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

Like any other new development in the repository, documentation additions should be made on a feature branch and added to the repo with a pull request as described in Development Getting Started Guide .

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 pymdown-extensions

pip install mdutils

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.

Alternative method: Using conda

The same python environment above can be achieved with conda. To do so, create a conda environment with a conda create -n e3sm_docs mkdocs-material pymdown-extensions mkdocs-monorepo-plugin mdutils mkdocs-bibtex then conda activate e3sm_docs to use the environment.

Use local environment to build/test documentation changes

Activate your virtual environment that you made in the above step.

source mkdocsenv/bin/activate

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

mkdocs build

A note on EAMxx docs

EAMxx docs use an automated routine to populate the namelist parameters. In order to avoid warnings on this step, please ensure you have a copy of the CIME submodule inside your main repo. Proceed to executing eamxx-params-docs-autogen in the components/eamxx/scripts directory. Then, you will be able to build with mkdocs build --strict --verbose (to convert any warning into an error, which we use in the PR checking).

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)

An alternative to mkdocs serve

An alternative to mkdocs serve is to access to the docs directly without serving them through a URL. To achieve this, one could you file:///E3SM_ROOT/site/index.html in a modern browser like Chrome (in place of a URL). In this case, E3SM_ROOT is the full path to the clone E3SM repository on your local machine. One could directly go to other pages as needed using the same method (e.g., file:///E3SM_ROOT/site/EAM/index.html).

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.

Markdown style guide

To help with maintainability, everyone is encouraged to follow best practices when it comes to writing markdown files. For example, popular IDEs support markdownlint (https://github.com/DavidAnson/markdownlint)

Automated preview during PRs

When you submit a PR, we have an automated process to build and test the docs (with --strict --verbose) and to preview them directly in the PR. An automated bot will leave a comment with a URL for you to review the docs.

Developing Documentation