Package `epispot`

epispot

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!

epispot's open-source contributors

Made with contributors-img.

Expand source code

"""
.. include:: ../README-nightly.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.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

Expand source code

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()