swcarpentry · fmichonneau · Jan 10, 2018 · Feb 14, 2018 · Feb 15, 2018 · Feb 15, 2018
diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,25 @@
+root = true
+
+[*]
+charset = utf-8
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+indent_size = 2
+indent_style = space
+max_line_length = 100  # Please keep this in sync with bin/lesson_check.py!
+
+[*.r]
+max_line_length = 80
+
+[*.py]
+indent_size = 4
+indent_style = space
+max_line_length = 79
+
+[*.sh]
+end_of_line = lf
+
+[Makefile]
+indent_style = tab
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -1,9 +1,11 @@
-Please delete the text below before submitting your contribution. 
+Please delete this line and the text below before submitting your contribution.
 
 ---
 
 Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
 
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. 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 Kate Hertweck ([email protected]).  
+If this issue is about a specific episode within a lesson, please provide its link or filename.
+
+Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. 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 Carpentries Team at [email protected].  
 
 ---
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,9 +1,9 @@
-Please delete the text below before submitting your contribution. 
+Please delete this line and the text below before submitting your contribution.
 
 ---
 
 Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
 
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. 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 Kate Hertweck ([email protected]).  
+Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. 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 Carpentries Team at [email protected].  
 
 ---
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,7 @@
 .sass-cache
 __pycache__
 _site
+.Rproj.user
+.Rhistory
+.RData
+
diff --git a/CODE_OF_CONDUCT.md b/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 --git a/CONDUCT.md b/CONDUCT.md
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,11 +1,10 @@
 ---
 layout: page
 title: "Licenses"
-permalink: /license/
 ---
 ## Instructional Material
 
-All Software Carpentry and Data Carpentry instructional material is
+All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is
 made available under the [Creative Commons Attribution
 license][cc-by-human]. The following is a human-readable summary of
 (and not a substitute for) the [full legal text of the CC BY 4.0
@@ -78,7 +77,6 @@ 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
+[mit-license]: https://opensource.org/licenses/mit-license.html
 [ci]: http://communityin.org/
-[osi]: http://opensource.org
-
+[osi]: https://opensource.org
diff --git a/Makefile b/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
@@ -38,7 +43,7 @@ clean :
 	@find . -name '*.pyc' -exec rm {} \;
 
 ## clean-rmd        : clean intermediate R files (that need to be committed to the repo).
-clear-rmd :
+clean-rmd :
 	@rm -rf ${RMD_DST}
 	@rm -rf fig/rmd-*
 
@@ -63,45 +68,40 @@ 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
 lesson-md : ${RMD_DST}
 
-# Use of .NOTPARALLEL makes rule execute only once
-${RMD_DST} : ${RMD_SRC}
-	@bin/knit_lessons.sh ${RMD_SRC}
+_episodes/%.md: _episodes_rmd/%.Rmd
+	@bin/knit_lessons.sh $< $@
 
 ## 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 :

diff --git a/_episodes/01-basics.md b/_episodes/01-basics.md
@@ -51,9 +51,9 @@ the same base document.
 A version control system is a tool that keeps track of these changes for us and
 helps us version and merge our files. It allows you to
 decide which changes make up the next version, called a
-[commit]({{ page.root }}/reference/#commit), and keeps useful metadata about them. The
+[commit]({% link reference.md %}#commit), and keeps useful metadata about them. The
 complete history of commits for a particular project and their metadata make up
-a [repository]({{ page.root }}/reference/#repository). Repositories can be kept in sync
+a [repository]({% link reference.md %}#repository). Repositories can be kept in sync
 across different computers facilitating collaboration among different people.
 
 > ## The Long History of Version Control Systems

diff --git a/_episodes/03-create-repo.md b/_episodes/03-create-repo.md
@@ -20,7 +20,7 @@ Lots of projects
 (and therefore version control repositories)
 start with a single text file in which someone writes down some initial ideas.
 
