added template files

.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

@@ -0,0 +1,7 @@
+*.pyc
+*~
+.DS_Store
+.ipynb_checkpoints
+.sass-cache
+__pycache__
+_site

CONDUCT.md

@@ -0,0 +1,45 @@
+---
+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,
+posting feature requests,
+updating documentation,
+submitting pull requests or patches,
+and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone,
+regardless of level of experience,
+gender,
+gender identity and expression,
+sexual orientation,
+disability,
+personal appearance,
+body size,
+race,
+ethnicity,
+age,
+or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery,
+derogatory comments or personal attacks,
+trolling,
+public or private harassment,
+insults,
+or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to our [Code of Conduct][coc].
+Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by following our [reporting guidelines][coc-reporting].
+
+
+- [Software and Data Carpentry Code of Conduct][coc]
+- [Code of Conduct Reporting Guide][coc-reporting]
+
+{% include links.md %}

LICENSE.md

@@ -1,42 +1,57 @@
-### Instructional Material
+---
+layout: page
+title: "Licenses"
+permalink: /license/
+---
+## Instructional Material
 
-All Data Carpentry instructional material is made available under
-the Creative Commons Attribution license. You are free:
+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].
 
-* to **Share**---to copy, distribute and transmit the work
-* to **Remix**---to adapt the work
+You are free:
 
-Under the following conditions:
+* to **Share**---copy and redistribute the material in any medium or format
+* to **Adapt**---remix, transform, and build upon the material
 
-* **Attribution**---You must attribute the work using "Copyright (c)
-  Data Carpentry" (but not in any way that suggests that we
-  endorse you or your use of the work).  Where practical, you must
-  also include a hyperlink to http://datacarpentry.org.
+for any purpose, even commercially.
 
-With the understanding that:
+The licensor cannot revoke these freedoms as long as you follow the
+license terms.
 
-* **Waiver**---Any of the above conditions can be waived if you get
-  permission from the copyright holder.
-* **Other Rights**---In no way are any of the following rights
-  affected by the license:
-    * Your fair dealing or fair use rights;
-    * The author's moral rights;
-    * Rights other persons may have either in the work itself or in
-      how the work is used, such as publicity or privacy rights.  *
-* **Notice**---For any reuse or distribution, you must make clear to
-  others the license terms of this work. The best way to do this is
-  with a link to
-  [http://creativecommons.org/licenses/by/3.0/](http://creativecommons.org/licenses/by/3.0/).
+Under the following terms:
 
-For the full legal text of this license, please see
-[http://creativecommons.org/licenses/by/3.0/legalcode](http://creativecommons.org/licenses/by/3.0/legalcode).
+* **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.
 
-### Software
+**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 Data Carpentry are made available under the
-[OSI](http://opensource.org)-approved
-[MIT license](http://opensource.org/licenses/mit-license.html).
+provided by Software Carpentry and Data Carpentry are made available under the
+[OSI][osi]-approved
+[MIT license][mit-license].
+>>>>>>> template/gh-pages
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
@@ -56,3 +71,17 @@ 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].
+
+[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
+

