Merge pull request #1 from datacarpentry/gh-pages

Update from master

.gitignore

@@ -5,3 +5,8 @@
 .sass-cache
 __pycache__
 _site
+.Rproj.user
+.Rhistory
+.RData
+
+/Gemfile.lock

.zenodo.json

@@ -0,0 +1,90 @@
+{
+  "contributors": [
+    {
+      "type": "Editor",
+      "name": "Roselyn Lemus"
+    },
+    {
+      "type": "Editor",
+      "name": "Mateusz Kuzak",
+      "orcid": "0000-0003-0087-6021"
+    },
+    {
+      "type": "Editor",
+      "name": "Rayna Harris",
+      "orcid": "0000-0002-7943-5650"
+    },
+    {
+      "type": "Editor",
+      "name": "Peter Hoyt",
+      "orcid": "0000-0002-2767-0923"
+    }
+  ],
+  "creators": [
+    {
+      "name": "Peter R. Hoyt",
+      "orcid": "0000-0002-2767-0923"
+    },
+    {
+      "name": "Deborah Paul",
+      "orcid": "0000-0003-2639-7520"
+    },
+    {
+      "name": "Tracy Teal",
+      "orcid": "0000-0002-9180-9598"
+    },
+    {
+      "name": "Amanda Charbonneau",
+      "orcid": "0000-0001-7376-7702"
+    },
+    {
+      "name": "Erin Alison Becker",
+      "orcid": "0000-0002-6832-0233"
+    },
+    {
+      "name": "François Michonneau",
+      "orcid": "0000-0002-9092-966X"
+    },
+    {
+      "name": "Taylor Reiter",
+      "orcid": "0000-0002-7388-421X"
+    },
+    {
+      "name": "Rayna Michelle Harris",
+      "orcid": "0000-0002-7943-5650"
+    },
+    {
+      "name": "Toby Hodges",
+      "orcid": "0000-0003-1766-456X"
+    },
+    {
+      "name": "Jason Williams",
+      "orcid": "0000-0003-3049-2010"
+    },
+    {
+      "name": "Bérénice Batut",
+      "orcid": "0000-0001-9852-1987"
+    },
+    {
+      "name": "Kevin Weitemier",
+      "orcid": "0000-0002-5793-0343"
+    },
+    {
+      "name": "Laura Williams"
+    },
+    {
+      "name": "Daniel O. S. Ouso",
+      "orcid": "0000-0003-0994-2558"
+    },
+    {
+      "name": "Juan A. Ugalde"
+    },
+    {
+      "name": "Paula Andrea Martinez",
+      "orcid": "0000-0002-8990-1985"
+    }
+  ],
+  "license": {
+    "id": "CC-BY-4.0"
+  }
+}

CITATION

@@ -1 +1,6 @@
-FIXME: describe how to cite this lesson.
+Please cite as:
+
+Roselyn Lemus, Yujuan Gui, Mateusz Kuzak (eds): "Data Carpentry: Genomics Organization Lesson."
+Version 2017.11.0, November 2017,
+http://www.datacarpentry.org/organization-genomics/,
+doi: 10.5281/zenodo.1064242

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 %}

CONTRIBUTING.md

@@ -46,23 +46,23 @@ and to meet some of our community members.
 ## Where to Contribute
 
 1.  If you wish to change this lesson,
-    please work in <https://github.com/swcarpentry/FIXME>,
-    which can be viewed at <https://swcarpentry.github.io/FIXME>.
+    please work in <https://github.com/datacarpentry/organization-genomics>,
+    which can be viewed at <https://datacarpentry.github.io/organization-genomics>.
 
 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
 
@@ -129,7 +129,8 @@ The maintainers are community volunteers,
 and have final say over what gets merged into the lesson.
 
 ## Issues Labels
-What issue lables in this repository mean? Think if you can asign one of the below labels to your issue.
+
+What issue labels in this repository mean? Think if you can asign one of the below labels to your issue.
 This will help maintainers to decide how to act and should result in quicker response to the issues.
 If you don't assign the label to an issue it will be assigned by the maintainers.
 
@@ -163,8 +164,8 @@ You can also [reach us by email][contact].
 [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/swcarpentry/FIXME/issues/
-[repo]: https://github.com/swcarpentry/FIXME/
+[issues]: https://github.com/datacarpentry/organization-genomics/issues/
+[repo]: https://github.com/datacarpentry/organization-genomics
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: http://software-carpentry.org/lessons/
 [swc-site]: http://software-carpentry.org/

Gemfile

@@ -0,0 +1,2 @@
+source 'https://rubygems.org'
+gem 'github-pages', group: :jekyll_plugins

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

@@ -3,7 +3,8 @@
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=jekyll
+JEKYLL=bundle exec 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 :

README.md

@@ -1,2 +1,5 @@
+[![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://swc-slack-invite.herokuapp.com/) 
+[![Slack Status](https://img.shields.io/badge/Slack_Channel-dc--genomics-E01563.svg)](https://swcarpentry.slack.com/messages/C9N1K7DCY) 
+
 # organization-genomics
-Lesson on data organization and project setup for genomics
+Lesson on data organization and project setup for genomics.