BEDbase documentation

This repository hosts the documentation for BEDbase and related tools. Please visit https://docs.bedbase.org to view this rendered documentation.

Documentation is written using mkdocs and themed with material for mkdocs. The repository has:

• mkdocs.yml: the primary configuration, as well as the structure of the documentation.
• /docs: the markdown files. Each tool gets its own folder.

How to write/update documentation

Each tool gets a nav section in mkdocs.yml, which maps to its own section/tab in the rendered documentation. So to add a new page, change titles, or change structure, edit mkdocs.yml. To edit the documentation itself, edit the .md documentation files in the subfolders under /docs.

Prereqs

pip install mkdocs-material

Building locally for development

I recommend previewing your changes locally before deploying. You can get a hot-reload server going by cloning this repository, and then just running:

mkdocs serve

You can also use mkdocs build to build a portable local version of the docs.

Publishing updates

The documentation is published automatically upon commits to master using a GitHub Action, which runs mkdocs gh-deploy. This builds the docs, and pushes them to the gh-pages branch. This branch is then published with GitHub Pages. There's no need to do this locally, just let the action deploy the updates for you automatically.

FAQ

Updating automatic documentation

In the past, I had a plugin that would auto-document 2 things: 1. Python docs using lucidoc, and 2. Jupyter notebooks. This plugin was neat, but it caused me a lot of maintenance issues as well. So now, I've made it much simpler; now it's no longer a plugin, just a simple Python script. Update all the auto-generated docs (stored in docs/autodoc_build) by running the update script manually:

python update_python_autodocs.py

Configuring lucidoc rendering

Auto-generated Python documentation with lucidoc rendering is configured in the lucidoc sections of mkdocs.yml.

lucidoc:
  peppy: path/to/output.md

Configuring jupyter rendering

Configure jupyter notebeeoks in the jupyter section, where you specify a list of in (for .ipynb files) and out (for .md files) locations.

jupyter:
  - in: path/to/notebook_folder1
    out: path/to/rendered_folder1
  - in: path/to/notebook_folder2
    out: path/to/rendered_folder2

There, you can specify which folders contain notebooks, and to where they should be rendered as markdown.

Rendering jupyter notebooks in this repository

By convention, we're putting jupyter notebooks in a /notebooks subfolder under each tool (look around for examples). These are then built into the code/<notebook_name>.md file by the authodoc.py. So, to add a new notebook:

1. put the notebook into a <module>/notebooks/<notebook_name>.ipynb
2. make sure that's listed in the jupyter section of the yaml (it already should be there if you're adding a notebook to an existing folder).
3. link to the notebook in mkdocs.yaml by linking to <module>/code/<notebook_name>.md.
4. you can build your rendered markdown version by running python autodoc.py.