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 this Code of Conduct.
+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 opening an issue or contacting one or more of the project maintainers.
+may be reported by following our [reporting guidelines][coc-reporting].
-This Code of Conduct is adapted from
-the [Contributor Covenant][contrib-covenant] Version 1.0.0.
-[contrib-covenant]: http://contributor-covenant.org/
+- [Software and Data Carpentry Code of Conduct][coc]
+- [Code of Conduct Reporting Guide][coc-reporting]
+
+{% include links.md %}
---
layout: page
title: "Licenses"
-permalink: /license/
+root: .
---
## Instructional Material
[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
+[numfocus]: https://numfocus.org/
+[osi]: https://opensource.org
index.md \
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.
${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
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
<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>
+ <a href="{{ site.lc_site }}"><img src="{{ page.root }}/assets/img/lc-icon-black.png" alt="Library Carpentry logo" /></a>
</div>
<div class="col-md-8">
- Library Carpentry is made by librarians to help librarians
+ <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;
--- /dev/null
+<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>
--- /dev/null
+<div class="row">
+ <div class="col-md-6">
+ <h3>Day 1</h3>
+ <table class="table table-striped">
+ <tr> <td>09:00</td> <td>Automating tasks with the Unix shell</td> </tr>
+ <tr> <td>10:30</td> <td>Coffee</td> </tr>
+ <tr> <td>12:00</td> <td>Lunch break</td> </tr>
+ <tr> <td>13:00</td> <td>Building programs with Python</td> </tr>
+ <tr> <td>14:30</td> <td>Coffee</td> </tr>
+ <tr> <td>16:00</td> <td>Wrap-up</td> </tr>
+ </table>
+ </div>
+ <div class="col-md-6">
+ <h3>Day 2</h3>
+ <table class="table table-striped">
+ <tr> <td>09:00</td> <td>Version control with Git</td> </tr>
+ <tr> <td>10:30</td> <td>Coffee</td> </tr>
+ <tr> <td>12:00</td> <td>Lunch break</td> </tr>
+ <tr> <td>13:00</td> <td>Managing data with SQL</td> </tr>
+ <tr> <td>14:30</td> <td>Coffee</td> </tr>
+ <tr> <td>16:00</td> <td>Wrap-up</td> </tr>
+ </table>
+ </div>
+</div>
--- /dev/null
+<div class="row">
+ <div class="col-md-6">
+ <h3 id="syllabus-shell">The Unix Shell</h3>
+ <ul>
+ <li>Files and directories</li>
+ <li>History and tab completion</li>
+ <li>Pipes and redirection</li>
+ <li>Looping over files</li>
+ <li>Creating and running shell scripts</li>
+ <li>Finding things</li>
+ <li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ <div class="col-md-6">
+ <h3 id="syllabus-python">Programming in Python</h3>
+ <ul>
+ <li>Using libraries</li>
+ <li>Working with arrays</li>
+ <li>Reading and plotting data</li>
+ <li>Creating and using functions</li>
+ <li>Loops and conditionals</li>
+ <li>Defensive programming</li>
+ <li>Using Python from the command line</li>
+ <li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ <!--
+ <div class="col-md-6">
+ <h3 id="syllabus-r">Programming in R</h3>
+ <ul>
+ <li>Working with vectors and data frames</li>
+ <li>Reading and plotting data</li>
+ <li>Creating and using functions</li>
+ <li>Loops and conditionals</li>
+ <li>Using R from the command line</li>
+ <li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ -->
+ <!--
+ <div class="col-md-6">
+ <h3 id="syllabus-matlab">Programming in MATLAB</h3>
+ <ul>
+ <li>Working with arrays</li>
+ <li>Reading and plotting data</li>
+ <li>Creating and using functions</li>
+ <li>Loops and conditionals</li>
+ <li>Defensive programming</li>
+ <li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ -->
+</div>
+
+<div class="row">
+ <div class="col-md-6">
+ <h3 id="syllabus-git">Version Control with Git</h3>
+ <ul>
+ <li>Creating a repository</li>
+ <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
+ <li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
+ <li>Ignoring files</li>
+ <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
+ <li>Resolving conflicts</li>
+ <li>Open licenses</li>
+ <li>Where to host work, and why</li>
+ <li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ <!--
+ <div class="col-md-6">
+ <h3 id="syllabus-sql">Managing Data with SQL</h3>
+ <ul>
+ <li>Reading and sorting data</li>
+ <li>Filtering with <code>where</code></li>
+ <li>Calculating new values on the fly</li>
+ <li>Handling missing values</li>
+ <li>Combining values using aggregation</li>
+ <li>Combining information from multiple tables using <code>join</code></li>
+ <li>Creating, modifying, and deleting data</li>
+ <li>Programming with databases</li>
+ <li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ -->
+ <div class="col-md-6">
+ <h3 id="syllabus-r">Open Refine</h3>
+ <ul>
+ <li>Introduction to OpenRefine</li>
+ <li>Importing data</li>
+ <li>Basic functions</li>
+ <li>Advanced Functions</li>
+ <li><a href="{{site.lc_pages}}library-openrefine/reference">Reference...</a></li>
+ </ul>
+ </div>
+</div>
--- /dev/null
+<p id="who">
+ <strong>Who:</strong>
+ The course is aimed at graduate students and other researchers.
