====== Creating a Reproducibility Guide using Github Pages ======

Let's do reproducible science! We can create a Github Page that goes along with our project repo (our project code on github) that walks others through our project, code, analyses, and how to reproduce or implement all code associated with a given publication.

To uses github's built-in support for the [[https://jekyllrb.com/|jekyll static site generator]],
a minimal documentation setup includes a ''docs/'' directory with two files: ''_config.yaml'' and ''index.md''.
<code>
docs/
  _config.yaml   # theme and configuration
  index.md       # actual documentation
</code>
===== Step 1. make docs/ =====

First, create a ''docs/'' directory in your local github repository

<code>
cd /path/to/mygithub/repo
mkdir docs
</code>

===== Step 2. docs/_config.yml =====

Create a ''_config.yml'' file in docs which includes the page **title**, **description**, **logo** (image file), and **theme** for your Project Page.
Your ''_config.yml'' file should look something like this:

<code>
title: <br>Cortical Myelin Maturation
description: <br>Project Information and Reproducibility Guide
logo: ./project_abstract.png
theme: jekyll-theme-minimal
</code>

  * The **title** appears at the top of the Project Page. This can be left blank, commented out, or deleted if desired.
  * The **description** appears somewhere below the title. This can be left blank, commented out, or deleted if desired.
  * If using a **logo** (eg ''project_abstract.png''), you must upload the image file to the selected branch (maybe ''gh-pages'' or ''main'', see below). This can be commented out or deleted if desired.
  * The **theme** controls what your Project Page looks like. Themes can be selected with ''jekyll-theme-**themename**''; supported themes are listed here https://pages.github.com/themes/ and you can preview what they look by searching here http://jekyllthemes.org/

===== Step 4. doc/index.md =====

Create an ''index.md'' file.
This file includes all of the text, links, etc. that you want to include on your Project Page! The text you write should comply to and will follow the formatting of Markdown syntax: https://github.com/Manuel83/sample/blob/master/index.md. Here is [[https://github.com/PennLINC/thalamocortical_development/blob/gh-pages/index.md | an example of an index.md file]] that served as one of Valerie’s study reproducibility guides. 

Here's a contrived example
<code>
# My Project
This project **does amazing things**. Use it like
```bash
./01_organize_data.bash
./02_run_stats.R
```

> [!NOTE]
> Watch out for this made up statistical //edge case//
</code>
===== Step 5. commit changes =====

Add, commit and push your config file, index file, and logo images. (Here we are using the ''main'' branch. Others may want to use ''gh-pages'' branch.)
<code>
git add docs 
git commit -m "initiating Project Page!" #edit the message after -m to your liking
git push origin main
</code>

===== Step 6. configure github =====
Finally, tell github to build your Project Page from /docs on your main branch.
Go to your github repository on github.com (in the web browser) and follow these steps:

  - Click on **Settings** on your repo page
  - Click on **Pages** on the left column
  - Under "__Build and deployment__" select **Deploy from a branch**
  - Under **Branch**, choose ''main'' and ''/docs'' (use ''gh-pages'' instead of ''main'' if you made that choice above).

Your site should be live 8-)! At https://labneurocogdevel.github.io/my_reponame or https://mygitusername.github.io/my_reponame (depending where your repo lives)

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