [cran-stringr]: https://cran.r-project.org/package=stringr
-[email]: mailto:[email protected]
+[dc-lessons]: http://www.datacarpentry.org/lessons/
+[email]: mailto:[email protected]
 [github-importer]: https://import.github.com/
 [importer]: https://github.com/new/import
 [jekyll-collection]: https://jekyllrb.com/docs/collections/
 [jekyll-install]: https://jekyllrb.com/docs/installation/
 [jekyll-windows]: http://jekyll-windows.juthilo.com/
 [jekyll]: https://jekyllrb.com/
 [jupyter]: https://jupyter.org/
+[lc-lessons]: https://librarycarpentry.org/#portfolio
 [lesson-example]: https://carpentries.github.io/lesson-example/
 [mit-license]: https://opensource.org/licenses/mit-license.html
 [morea]: https://morea-framework.github.io/
@@ -32,6 +34,7 @@
 [ruby-installer]: https://rubyinstaller.org/
 [rubygems]: https://rubygems.org/pages/download/
 [styles]: https://github.com/carpentries/styles/
+[swc-lessons]: https://software-carpentry.org/lessons/ 
 [swc-releases]: https://github.com/swcarpentry/swc-releases
 [workshop-repo]: {{ site.workshop_repo }}
 [yaml]: http://yaml.org/

Diff for: _includes/navbar.html

@@ -38,7 +38,7 @@
       <ul class="nav navbar-nav">
 
 	{% comment %} Always show code of conduct. {% endcomment %}
-        <li><a href="{{ page.root }}{% link CONDUCT.md %}">Code of Conduct</a></li>
+        <li><a href="{{ page.root }}{% link CODE_OF_CONDUCT.md %}">Code of Conduct</a></li>
 
         {% if site.kind == "lesson" %}
 	{% comment %} Show setup instructions. {% endcomment %}

Diff for: bin/boilerplate/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 %}

Diff for: bin/boilerplate/CONTRIBUTING.md

@@ -15,7 +15,7 @@ In exchange,
 we will address your issues and/or assess your change proposal as promptly as we can,
 and help you become a member of our community.
 Everyone involved in [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
-agrees to abide by our [code of conduct](CONDUCT.md).
+agrees to abide by our [code of conduct](CODE_OF_CONDUCT.md).
 
 ## How to Contribute
 
@@ -50,19 +50,19 @@ and to meet some of our community members.
     which can be viewed at <https://swcarpentry.github.io/FIXME>.
 
 2.  If you wish to change the example lesson,
-    please work in <https://github.com/swcarpentry/lesson-example>,
+    please work in <https://github.com/carpentries/lesson-example>,
     which documents the format of our lessons
-    and can be viewed at <https://swcarpentry.github.io/lesson-example>.
+    and can be viewed at <https://carpentries.github.io/lesson-example>.
 
 3.  If you wish to change the template used for workshop websites,
-    please work in <https://github.com/swcarpentry/workshop-template>.
+    please work in <https://github.com/carpentries/workshop-template>.
     The home page of that repository explains how to set up workshop websites,
-    while the extra pages in <https://swcarpentry.github.io/workshop-template>
+    while the extra pages in <https://carpentries.github.io/workshop-template>
     provide more background on our design choices.
 
 4.  If you wish to change CSS style files, tools,
     or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
-    please work in <https://github.com/swcarpentry/styles>.
+    please work in <https://github.com/carpentries/styles>.
 
 ## What to Contribute
 
@@ -145,4 +145,4 @@ You can also [reach us by email][email].
 [issues]: https://guides.github.com/features/issues/
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: https://software-carpentry.org/lessons/
-[swc-site]: https://software-carpentry.org/
+[swc-site]: https://software-carpentry.org/

Diff for: bin/boilerplate/README.md

@@ -25,4 +25,4 @@ A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
 
 To cite this lesson, please consult with [CITATION](CITATION)
 
-[lesson-example]: https://swcarpentry.github.io/lesson-example
+[lesson-example]: https://carpentries.github.io/lesson-example

Diff for: bin/boilerplate/_config.yml

@@ -2,17 +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: "swc"
 
