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Merge pull request #96 from aaren/fix-remove-excess-html 

remove layout, faq, design html
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<meta name="generator" content="pandoc">
<title>Software Carpentry: </title>
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</div>
<div class="row-fluid">
<div class="span10 offset1">
<h1 class="title"></h1>
<h2 id="background-and-design">Background and Design</h2>
<p>There are a few things you need to know in order to understand why this template is organized the way it is:</p>
<ol style="list-style-type: decimal">
<li><p>Git uses the term <em>clone</em> to mean &quot;a copy of a repository&quot;. GitHub uses the term <em>fork</em> to mean, &quot;a copy of a GitHub-hosted repo that is also hosted on GitHub&quot;, and the term <em>clone</em> to mean &quot;a copy of a GitHub-hosted repo that's located on someone else's machine&quot;. In both cases, the duplicate has a remote called <code>origin</code> that points to the original repo; other remotes can be added manually.</p></li>
<li><p>A user on GitHub can only have one fork of a particular repo. This is a problem for us because an author may be involved in writing several lessons, each of which has its own website repo. Those website repositories ought to be forks of this one, but since GitHub doesn't allow that, we've had to find a workaround.</p></li>
<li><p>If a repository has a branch called <code>gh-pages</code> (which stands for &quot;GitHub pages&quot;), then GitHub uses the HTML and Markdown files in that branch to create a website for the repository. If the repository's URL is <code>http://github.com/darwin/finches</code>, the URL for the website is <code>http://darwin.github.io/finches</code>.</p></li>
<li><p>We use Markdown for writing pages because it's simple to learn, and isn't tied to any specific language (the ReStructured Text format popular in the Python world, for example, is a complete unknown to R programmers). If authors want to use something else to author their lessons (e.g., IPython Notebooks), it's up to them to generate and commit Markdown formatted according to the rules below.</p>
<p><strong>Note:</strong> we do <em>not</em> prescribe what tools instructors should use when actually teaching. The IPython Notebook, Python IDEs like Spyder, and the GOCLI (Good Ol' Command Line Interpreter) are all equally welcome up on stage --- all we specify is the format of the lesson notes.</p></li>
<li><p>We use Pandoc to process pages instead of Jekyll (GitHub's default conversion tool) because Pandoc supports a much richer dialect of Markdown than Jekyll. Like Jekyll, Pandoc looks for a header at the top of each page formatted like this:</p>
<pre><code>---
variable: value
other_variable: other_value
---
...stuff in the page...</code></pre>
<p>and inserts the values of those variables into the page when formatting this. Lesson authors will usually not have to worry about this.</p></li>
<li><p>Using Pandoc instead of Jekyll means that we have to compile our Markdown into HTML on our own machines and commit it to the <code>gh-pages</code> branch of the lesson's GitHub repository.</p>
<p>It's considered bad practice to put computer-generated files under version control, but the HTML pages put into the lesson's root directory by Pandoc <em>must</em> be committed to version control in order for the lesson to be displayed properly on GitHub.</p>
<p>It's also considered bad practice to put generated files in the same directory as source files. We do it because some authors may use auxiliary source files such as R Markdown and IPython Notebook files which are executable, and contain paths to things like images and data files. If we put our source files in a sub-directory, those paths won't work (or conversely, if we put our generated files in a different directory, the paths won't work there).</p></li>
<li><p>In order to display properly, our generated HTML pages need artwork, CSS style files, and a few bits of Javascript. We could load these from the web, but that would make offline authoring difficult. Instead, each lesson's repository has a copy of these files, and a way of updating them (and only them) on demand.</p></li>
</ol>
<p>One final note: we try not to put HTML inside Markdown because it's ugly to read and write, and error-prone to process. Instead, we put things that ought to be in <code>&lt;div&gt;</code> blocks, like the learning objectives and challenge exercises, in blockquotes indented with <code>&gt;</code>, and do a bit of post-processing to attach the right CSS classes to these blocks.</p>
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<div class="span10 offset1">
<h1 class="title"></h1>
<h2 id="faq">FAQ</h2>
<ul>
<li><p><em>Where can I get help?</em></p>
<p>Mail <script type="text/javascript">
<!--
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<li><p><em>Where can I report problems or suggest improvements?</em></p>
<p>Please <a href="https://github.com/swcarpentry/lesson-template/issues?q=is%3Aopen+is%3Aissue">file an issue</a> or <script type="text/javascript">
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<li><p><em>Why does the lesson repository have to be created from scratch? Why not fork <code>lesson-template</code> on GitHub?</em></p>
