flepimop2-extras

A collection of common modules that are used frequently in practice in conjunction with flepimop2.

These modules have been separated from core flepimop2 because they're specialized or require major dependencies. It also makes it much easier for developers to contribute/work on individual modules without having to think about affecting core flepimop2 pipeline elements.

Installation

Packages in this repository can be installed by a user one of two ways:

1. Installing the module package directly, or
2. Installing modules via the flepimop2-extras meta package.

Installing Directly

For example, suppose you want to install the flepimop2-ipynbrender package with provides the ipynbrender process module:

pip install "flepimop2-ipynbrender@git+https://github.com/ACCIDDA/flepimop2-extras.git@main#subdirectory=packages/flepimop2-ipynbrender"

To install other packages directly you can replace flepimop2-ipynbrender in the command above with your preferred package.

Installing From the flepimop2-extras Meta Package

To make working on the codebase easier for the developers of this package the individual packages are managed via a uv workspace. This means that the dependencies across all constituent packages are consistently managed together and the flepimop2-extras package is a thin meta package. You can install the desired modules by installing flepimop2-extras package with the appropriate extra:

# If you want to install the `flepimop2-ipynbrender` module:
pip install "flepimop2-extras[ipynbrender]@git+https://github.com/ACCIDDA/flepimop2-extras.git@main"

# If you want to install multiple modules, such as `flepimop2-ipynbrender` and `flepimop2-slurm`:
pip install "flepimop2-extras[ipynbrender,slurm]@git+https://github.com/ACCIDDA/flepimop2-extras.git@main"

# If you want to install all modules in the `flepimop2-extras` package:
pip install "flepimop2-extras[all]@git+https://github.com/ACCIDDA/flepimop2-extras.git@main"

Package Index

Below is an index of the current packages included in flepimop2-extras.

• Module Name: Corresponds to the name of the module provided. I.e. the string you'd use to reference the module in configuration.
• Module Type: Corresponds to the type of module provided. I.e. the configuration section where you'd reference the module.
• Package: The name of the package if you wanted to install it directly.
• flepimop2-extras Extras: The extra groups that the module is included in.
• Documentation: Link to the documentation for the module.

Module Name	Module Type	Package	flepimop2-extras Extras	Documentation
ipynbrender	process	flepimop2-ipynbrender	all, ipynbrender	Link
slurm	job	flepimop2-slurm	all, slurm	Link

Contributing

Contributions are welcomed and appreciated! Please see the contributing guide for details on development setup, code standards, testing, and the pull request process.

Funding Acknowledgement

This project was made possible by the Insight Net cooperative agreement CDC-RFA-FT-23-0069 from the CDC’s Center for Forecasting and Outbreak Analytics. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention.