Update to styles v9.5.2

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete 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]).  
+
+---

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete 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]).  
+
+---

.gitignore

@@ -10,4 +10,6 @@ data/.DS_Store
 .sass-cache
 __pycache__
 _site
-_episodes_rmd/_episodes_rmd.Rproj
+.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

@@ -1,116 +1,84 @@
-CC0 1.0 Universal
-
-Statement of Purpose
-
-The laws of most jurisdictions throughout the world automatically confer
-exclusive Copyright and Related Rights (defined below) upon the creator and
-subsequent owner(s) (each and all, an "owner") of an original work of
-authorship and/or a database (each, a "Work").
-
-Certain owners wish to permanently relinquish those rights to a Work for the
-purpose of contributing to a commons of creative, cultural and scientific
-works ("Commons") that the public can reliably and without fear of later
-claims of infringement build upon, modify, incorporate in other works, reuse
-and redistribute as freely as possible in any form whatsoever and for any
-purposes, including without limitation commercial purposes. These owners may
-contribute to the Commons to promote the ideal of a free culture and the
-further production of creative, cultural and scientific works, or to gain
-reputation or greater distribution for their Work in part through the use and
-efforts of others.
-
-For these and/or other purposes and motivations, and without any expectation
-of additional consideration or compensation, the person associating CC0 with a
-Work (the "Affirmer"), to the extent that he or she is an owner of Copyright
-and Related Rights in the Work, voluntarily elects to apply CC0 to the Work
-and publicly distribute the Work under its terms, with knowledge of his or her
-Copyright and Related Rights in the Work and the meaning and intended legal
-effect of CC0 on those rights.
-
-1. Copyright and Related Rights. A Work made available under CC0 may be
-protected by copyright and related or neighboring rights ("Copyright and
-Related Rights"). Copyright and Related Rights include, but are not limited
-to, the following:
-
-  i. the right to reproduce, adapt, distribute, perform, display, communicate,
-  and translate a Work;
-
-  ii. moral rights retained by the original author(s) and/or performer(s);
-
-  iii. publicity and privacy rights pertaining to a person's image or likeness
-  depicted in a Work;
-
-  iv. rights protecting against unfair competition in regards to a Work,
-  subject to the limitations in paragraph 4(a), below;
-
-  v. rights protecting the extraction, dissemination, use and reuse of data in
-  a Work;
-
-  vi. database rights (such as those arising under Directive 96/9/EC of the
-  European Parliament and of the Council of 11 March 1996 on the legal
-  protection of databases, and under any national implementation thereof,
-  including any amended or successor version of such directive); and
-
-  vii. other similar, equivalent or corresponding rights throughout the world
-  based on applicable law or treaty, and any national implementations thereof.
-
-2. Waiver. To the greatest extent permitted by, but not in contravention of,
-applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and
-unconditionally waives, abandons, and surrenders all of Affirmer's Copyright
-and Related Rights and associated claims and causes of action, whether now
-known or unknown (including existing as well as future claims and causes of
-action), in the Work (i) in all territories worldwide, (ii) for the maximum
-duration provided by applicable law or treaty (including future time
-extensions), (iii) in any current or future medium and for any number of
-copies, and (iv) for any purpose whatsoever, including without limitation
-commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes
-the Waiver for the benefit of each member of the public at large and to the
-detriment of Affirmer's heirs and successors, fully intending that such Waiver
-shall not be subject to revocation, rescission, cancellation, termination, or
-any other legal or equitable action to disrupt the quiet enjoyment of the Work
-by the public as contemplated by Affirmer's express Statement of Purpose.
-
-3. Public License Fallback. Should any part of the Waiver for any reason be
-judged legally invalid or ineffective under applicable law, then the Waiver
-shall be preserved to the maximum extent permitted taking into account
-Affirmer's express Statement of Purpose. In addition, to the extent the Waiver
-is so judged Affirmer hereby grants to each affected person a royalty-free,
-non transferable, non sublicensable, non exclusive, irrevocable and
-unconditional license to exercise Affirmer's Copyright and Related Rights in
-the Work (i) in all territories worldwide, (ii) for the maximum duration
