--- /dev/null
+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
__pycache__
_site
.Rproj.user
+.Rhistory
+.RData
+
---
layout: page
title: "Contributor Code of Conduct"
-permalink: /conduct/
---
As contributors and maintainers of this project,
we pledge to follow the [Carpentry Code of Conduct][coc].
# Settings
MAKEFILES=Makefile $(wildcard *.mk)
JEKYLL=jekyll
+JEKYLL_VERSION=3.7.3
PARSER=bin/markdown_ast.rb
DST=_site
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
@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-*
## 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-fixme
{% comment %}
Display key points of all episodes for reference.
{% endcomment %}
+
+{% include base_path.html %}
+
<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>
+ <a href="{{ relative_root_path }}{{ episode.url }}">{{ episode.title }}</a>
</td>
<td class="col-md-9">
<ul>
--- /dev/null
+{% comment %}
+This is adapted from: https://ricostacruz.com/til/relative-paths-in-jekyll
+
+`page.url` gives the URL of the current page with a leading /:
+
+- when the URL ends with the extension (e.g., /foo/bar.html) then we can get
+ the depth by counting the number of / and remove - 1
+- when the URL ends with a / (e.g. /foo/bar/) then the number / gives the depth
+ directly
+{% endcomment %}
+
+{% assign relative_root_path = '' %}
+
+{% assign last_char = page.url | slice: -1 %}
+
+{% if last_char == "/"}
+{% assign offset = 0 %}
+{% else %}
+{% assign offset = 1 %}
+{% endif %}
+
+{% assign depth = page.url | split: '/' | size | minus: offset %}
+{% if depth <= 1 %}{% assign relative_root_path = '.' %}
+{% elsif depth == 2 %}{% assign relative_root_path = '..' %}
+{% elsif depth == 3 %}{% assign relative_root_path = '../..' %}
+{% elsif depth == 4 %}{% assign relative_root_path = '../../..' %}
+{% endif %}
{% comment %}
General description of Software and Data Carpentry.
{% endcomment %}
+
+{% include base_path.html %}
+
<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>
+ <a href="{{ site.carpentries_site }}"><img src="{{ relative_root_path }}/assets/img/cp-logo-blue.svg" alt="The Carpentries 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.
+ <p><a href="{{ site.carpentries_site }}">The Carpentries</a> comprises
+ Software Carpentry and Data Carpentry, communities of Instructors, Trainers,
+ Maintainers, helpers, and supporters who share a mission to teach
+ foundational coding and data science skills to researchers. In January,
+ 2018, The Carpentries was formed by the merger of Software Carpentry and
+ Data Carpentry.</p>
+
+ <p>While individual lessons and workshops continue to be run under each
+ lesson project, The Carpentries provide overall staffing and governance, as
+ well as support for assessment, instructor training and mentoring.
+ Memberships are joint, and the Carpentries project maintains a shared Code
+ of Conduct. The Carpentries is a fiscally sponsored project of Community
+ Initiatives, a registered 501(c)3 non-profit based in California, USA.</p>
+ </div>
+</div>
+<div class="row">
+ <div class="col-md-2" align="center">
+ <a href="{{ site.swc_site }}"><img src="{{ relative_root_path }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" /></a>
+ </div>
+ <div class="col-md-8">
+ <p>Since 1998, <a href="{{ site.swc_site }}">Software Carpentry</a> has
+ been teaching researchers across all disciplines the foundational coding
+ 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
+ around the world. Now that all research involves some degree of
+ computational work, whether with big data, cloud computing, or simple task
+ automation, these skills are needed more than ever.</p>
</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>
+ <a href="{{ site.dc_site }}"><img src="{{ relative_root_path }}/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.
+ <p><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. Data Carpentry workshops take researchers through the entire
+ data life cycle.</p>
</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.png" alt="Library Carpentry logo" /></a>
+ <a href="{{ site.lc_site }}"><img src="{{ relative_root_path }}/assets/img/lc-icon-black.png" alt="Library Carpentry logo" /></a>
</div>
<div class="col-md-8">
- <a href="{{ site.lc_site }}">Library Carpentry</a> 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>.
+ <p><a href="{{ site.lc_site }}">Library Carpentry</a> is in discussions with
+ The Carpentries to be a Lesson Project, like Software Carpentry*
+ and Data Carpentry. Library Carpentry develops lessons and
+ teaches workshops for and with people working in library- and
+ information-related roles. Its goal is to create an on-ramp to empower this
+ community to use software and data in their own work, as well as be
+ advocates for and train others in efficient, effective and reproducible data
+ and software practices.</p>
</div>
</div>
+{% comment %}
+For some reason, the relative_root_path seems out of scope in this file, so we
+need to re-assign it here
+{% endcomment %}
+
+{% include base_path.html %}
+
{% comment %}
Navigation bar for an episode.