+ <strong>
+ You don't need to have any previous knowledge of the tools
+ that will be presented at the workshop.
+ </strong>
+</p>
Navigation bar for an episode.
{% endcomment %}
<div class="row">
- <div class="col-md-1">
- <h3>
+ <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>
{% else %}
{% endif %}
</h3>
</div>
- <div class="col-md-10">
+ <div class="col-xs-10">
{% if include.episode_navbar_title %}
<h3 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a></h3>
- <h1 class="maintitle">{{ page.title }}</h1>
{% endif %}
</div>
- <div class="col-md-1">
- <h3>
+ <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>
{% else %}
-{% comment %}
- Find previous and next episodes (if any).
-{% endcomment %}
-{% for episode in site.episodes %}
- {% if episode.url == page.url %}
- {% unless forloop.first %}
- {% assign prev_episode = prev %}
- {% endunless %}
- {% unless forloop.last %}
- {% assign next_episode = site.episodes[forloop.index] %}
- {% endunless %}
- {% endif %}
- {% assign prev = episode %}
-{% endfor %}
-
-{% comment %}
- Display title and prev/next links.
-{% endcomment %}
<div class="row">
<div class="col-md-1">
- <h3>
- {% if prev_episode %}
- <a href="{{ page.root }}{{ prev_episode.url }}"><span class="glyphicon glyphicon-menu-left"></span></a>
- {% else %}
- <a href="{{ page.root }}"><span class="glyphicon glyphicon-menu-up"></span></a>
- {% endif %}
- </h3>
</div>
<div class="col-md-10">
- <h3 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a></h3>
<h1 class="maintitle">{{ page.title }}</h1>
</div>
<div class="col-md-1">
- <h3>
- {% if next_episode %}
- <a href="{{ page.root }}{{ next_episode.url }}"><span class="glyphicon glyphicon-menu-right"></span></a>
- {% else %}
- <a href="{{ page.root }}"><span class="glyphicon glyphicon-menu-up"></span></a>
- {% endif %}
- </h3>
</div>
</div>
--- /dev/null
+<p>
+ <a href="{{site.lc_site}}">Library Carpentry</a>
+ is made by librarians, for librarians to help you:
+</p>
+<ul>
+ <li>automate repetitive, boring, error-prone tasks</li>
+ <li>create, maintain and analyse 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>
+</ul>
+<p align="center">
+ <em>
+ Library Carpentry introduces you to the fundamentals of computing
+ and provides you with a platform for further self-directed learning.
+ For more information on what we teach and why, please see our paper
+ "<a href="http://doi.org/10.18352/lq.10176">Library Carpentry: software skills training for library professionals</a>".
