Package `epispot`

epispot

epispot v2

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.

Features

The epispot package currently only supports compartmental models, though we plan to expand the package to work for stochastic agent-based and spatial models as well. Currently, epispot offers the following:

Quick compilation of compartmental models with the following compartments:
Susceptible
Infected
Recovered
Removed
Exposed
Dead
Critical
Hospitalized
Custom-defined compartments for research
Built-in graphing and visualization engine
Plots model predictions interactively
Creates comparisons between models

Due to its diverse range of features, epispot can be used for both research and experimental modeling. If you would like to add more modeling support, please see the contributing section.

Installation

The epispot package can be installed from PyPI, Anaconda, or be built from the source. Before reading this guide, it is important to note that there are actually two different versions of the epispot package. The first of which is the master package, which will always have a version tag like v#.#.#. This package is used to release stable versions of epispot. However, during important events, like the COVID-19 pandemic, the nightly package is used to publish new features quickly. However, these versions may be unstable.

PyPI

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

pip install epispot

For the nightly version, use

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 for the CLI. These can be installed beforehand with:

pip install numpy
pip install matplotlib
pip install fire

Anaconda

Please note that the nightly version is not available on the conda package registry. However, it is still possible to install on conda-based systems with

pip install epispot-nightly

which uses pip from Anaconda to install it.

The standard version of epispot is published to conda using the conda-forge channel. To install, please use:

conda config --add channels conda-forge
conda install -c conda-forge epispot

Building from the source

This is the hardest way to install epispot and it is recommended that you use either PyPI or Anaconda to install it instead. However, if you would like to contribute to the repository, this will be particularly useful.

Clone the repository with:

git clone https://github.com/epispot/epispot  # clone epispot/epispot
cd epispot  # open project
pip install -r requirements.txt  # install package requirements
pip install -r bin/requirements.txt  # Install CLI requirements

Then, build the nightly version with

python setup-nightly.py install

For the stable version, first checkout a release branch with something like:

git checkout v2.1.1
python setup.py install

Quick Demo

Using epispot in a Python REPL to create the well-known SIR model (in less than three lines of code):

Quick demo GIF

Documentation

The documentation for the epispot package is generated automatically from the Python source code using Pdoc3. You can view the documentation for both the nightly and stable builds of epispot here.

At first, the documentation may seem a bit hard to understand, especially if you're new to epidemiology. That's why epispot has put together an entire manual describing some basic concepts you'll need to know to master epispot. You can view it here. The GitHub source is available here.

Usage/Examples

The GitHub repository has a vast array of samples using epispot. You can start by checking out the explorables/ directory. In it, you'll find many programs designed for helping you get started with epispot and some hands-on examples.

Badges

latest-release conda open-issues

Statuses

Pipeline	Status
Travis CI
CodeCov
PyPI main
PyPI nightly
Security

Feedback

If you have any feedback, please

Create a discussion on GitHub
Create an issue if you've found a bug
Submit a PR if you want to add a new feature
Contact a CODEOWNER

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

Citation

If you plan on using epispot in your project, please abide by the GPLv3 license. This requires that any changes you make to epispot must be open-sourced under the GPLv3 license as well and that you give credit to the author, which you can do by citing the project in your research, linking back to the original repository, or mentioning the author @quantum9innovation.

For research, you can also use epispot's DOI to reference the project:

The recommended citation for epispot is:

quantum9innovation (2021, April 2). epispot/epispot: (Version 2.1.0). Zenodo. http://doi.org/10.5281/zenodo.4624423

There are many related projects to epispot, although we believe that epispot has greater extensibility than many of these other projects. Additionally, epispot is quite portable (graphs can be used as web components/displayed as images/etc.). However, below we would like to acknowledge a few projects that may be better suited to certain use cases:

EpiJS by @Quantalabs is a disease modeling package for Javascript
covasim by the Institute for Disease Modeling offers agent-based stochastic models which epispot unfortunately does not support as of yet
CovsirPhy by @lisphilar offers greater support for loading and analyzing real COVID-19 data, which epispot strives to add soon

Authors

Please see our CODEOWNERS file for authors. Because epispot is an open-source project, different pieces of our code have different authors. However, if citing epispot or using it in another project, you can put @quantum9innovation as the lead author.

Acknowledgements

Idea & Inspiration

The original idea for epispot came from a 3Blue1Brown video on basic infectious disease dynamics and an interactive article in the Washington Post. This in turn inspired the very basic infectious disease dynamics simulated here. However, what finally set the package into motion was a series of articles by Henry Froese, available on Medium here, along with their corresponding interactive notebooks.