{% endcomment %}
+
<div class="row">
<div class="col-xs-1">
<h3 class="text-left">
{% if page.previous.url %}
- <a href="{{ page.root }}{{ page.previous.url }}"><span class="glyphicon glyphicon-menu-left" aria-hidden="true"></span><span class="sr-only">previous episode</span></a>
+ <a href="{{ relative_root_path }}{{ page.previous.url }}"><span class="glyphicon glyphicon-menu-left" aria-hidden="true"></span><span class="sr-only">previous episode</span></a>
{% else %}
- <a href="{{ page.root }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
+ <a href="{{ relative_root_path }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
{% endif %}
</h3>
</div>
<div class="col-xs-10">
{% if include.episode_navbar_title %}
- <h3 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a></h3>
+ <h3 class="maintitle"><a href="{{ relative_root_path }}/">{{ site.title }}</a></h3>
{% endif %}
</div>
<div class="col-xs-1">
<h3 class="text-right">
{% if page.next.url %}
- <a href="{{ page.root }}{{ page.next.url }}"><span class="glyphicon glyphicon-menu-right" aria-hidden="true"></span><span class="sr-only">next episode</span></a>
+ <a href="{{ relative_root_path }}{{ page.next.url }}"><span class="glyphicon glyphicon-menu-right" aria-hidden="true"></span><span class="sr-only">next episode</span></a>
{% else %}
- <a href="{{ page.root }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
+ <a href="{{ relative_root_path }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
{% endif %}
</h3>
</div>
-{% assign favicon_url = site.baseurl | append: '/assets/favicons/' | append: site.carpentry | prepend: site.url %}
+{% assign favicon_url = relative_root_path | append: '/assets/favicons/' | append: site.carpentry %}
{% if site.carpentry == 'swc' %}
{% assign carpentry = 'Software Carpentry' %}
--- /dev/null
+{% comment %}
+When rendering websites locally, `site.github.url` doesn't get resolved properly
+unless a GitHub Personal Access Token is set up and available in the
+environment. This leads to warnings and errors when trying to serve the site
+locally. To work around this, we use the `jekyll.environment` variable which is
+set to `development` when rendering the site locally, and set to `production` on
+GitHub where `site.github.url` is defined.
+{% endcomment %}
+
+{% if jekyll.environment == "production" %}
+
+{% comment %}
+First, get the name of the repository
+{% endcomment %}
+{% assign repo_name = site.github.repository_name %}
+
+{% comment %}
+`site.github.public_repositories` contains comprehensive information for all public repositories for the organization. We use `where` to extract the part
+of the metadata that is relevant to the present repository.
+{% endcomment %}
+{% assign repo_info = site.github.public_repositories | where: "name", repo_name %}
+
+{% comment %}
+Now, we can extract the default branch for the repo
+{% endcomment %}
+{% assign default_branch = repo_info[0].default_branch %}
+
+{% comment %}
+Other variables requested by the template
+{% endcomment %}
+{% assign repo_url = site.github.repository_url %}
+{% assign search_domain_url = site.github.url %}
+{% assign project_title = site.github.project_title %}
+{% assign source_branch = site.github.source.branch %}
+
+{% elsif jekyll.environment == "development" %}
+
+{% assign repo_name = "" %}
+{% assign repo_url = "" %}
+{% assign default_branch = "" %}
+{% assign search_domain_url = "" %}
+{% assign project_title = "" %}
+{% assign source_branch = "" %}
+
+{% endif %}
{% comment %}
- Javascript used in lesson and workshop pages.
+ JavaScript used in lesson and workshop pages.
{% endcomment %}
-<script src="{{ page.root }}/assets/js/jquery.min.js"></script>
-<script src="{{ page.root }}/assets/js/bootstrap.min.js"></script>
-<script src="{{ page.root }}/assets/js/lesson.js"></script>
+<script src="{{ relative_root_path }}/assets/js/jquery.min.js"></script>
+<script src="{{ relative_root_path }}/assets/js/bootstrap.min.js"></script>
+<script src="{{ relative_root_path }}/assets/js/lesson.js"></script>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
</p>
<ul>
<li>automate repetitive, boring, error-prone tasks</li>
- <li>create, maintain and analyse sustainable and reusable data</li>
+ <li>create, maintain and analyze sustainable and reusable data</li>
<li>work effectively with IT and systems colleagues</li>
<li>better understand the use of software in research</li>
<li>and much more...</li>
{% comment %}
Footer for lesson pages.