+ </em>
+</p>
--- /dev/null
+<div class="row">
+ <div class="col-md-6">
+ <h3>Day 1</h3>
+ <table class="table table-striped">
+ <tr> <td>09:00</td> <td>Data Intro for Librarians</td> </tr>
+ <tr> <td>10:30</td> <td>Coffee</td> </tr>
+ <tr> <td>12:00</td> <td>Lunch break</td> </tr>
+ <tr> <td>13:00</td> <td>Shell Lessons for Libraries</td> </tr>
+ <tr> <td>14:30</td> <td>Coffee</td> </tr>
+ <tr> <td>16:00</td> <td>Wrap-up</td> </tr>
+ </table>
+ </div>
+ <div class="col-md-6">
+ <h3>Day 2</h3>
+ <table class="table table-striped">
+ <tr> <td>09:00</td> <td>Git Intro for Librarians</td> </tr>
+ <tr> <td>10:30</td> <td>Coffee</td> </tr>
+ <tr> <td>12:00</td> <td>Lunch break</td> </tr>
+ <tr> <td>13:00</td> <td>OpenRefine for Librarians</td> </tr>
+ <tr> <td>14:30</td> <td>Coffee</td> </tr>
+ <tr> <td>16:00</td> <td>Wrap-up</td> </tr>
+ </table>
+ </div>
+</div>
--- /dev/null
+<div class="row">
+ <div class="col-md-6">
+ <h3 id="syllabus-python">Data Intro</h3>
+ <ul>
+ <li>Intro to data</li>
+ <li>Jargon busting</li>
+ <li>Keyboard shortcuts</li>
+ <li>Plain text formats</li>
+ <li>Naming files</li>
+ <li>Regular expressions</li>
+ <li><a href="https://data-lessons.github.io/library-data-intro/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ <div class="col-md-6">
+ <h3 id="syllabus-shell">The Unix Shell</h3>
+ <ul>
+ <li>Files and directories</li>
+ <li>History and tab completion</li>
+ <li>Counting and sorting contents in files</li>
+ <li>Pipes and redirection</li>
+ <li>Mining or searching in files</li>
+ <li><a href="https://data-lessons.github.io/library-shell/reference/">Reference...</a></li>
+ </ul>
+ </div>
+
+</div>
+
+<div class="row">
+ <div class="col-md-6">
+ <h3 id="syllabus-git">Version Control with Git</h3>
+ <ul>
+ <li>Creating a repository</li>
+ <li>Configuring git</li>
+ <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
+ <li>Viewing state changes with <code>status</code></li>
+ <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
+ <li>Where to host work, and why</li>
+ <li><a href="https://data-lessons.github.io/library-git/reference">Reference...</a></li>
+ </ul>
+ </div>
+ <div class="col-md-6">
+ <div class="col-md-6">
+ <h3 id="syllabus-r">Open Refine</h3>
+ <ul>
+ <li>Introduction to OpenRefine</li>
+ <li>Importing data</li>
+ <li>Basic functions</li>
+ <li>Advanced Functions</li>
+ <li><a href="https://data-lessons.github.io/library-openrefine/reference">Reference...</a></li>
+ </ul>
+ </div>
+ </div>
+</div>
+<!--div class="row">
+ <div class="col-md-6">
+ <h3 id="syllabus-sql">SQL Intro</h3>
+ <ul>
+ <li>What is SQL?</li>
+ <li>Intro to SQLite Manager</li>
+ <li>Importing a database</li>
+ <li>Reading and sorting data</li>
+ <li>Filtering with <code>where</code></li>
+ <li>Combining values using aggregation</li>
+ <li>Combining information from multiple tables using <code>join</code></li>
+ <li><a href="https://data-lessons.github.io//library-sql/reference/">Reference...</a></li>
+ </ul>
+ </div>
+</div>
+-->
--- /dev/null
+<p id="who">
+ <strong>Who:</strong>
+ The course is for librarians, archivists, and other information workers.
+ <strong>
+ You don't need to have any previous knowledge of the tools that
+ will be presented at the workshop.
+ </strong>
+</p>
/
<a href="{{ site.github.repository_url }}/blob/gh-pages/CITATION">Cite</a>
/
- <a href="{{ site.contact }}">Contact</a>
+ <a href="{{ site.email }}">Contact</a>
</h4>
</div>
</div>
--- /dev/null
+[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
+[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[concept-maps]: https://carpentries.github.io/instructor-training/05-memory/
+[email]: mailto:lessons@software-carpentry.org
+[contrib-covenant]: https://contributor-covenant.org/
+[contributing]: {{ site.github.repository_url }}/blob/gh-pages/CONTRIBUTING.md
+[cran-checkpoint]: https://cran.r-project.org/web/packages/checkpoint/index.html
+[cran-knitr]: https://cran.r-project.org/web/packages/knitr/index.html
+[cran-stringr]: https://cran.r-project.org/web/packages/stringr/index.html
+[github-importer]: https://import.github.com/
+[importer]: https://github.com/new/import
+[jekyll-collection]: https://jekyllrb.com/docs/collections/
+[jekyll-install]: https://jekyllrb.com/docs/installation/
+[jekyll-windows]: http://jekyll-windows.juthilo.com/
+[jekyll]: https://jekyllrb.com/
+[jupyter]: https://jupyter.org/
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[morea]: https://morea-framework.github.io/
+[numfocus]: https://numfocus.org/
+[osi]: https://opensource.org
+[pandoc]: https://pandoc.org/
+[paper-now]: https://github.com/PeerJ/paper-now
+[python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/
+[pyyaml]: https://pypi.python.org/pypi/PyYAML
+[r-markdown]: http://rmarkdown.rstudio.com/
+[rstudio]: https://www.rstudio.com/
+[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/
+[training]: https://swcarpentry.github.io/instructor-training/
+[workshop-repo]: {{ site.workshop_repo }}
+[yaml]: http://yaml.org/
+[coc]: https://software-carpentry.org/conduct/
+[coc-reporting]: https://software-carpentry.org/CoC-reporting/
{% comment %}
Main title for lesson pages.
