HNN Textbook Source Code

Where to access the deployed verison of this website?

Click here: https://jonescompneurolab.github.io/textbook/content/preface.html

How to use this repository

1. Content creation step: First, you add or edit the actual content. Specifically, this means adding to or editing the various Markdown (filetype .md) files located in content/.

   • TODO: We should gradually describe with more detail here.

2. "Building" step: Second, you should "build" the Markdown content into actual HTML pages. This is done automatically when you run python build.py or make from the main directory. For installation of the python packages/environment, see below.

3. Git push step: At this point, you should be ready to push! Make a PR from your fork so we can then merge your changes.

Install environment (Mac or Linux)

1. Ensure that Anaconda is installed.
2. Ensure that make is installed. You can test if make is installed by running the command which make which should then return a filename. If it returns nothing, then you need to install it.
   • (MacOS) If you don't have make, then you can install it via installing "Xcode Command-Line Tools", which is needed for HNN. To do this, simply run the command xcode-select --install and select all the default options. Make sure you restart your computer after installing this
   • (Linux) If you don't have make on Linux, then you should install whatever the "basic software building tools" package your distribution uses. As an example, on Ubuntu, this is build-essential. So, in the case of Ubuntu, you could install this using the following command: sudo apt install build-essential.
3. Once you have the above dependencies, you can easily create a new conda environment using the following command:

make create-conda-env-mpi

The above will create a new Conda environment named textbook-env-mpi which you should use for building the HTML output in this repo.