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. NOTE: the Markdown files are converted to html. They will look different if you view them directly with a Markdown renderer.
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.
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
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)
NOTE: Don’t rely on direct Markdown viewers to see how things look. You need to look at the derived html because that is what will be served at github.io.
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 a 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.