{% endcomment %}
+
+{% include gh_variables.html %}
+
<footer>
<div class="row">
<div class="col-md-6 copyright" align="left">
{% if site.carpentry == "swc" %}
- Copyright © 2018–{{ 'now' | date: "%Y" }}
- <a href="{{ site.carpentries_site }}">The Carpentries</a>
+ Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
+
by <a href="{{ site.carpentries_site }}">The Carpentries</a>
<br>
- Copyright © 2016–2018
- <a href="{{ site.swc_site }}">Software Carpentry Foundation</a>
+ Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
+
by <a href="{{ site.swc_site }}">Software Carpentry Foundation</a>
{% elsif site.carpentry == "dc" %}
- Copyright © 2018–{{ 'now' | date: "%Y" }}
- <a href="{{ site.carpentries_site }}">The Carpentries</a>
+ Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
+
by <a href="{{ site.carpentries_site }}">The Carpentries</a>
<br>
- Copyright © 2016–2018
- <a href="{{ site.dc_site }}">Data Carpentry</a>
+ Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
+
by <a href="{{ site.dc_site }}">Data Carpentry</a>
{% elsif site.carpentry == "lc" %}
- Copyright © 2016–{{ 'now' | date: "%Y" }}
- <a href="{{ site.lc_site }}">Library Carpentry</a>
+ Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–{{ 'now' | date: "%Y" }}
+
by <a href="{{ site.lc_site }}">Library Carpentry</a>
{% elsif site.carpentry == "cp" %}
- Copyright © 2018–{{ 'now' | date: "%Y" }}
- <a href="{{ site.carpentries_site }}">The Carpentries</a>
+ Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
+
by <a href="{{ site.carpentries_site }}">The Carpentries</a>
{% endif %}
</div>
<div class="col-md-6 help-links" align="right">
{% if page.source %}
{% if page.source == "Rmd" %}
- <a href="{{site.github.repository_url}}/edit/gh-pages/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}">Edit on GitHub</a>
+ <a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}">Edit on GitHub</a>
{% endif %}
{% else %}
- <a href="{{site.github.repository_url}}/edit/gh-pages/{{page.path}}">Edit on GitHub</a>
+ <a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}">Edit on GitHub</a>
{% endif %}
/
- <a href="{{ site.github.repository_url }}/blob/gh-pages/CONTRIBUTING.md">Contributing</a>
+ <a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md">Contributing</a>
/
- <a href="{{ site.github.repository_url }}/">Source</a>
+ <a href="{{ repo_url }}/">Source</a>
/
- <a href="{{ site.github.repository_url }}/blob/gh-pages/CITATION">Cite</a>
+ <a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION">Cite</a>
/
<a href="mailto:{{ site.email }}">Contact</a>
</div>
</div>
<div class="row">
<div class="col-md-12" align="center">
- Using <a href="https://github.com/swcarpentry/styles/">The Carpentries style</a>
- version <a href="https://github.com/swcarpentry/styles/releases/tag/v9.5.0">9.5.0</a>.
+ Using <a href="https://github.com/carpentries/styles/">The Carpentries style</a>
+ version <a href="https://github.com/carpentries/styles/releases/tag/v9.5.3">9.5.3</a>.
</div>
</div>
</footer>
--- /dev/null
+
+{% if site.life_cycle == "pre-alpha" %}
+
+<div class="panel panel-default life-cycle">
+ <div id="life-cycle" class="panel-body pre-alpha">
+ This lesson is still being designed and assembled (Pre-Alpha version)
+ </div>
+</div>
+
+
+{% elsif site.life_cycle == "alpha" %}
+
+<div class="panel panel-default life-cycle">
+ <div id="life-cycle" class="panel-body alpha">
+ This lesson is in the early stages of development (Alpha version)
+ </div>
+</div>
+
+
+{% elsif site.life_cycle == "beta" %}
+
+<div class="panel panel-default life-cycle">
+ <div id="life-cycle" class="panel-body beta">
+ This lesson is being piloted (Beta version)
+ </div>
+</div>
+
+{% elsif site.life_cycle == "stable" %}
+
+{% comment %}
+We don't do anything special for now
+{% endcomment %}
+
+{% endif %}
+{% include gh_variables.html %}
+
[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
[ci]: http://communityin.org/
[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
[concept-maps]: https://carpentries.github.io/instructor-training/05-memory/
[contrib-covenant]: https://contributor-covenant.org/
-[contributing]: {{ site.github.repository_url }}/blob/gh-pages/CONTRIBUTING.md
+[contributing]: {{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md
[cran-checkpoint]: https://cran.r-project.org/package=checkpoint
[cran-knitr]: https://cran.r-project.org/package=knitr
[cran-stringr]: https://cran.r-project.org/package=stringr
-[email]: mailto:lessons@software-carpentry.org
+[dc-lessons]: http://www.datacarpentry.org/lessons/
+[email]: mailto:team@carpentries.org
[github-importer]: https://import.github.com/
[importer]: https://github.com/new/import
[jekyll-collection]: https://jekyllrb.com/docs/collections/
[jekyll-windows]: http://jekyll-windows.juthilo.com/
[jekyll]: https://jekyllrb.com/
[jupyter]: https://jupyter.org/
-[lesson-example]: https://swcarpentry.github.io/lesson-example/
+[lc-lessons]: https://librarycarpentry.org/#portfolio
+[lesson-example]: https://carpentries.github.io/lesson-example/
[mit-license]: https://opensource.org/licenses/mit-license.html
[morea]: https://morea-framework.github.io/
[numfocus]: https://numfocus.org/
[ruby-install-guide]: https://www.ruby-lang.org/en/downloads/
[ruby-installer]: https://rubyinstaller.org/
[rubygems]: https://rubygems.org/pages/download/
-[styles]: https://github.com/swcarpentry/styles/
+[styles]: https://github.com/carpentries/styles/
+[swc-lessons]: https://software-carpentry.org/lessons/
[swc-releases]: https://github.com/swcarpentry/swc-releases
[workshop-repo]: {{ site.workshop_repo }}
[yaml]: http://yaml.org/
{% comment %}
Main title for lesson pages.
{% endcomment %}
-<h1 class="maintitle"><a href="{{ page.root }}{% link index.md %}">{{ site.title }}</a>{% if page.title %}: {{ page.title }}{% endif %}</h1>
+
+{% include base_path.html %}
+
+<h1 class="maintitle"><a href="{{ relative_root_path }}{% link index.md %}">{{ site.title }}</a>{% if page.title %}: {{ page.title }}{% endif %}</h1>
{% comment %}
Lesson navigation bar.
