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tools:project_reproducibility_guides_with_gh-pages [2025/08/18 10:37] – [Step 6. configure github] willtools:project_reproducibility_guides_with_gh-pages [2025/08/18 10:44] (current) – [Step 4. doc/index.md] will
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 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. 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/ ===== ===== Step 1. make docs/ =====
  
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 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.  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 ===== ===== Step 5. commit changes =====
  
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 <code> <code>
 git add docs  git add docs 
-git commit -m “initiating Project Page!” #edit the message after -m to your liking+git commit -m "initiating Project Page!" #edit the message after -m to your liking
 git push origin main git push origin main
 </code> </code>