{% endcomment %}
-<h1 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a>{% if page.title %}: {{ page.title }}{% endif %}</h1>
+<h1 class="maintitle"><a href="{{ page.root }}{% link index.md %}">{{ site.title }}</a>{% if page.title %}: {{ page.title }}{% endif %}</h1>
</a>
{% elsif page.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" />
- </a>
- {% elsif 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" />
- </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" />
- </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="{{ page.root }}/assets/img/lc-icon-black.png" alt="Library Carpentry logo" />
</a>
{% endif %}
{% comment %} Always show link to home page. {% endcomment %}
- <a class="navbar-brand" href="{{ page.root }}/">Home</a>
+ <a class="navbar-brand" href="{{ page.root }}{% 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 }}/conduct/">Code of Conduct</a></li>
+ <li><a href="{{ page.root }}{% link CONDUCT.md %}">Code of Conduct</a></li>
- {% comment %} Show setup instructions, reference guide, and lesson episodes for lessons. {% endcomment %}
{% if site.kind == "lesson" %}
- <li><a href="{{ page.root }}/setup/">Setup</a></li>
+ {% comment %} Show setup instructions. {% endcomment %}
+ <li><a href="{{ page.root }}{% 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>
<ul class="dropdown-menu">
{% for episode in site.episodes %}
<li><a href="{{ page.root }}{{ 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>
</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" or site.github.repository_name == "workshop-template" %}
+ {% 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>
<ul class="dropdown-menu">
- <li><a href="{{ page.root }}/reference/">Reference</a></li>
+ <li><a href="{{ page.root }}{% link reference.md %}">Reference</a></li>
{% for extra in site.extras %}
<li><a href="{{ page.root }}{{ extra.url }}">{{ extra.title }}</a></li>
{% endfor %}
{% endif %}
{% comment %} Always show license. {% endcomment %}
- <li><a href="{{ page.root }}/license/">License</a></li>
+ <li><a href="{{ page.root }}{% 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>
--- /dev/null
+<p>
+ <a href="{{site.swc_site}}">Software 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>
--- /dev/null
+<div class="row">
+ <div class="col-md-6">
+ <h3>Day 1</h3>
+ <table class="table table-striped">
+ <tr> <td>09:00</td> <td>Automating tasks with the Unix shell</td> </tr>
+ <tr> <td>10:30</td> <td>Coffee</td> </tr>
+ <tr> <td>12:00</td> <td>Lunch break</td> </tr>
+ <tr> <td>13:00</td> <td>Building programs with Python</td> </tr>
+ <tr> <td>14:30</td> <td>Coffee</td> </tr>
+ <tr> <td>16:00</td> <td>Wrap-up</td> </tr>
+ </table>
+ </div>
+ <div class="col-md-6">
+ <h3>Day 2</h3>
+ <table class="table table-striped">
+ <tr> <td>09:00</td> <td>Version control with Git</td> </tr>
+ <tr> <td>10:30</td> <td>Coffee</td> </tr>
+ <tr> <td>12:00</td> <td>Lunch break</td> </tr>
+ <tr> <td>13:00</td> <td>Managing data with SQL</td> </tr>
+ <tr> <td>14:30</td> <td>Coffee</td> </tr>
+ <tr> <td>16:00</td> <td>Wrap-up</td> </tr>
+ </table>
+ </div>
+</div>
--- /dev/null
+<div class="row">
+ <div class="col-md-6">
+ <h3 id="syllabus-shell">The Unix Shell</h3>
+ <ul>
+ <li>Files and directories</li>
+ <li>History and tab completion</li>
+ <li>Pipes and redirection</li>
+ <li>Looping over files</li>
+ <li>Creating and running shell scripts</li>
+ <li>Finding things</li>
+ <li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ <div class="col-md-6">
+ <h3 id="syllabus-python">Programming in Python</h3>
+ <ul>
+ <li>Using libraries</li>
+ <li>Working with arrays</li>
+ <li>Reading and plotting data</li>
+ <li>Creating and using functions</li>
+ <li>Loops and conditionals</li>
+ <li>Defensive programming</li>
+ <li>Using Python from the command line</li>
+ <li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ <!--
+ <div class="col-md-6">
+ <h3 id="syllabus-r">Programming in R</h3>
+ <ul>