-Now that we have Mercurial [configured]({{ page.root }}/02-configuration/),
+Now that we have Mercurial [configured]({% link _episodes/02-configuration.md %}),
 we can start using it.
 Let's create a directory for Susan's NEMO forecast project:
 
@@ -30,7 +30,7 @@ $ cd forecast
 ~~~
 {: .bash}
 
-and tell Mercurial to make it a [repository]({{ page.root }}/reference/#repository):
+and tell Mercurial to make it a [repository]({% link reference.md %}#repository):
 a place where Mercurial can store versions of our files:
 
 ~~~

diff --git a/_episodes/04-tracking.md b/_episodes/04-tracking.md
@@ -110,8 +110,8 @@ $ hg commit -m "Starting to plan the daily NEMO forecast system."
 When we run `hg commit`,
 Mercurial takes the file we have told it about by using `hg add` and stores
 a copy permanently inside the special `.hg` directory.
-That permanent copy is called a [commit]({{ page.root }}/reference/#commit)
-(or [revision]({{ page.root }}/reference/#revision)).
+That permanent copy is called a [commit]({% link reference.md %}#commit)
+(or [revision]({% link reference.md %}#revision)).
 
 We use the `-m` flag (for "message") to record a comment that will help us
 remember later on what we did and why.
@@ -156,7 +156,7 @@ summary:     Starting to plan the daily NEMO forecast system.
 
 `hg log` lists all changes committed to a repository,
 starting with the most recent.
-The listing for each [changeset]({{ page.root }}/reference/#changeset) includes:
+The listing for each [changeset]({% link reference.md %}#changeset) includes:
 
 * the changeset's revision number and identifier
   (`0` and `1320339bbcae` in this case,

diff --git a/_episodes/09-remote-repos.md b/_episodes/09-remote-repos.md
@@ -235,6 +235,6 @@ this command would download them to our local repository.
 > that you can generate for yourself.
 > Getting that set up is a distraction from the topics of this workshop,
 > but after the workshop you should read the Bitbucket
-> [Setting up SSH for Mercurial](https://confluence.atlassian.com/bitbucket/set-up-ssh-for-mercurial-728138122.html)
+> [Setting up SSH for Mercurial](https://confluence.atlassian.com/bitbucket/set-up-an-ssh-key-728138079.html)
 > documentation on your own and set up ssh keys for yourself.
 {: .callout}
diff --git a/_episodes/12-merges.md b/_episodes/12-merges.md
@@ -94,7 +94,7 @@ abort: push creates new remote head e0747e3feea1!
 Mercurial detects that our changes have diverged with the changes in the remote
 repo on Bitbucket and stops us from creating a confusing situation on there.
 What we have to do is pull the changes from Bitbucket,
-[merge]({{ page.root }}/reference/#merge) them into the copy we're currently working in,
+[merge]({% link reference.md %}#merge) them into the copy we're currently working in,
 and then push that.
 Let's start by pulling:
 

diff --git a/_episodes/15-licensing.md b/_episodes/15-licensing.md
@@ -54,7 +54,7 @@ the most popular, including the following:
 
 The GPL is different from most other open source licenses in that it
 is
-[infective]({{ page.root }}/reference/#infective):
+[infective]({% link reference.md %}#infective):
 anyone who distributes a modified version of the code, or anything
 that includes GPL'ed code, must make *their* code freely available as
 well.

diff --git a/_extras/about.md b/_extras/about.md
@@ -1,6 +1,5 @@
 ---
 layout: page
 title: About
-permalink: /about/
 ---
 {% include carpentries.html %}
diff --git a/_extras/discuss.md b/_extras/discuss.md
@@ -13,7 +13,7 @@ it won't be covered by the instructor.
 
 ## More Advanced Mercurial Configuration
 
-In the [Setting Up]({{ page.root }}/01-backup/#setting-up) section we edited a
+In the [Setting Up]({% link _episodes/01-basics.md %}#setting-up) section we edited a
 Mercurial configuration file in our home directory called
 `$USERPROFILE/Mercurial.ini` or `~/.hgrc`.  You can quickly open that
 file for editing with the command `hg config --edit`.
@@ -41,7 +41,7 @@ editing with the command `hg config --local`.
 
 ## Non-text Files
 
-Recall when we discussed [Conflicts]({{ page.root }}/03-conflict/) there was a
+Recall when we discussed [Conflicts]({% link _episodes/13-conflicts.md %}) there was a
 challenge that asked, "What does hg do when there is a conflict in an
 image or some other non-textual file that is stored in version
 control?"  We will now revisit this in more detail.

diff --git a/_extras/figures.md b/_extras/figures.md
@@ -1,6 +1,5 @@
 ---
 layout: page
 title: Figures
-permalink: /figures/
 ---
 {% include all_figures.html %}