Code Development & Maintenance

The epispot project is built on open source code and is itself open-source. The initial core development was fueled by @quantum9innovation and much of the codebase was maintained by @Quantalabs. Additionally, thank you to all of epispot's open-source contributors!

epispot's open-source contributors

Dependencies

The epispot team also relies on the following open-source projects as dependencies:

NumPy (GitHub), the fundamental package for scientific computing with Python
Matplotlib (GitHub), plotting with Python
Google Fire (Github), a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

External Code Management Tools

For code maintenance, epispot uses various tools including:

Coverage.py (PyPI) for code coverage report generation
Pdoc3 (GitHub) for automatic documentation generation
GitBook (Website) for documentation hosting
CodeCov (Website) for code coverage report analysis
LGTM (Website) for CodeQL analysis
DeepSource (Website) for static code analysis
GitLocalize (Website) for localization of documentation
Zenodo (Website) for automatic DOI & citations

Expand source code

"""
.. include:: ../README.md
<!-- 
Documentation available at: 
https://epispot.github.io/epispot/en/v3.0.0-alpha-3 
-->
"""


def _dependency_check():
    """Checks dependencies"""
    try:
        import numpy
    except ImportError:  # pragma: no cover
        raise ImportError('In order to integrate `epispot` models, '
                          '`numpy` is a required dependency.\n'
                          'Install with either:\n'
                          ' $ pip install epispot\n'
                          ' $ conda install epispot')
    try:
        import matplotlib  # lgtm [py/import-and-import-from]
    except ImportError:  # pragma: no cover
        raise ImportError('In order to display plots, `matplotlib` is '
                          'a required dependency.\n'
                          'Install with either:\n'
                          ' $ pip install matplotlib\n'
                          ' $ conda install matplotlib')


# imports
import warnings
import random


# dependencies
_dependency_check()  # check for uninstalled dependencies
del _dependency_check
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import colors


# local
from . import comps
from . import models
from . import pre
from . import fitters
from . import plots


# helper funcs
def _check_versions():
    """Checks for version conflicts"""
    pass

def _check_install():  # pragma: no cover
    """Checks for installation errors"""
    pass

def _check_updates():
    """Checks for updates"""
    pass

def sanity_check():
    """
    Sanity check to check for basic installation errors, 
    version conflicts, upgrades, etc.

    **Run this if you experience any problems with epispot and before 
    submitting any issues**
    
    """
    # check for installation errors
    if not source or not version:  # pragma: no cover
        _check_install()

    # check for version conflicts
    import sys
    if (sys.version_info[0] < 3) or \
           (sys.version_info[0] == 3 and sys.version_info[1] < 7):
        raise RuntimeError('Epispot requires Python 3.7 or later')  # pragma: no cover
    _check_versions()

    # check for updates
    _check_updates()


# version info
version = '3.0.0-alpha-3'
"""
Epispot's version info (updated every release)\n
Check version information with:

```
    >>> print(epispot.version)
```

Version information is also available through the `__version__` 
property, included for legacy support.
"""
__version__ = version  # alias for version

stable = False
"""
Build stability:

- True ⇒ main package (stable)
- False ⇒ nightly package (possibly unstable)
"""

# metadata
source = 'https://www.github.com/epispot/epispot'
"""URL to VCS source"""
raw = f'https://raw.githubusercontent.com/epispot/epispot/v{version}/'
"""URL to raw VCS source (must append file path)"""
docs = f'https://epispot.github.io/epispot/en/v{version}/'
"""Project documentation (version-specific)"""
issues = 'https://www.github.com/epispot/epispot/issues'
"""Bug tracker"""

Sub-modules

epispot.comps: The epispot.comps module is a collection of compartments used to initialize the Model object to create a compartmental model. Each of these …
epispot.fitters: This module contains all available fitting algorithms. These operate separately from the Model class …
epispot.models: The epispot.models classes store different types of epidemiological models in a compact form useful for integration. Models can be differentiated, …
epispot.params: The epispot.params module stores various parameter distributions and estimations, many of which have been pulled from the literature. These …
epispot.plots: This sub-package is responsible for plotting epispot models of the Model class. This is done independently of any other modules and …
epispot.pre: This module (short for 'pre-compiled') contains models that have already been compiled and can be put to use immediately. Each function returns an …

Global variables

var docs

Project documentation (version-specific)

var issues

Bug tracker

var raw

URL to raw VCS source (must append file path)

var source

URL to VCS source

var stable

Build stability:

True ⇒ main package (stable)
False ⇒ nightly package (possibly unstable)

var version

Epispot's version info (updated every release)

Check version information with:

    >>> print(epispot.version)

Version information is also available through the __version__ property, included for legacy support.

Functions

def sanity_check()

Sanity check to check for basic installation errors, version conflicts, upgrades, etc.

Run this if you experience any problems with epispot and before submitting any issues