 # Overall title for pages.
 title: "Lesson Title"
 
-# Contact.  This *must* include the protocol: if it's an email
-# address, it must look like "mailto:[email protected]",
-# or if it's a URL, "https://gitter.im/username/ProjectName".
-email: "mailto:[email protected]"
-
 #------------------------------------------------------------
 # Generic settings (should not need to change).
 #------------------------------------------------------------
@@ -22,24 +21,28 @@ 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: "[email protected]"
+
 # 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/swcarpentry/lesson-example"
-example_site: "https://swcarpentry.github.com/lesson-example"
+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_pages: "https://swcarpentry.github.io"
 swc_site: "https://software-carpentry.org"
-template_repo: "https://github.com/swcarpentry/styles"
-training_site: "https://swcarpentry.github.io/instructor-training"
-workshop_repo: "https://github.com/swcarpentry/workshop-template"
-workshop_site: "https://swcarpentry.github.io/workshop-template"
+template_repo: "https://github.com/carpentries/styles"
+training_site: "https://carpentries.github.io/instructor-training"
+workshop_repo: "https://github.com/carpentries/workshop-template"
+workshop_site: "https://carpentries.github.io/workshop-template"
 
 # Surveys.
 pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="

Diff for: bin/boilerplate/_episodes/01-introduction.md

@@ -3,9 +3,12 @@ title: "Introduction"
 teaching: 0
 exercises: 0
 questions:
-- "Key question"
+- "Key question (FIXME)"
 objectives:
-- "First objective."
+- "First objective. (FIXME)"
 keypoints:
-- "First key point."
----
+- "First key point. (FIXME)"
+---
+FIXME
+
+{% include links.md %}

Diff for: bin/boilerplate/_extras/about.md

@@ -2,3 +2,4 @@
 title: About
 ---
 {% include carpentries.html %}
+{% include links.md %}

Diff for: bin/boilerplate/_extras/discuss.md

@@ -2,3 +2,5 @@
 title: Discussion
 ---
 FIXME
+
+{% include links.md %}

Diff for: bin/boilerplate/_extras/figures.md

@@ -36,3 +36,5 @@ Create anchor for each one of the episodes.
 {% for episode in site.episodes %}
 <article id="{{ episode.url }}"></article>
 {% endfor %}
+
+{% include links.md %}

Diff for: bin/boilerplate/_extras/guide.md

@@ -2,3 +2,5 @@
 title: "Instructor Notes"
 ---
 FIXME
+
+{% include links.md %}

Diff for: bin/boilerplate/index.md

@@ -9,3 +9,5 @@ FIXME: home page introduction
 >
 > FIXME
 {: .prereq}
+
+{% include links.md %}

Diff for: bin/boilerplate/reference.md

@@ -5,3 +5,5 @@ layout: reference
 ## Glossary
 
 FIXME
+
+{% include links.md %}

Diff for: bin/boilerplate/setup.md

@@ -2,3 +2,6 @@
 title: Setup
 ---
 FIXME
+
+
+{% include links.md %}

Diff for: bin/lesson_check.py

@@ -26,7 +26,7 @@
 # specially. This list must include all the Markdown files listed in the
 # 'bin/initialize' script.
 REQUIRED_FILES = {
-    '%/CONDUCT.md': True,
+    '%/CODE_OF_CONDUCT.md': True,
     '%/CONTRIBUTING.md': False,
     '%/LICENSE.md': True,
     '%/README.md': False,
@@ -171,7 +171,7 @@ def check_config(reporter, source_dir):
     reporter.check_field(config_file, 'configuration',
                          config, 'kind', 'lesson')
     reporter.check_field(config_file, 'configuration',
-                         config, 'carpentry', ('swc', 'dc', 'lc'))
+                         config, 'carpentry', ('swc', 'dc', 'lc', 'cp'))
     reporter.check_field(config_file, 'configuration', config, 'title')
     reporter.check_field(config_file, 'configuration', config, 'email')
 

Diff for: bin/lesson_initialize.py

@@ -11,6 +11,7 @@
     '.travis.yml',
     'AUTHORS',
     'CITATION',
+    'CODE_OF_CONDUCT.md',
     'CONTRIBUTING.md',
     'README.md',
     '_config.yml',