common-workflow-language · mr-c · Oct 19, 2018 · May 25, 2018 · May 30, 2018 · May 30, 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/.gitignore b/.gitignore
@@ -5,3 +5,7 @@
 .sass-cache
 __pycache__
 _site
+.Rproj.user
+.Rhistory
+.RData
+
diff --git a/.zenodo.json b/.zenodo.json
@@ -7,12 +7,12 @@
     "creators": [
         {
             "affiliation": "European Molecular Biology Laboratory",
-            "orcid": "http://orcid.org/0000-0003-1766-456X",
+            "orcid": "https://orcid.org/0000-0003-1766-456X",
             "name": "Toby Hodges"
         },
         {
             "affiliation": "Common Workflow Language project",
-            "orcid": "http://orcid.org/0000-0002-2961-9670",
+            "orcid": "https://orcid.org/0000-0002-2961-9670",
             "name": "Michael R. Crusoe"
         }
     ],

diff --git a/AUTHORS b/AUTHORS
diff --git a/CITATION b/CITATION
@@ -11,7 +11,7 @@ https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 
 @data{cwl,
   doi = {10.6084/m9.figshare.3115156.v2},
-  url = {http://dx.doi.org/10.6084/m9.figshare.3115156.v2},
+  url = {https://doi.org/10.6084/m9.figshare.3115156.v2},
   author = {Peter Amstutz; Michael R. Crusoe; Nebojša Tijanić; Brad Chapman;
 John Chilton; Michael Heuer; Andrey Kartashov; John Kern; Dan Leehr;
 Hervé Ménager; Maya Nedeljkovich; Matt Scales; Stian Soiland-Reyes;

diff --git a/CONDUCT.md → CODE_OF_CONDUCT.md b/CONDUCT.md → 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 respect all people who contribute through reporting issues,
@@ -10,8 +9,16 @@ updating documentation,
 submitting pull requests or patches,
 and other activities.
 
-The CWL Project is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form.
+The CWL Project is dedicated to providing a harassment-free experience for
+everyone, regardless of gender, gender identity and expression, sexual
+orientation, disability, physical appearance, body size, age, race, or religion.
+We do not tolerate harassment of participants in any form.
 
-This code of conduct applies to all CWL Project spaces, including the Google Group, the Gitter chat room, the Google Hangouts chats, both online and off. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the leadership team.
+This code of conduct applies to all CWL Project spaces, including the Google
+Group, the Gitter chat room, the Google Hangouts chats, both online and off.
+Anyone who violates this code of conduct may be sanctioned or expelled from
+these spaces at the discretion of the leadership team.
 
 For more details, see the [complete CWL project code of conduct](https://github.com/common-workflow-language/common-workflow-language/blob/master/CODE_OF_CONDUCT.md).
+
+{% include links.md %}
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -27,7 +27,7 @@ This is a good way to introduce yourself
 and to meet some of our community members.
 
 1.  If you do not have a [GitHub][github] account,
-    you can [send us comments by email][contact].
+    you can [send us comments by email][discuss-list].
     However,
     we will be able to respond more quickly if you use one of the other methods described below.
 
@@ -47,24 +47,29 @@ and to meet some of our community members.
 
 1.  If you wish to change this lesson,
     please work in <https://github.com/common-workflow-language/user_guide>,
-    which can be viewed at <http://www.commmonwl.org/user_guide/>.
+    which can be viewed at <https://www.commmonwl.org/user_guide/>.
 
 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 CSS style files, tools,
+3.  If you wish to change the template used for workshop websites,
+    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://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> if those changes are
-    generic or here if they are specific to the CWL user guide.
+    please work in <https://github.com/carpentries/styles>.
 
 ## What to Contribute
 
 There are many ways to contribute,
 from writing new exercises and improving existing ones
 to updating or filling in the documentation
-and and submitting [bug reports][issues]
+and submitting [bug reports][issues]
 about things that don't work, aren't clear, or are missing.
 If you are looking for ideas,
 please see [the list of issues for this repository][issues],
@@ -90,39 +95,36 @@ The first encourages contributors to be honest about requirements;
 the second, to think hard about priorities.
 
 We are also not looking for exercises or other material that only run on one platform.
-Our workshops typically contain a mixture of Windows, Mac OS X, and Linux users;
+Our workshops typically contain a mixture of Windows, macOS, and Linux users;
 in order to be usable,
 our lessons must run equally well on all three.
 -->
 ## Using GitHub
 