+ <li>Working with vectors and data frames</li>
+ <li>Reading and plotting data</li>
+ <li>Creating and using functions</li>
+ <li>Loops and conditionals</li>
+ <li>Using R from the command line</li>
+ <li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ -->
+ <!--
+ <div class="col-md-6">
+ <h3 id="syllabus-matlab">Programming in MATLAB</h3>
+ <ul>
+ <li>Working with arrays</li>
+ <li>Reading and plotting data</li>
+ <li>Creating and using functions</li>
+ <li>Loops and conditionals</li>
+ <li>Defensive programming</li>
+ <li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ -->
+</div>
+
+<div class="row">
+ <div class="col-md-6">
+ <h3 id="syllabus-git">Version Control with Git</h3>
+ <ul>
+ <li>Creating a repository</li>
+ <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
+ <li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
+ <li>Ignoring files</li>
+ <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
+ <li>Resolving conflicts</li>
+ <li>Open licenses</li>
+ <li>Where to host work, and why</li>
+ <li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ <!--
+ <div class="col-md-6">
+ <h3 id="syllabus-sql">Managing Data with SQL</h3>
+ <ul>
+ <li>Reading and sorting data</li>
+ <li>Filtering with <code>where</code></li>
+ <li>Calculating new values on the fly</li>
+ <li>Handling missing values</li>
+ <li>Combining values using aggregation</li>
+ <li>Combining information from multiple tables using <code>join</code></li>
+ <li>Creating, modifying, and deleting data</li>
+ <li>Programming with databases</li>
+ <li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
+ </ul>
+ </div>
+ -->
+ <div class="col-md-6">
+ <h3 id="syllabus-r">Open Refine</h3>
+ <ul>
+ <li>Introduction to OpenRefine</li>
+ <li>Importing data</li>
+ <li>Basic functions</li>
+ <li>Advanced Functions</li>
+ <li><a href="{{site.lc_pages}}library-openrefine/reference">Reference...</a></li>
+ </ul>
+ </div>
+</div>
--- /dev/null
+<p id="who">
+ <strong>Who:</strong>
+ The course is aimed at graduate students and other researchers.
+ <strong>
+ You don't need to have any previous knowledge of the tools
+ that will be presented at the workshop.
+ </strong>
+</p>
<tr>
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- <td class="col-md-3"><a href="{{ page.root }}/setup">Setup</a></td>
+ <td class="col-md-3"><a href="{{ page.root }}{% link setup.md %}">Setup</a></td>
<td class="col-md-7">Download files required for the lesson</td>
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+ <div class="col-md-6" align="left">
+ <h4>
+ Copyright © 2016
+ {% if site.carpentry == "swc" %}
+ <a href="{{ site.swc_site }}">Software Carpentry Foundation</a>
+ {% elsif site.carpentry == "dc" %}
+ <a href="{{ site.dc_site }}">Data Carpentry</a>
+ {% elsif site.carpentry == "lc" %}
+ <a href="{{ site.lc_site }}">Library Carpentry</a>
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+ <h4>
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\ No newline at end of file
// Handle foldable challenges and solutions (on click and at start).
-$(".challenge,.discussion,.solution").click(function(event) {
+$(".solution").click(function(event) {
var trigger = $(event.target).has(".fold-unfold").size() > 0
|| $(event.target).filter(".fold-unfold").size() > 0;
if (trigger) {
event.stopPropagation();
}
});
-$(".challenge,.discussion,.solution").each(function() {
+$(".solution").each(function() {
$(">*:not(h2)", this).toggle();
var h2 = $("h2:first", this);
h2.append("<span class='fold-unfold glyphicon glyphicon-collapse-down'></span>");
hook_in <- function(x, options) {
stringr::str_c("\n\n~~~\n",
paste0(x, collapse="\n"),
- "\n~~~\n{: .r}\n\n")
+ "\n~~~\n{: .language-r}\n\n")
}
hook_out <- function(x, options) {
+++ /dev/null
-#!/usr/bin/env python
-
-from __future__ import print_function
-import sys
-import os
-import glob
-from optparse import OptionParser
-
-from util import Reporter, read_markdown, IMAGE_FILE_SUFFIX
-
-def main():
- """Main driver."""