<p>Because any particular user can only have one fork of a repository, but instructors frequently need to work on several workshops at once.</p></li>
<li><p><em>Why use Pandoc? Why not some other markup language and some other converter?</em></p>
<p>Because it supports a richer dialect of Markdown than Jekyll (the converter that GitHub uses by default). In particular, Pandoc can do tables and allows us to add styles to headings.</p></li>
<li><p><em>What do the <a href="https://github.com/swcarpentry/lesson-template/issues?q=is%3Aopen+is%3Aissue">labels</a> mean?</em></p>
<ul>
<li><code>bug</code>: something is wrong in our tools or documentation</li>
<li><code>defer</code>: marks an issue that we will work on, but not now</li>
<li><code>discussion</code>: marks issues used for conversations about specific problems and questions</li>
<li><code>duplicate</code>: marks an issue that was closed as redundant (include the number of the original issue in the closing comment)</li>
<li><code>enhancement</code>: asks for, or adds, a new feature or new information</li>
<li><code>filed-by-newcomer</code>: issue or pull request was filed by someone who is relatively new to GitHub and/or this project, and would appreciate guidance as well as feedback</li>
<li><code>getting-started</code>: issue or pull request is suitable for someone new to GitHub and/or this project</li>
<li><code>help-wanted</code>: a question or request for assistance</li>
<li><code>left-as-was</code>: marks an issue closed because the item in question will be left as it was</li>
<li><code>suitable-for-newcomer</code>: issue or pull request is a good starting point for someone who is relatively new to GitHub and/or this project</li>
<li><code>work-in-progress</code>: a pull request that is not yet ready for review</li>
</ul></li>
</ul>
<h2 id="debugging">Debugging</h2>
<p>Please add notes about problems and solutions below.</p>
<ul>
<li><p><code>pandoc: command not found</code></p>
<p>Probably you didn't install <a href="http://pandoc.org/installing.html">Pandoc</a>.</p></li>
<li><p><code>pandoc: Error running filter tools/filters/blockquote2div.py</code> due <code>ImportError: No module named 'pandocfilters'</code></p>
<p>Probably you didn't install <a href="https://pypi.python.org/pypi/pandocfilters/1.2.3">pandocfilters</a>.</p></li>
</ul>
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<title>Software Carpentry: </title>
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<div class="span10 offset1">
<h1 class="title"></h1>
<h1 id="lesson-layout">Lesson Layout</h1>
<p>Each lesson is stored in a directory laid out as described below. That directory is a self-contained Git repository (i.e., there are no submodules or clever tricks with symbolic links).</p>
<ol style="list-style-type: decimal">
<li><p><code>README.md</code>: initially a copy of this file. It should be overwritten with short description of the lesson, but should include the following blockquote to help people find these instructions:</p>
<pre><code>&gt; Please see [https://github.com/swcarpentry/lesson-template](https://github.com/swcarpentry/lesson-template)
&gt; for instructions on formatting, building, and submitting lessons,
&gt; or run `make` in this directory for a list of helpful commands.</code></pre></li>
<li><p>Other files in the root directory: the source of the lesson's web pages (and possibly auxiliary files like IPython Notebooks and R Markdown files).</p></li>
<li><p><code>code/</code>, <code>data/</code>, and <code>fig/</code>: sub-directories containing sample code, data files, and figures. See &quot;Code, Data, and Figures&quot; below.</p></li>
<li><p><code>css/</code>, <code>img/</code>, <code>js/</code>, and <code>deck.js/</code>: style sheets, artwork, and Javascript used in the lesson's web site. See &quot;Support Files&quot; below.</p></li>
<li><p><code>_layouts/</code> and <code>_includes/</code>: page templates and inclusions. See &quot;Support Files&quot; below.</p></li>
<li><p><code>tools/</code>: tools for managing lessons. See &quot;Tools&quot; below.</p></li>
</ol>
<h1 id="code-data-and-figures">Code, Data, and Figures</h1>
<p>All of the software samples used in the lesson must go in a directory called <code>code/</code>. Stand-alone data files must go in a directory called <code>data/</code>. Groups of related data files must be put together in a sub-directory of <code>data/</code> with a meaningful (short) name. Figures, plots, and diagrams used in the lessons must go in a <code>fig/</code> directory.</p>
<p><strong>Notes:</strong></p>
<ol style="list-style-type: decimal">
<li><p>This mirrors the layout a scientist would use for actual work. However, it may cause novice learners problems. If a program is in <code>code/a.py</code>, and contains a reference to a data file <code>../data/b.csv</code>, then if the user runs the program from the root directory using <code>python code/a.py</code>, it will be unable to find the data file (since the program's working directory will be the root directory, not the <code>data</code> directory).</p></li>