-If you choose to contribute via GitHub,
-you may want to look at
+If you choose to contribute via GitHub, you may want to look at
 [How to Contribute to an Open Source Project on GitHub][how-contribute].
-In brief:
-
-1.  The published copy of the lesson is in the `gh-pages` branch of the repository
-    (so that GitHub will regenerate it automatically).
-    Please create all branches from that,
-    and merge the [master repository][repo]'s `gh-pages` branch into your `gh-pages` branch
-    before starting work.
-    Please do *not* work directly in your `gh-pages` branch,
-    since that will make it difficult for you to work on other contributions.
-
-2.  We use [GitHub flow][github-flow] to manage changes:
-    1.  Create a new branch in your desktop copy of this repository for each significant change.
-    2.  Commit the change in that branch.
-    3.  Push that branch to your fork of this repository on GitHub.
-    4.  Submit a pull request from that branch to the [master repository][repo].
-    5.  If you receive feedback,
-        make changes on your desktop and push to your branch on GitHub:
-        the pull request will update automatically.
-3. Please add yourself to the authors file if you aren't already present: https://github.com/common-workflow-language/user_guide/blob/gh-pages/.zenodo.json
-
-Each lesson has two maintainers who review issues and pull requests
-or encourage others to do so.
-The maintainers are community volunteers,
-and have final say over what gets merged into the lesson.
+To manage changes, we follow [GitHub flow][github-flow].
+Each lesson has two maintainers who review issues and pull requests or encourage others to do so.
+The maintainers are community volunteers and have final say over what gets merged into the lesson.
+To use the web interface for contributing to a lesson:
+
+1.  Fork the originating repository to your GitHub profile.
+2.  Within your version of the forked repository, move to the `gh-pages` branch and
+create a new branch for each significant change being made.
+3.  Navigate to the file(s) you wish to change within the new branches and make revisions as required.
+4.  Commit all changed files within the appropriate branches.
+5.  Create individual pull requests from each of your changed branches
+to the `gh-pages` branch within the originating repository.
+6.  If you receive feedback, make changes using your issue-specific branches of the forked
+repository and the pull requests will update automatically.
+7.  Repeat as needed until all feedback has been addressed.
+
+When starting work, please make sure your clone of the originating `gh-pages` branch is up-to-date
+before creating your own revision-specific branch(es) from there.
+Additionally, please only work from your newly-created branch(es) and *not*
+your clone of the originating `gh-pages` branch.
+Lastly, published copies of all the lessons are available in the `gh-pages` branch of the originating
+repository for reference while revising.
 
 ## Other Resources
 
@@ -134,13 +136,13 @@ which everyone is welcome to join.
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/
 [discuss-list]: https://groups.google.com/forum/#!forum/common-workflow-language
-[github]: http://github.com
+[github]: https://github.com
 [github-flow]: https://guides.github.com/introduction/flow/
 [github-join]: https://github.com/join
 [how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
 [issues]: https://github.com/common-workflow-language/user_guide/issues
 [repo]: https://github.com/common-workflow-language/user_guide
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: http://software-carpentry.org/lessons/
-[swc-site]: http://software-carpentry.org/
-[cwl-site]: http://www.commonwl.org/
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
+[cwl-site]: https://www.commonwl.org/
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,7 +1,7 @@
 ---
 layout: page
 title: "Licenses"
-permalink: /license/
+root: .
 ---
 ## Instructional Material
 
@@ -30,7 +30,7 @@ Under the following terms:
 * **Attribution**---You must give appropriate credit (mentioning that
   your work is derived from work that is Copyright © the Common Workflow
   Language project, and Copyright © Software Carpentry, and, where practical, linking to
-  http://www.commonwl.org/ and http://software-carpentry.org/), provide a [link to the
+  https://www.commonwl.org/ and https://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.
@@ -65,10 +65,10 @@ limitations under the License.
 ## 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
 [apache-2.0-license]: https://opensource.org/licenses/Apache-2.0
-[numfocus]: http://numfocus.org/
-[osi]: http://opensource.org
+[ci]: http://communityin.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-*
 
@@ -63,7 +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 \
@@ -83,31 +88,20 @@ HTML_DST = \
 ## 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
-
-RUNNER=cwl-runner
-
-## unittest-examples: run unit tests for the examples
-unittest-examples :
-	cd _includes/cwl; cwltest --test=conformance-test.yml --tool=${RUNNER}
+	@bin/test_lesson_check.py
 
 ## lesson-files     : show expected names of generated files for debugging.
 lesson-files :

diff --git a/README.md b/README.md
@@ -2,15 +2,37 @@
 
 [![Syntax Check](https://travis-ci.org/common-workflow-language/user_guide.svg?branch=gh-pages)](https://travis-ci.org/common-workflow-language/user_guide)
 
-[User guide for CWL v1.0.1](http://www.commonwl.org/user_guide/)
+[User guide for CWL v1.0.2](https://www.commonwl.org/user_guide/)
 
 Original source:
 https://github.com/common-workflow-language/common-workflow-language/blob/a2a8a08b8c8d56f8f2ca6284ca4e9cbf23d19346/v1.0/UserGuide.yml
 
+## Contributing
+
+We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any
+questions, concerns, or experience any difficulties along the way.
 To edit the user guide:
 
+We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md) and have a look at
+the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
+how to write new episodes.
+
 - The text files for each tutorial can be found in the directory [_episodes](_episodes)
 
 - The cwl and yaml code files linked to each tutorial can be found in the directory [_includes/cwl](_includes/cwl)
 
 This repo is based upon https://github.com/swcarpentry/styles and should be periodically resynced.
+
+## Maintainer(s)
+
+* FIXME
+
+## Authors
+
+A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
+
+## Citation
+
+To cite this lesson, please consult with [CITATION](CITATION)
+
+[lesson-example]: https://carpentries.github.io/lesson-example