The E3SM source code includes the documentation of the model in text files stored along with source code in the main repository.

Our documentation is written in Markdown language. See https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax to get started.

Doing local development of documentation

Just like you compile and test your Fortran before committing it, you should “compile” and view your documentation before committing and pushing the branch. Unlike compiling and running the model, the documentation can be easily built and displayed on your laptop. Here is one way to do that.

Create a local python virtual environment for the doc building packages (one time setup)

On your local laptop in your home directory, create a python virtual environment called “mkdocsenv”

python3 -m venv mkdocsenv (you can call it something else besides “mkdocsenv”)

Now enter that environment with

source mkdocsenv/bin/activate

Install the python packages needed:

pip install mkdocs-material

pip install mkdocs-monorepo-plugin

pip install mkdocs-bibtex

Leave the environment by typing

deactivate

The creation of mkdocsenv and the pip install commands only have to be done once on each platform you want to do documentation development.

Installing a python package in a virtual environment keeps it from being installed system wide which is good practice and also useful if you don’t have permissions to install system-level packages.

Use local environment to build/test documentation changes

Activate your virtual environment

source mkdocsenv/bin/activate

cd top the top level E3SM directory and see if you can build the current docs by typing

mkdocs build

You can view the docs locally in your browser with the built-in server

mkdocs serve

(Follow the instructions output by the above command to display in your browser. control-C to end server)

As you edit the documentation, rerun the “mkdocs build” command and refresh the website in your browser. The output of “mkdocs build” will tell you if you have a syntax error in your markdown files. The website in your browser will let you know if it looks as you intended

Documentation organization

The documentation for a model should be stored within that model’s source code directory.

The first file needed is mkdocs.yml which should be in E3SM/components/<model>. See E3SM/components/eam/mkdocs.yml for an example:

site_name: EAM

nav:
 - Introduction: 'index.md'
 - Users's Guide: user-guide/index.md
 - Developers's Guide: dev-guide/index.md
 - Technical Guide: tech-guide/index.md

The “site_name” is keyword used in the E3SM/docs/index.md file to reference all the model’s documentation. (That file must be edited when adding a new model’s documentation).

All other files should be stored under E3SM/components/<model>/docs

The basic structure under “docs” is

index.md - top level introductory text and links to main sections
dev-guide/ - subdir for development guide
tech-guide/ - subidr for technical guide
user-guide/ - subdir for user guide

Each of the sub-dirs should also have an “index.md” file to organize their content.

Files and sections

A subsection of your documentation should be contained entirely in a single file. Short sections can be grouped in to one file.

Equation numbering and references to equations are local to an individual markdown file.

Figures

When you start adding figures to your documentation, keep in mind that binary files can lead to repo size bloat IF they change a lot so don’t commit a figure to the repo until you are confident its the near-final version.

Figures should be in png format and under 500 pixels on the longest side.

Keep figures in the same directory as the Markdown file referencing them.