-
- args = parse_args()
- images = []
- for filename in args.filenames:
- images += get_images(args.parser, filename)
- save(sys.stdout, images)
-
-
-def parse_args():
- """Parse command-line arguments."""
-
- parser = OptionParser()
- parser.add_option('-p', '--parser',
- default=None,
- dest='parser',
- help='path to Markdown parser')
-
- args, extras = parser.parse_args()
- require(args.parser is not None,
- 'Path to Markdown parser not provided')
- require(extras,
- 'No filenames specified')
-
- args.filenames = extras
- return args
-
-
-def get_filenames(source_dir):
- """Get all filenames to be searched for images."""
-
- return glob.glob(os.path.join(source_dir, '*.md'))
-
-
-def get_images(parser, filename):
- """Extract all images from file."""
-
- content = read_markdown(parser, filename)
- result = []
- find_image_nodes(content['doc'], result)
- find_image_links(content['doc'], result)
- return result
-
-
-def find_image_nodes(doc, result):
- """Find all nested nodes representing images."""
-
- if (doc['type'] == 'img') or \
- ((doc['type'] == 'html_element') and (doc['value'] == 'img')):
- alt = doc['attr'].get('alt', '')
- result.append({'alt': alt, 'src': doc['attr']['src']})
- else:
- for child in doc.get('children', []):
- find_image_nodes(child, result)
-
-
-def find_image_links(doc, result):
- """Find all links to files in the 'fig' directory."""
-
- if ((doc['type'] == 'a') and ('attr' in doc) and ('href' in doc['attr'])) \
- or \
- ((doc['type'] == 'html_element') and (doc['value'] == 'a') and ('href' in doc['attr'])):
- path = doc['attr']['href']
- if os.path.splitext(path)[1].lower() in IMAGE_FILE_SUFFIX:
- result.append({'alt':'', 'src': doc['attr']['href']})
- else:
- for child in doc.get('children', []):
- find_image_links(child, result)
-
-
-def save(stream, images):
- """Save results as Markdown."""
-
- text = '\n<hr/>\n'.join(['<p><img alt="{0}" src="{1}" /></p>'.format(img['alt'], img['src']) for img in images])
- print(text, file=stream)
-
-
-def require(condition, message):
- """Fail if condition not met."""
-
- if not condition:
- print(message, file=sys.stderr)
- sys.exit(1)
-
-
-if __name__ == '__main__':
- main()
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")) {
+ if (require("checkpoint") && packageVersion("checkpoint") >= '0.4.0') {
required_pkgs <-
- checkpoint:::projectScanPackages(project = "_episodes_rmd",
- verbose=FALSE, use.knitr = TRUE)$pkgs
+ checkpoint:::scanForPackages(project = "_episodes_rmd",
+ verbose=FALSE, use.knitr = TRUE)$pkgs
} else {
- stop("The checkpoint package is required to build the lessons.")
+ stop("The checkpoint package (>= 0.4.0) is required to build the lessons.")
}
missing_pkgs <- required_pkgs[!(required_pkgs %in% rownames(installed.packages()))]
install.packages(missing_pkgs)
}
- ## find all the Rmd files, and generates the paths for their respective outputs
+ ## find all the Rmd files, and generate the paths for their respective outputs
src_rmd <- list.files(pattern = "??-*.Rmd$", 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)
-
+
+ # Read the generated md files and add comments advising not to edit them
+ vapply(dest_md, function(y) {
+ con <- file(y)
+ mdfile <- readLines(con)
+ 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",
+ basename(y), "in _episodes_rmd/"), after = 2)
+ writeLines(mdfile, con)
+ close(con)
+ return(paste("Warning added to YAML header of", y))
+ },
+ character(1))
}
generate_md_episodes()
'%/LICENSE.md': True,
'%/README.md': False,
'%/_extras/discuss.md': True,
- '%/_extras/figures.md': True,
'%/_extras/guide.md': True,
'%/index.md': True,
'%/reference.md': True,
'error',
'output',
'source',
- 'bash',
- 'make',
- 'matlab',
- 'python',
- 'r',
- 'sql'
+ 'language-bash',
+ 'html',
+ 'language-make',
+ 'language-matlab',
+ 'language-python',
+ 'language-r',
+ 'language-shell',
+ 'language-sql'
}
# What fields are required in teaching episode metadata?
for filename in docs.keys():
checker = create_checker(args, filename, docs[filename])
checker.check()
- check_figures(args.source_dir, args.reporter)
args.reporter.report()
reporter.check_field(config_file, 'configuration', config, 'kind', 'lesson')
reporter.check_field(config_file, 'configuration', config, 'carpentry', ('swc', 'dc', 'lc'))
reporter.check_field(config_file, 'configuration', config, 'title')
- reporter.check_field(config_file, 'configuration', config, 'contact')
+ reporter.check_field(config_file, 'configuration', config, 'email')
reporter.check({'values': {'root': '..'}} in config.get('defaults', []),
'configuration',
seen)
-def check_figures(source_dir, reporter):
- """Check that all figures are present and referenced."""