{% endcomment %}
+
+{% include gh_variables.html %}
+
<nav class="navbar navbar-default">
<div class="container-fluid">
<div class="navbar-header">
{% comment %} Select what logo to display. {% endcomment %}
{% if site.carpentry == "swc" %}
<a href="{{ site.swc_site }}" class="pull-left">
- <img class="navbar-logo" src="{{ page.root }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" />
+ <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/swc-icon-blue.svg %}" alt="Software Carpentry logo" />
</a>
{% elsif site.carpentry == "dc" %}
<a href="{{ site.dc_site }}" class="pull-left">
- <img class="navbar-logo" src="{{ page.root }}/assets/img/dc-icon-black.svg" alt="Data Carpentry logo" />
+ <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/dc-icon-black.svg %}" alt="Data Carpentry logo" />
</a>
{% elsif site.carpentry == "lc" %}
<a href="{{ site.lc_site }}" class="pull-left">
- <img class="navbar-logo" src="{{ page.root }}/assets/img/lc-icon-black.svg" alt="Library Carpentry logo" />
+ <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/lc-icon-black.svg %}" alt="Library Carpentry logo" />
</a>
{% elsif site.carpentry == "cp" %}
<a href="{{ site.carpentries_site }}" class="pull-left">
- <img class="navbar-logo" src="{{ page.root }}/assets/img/cp-logo-blue.svg" alt="The Carpentries logo" />
+ <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/cp-logo-blue.svg %}" alt="The Carpentries logo" />
</a>
{% endif %}
{% comment %} Always show link to home page. {% endcomment %}
- <a class="navbar-brand" href="{{ page.root }}{% link index.md %}">Home</a>
+ <a class="navbar-brand" href="{{ relative_root_path }}{% link index.md %}">Home</a>
</div>
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav">
{% comment %} Always show code of conduct. {% endcomment %}
- <li><a href="{{ page.root }}{% link CODE_OF_CONDUCT.md %}">Code of Conduct</a></li>
+ <li><a href="{{ relative_root_path }}{% link CODE_OF_CONDUCT.md %}">Code of Conduct</a></li>
{% if site.kind == "lesson" %}
{% comment %} Show setup instructions. {% endcomment %}
- <li><a href="{{ page.root }}{% link setup.md %}">Setup</a></li>
+ <li><a href="{{ relative_root_path }}{% link setup.md %}">Setup</a></li>
{% comment %} Show lesson episodes for lessons. {% endcomment %}
<li class="dropdown">
- <a href="{{ page.root }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Episodes <span class="caret"></span></a>
+ <a href="{{ relative_root_path }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Episodes <span class="caret"></span></a>
<ul class="dropdown-menu">
{% for episode in site.episodes %}
- <li><a href="{{ page.root }}{{ episode.url }}">{{ episode.title }}</a></li>
+ <li><a href="{{ relative_root_path }}{{ episode.url }}">{{ episode.title }}</a></li>
{% endfor %}
<li role="separator" class="divider"></li>
- <li><a href="{{ page.root }}{% link aio.md %}">All in one page (Beta)</a></li>
+ <li><a href="{{ relative_root_path }}{% link aio.md %}">All in one page (Beta)</a></li>
</ul>
</li>
{% endif %}
{% comment %} Show extras for lessons or if this is the main workshop-template repo (where they contain documentation). {% endcomment %}
{% if site.kind == "lesson" %}
<li class="dropdown">
- <a href="{{ page.root }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Extras <span class="caret"></span></a>
+ <a href="{{ relative_root_path }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Extras <span class="caret"></span></a>
<ul class="dropdown-menu">
- <li><a href="{{ page.root }}{% link reference.md %}">Reference</a></li>
+ <li><a href="{{ relative_root_path }}{% link reference.md %}">Reference</a></li>
{% for extra in site.extras %}
- <li><a href="{{ page.root }}{{ extra.url }}">{{ extra.title }}</a></li>
+ <li><a href="{{ relative_root_path }}{{ extra.url }}">{{ extra.title }}</a></li>
{% endfor %}
</ul>
</li>
{% endif %}
{% comment %} Always show license. {% endcomment %}
- <li><a href="{{ page.root }}{% link LICENSE.md %}">License</a></li>
+ <li><a href="{{ relative_root_path }}{% link LICENSE.md %}">License</a></li>
{% if page.source %}
{% if page.source == "Rmd" %}
- <li><a href="{{site.github.repository_url}}/edit/gh-pages/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}">Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
+ <li><a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}">Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
{% endif %}
{% else %}
- <li><a href="{{site.github.repository_url}}/edit/gh-pages/{{page.path}}">Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
+ <li><a href="{{repo_url}}/edit/{{ default_branch}}/{{page.path}}">Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
{% endif %}
</ul>
<form class="navbar-form navbar-right" role="search" id="search" onsubmit="google_search(); return false;">
+{% include base_path.html %}
+
{% comment %}
Display syllabus in tabular form.
Days are displayed if at least one episode has 'start = true'.
