epispot-nightly 3.0.0a3

The nightly version of the epispot package.

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epispot nightly

A Python package for the mathematical modeling of infectious diseases via compartmental models. Originally designed for epidemiologists, epispot can be adapted for almost any type of modeling scenario.

This is a nightly version of epispot and may contain possibly unstable code.
Please see usage instructions prior to adding this project as a dependency
If you prefer to use the stable version of epispot, please see the project on PyPI

Installation

The epispot package can be installed from PyPI, Anaconda, or be built from the source. However, as epispot's nightly versions cannot be released per-commit to the conda packaging registry, using Anaconda means that epispot will have to be installed via the built-in pip installer. Instructions for each platform are listed below.

PyPI

This is the easiest way to install epispot nightly. Fire up a terminal and type:

pip install epispot-nightly

Pip will ask you to install numpy and matplotlib as dependencies if you haven't already. Additionally, it may require you to install fire, plotly, and SciencePlots for some nightly experiments. These can be installed beforehand with:

pip install numpy
pip install matplotlib
pip install fire
pip install plotly
pip install SciencePlots

Update the package regularly with:

pip install epispot-nightly --upgrade

Anaconda

Please note that the nightly version is not available on the conda package registry (although we may add it in the future). However, it is still possible to install on conda-based systems with

pip install epispot-nightly

which uses pip from Anaconda to install it. All dependencies are available on the conda package registry (except SciencePlots), but you may prefer to install them via pip to avoid cross-referencing packages installed on different registries.

SciencePlots can be installed using pip with:

pip install SciencePlots

Update the package regularly with:

pip install epispot-nightly --upgrade

If you installed the dependencies on conda instead of pip you may have to update them too after major releases. You can do that with:

conda update numpy
conda update matplotlib
conda update fire
conda update -c conda-forge plotly

Building from the source

This is the hardest way to install epispot-nightly but it can be particularly useful if you plan on helping out with the development process. The main downside of this approach is that you will have to continuously run git pull and then rerun the steps listed below to get the latest version.

Clone the repository with:

git clone https://github.com/epispot/epispot
cd epispot/requirements
pip install -r pre-requirements.txt  # helps avoid version conflicts
pip install -r requirements-nightly.txt

If you're planning on helping out in the development process, it will be helpful to install a few extra requirements with:

pip install -r requirements-dev.txt

Then, build the nightly version with:

python setup-nightly.py install

If you're working on a patch, you may find it helpful to use

python setup-nightly.py develop

instead because it will greatly simplify the constant reinstallation of the package.

Usage

It is important to note that this package was designed specifically for getting releases out as soon as possible when modeling is important. During the COVID-19 pandemic, this strategy allowed epispot to distribute versions quickly on PyPI; additionally, this package is used to ship alpha releases and other unstable code that is currently being developed in the epispot repository. beta-tagged releases and release candidates will be published on the stable package.

Please also note that security updates are not provided on previous nightly versions. To make sure that your version has no vulnerabilities, upgrade to the latest published version regularly. The latest version of the nightly package is the one that is maintained by our development team.

Getting Started

Make sure you are already familiar with epispot. If not, continue reading the auto-generated documentation published to this site. Additionally, we highly recommend reading the epispot manual to get a better understanding of the documentation and how to use epispot.

Current Statuses

Please note that these statuses reflect the most recent CI checks and are not related to this specific version. The following statuses show the progress of the current development.

Pipeline	Status
Build (3.7-3.9)
CodeCov
PyPI main (latest)
PyPI nightly (latest)

Contributing

Contributions are always welcome! See CONTRIBUTING.md for instructions on how to get started, including environment setup and instructions to build from the source. Please note also that epispot has many guides dedicated to certain types of contributions. Please see

• DOCUMENTATION.md for documentation additions
• SECURITY.md for epispot's security policy

Thank you to all contributors!

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