<li><p>IPython Notebooks and R Markdown files, which are both code and the source for web pages, should go in the root directory. These will not be checked by our validation tool, or indexed by other tools we plan to build.</p></li>
<li><p>We strongly prefer SVG for line drawings, since they are smaller, scale better, and are easier to edit. Screenshots and other raster images must be PNG or JPEG format.</p></li>
</ol>
<h1 id="support-files">Support Files</h1>
<p>Files used to display the lesson, such as artwork, CSS, and Javascript, are stored in <code>img/</code>, <code>css/</code>, and <code>js/</code> directories of their own, while the <code>deck.js/</code> directory contains files used to make HTML slideshows. We keep website artwork in the <code>img/</code> directory separate from figures used in the lesson (which are stored in <code>fig/</code>) to make it simple to update the former automatically. Most authors should not need to modify any of the support files themselves.</p>
<p>The <code>_layouts/</code> directory holds the page templates used to translate Markdown to HTML, while the <code>_includes/</code> directory holds snippets of HTML that are used in several page layouts. These directories have underscores at the start of their names to be consistent with Jekyll's naming conventions, but the files they contain are for Pandoc.</p>
<h1 id="tools">Tools</h1>
<p>The <code>tools/</code> directory contains tools to help create and maintain lessons:</p>
<ul>
<li><code>tools/check</code>: make sure that everything is formatted properly, and print error messages identifying problems if it's not.</li>
</ul>
<h1 id="pages">Pages</h1>
<p>The root directory holds the content of the lesson, and must contain:</p>
<ol style="list-style-type: decimal">
<li><p><code>Makefile</code>: contains commands to check, preview, and update the repository. Authors should not need to modify this file.</p></li>
<li><p><code>index.md</code>: the home page for the lesson. (See &quot;Home Page&quot; below.)</p></li>
<li><p><code>dd-slug.md</code>: the topics in the lesson. <code>dd</code> is a sequence number such as <code>01</code>, <code>02</code>, etc., and <code>slug</code> is an abbreviated single-word mnemonic for the topic. Thus, <code>03-filesys.md</code> is the third topic in this lesson, and is about the filesystem. (Note that we use hyphens rather than underscores in filenames.) See &quot;Topics&quot; below.</p></li>
<li><p><code>motivation.md</code>: slides for a short introductory presentation (three minutes or less) explaining what the lesson is about and why people would want to learn it. See &quot;Introductory Slides&quot; below.</p></li>
<li><p><code>reference.md</code>: a cheat sheet summarizing key terms and commands, syntax, etc., that can be printed and given to learners. See &quot;Reference Guide&quot; below.</p></li>
<li><p><code>discussion.md</code>: notes about more advanced ideas that would distract from the main lesson, and pointers to where to go next. See &quot;Discussion Page&quot; below.</p></li>
<li><p><code>instructors.md</code>: the instructor's guide for the lesson. See &quot;Instructor's Guide&quot; below.</p></li>
</ol>
<p>Note that the lesson's title is repeated in several files. We could put this in the Makefile, and insert it into pages when compiling, but then authors would have to edit the Makefile (which we want to avoid). We could also put it in some sort of configuration file, but again, we're trying to avoid those.</p>
<h2 id="home-page">Home Page</h2>
<p><code>index.md</code> must be structured as follows:</p>
<pre><code>---
layout: lesson
title: Lesson Title
---
Paragraph(s) of introductory material.
&gt; ## Prerequisites {.prereq}
&gt;
&gt; What learners need to know before tackling this lesson.
## Topics
1. [Topic Title 1](01-slug.html)
2. [Topic Title 2](02-slug.html)
## Other Resources
* [Motivation](motivation.html)
* [Reference](reference.html)
* [Discussion](discussion.html)
* [Instructor&#39;s Guide](instructors.html)</code></pre>
<p><strong>Notes:</strong></p>
<ol style="list-style-type: decimal">
<li><p>The description of prerequisites is prose for human consumption, not a machine-comprehensible list of dependencies. We may supplement the former with the latter once we have more experience with this lesson format and know what we actually want to do.</p></li>
<li><p>Software installation and configuration instructions <em>aren't</em> in the lesson, since they may be shared with other lessons. They will be stored centrally on the Software Carpentry web site and linked from the lessons that need them.</p></li>
</ol>
<h2 id="topics">Topics</h2>
<p>Each topic page must be structured as follows:</p>
<pre><code>---
layout: page
title: Lesson Title
subtitle: Topic Title
minutes: 10
---
&gt; ## Learning Objectives
&gt;
&gt; * Learning objective 1
&gt; * Learning objective 2
Paragraphs of text --- possibly including **definitions** ---
mixed with:
~~~ {.python}
some code:
to be displayed
~~~
and:
~~~ {.output}
output
from
program
~~~
and:
~~~ {.error}
error reports from programs (if any)
~~~
and possibly including some of these:
&gt; ## Callout Box {.callout}
&gt;
&gt; An aside of some kind.
and one or more of these:
&gt; ## Challenge Title {.challenge}
&gt;
&gt; Description of a single challenge.