<tr>
{% if multiday %}<td class="col-md-1"></td>{% endif %}
<td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}"></td>
- <td class="col-md-3"><a href="{{ page.root }}{% link setup.md %}">Setup</a></td>
+ <td class="col-md-3"><a href="{{ relative_root_path }}{% link setup.md %}">Setup</a></td>
<td class="col-md-7">Download files required for the lesson</td>
</tr>
{% for episode in site.episodes %}
<td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
<td class="col-md-3">
{% assign lesson_number = lesson_number | plus: 1 %}
- {{ lesson_number }}. <a href="{{ page.root }}{{ episode.url }}">{{ episode.title }}</a>
+ {{ lesson_number }}. <a href="{{ relative_root_path }}{{ episode.url }}">{{ episode.title }}</a>
</td>
<td class="col-md-7">
{% if episode.break %}
--- /dev/null
+<a href="//calendar.google.com/calendar/render?action=TEMPLATE&text={% if page.carpentry == "swc" %}Software{% elsif page.carpentry == "dc" %}Data{% endif %} Carpentry Workshop&dates={{ page.startdate | replace: "-", "" }}/{{ page.enddate | replace: "-", "" | plus: 0}}&trp=false&sprop&sprop=name:&sf=true&output=xml&location={{ page.address }}&details={% if page.carpentry == "swc" %}Software{% elsif page.carpentry == "dc" %}Data{% endif %} Carpentry Workshop at {{ page.venue }}">Add to your Google Calendar.</a>
---
---
+{% include base_path.html %}
+{% include gh_variables.html %}
+
<!doctype html>
<html lang="en">
<head>
<meta http-equiv="last-modified" content="{{ site.time }}">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!-- meta "search-domain" used for google site search function google_search() -->
- <meta name="search-domain" value="{{ site.github.url }}">
- <link rel="stylesheet" type="text/css" href="{{ page.root }}/assets/css/bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="{{ page.root }}/assets/css/bootstrap-theme.css" />
- <link rel="stylesheet" type="text/css" href="{{ page.root }}/assets/css/lesson.css" />
- <link rel="stylesheet" type="text/css" href="{{ page.root }}/assets/css/syntax.css" />
+ <meta name="search-domain" value="{{ search_domain_url }}">
+ <link rel="stylesheet" type="text/css" href="{{ relative_root_path }}/assets/css/bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="{{ relative_root_path }}/assets/css/bootstrap-theme.css" />
+ <link rel="stylesheet" type="text/css" href="{{ relative_root_path }}/assets/css/lesson.css" />
+ <link rel="stylesheet" type="text/css" href="{{ relative_root_path }}/assets/css/syntax.css" />
{% include favicons.html %}
<title>{{ site.title }}{% if page.title %}: {{ page.title }}{% endif %}</title>
</head>
<body>
+
+ {% include life_cycle.html %}
+
<div class="container">
{% include navbar.html %}
{{ content }}
layout: base
---
{% include main_title.html %}
-{{ content }}
+<article>
+ {{ content }}
+</article>
{% include syllabus.html %}
layout: base
---
{% include main_title.html %}
+<article>
{{content}}
+</article>
---
---
+{% include base_path.html %}
+{% include gh_variables.html %}
+
<!doctype html>
<html lang="en">
<head>
- <meta name="slug" content="{{site.github.project_title}}" />
+ <meta name="slug" content="{{project_title}}" />
<meta name="startdate" content="{{page.startdate}}" />
<meta name="enddate" content="{{page.enddate}}" />
<meta name="humandate" content="{{page.humandate}}" />
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta http-equiv="last-modified" content="{{ site.time }}">
<meta name="viewport" content="width=device-width, initial-scale=1">
- <link rel="stylesheet" type="text/css" href="{{ page.root }}/assets/css/bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="{{ page.root }}/assets/css/bootstrap-theme.css" />
- <link rel="stylesheet" type="text/css" href="{{ page.root }}/assets/css/lesson.css" />
+ <link rel="stylesheet" type="text/css" href="{{ relative_root_path }}/assets/css/bootstrap.css" />
+
+ <link rel="stylesheet" type="text/css" href="{{ relative_root_path }}/assets/css/bootstrap-theme.css" />
+ <link rel="stylesheet" type="text/css" href="{{ relative_root_path }}/assets/css/lesson.css" />
{% include favicons.html %}
//----------------------------------------
@mixin cdSetup($color) {
- color: $color;
- border-left: solid 5px $color;
- margin-bottom: 0px;
- border-radius: 4px 0 0 4px;
+ color: $color;
+ border-left: solid 5px $color;
+ margin: 15px 0;
+ border-radius: 4px 0 0 4px;
}
.error { @include cdSetup($color-error); }
.matlab, .language-matlab { @include cdSetup($color-source); }
.python, .language-python { @include cdSetup($color-source); }
.r, .language-r { @include cdSetup($color-source); }
-.sql, .langauge-sql { @include cdSetup($color-source); }
+.sql, .language-sql { @include cdSetup($color-source); }
.error pre,
.output pre,
padding-right: 0;
border: 1px solid;
border-color: $color;
+ border-radius: 4px;
padding-bottom: $codeblock-padding;
+ margin: 15px 0;
+
h2 {
padding-top: $codeblock-padding;
padding-bottom: $codeblock-padding;
font-size: 18px;
}
+blockquote p {
+ margin: 5px;
+}
+
//----------------------------------------
// Override Bootstrap settings.
