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update readme
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micokoch authored Jan 29, 2025
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# Documentation for Infectious Disease Modeling Hubs
# Documentation for Collaborative Modeling Hubs

This repository includes the content needed to generate the Hubverse static
documentation site. Included is documentation about how to build, manage, and
maintain collaborative modeling hubs.
This repository includes the content needed to generate the [Hubverse static
documentation site](https://hubverse.io/en/latest/). The website includes documentation
about how to build, manage, and maintain collaborative modeling hubs.

Below you can find instructions on how to build and edit the Hubverse
documentation site locally on your computer.

## Sections

Expand All @@ -19,23 +22,23 @@ maintain collaborative modeling hubs.
This site uses [ReadTheDocs](https://readthedocs.org/) and
[Sphinx](https://www.sphinx-doc.org/en/master/index.html) for building and
maintaining the content. The
[live version of the documentation can be found in this page](https://hubverse.io/en/latest/).
[live version of the website can be found in this page](https://hubverse.io/en/latest/).

Useful links:

- Documentation for our current theme, [Jupyter Book](https://jupyterbook.org/en/stable/intro.html)
- Documentation for our current theme, [Sphinx Book Theme](https://sphinx-book-theme.readthedocs.io/en/stable/)
- Getting started guide for [Read the Docs and Sphinx](https://docs.readthedocs.io/en/stable/intro/getting-started-with-sphinx.html)

## Local development

This project uses [`uv`](https://docs.astral.sh/uv/) to manage Python installs,
This project uses [`uv`](https://docs.astral.sh/uv/) to manage **Python** installs,
dependencies, and virtual environments. The result is less work to set up
a development environment.

However, contributors who prefer different Python tools can still use them as
long as dependency updates follow the workflow of adding (or removing)
dependencies from `pyproject.toml` and re-generating an annotated
`requirements/requirements.txt` file. In other words, don't add update
`requirements/requirements.txt` file. In other words, don't update
the requirements.txt file directly.

> [!IMPORTANT]
Expand All @@ -48,15 +51,21 @@ the requirements.txt file directly.
### Updating Hubverse documentation

The main content of the Hubverse documentation lives in
[`docs/source`](docs/source/). That is where you will add/edit Markdown files
to change the site's content.
[`docs/source`](docs/source/). To update and make changes to the
Hubverse documentation site on your computer, it is best to first
[clone this repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository).

Once you have cloned the repository on your computer, you can
add/edit the
[Markdown files](https://www.markdownguide.org/getting-started/)
in [`docs/source`](docs/source/) to change the site's content.

To preview the site locally after making updates:

1. Install uv on your machine (you will only need to do this once):
<https://docs.astral.sh/uv/getting-started/installation/>
2. Clone this repository. The rest of the instructions should be executed from
the repo's root directory.
2. The rest of the instructions should be executed from the cloned repository's root directory
(e.g., `/Users/hubUser/repositories/hubDocs`).
3. Create a virtual environment for the project:

```script
Expand All @@ -82,7 +91,8 @@ the repo's root directory.
The output of this command provides the url to use for viewing the
documentation. In the example below, you can see the built page by
going to http://127.0.0.1:8000. Use CTRL+C to stop serving the local build.
going to http://127.0.0.1:8000. Once you are finished reviewing the
site, use CTRL+C to stop serving the local build.
```script
build succeeded, 4 warnings.
Expand Down Expand Up @@ -184,4 +194,5 @@ In general, contributions should be made via pull requests to the `main` branch.
- Formatting of pages should try to use (1) native Markdown formatting first, (2) HTML formatting when Markdown formatting is insufficient or inadequate, (3) customization of HTML through CSS using `custom.css` (`docs/_static/css/custom.css`).
- Images used in Markdown pages should be stored in `docs/source/images` or in some instances under `docs/_static`.
- Files that are not Markdown files (e.g., html files, json files, pdf files) should be stored in `docs/source/files` or in some instances under `docs/_static`.
- Scripts that are meant to be regularly run for updating content should be stored in `scripts/`.
- Additional stylistic suggestions can be found in [this style guide for Sphinx-based documentations](https://documentation-style-guide-sphinx.readthedocs.io/en/latest/).

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