&gt; There may be several challenges.</code></pre>
<p><strong>Notes:</strong></p>
<ol style="list-style-type: decimal">
<li><p>The &quot;expected time&quot; heading is called minutes to encourage people to create topics that are short (10-15 minutes at most).</p></li>
<li><p>There are no sub-headings inside a topic other than the ones shown. (If a topic needs sub-headings, it should be broken into two or more topics.)</p></li>
<li><p>Every challenge should relate explicitly back to a learning objective.</p></li>
<li><p>Definitions of terms are marked in <strong>bold</strong> (like <code>**this**</code>). Nothing else should be marked as bold text --- use <em>italics</em> for for all other emphasis.</p></li>
</ol>
<h2 id="motivational-slides">Motivational Slides</h2>
<p>Every lesson must include a short slide deck suitable for a short presentation (3 minutes or less) that the instructor can use to explain to learners how knowing the subject will help them. The slides must be laid out like this:</p>
<pre><code>---
layout: slides
title: Lesson Title
subtitle: Motivation
---
&lt;section class=&quot;slide&quot;&gt;
## Why This Topic?
&lt;/section&gt;
&lt;section class=&quot;slide&quot;&gt;
## Some Other Point
&lt;/section&gt;</code></pre>
<p><strong>Notes:</strong></p>
<ol style="list-style-type: decimal">
<li><p>This is the one place where we <em>must</em> use HTML tags in our Markdown (to delimit slides). Everything inside the section markers should be Markdown if possible.</p></li>
<li><p>We use <a href="http://imakewebthings.com/deck.js/">deck.js</a> for our slides as it is simpler and prettier than alternatives like <a href="http://lab.hakim.se/reveal-js/">reveal.js</a>.</p></li>
</ol>
<h2 id="reference-guide">Reference Guide</h2>
<p>The reference guide is a cheat sheet for learners to print, doodle on, and take away. Its format is deliberately unconstrained for now, since we'll need to see a few before we can decide how they ought to be laid out (or whether they need to be laid out the same way at all).</p>
<p>The last section of the reference guide must be a glossary laid out as a definition list:</p>
<pre><code>---
layout: page
title: Lesson Title
subtitle: Reference
---
...commands and examples...
## Glossary
Key Word 1
: Definition of first term
Key Word 2
: Definition of second term</code></pre>
<h2 id="discussion-page">Discussion Page</h2>
<p>The discussion page</p>
<pre><code>---
layout: page
title: Lesson Title
subtitle: Discussion
---
* First point of general discussion.
This may span several paragraphs.
* Second point of general discussion.</code></pre>
<h2 id="instructors-guide">Instructor's Guide</h2>
<p>Learners may go through lessons outside of class, so it seems best to keep material for instructors in a separate document, rather than interleaved in the lesson itself. Its structure is:</p>
<pre><code>---
layout: page
title: Lesson Title
subtitle: Instructor&#39;s Guide
---
## Legend
One or more paragraphs laying out the lesson&#39;s legend (i.e., the story
behind its running example).
## Overall
* Point
* Point
## [Topic Title 1](01-slug.html)
* Point
* Point
1. Discussion of first challenge.
2. Discussion of second challenge.
## [Topic Title 2](02-slug.html)
* Point
* Point
1. Discussion of first challenge.
2. Discussion of second challenge.</code></pre>
<p><strong>Notes:</strong></p>
<ol style="list-style-type: decimal">
<li><p>The topic headings must match the topic titles. (Yes, we could define these as variables in a configuration file and refer to those variables everywhere, but in this case, repetition will be a lot easier to read, and our validator can check that the titles line up.)</p></li>
<li><p>The points can be anything: specific ways to introduce ideas, common mistakes learners make and how to get out of them, or anything else.</p></li>
<li><p>Full solutions to the challenges do not have to be presented, but every challenge should be discussed, and that discussion should mention how long it typically takes to do. (Those estimates do not go in the challenge itself, since they can increase learners' stress levels.)</p></li>
</ol>
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