//----------------------------------------
background-color: #e7e7e7;
}
-img {
- max-width: 100%;
+article img {
+ display: block;
+ margin: 20px auto;
+ max-width: 100%;
+}
+
+article h2 {
+ margin: 48px 0 16px;
+ border-bottom: solid 1px #eaecef;
+ padding-bottom: 0.3em;
+ line-height: 1.25;
}
+article h3 { margin: 40px 0 16px; }
+
//----------------------------------------
// Miscellaneous.
//----------------------------------------
+.figures h2 { margin-top: 100px; }
+
.maintitle {
text-align: center;
}
footer .copyright,
footer .help-links
{
- font-size: 18px;
+ font-size: inherit;
margin-top: 10px;
margin-bottom: 10px;
font-weight: 500;
}
+//----------------------------------------
+// Life cycle box
+//----------------------------------------
+
+div.life-cycle {
+ position: -webkit-sticky; /* Safari */
+ position: sticky;
+ top: 0;
+ z-index: 100;
+ font-size: 1.2em;
+ text-align: center;
+ margin-bottom: -1px;
+ border-radius: 0;
+}
+
+.pre-alpha {
+ color: #a94442;
+ background: #f2dede;
+}
+
+.alpha {
+ color: #8a6d3b;
+ background: #fcf8e3;
+}
+
+.beta {
+ color: #31708f;
+ background: #d9edf7;
+}
+
+
//----------------------------------------
// keyboard key style, from StackExchange.
//----------------------------------------
var domain = $("meta[name=search-domain]").attr("value");
window.open("https://www.google.com/search?q=" + query + "+site:" + domain);
}
+
+// function to shrink the life cycle bar when scrolling
+$(function(){
+ $('#life-cycle').data('size','big');
+});
+
+$(window).scroll(function(){
+ if($(document).scrollTop() > 0)
+ {
+ if($('#life-cycle').data('size') == 'big')
+ {
+ $('#life-cycle').data('size','small');
+ $('#life-cycle').stop().animate({
+ padding: '5px'
+ },100);
+ }
+ }
+ else
+ {
+ if($('#life-cycle').data('size') == 'small')
+ {
+ $('#life-cycle').data('size','big');
+ $('#life-cycle').stop().animate({
+ padding: '15px'
+ },100);
+ }
+ }
+});
which can be viewed at <https://swcarpentry.github.io/FIXME>.
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
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.
[issues]: https://guides.github.com/features/issues/
[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
[swc-lessons]: https://software-carpentry.org/lessons/
-[swc-site]: https://software-carpentry.org/
\ No newline at end of file
+[swc-site]: https://software-carpentry.org/
To cite this lesson, please consult with [CITATION](CITATION)
-[lesson-example]: https://swcarpentry.github.io/lesson-example
\ No newline at end of file
+[lesson-example]: https://carpentries.github.io/lesson-example
# Values for this lesson.
#------------------------------------------------------------
-# Which carpentry is this ("swc", "dc", or "lc")?
+# Which carpentry is this ("swc", "dc", "lc", or "cp")?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor traning for instance)
carpentry: "swc"
# Overall title for pages.
title: "Lesson Title"
-# Email address, no mailto:
-email: "lessons@software-carpentry.org"
+# Life cycle stage of the lesson
+# possible values: "pre-alpha", "alpha", "beta", "stable"
+life_cycle: "pre-alpha"
#------------------------------------------------------------
# Generic settings (should not need to change).
# Magic to make URLs resolve both locally and on GitHub.
# See https://help.github.com/articles/repository-metadata-on-github-pages/.
+# Please don't change it: <USERNAME>/<PROJECT> is correct.
repository: <USERNAME>/<PROJECT>
+# Email address, no mailto:
+email: "team@carpentries.org"
+
# Sites.
amy_site: "https://amy.software-carpentry.org/workshops"
carpentries_github: "https://github.com/carpentries"
carpentries_pages: "https://carpentries.github.io"
carpentries_site: "https://carpentries.org/"
dc_site: "http://datacarpentry.org"
-example_repo: "https://github.com/swcarpentry/lesson-example"
-example_site: "https://swcarpentry.github.com/lesson-example"
-lc_site: "https://librarycarpentry.github.io/"
+example_repo: "https://github.com/carpentries/lesson-example"
+example_site: "https://carpentries.github.io/lesson-example"
+lc_site: "https://librarycarpentry.org/"
swc_github: "https://github.com/swcarpentry"
swc_pages: "https://swcarpentry.github.io"
swc_site: "https://software-carpentry.org"
-template_repo: "https://github.com/swcarpentry/styles"
-training_site: "https://swcarpentry.github.io/instructor-training"
-workshop_repo: "https://github.com/swcarpentry/workshop-template"
-workshop_site: "https://swcarpentry.github.io/workshop-template"
+template_repo: "https://github.com/carpentries/styles"
+training_site: "https://carpentries.github.io/instructor-training"
+workshop_repo: "https://github.com/carpentries/workshop-template"
+workshop_site: "https://carpentries.github.io/workshop-template"
+cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
# Surveys.
-pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
-post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
+swc_pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
+swc_post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training"
+dc_pre_survey: "https://www.surveymonkey.com/r/dcpreworkshopassessment?workshop_id="
+dc_post_survey: "https://www.surveymonkey.com/r/dcpostworkshopassessment?workshop_id="
+lc_pre_survey: "https://www.surveymonkey.com/r/lcpreworkshopsurvey?workshop_id="
+lc_post_survey: "https://www.surveymonkey.com/r/lcpostworkshopsurvey?workshop_id="
+instructor_pre_survey: "https://www.surveymonkey.com/r/instructor_training_pre_survey?workshop_id="
+instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post_survey?workshop_id="
+
# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
start_time: 0
teaching: 0
exercises: 0
questions:
-- "Key question"
+- "Key question (FIXME)"
objectives:
-- "First learning objective."