-provided by applicable law or treaty (including future time extensions), (iii)
-in any current or future medium and for any number of copies, and (iv) for any
-purpose whatsoever, including without limitation commercial, advertising or
-promotional purposes (the "License"). The License shall be deemed effective as
-of the date CC0 was applied by Affirmer to the Work. Should any part of the
-License for any reason be judged legally invalid or ineffective under
-applicable law, such partial invalidity or ineffectiveness shall not
-invalidate the remainder of the License, and in such case Affirmer hereby
-affirms that he or she will not (i) exercise any of his or her remaining
-Copyright and Related Rights in the Work or (ii) assert any associated claims
-and causes of action with respect to the Work, in either case contrary to
-Affirmer's express Statement of Purpose.
-
-4. Limitations and Disclaimers.
-
-  a. No trademark or patent rights held by Affirmer are waived, abandoned,
-  surrendered, licensed or otherwise affected by this document.
-
-  b. Affirmer offers the Work as-is and makes no representations or warranties
-  of any kind concerning the Work, express, implied, statutory or otherwise,
-  including without limitation warranties of title, merchantability, fitness
-  for a particular purpose, non infringement, or the absence of latent or
-  other defects, accuracy, or the present or absence of errors, whether or not
-  discoverable, all to the greatest extent permissible under applicable law.
-
-  c. Affirmer disclaims responsibility for clearing rights of other persons
-  that may apply to the Work or any use thereof, including without limitation
-  any person's Copyright and Related Rights in the Work. Further, Affirmer
-  disclaims responsibility for obtaining any necessary consents, permissions
-  or other rights required for any use of the Work.
-
-  d. Affirmer understands and acknowledges that Creative Commons is not a
-  party to this document and has no duty or obligation with respect to this
-  CC0 or use of the Work.
-
-For more information, please see
-<http://creativecommons.org/publicdomain/zero/1.0/>
+---
+layout: page
+title: "Licenses"
+root: .
+---
+## Instructional Material
+
+All Software Carpentry and Data 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
+license][cc-by-legal].
+
+You are free:
+
+* to **Share**---copy and redistribute the material in any medium or format
+* to **Adapt**---remix, transform, and build upon the material
+
+for any purpose, even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the
+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.
+
+**No additional restrictions**---You may not apply legal terms or
+technological measures that legally restrict others from doing
+anything the license permits.  With the understanding that:
+
+Notices:
+
+* You do not have to comply with the license for elements of the
+  material in the public domain or where your use is permitted by an
+  applicable exception or limitation.
+* No warranties are given. The license may not give you all of the
+  permissions necessary for your intended use. For example, other
+  rights such as publicity, privacy, or moral rights may limit how you
+  use the material.
+
+## Software
+
+Except where otherwise noted, the example programs and other software
+provided by Software Carpentry and Data Carpentry are made available under the
+[OSI][osi]-approved
+[MIT license][mit-license].
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+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.
+
+## Trademark
+
+"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
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[ci]: http://communityin.org/
+[osi]: https://opensource.org
+

Makefile

@@ -4,23 +4,29 @@
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
 JEKYLL=jekyll
+JEKYLL_VERSION=3.7.3
 PARSER=bin/markdown_ast.rb
 DST=_site
 
 # Controls
 .PHONY : commands clean files
+.NOTPARALLEL:
 all : commands
 
 ## commands         : show 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-rmd
+serve : lesson-md
 	${JEKYLL} serve
 
 ## site             : build files but do not run a server.
-site : lesson-rmd
+site : lesson-md
 	${JEKYLL} build
 
 # repo-check        : check repository settings.
@@ -53,7 +59,7 @@ workshop-check :
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
 
 # RMarkdown files
 RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
@@ -62,42 +68,41 @@ 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-rmd       : convert Rmarkdown files to markdown
-lesson-rmd: $(RMD_SRC)
-	@bin/knit_lessons.sh $(RMD_SRC)
+## 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}
 
 ## lesson-check     : validate lesson Markdown.
-lesson-check :
-	@bin/lesson_check.py -s . -p ${PARSER}
+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 :