Makefile

@@ -0,0 +1,121 @@
+## ========================================
+## Commands for both workshop and lesson websites.
+
+# Settings
+MAKEFILES=Makefile $(wildcard *.mk)
+JEKYLL=jekyll
+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'
+
+## serve            : run a local server.
+serve : lesson-md
+	${JEKYLL} serve
+
+## site             : build files but do not run a server.
+site : lesson-md
+	${JEKYLL} build
+
+# repo-check        : check repository settings.
+repo-check :
+	@bin/repo_check.py -s .
+
+## clean            : clean up junk files.
+clean :
+	@rm -rf ${DST}
+	@rm -rf .sass-cache
+	@rm -rf bin/__pycache__
+	@find . -name .DS_Store -exec rm {} \;
+	@find . -name '*~' -exec rm {} \;
+	@find . -name '*.pyc' -exec rm {} \;
+
+## clean-rmd        : clean intermediate R files (that need to be committed to the repo).
+clear-rmd :
+	@rm -rf ${RMD_DST}
+	@rm -rf fig/rmd-*
+
+## ----------------------------------------
+## Commands specific to workshop websites.
+
+.PHONY : workshop-check
+
+## workshop-check   : check workshop homepage.
+workshop-check :
+	@bin/workshop_check.py .
+
+## ----------------------------------------
+## Commands specific to lesson websites.
+
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+
+# RMarkdown files
+RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
+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 \
+  setup.md \
+  $(wildcard _episodes/*.md) \
+  reference.md \
+  $(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)) \
+  ${DST}/reference/index.html \
+  $(patsubst _extras/%.md,${DST}/%/index.html,$(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}
+
+## lesson-check     : validate lesson Markdown.
+lesson-check :
+	@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
+
+## unittest         : run unit tests on checking tools.
+unittest :
+	python bin/test_lesson_check.py
+
+## lesson-files     : show expected names of generated files for debugging.
+lesson-files :
+	@echo 'RMD_SRC:' ${RMD_SRC}
+	@echo 'RMD_DST:' ${RMD_DST}
+	@echo 'MARKDOWN_SRC:' ${MARKDOWN_SRC}
+	@echo 'HTML_DST:' ${HTML_DST}
+
+## lesson-fixme     : show FIXME markers embedded in source files.
+lesson-fixme :
+	@fgrep -i -n FIXME ${MARKDOWN_SRC} || true
+
+#-------------------------------------------------------------------------------
+# Include extra commands if available.
+#-------------------------------------------------------------------------------
+
+-include commands.mk

_includes/all_keypoints.html

@@ -0,0 +1,22 @@
+{% comment %}
+  Display key points of all episodes for reference.
+{% endcomment %}
+<h2>Key Points</h2>
+<table class="table table-striped">
+{% for episode in site.episodes %}
+  {% unless episode.break %}
+    <tr>
+      <td class="col-md-3">
+        <a href="{{ page.root }}{{ episode.url }}">{{ episode.title }}</a>
+      </td>
+      <td class="col-md-9">
+        <ul>
+        {% for keypoint in episode.keypoints %}
+        <li>{{ keypoint|markdownify }}</li>
+        {% endfor %}
+        </ul>
+      </td>
+    </tr>
+  {% endunless %}
+{% endfor %}
+</table>

_includes/carpentries.html

@@ -0,0 +1,44 @@
+{% comment %}
+  General description of Software and Data Carpentry.
+{% endcomment %}
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.swc_site }}"><img src="{{ page.root }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    Since 1998,
+    <a href="{{ site.swc_site }}">Software Carpentry</a>
+    has been teaching researchers in science, engineering, medicine, and related disciplines
+    the computing skills they need to get more done in less time and with less pain.
+    Its volunteer instructors have run hundreds of events
+    for thousands of learners in the past two and a half years.
+  </div>
+</div>
+<br/>
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.dc_site }}"><img src="{{ page.root }}/assets/img/dc-icon-black.svg" alt="Data Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    <a href="{{ site.dc_site }}">Data Carpentry</a> develops and teaches workshops on the fundamental data skills needed to conduct research.
+    Its target audience is researchers who have little to no prior computational experience,
+    and its lessons are domain specific,
+    building on learners' existing knowledge to enable them to quickly apply skills learned to their own research.
+  </div>
+</div>
+<br/>
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.lc_site }}"><img src="{{ page.root }}/assets/img/lc-icon-black.svg" alt="Library Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    Library Carpentry is made by librarians to help librarians
+    automate repetitive, boring, error-prone tasks;
+    create, maintain and analyse sustainable and reusable data;
+    work effectively with IT and systems colleagues;
+    better understand the use of software in research;
+    and much more.
+    Library Carpentry was the winner of the 2016
+    <a href="http://labs.bl.uk/British+Library+Labs+Awards">British Library Labs Teaching and Learning Award</a>.
+  </div>
+</div>

_includes/dc/intro.html

@@ -0,0 +1,18 @@
+<p>
+  <a href="{{site.dc_site}}">Data Carpentry</a>
+  aims to help researchers get their work done
+  in less time and with less pain
+  by teaching them basic research computing skills.
+  This hands-on workshop will cover basic concepts and tools,
+  including program design, version control, data management,
+  and task automation.
+  Participants will be encouraged to help one another
+  and to apply what they have learned to their own research problems.
+</p>
+<p align="center">
+  <em>
+    For more information on what we teach and why,
+    please see our paper
+    "<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">Best Practices for Scientific Computing</a>".
+  </em>
+</p>