+- "First learning objective. (FIXME)"
keypoints:
-- "First key point. Brief Answer to questions."
+- "First key point. Brief Answer to questions. (FIXME)"
---
+FIXME
+
+{% include links.md %}
+
title: About
---
{% include carpentries.html %}
+{% include links.md %}
title: Discussion
---
FIXME
+
+{% include links.md %}
---
title: Figures
---
+
+{% include base_path.html %}
+
<script>
window.onload = function() {
var lesson_episodes = [
{% for episode in site.episodes %}
- "{{ episode.url}}"{% unless forloop.last %},{% endunless %}
+ "{{ episode.url }}"{% unless forloop.last %},{% endunless %}
{% endfor %}
];
+
var xmlHttp = []; /* Required since we are going to query every episode. */
for (i=0; i < lesson_episodes.length; i++) {
+
xmlHttp[i] = new XMLHttpRequest();
xmlHttp[i].episode = lesson_episodes[i]; /* To enable use this later. */
xmlHttp[i].onreadystatechange = function() {
+
if (this.readyState == 4 && this.status == 200) {
- var article_here = document.getElementById(this.episode);
var parser = new DOMParser();
var htmlDoc = parser.parseFromString(this.responseText,"text/html");
var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
- article_here.appendChild(htmlDocArticle.getElementsByTagName("h1")[0]);
- for (let image of htmlDocArticle.getElementsByTagName("img")) {
- article_here.appendChild(image);
+
+ var article_here = document.getElementById(this.episode);
+ var images = htmlDocArticle.getElementsByTagName("img");
+
+ if (images.length > 0) {
+ var h1text = htmlDocArticle.getElementsByTagName("h1")[0].innerHTML;
+
+ var htitle = document.createElement('h2');
+ htitle.innerHTML = h1text;
+ article_here.appendChild(htitle);
+
+ var image_num = 0;
+ for (let image of images) {
+ image_num++;
+
+ var title = document.createElement('p');
+ title.innerHTML = "<strong>Figure " + image_num + ".</strong> " + image.alt;
+ article_here.appendChild(title);
+
+ article_here.appendChild(image.cloneNode(false));
+
+ if (image_num < images.length) {
+ var hr = document.createElement('hr');
+ article_here.appendChild(hr);
+ }
+ }
}
}
}
- episode_url = "{{ page.root }}" + lesson_episodes[i];
+ episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
xmlHttp[i].open("GET", episode_url);
xmlHttp[i].send(null);
}
Create anchor for each one of the episodes.
{% endcomment %}
{% for episode in site.episodes %}
-<article id="{{ episode.url }}"></article>
+<article id="{{ episode.url }}" class="figures"></article>
{% endfor %}
+
+{% include links.md %}
title: "Instructor Notes"
---
FIXME
+
+{% include links.md %}
---
---
+
+{% include base_path.html %}
+
<script>
window.onload = function() {
var lesson_episodes = [
article_here.innerHTML = htmlDocArticle.innerHTML;
}
}
- episode_url = "{{ page.root }}" + lesson_episodes[i];
+ episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
xmlHttp[i].open("GET", episode_url);
xmlHttp[i].send(null);
}
>
> FIXME
{: .prereq}
+
+{% include links.md %}
## Glossary
FIXME
+
+{% include links.md %}
title: Setup
---
FIXME
+
+
+{% include links.md %}
opts_chunk$set(fig.path = new_path)
}
-## We use the rmd- prefix for the figures generated by the lssons so
+## We use the rmd- prefix for the figures generated by the lessons so
## they can be easily identified and deleted by `make clean-rmd`. The
## working directory when the lessons are generated is the root so the
## figures need to be saved in fig/, but when the site is generated,
opts_chunk$set(tidy = FALSE, results = "markup", comment = NA,
fig.align = "center", fig.path = "fig/rmd-",
- fig.process = fix_fig_path)
+ fig.process = fix_fig_path,
+ fig.width = 8.5, fig.height = 8.5,
+ fig.retina = 2)
# The hooks below add html tags to the code chunks and their output so that they
# are properly formatted when the site is built.
hook_out <- function(x, options) {
x <- gsub("\n$", "", x)
stringr::str_c("\n\n~~~\n",
- paste0(x, collapse="\n"),
+ paste0(x, collapse="\n"),
"\n~~~\n{: .output}\n\n")
}
generate_md_episodes <- function() {
- library("methods")
-
- if (require("knitr") && packageVersion("knitr") < '1.9.19')
- stop("knitr must be version 1.9.20 or higher")
-
- if (!require("stringr"))
- stop("The package stringr is required for generating the lessons.")