-
- # Get references.
- try:
- all_figures_html = os.path.join(source_dir, '_includes', 'all_figures.html')
- with open(all_figures_html, 'r') as reader:
- text = reader.read()
- figures = P_FIGURE_REFS.findall(text)
- referenced = [os.path.split(f)[1] for f in figures if '/fig/' in f]
- except FileNotFoundError as e:
- reporter.add(all_figures_html,
- 'File not found')
- return
-
- # Get actual image files (ignore non-image files).
- fig_dir_path = os.path.join(source_dir, 'fig')
- actual = [f for f in os.listdir(fig_dir_path) if os.path.splitext(f)[1] in IMAGE_FILE_SUFFIX]
-
- # Report differences.
- unexpected = set(actual) - set(referenced)
- reporter.check(not unexpected,
- None,
- 'Unexpected image files: {0}',
- ', '.join(sorted(unexpected)))
- missing = set(referenced) - set(actual)
- reporter.check(not missing,
- None,
- 'Missing image files: {0}',
- ', '.join(sorted(missing)))
-
-
def create_checker(args, filename, info):
"""Create appropriate checker for file."""
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][email].
However,
we will be able to respond more quickly if you use one of the other methods described below.
General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
happens on the [discussion mailing list][discuss-list],
which everyone is welcome to join.
-You can also [reach us by email][contact].
+You can also [reach us by email][email].
-[contact]: mailto:admin@software-carpentry.org
+[email]: mailto:admin@software-carpentry.org
[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
[dc-lessons]: http://datacarpentry.org/lessons/
[dc-site]: http://datacarpentry.org/
[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
-[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/swcarpentry/FIXME/issues/
[repo]: https://github.com/swcarpentry/FIXME/
[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: http://software-carpentry.org/lessons/
-[swc-site]: http://software-carpentry.org/
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
'''
ROOT_CONFIG_YML = '''\
# Contact. This *must* include the protocol: if it's an email
# address, it must look like "mailto:lessons@software-carpentry.org",
# or if it's a URL, "https://gitter.im/username/ProjectName".
-contact: "mailto:lessons@software-carpentry.org"
+email: "mailto:lessons@software-carpentry.org"
#------------------------------------------------------------
# Generic settings (should not need to change).
swc_github: "https://github.com/swcarpentry"
swc_site: "https://software-carpentry.org"
swc_pages: "https://swcarpentry.github.io"
-lc_site: "http://librarycarpentry.github.io/"
+lc_site: "https://librarycarpentry.github.io/"
template_repo: "https://github.com/swcarpentry/styles"
example_repo: "https://github.com/swcarpentry/lesson-example"
example_site: "https://swcarpentry.github.com/lesson-example"
collections:
episodes:
output: true
- permalink: /:path/
+ permalink: /:path/index.html
extras:
output: true
+ permalink: /:path/index.html
# Set the default layout for things in the episodes collection.
defaults:
- Makefile
- bin
-# Turn off built-in syntax highlighting.
-highlighter: false
+# Turn on built-in syntax highlighting.
+highlighter: rouge
'''
ROOT_INDEX_MD = '''\
---
layout: lesson
root: .
+permalink: index.html # Is the only page that don't follow the partner /:path/index.html
---
FIXME: home page introduction
ROOT_REFERENCE_MD = '''\
---
layout: reference
-permalink: /reference/
+root: .
---
## Glossary
---
layout: page
title: Setup
-permalink: /setup/
+root: .
---
FIXME
'''
+ROOT_AIO_MD = '''\
+---
+layout: page
+root: .
+---
+<script>
+ window.onload = function() {
+ var lesson_episodes = [
+ {% for episode in site.episodes %}
+ "{{ 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.innerHTML = htmlDocArticle.innerHTML;
+ }
+ }
+ episode_url = "{{ page.root }}" + lesson_episodes[i];
+ xmlHttp[i].open("GET", episode_url);
+ xmlHttp[i].send(null);
+ }
+ }
+</script>
+{% comment %}
+Create anchor for each one of the episodes.
