HNN Textbook Source Code

How to contribute webpages or Jupyter notebooks

This repository ( https://github.com/jonescompneurolab/textbook ) is how we are developing our new HNN Textbook website ( published here https://jonescompneurolab.github.io/textbook/content/preface.html ). We've finished building the core functionality to power the website, and we are now ready to begin accepting changes and additions from lab members. This new Textbook website is intended to be the primary resource for users to learn both the underlying scientific basics of HNN and how to use the HNN software itself (both the Python API and the GUI). All lab members (and non-lab members) are welcome to contribute! This is where we will be making changes as we perform a "Pedagogy Update" over 2026.

Step 1. Create a fork of this repository

Go to https://github.com/jonescompneurolab/textbook , click "Fork" in the upper right, then click "Create fork". (You only need to do this once.)

Step 2. Setup Github Pages

Next, before you do anything else, you need to set up your fork of textbook to publish to Github Pages. (You only need to do this once.)

1. Go to the page for your fork of the textbook repository.

2. Click the dropdown that says main on the left.

3. If you don't see an entry for a branch named gh-pages, then you need to create one. You can do this easily by typing in gh-pages in the textbox, then clicking where it says "Create branch gh-pages from main". The branch should now be created.

4. Go to the "Settings" tab of your fork's repository.

5. On the left-hand side, in the "Code and automation" section, click the section named "Pages".

6. If you see something at the top like "Your site is live at (URL)", then you're done, and you don't need to do step 7.

7. If you don't see that at the top, then under the "Build and deployment" section, do the following:

   a. Make sure the "Source" option says "Deploy from a branch" (it probably will by default). b. Under "Branch", click the dropdown and change it to gh-pages. c. Hit the "Save" button. d. You should done now.

Step 3. Add or edit webpages (Markdown) and Jupyter Notebooks!

Now you're ready to add or change webpages on the website (using your fork)!

• "Short" version: You can add or edit Markdown (.md) and Jupyter Notebook (.ipynb) files inside the content directory. All files are organized according to a content/<section>/<page> layout, where Markdown files produce pages, and Markdown files determine where the Jupyter notebooks are displayed. You can add images and display images by putting them in content/<section>/images and then referencing them appropriately. You do not need to install hnn-core in order to make your changes, you only need to change the Markdown files (and, optionally, Jupyter Notebook and image files). We prefer that you contribute changes by "forking" this repository to your personal Github account, making your changes on a new branch, and then making a "Pull Request" to this repository. If you don't know how to use Github and git, then you can also send the files containing your changes directly to Austin and he’ll make the changes for you. You can run a local "build" of the website to inspect what the output looks like (see the Contributing Guide), but that is optional.

• Long version: We have a more comprehensive Contributing Guide here.