-
- if (require("checkpoint") && packageVersion("checkpoint") >= '0.4.0') {
- required_pkgs <-
- checkpoint:::scanForPackages(project = "_episodes_rmd",
- verbose=FALSE, use.knitr = TRUE)$pkgs
- } else {
- stop("The checkpoint package (>= 0.4.0) is required to build the lessons.")
- }
-
- missing_pkgs <- required_pkgs[!(required_pkgs %in% rownames(installed.packages()))]
-
- if (length(missing_pkgs)) {
- message("Installing missing required packages: ",
- paste(missing_pkgs, collapse=", "))
- install.packages(missing_pkgs)
- }
-
- ## find all the Rmd files, and generate the paths for their respective outputs
- src_rmd <- list.files(pattern = "??-*.Rmd$", path = "_episodes_rmd", full.names = TRUE)
- dest_md <- file.path("_episodes", gsub("Rmd$", "md", basename(src_rmd)))
-
- ## knit the Rmd into markdown
- mapply(function(x, y) {
- knitr::knit(x, output = y)
- }, src_rmd, dest_md)
-
+ library("methods")
+
+ if (!require("remotes", quietly = TRUE)) {
+ install.packages("remotes", repos = c(CRAN = "https://cloud.r-project.org/"))
+ }
+
+ if (!require("requirements", quietly = TRUE)) {
+ remotes::install_github("hadley/requirements")
+ }
+
+ required_pkgs <- unique(c(
+ ## Packages for episodes
+ requirements:::req_dir("_episodes_rmd"),
+ ## Pacakges for tools
+ requirements:::req_dir("bin")
+ ))
+
+ missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
+
+ if (length(missing_pkgs)) {
+ message("Installing missing required packages: ",
+ paste(missing_pkgs, collapse=", "))
+ install.packages(missing_pkgs)
+ }
+
+ if (require("knitr") && packageVersion("knitr") < '1.9.19')
+ stop("knitr must be version 1.9.20 or higher")
+
+ ## get the Rmd file to process from the command line, and generate the path for their respective outputs
+ args <- commandArgs(trailingOnly = TRUE)
+ if (!identical(length(args), 2L)) {
+ stop("input and output file must be passed to the script")
+ }
+
+ src_rmd <- args[1]
+ dest_md <- args[2]
+
+ ## knit the Rmd into markdown
+ knitr::knit(src_rmd, output = dest_md)
+
# Read the generated md files and add comments advising not to edit them
vapply(dest_md, function(y) {
con <- file(y)
if (mdfile[1] != "---")
stop("Input file does not have a valid header")
mdfile <- append(mdfile, "# Please do not edit this file directly; it is auto generated.", after = 1)
- mdfile <- append(mdfile, paste("# Instead, please edit",
+ mdfile <- append(mdfile, paste("# Instead, please edit",
basename(y), "in _episodes_rmd/"), after = 2)
writeLines(mdfile, con)
close(con)
# The Makefile passes in the names of files.
if [ $# -ne 0 ] ; then
- Rscript -e "source('bin/generate_md_episodes.R')"
+ Rscript -e "source('bin/generate_md_episodes.R')" "$@"
fi
# Where to look for source Markdown files.
SOURCE_DIRS = ['', '_episodes', '_extras']
+# Where to look for source Rmd files.
+SOURCE_RMD_DIRS = ['_episodes_rmd']
+
# Required files: each entry is ('path': YAML_required).
# FIXME: We do not yet validate whether any files have the required
# YAML headers, but should in the future.
}
# How long are lines allowed to be?
+# Please keep this in sync with .editorconfig!
MAX_LINE_LEN = 100
args = parse_args()
args.reporter = Reporter()
check_config(args.reporter, args.source_dir)
+ check_source_rmd(args.reporter, args.source_dir, args.parser)
args.references = read_references(args.reporter, args.reference_path)
docs = read_all_markdown(args.source_dir, args.parser)
reporter.check_field(config_file, 'configuration',
config, 'kind', 'lesson')
reporter.check_field(config_file, 'configuration',
- config, 'carpentry', ('swc', 'dc', 'lc'))
+ config, 'carpentry', ('swc', 'dc', 'lc', 'cp'))
reporter.check_field(config_file, 'configuration', config, 'title')
reporter.check_field(config_file, 'configuration', config, 'email')
'configuration',
'"root" not set to "." in configuration')
+def check_source_rmd(reporter, source_dir, parser):
+ """Check that Rmd episode files include `source: Rmd`"""
+
+ episode_rmd_dir = [os.path.join(source_dir, d) for d in SOURCE_RMD_DIRS]
+ episode_rmd_files = [os.path.join(d, '*.Rmd') for d in episode_rmd_dir]
+ results = {}
+ for pat in episode_rmd_files:
+ for f in glob.glob(pat):
+ data = read_markdown(parser, f)
+ dy = data['metadata']
+ if dy:
+ reporter.check_field(f, 'episode_rmd',
+ dy, 'source', 'Rmd')
def read_references(reporter, ref_path):
"""Read shared file of reference links, returning dictionary of valid references
projects / rnaseq-cwl-training.git / commitdiff