+{% endcomment %}
+{% for episode in site.episodes %}
+<article id="{{ episode.url }}"></article>
+{% endfor %}
+'''
+
EPISODES_INTRODUCTION_MD = '''\
---
title: "Introduction"
---
layout: page
title: About
-permalink: /about/
---
{% include carpentries.html %}
'''
---
layout: page
title: Discussion
-permalink: /discuss/
---
FIXME
'''
---
layout: page
title: Figures
-permalink: /figures/
---
-{% include all_figures.html %}
+<script>
+ window.onload = function() {
+ var lesson_episodes = [
+ {% for episode in site.episodes %}
+ "{{ 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);
+ }
+ }
+ }
+ episode_url = "{{ page.root }}" + lesson_episodes[i];
+ xmlHttp[i].open("GET", episode_url);
+ xmlHttp[i].send(null);
+ }
+ }
+</script>
+{% comment %}
+Create anchor for each one of the episodes.
+{% endcomment %}
+{% for episode in site.episodes %}
+<article id="{{ episode.url }}"></article>
+{% endfor %}
'''
EXTRAS_GUIDE_MD = '''\
---
layout: page
title: "Instructor Notes"
-permalink: /guide/
---
FIXME
'''
-INCLUDES_ALL_FIGURES_HTML = '''\
-<!-- empty -->
-'''
-
BOILERPLATE = (
('AUTHORS', ROOT_AUTHORS),
('CITATION', ROOT_CITATION),
('index.md', ROOT_INDEX_MD),
('reference.md', ROOT_REFERENCE_MD),
('setup.md', ROOT_SETUP_MD),
+ ('aio.md', ROOT_AIO_MD),
('_episodes/01-introduction.md', EPISODES_INTRODUCTION_MD),
('_extras/about.md', EXTRAS_ABOUT_MD),
('_extras/discuss.md', EXTRAS_DISCUSS_MD),
('_extras/figures.md', EXTRAS_FIGURES_MD),
('_extras/guide.md', EXTRAS_GUIDE_MD),
- ('_includes/all_figures.html', INCLUDES_ALL_FIGURES_HTML)
)
CARPENTRIES = ("dc", "swc")
DEFAULT_CONTACT_EMAIL = 'admin@software-carpentry.org'
-USAGE = 'Usage: "check-workshop path/to/root/directory"'
+USAGE = 'Usage: "workshop_check.py path/to/root/directory"'
# Country and language codes. Note that codes mean different things: 'ar'
# is 'Arabic' as a language but 'Argentina' as a country.
@look_for_fixme
def check_email(email):
"""
- 'contact' must be a valid email address consisting of characters,
- an '@', and more characters. It should not be the default contact
- email address 'admin@software-carpentry.org'.
+ 'email' must be a comma-separated list of valid email addresses.
+ The list may be empty. A valid email address consists of characters,
+ an '@', and more characters. It should not contain the default contact
"""
- return bool(re.match(EMAIL_PATTERN, email)) and \
- (email != DEFAULT_CONTACT_EMAIL)
+ # YAML automatically loads list-like strings as lists.
+ if (isinstance(emails, list) and len(emails) >= 0):
+ for email in emails:
+ if ((not bool(re.match(EMAIL_PATTERN, email))) or (email == DEFAULT_CONTACT_EMAIL)):
+ return False
+ else:
+ return False
+
+ return True
def check_eventbrite(eventbrite):
@look_for_fixme
-def check_etherpad(etherpad):
+def check_collaborative_notes(collaborative_notes):
"""
- 'etherpad' must be a valid URL.
+ 'collaborative_notes' must be a valid URL.
"""
- return bool(re.match(URL_PATTERN, etherpad))
+ return bool(re.match(URL_PATTERN, collaborative_notes))
@look_for_fixme
'helper list isn\'t a valid list of format ' +
'["First helper", "Second helper",..]'),
- 'contact': (True, check_email,
- 'contact email invalid or still set to ' +
+ 'email': (True, check_emails,
+ 'contact email list isn\'t a valid list of format ' +
+ '["me@example.org", "you@example.org",..] or contains incorrectly formatted email addresses or ' +
'"{0}".'.format(DEFAULT_CONTACT_EMAIL)),
'eventbrite': (False, check_eventbrite, 'Eventbrite key appears invalid'),
- 'etherpad': (False, check_etherpad, 'Etherpad URL appears invalid'),
+ 'collaborative_notes': (False, check_collaborative_notes, 'Collaborative Notes URL appears invalid'),
'venue': (False, check_pass, 'venue name not specified'),
projects / rnaseq-cwl-training.git / commitdiff
