GitBook Documentation Restructuring

[TimothyWillard]

Beyond the usual maintenance I think it might be time to consider restructuring the GitBook documentation for flepiMoP. As an "newer" user I find the GitBook documentation challenging to navigate and determine if it contains what I need quickly. Some of my initial thoughts are:

• We should think carefully about top level topics and make them clear, specific, and as mutually exclusive as possible.
  • i.e. If I have a question I should be able to scan the top level topic names and know where to look first.
• Make it easy to update documentation quickly to encourage keeping documentation up to date with code.

My suggestions on top level topics (not necessarily in order) are:

• Home: The landing page with an overview of the project, current home seems good.
• Getting Started: Installation guide(s), doing a basic simulation run, doing a basic inference run, plotting outputs, etc.
• Methodology: IDD compartmental models overview, flepiMoP's take on IDD compartmental models, inference methodology and subsection for dual likelihood, etc.
• Configuration: Overview of configuration sections, guides on each individual section.
• Model Input/Output: Directory structure, inputs (besides configuration), outputs, etc.
• Advanced Runs: Guides for installing/running flepiMoP on rockfish, longleaf, aws, etc.
• Core Development: Steps to install extra dependencies and run linting/unit tests, high level overview of the codebase, etc.
• Pre/Post Processing: Overview of these scripts, examples of these scripts, a guide to develop one, etc.

I'm also open to the view point that the documentation doesn't need restructuring if there's a strong argument for that. Also want to get some feedback on the top level topics and their contents before beginning to restructure/rewrite the GitBook documentation. Will make a separate GitHub issue with concrete details that come from this discussion.