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epydemic

Epidemic processes on networks in Python

https://github.com/simoninireland/epydemic

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Epidemic processes on networks in Python

Basic Info
  • Host: GitHub
  • Owner: simoninireland
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 2.47 MB
Statistics
  • Stars: 50
  • Watchers: 8
  • Forks: 13
  • Open Issues: 1
  • Releases: 5
Created over 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.rst 

epydemic: Epidemic (and other) simulations on networks in Python
================================================================

.. image:: https://badge.fury.io/py/epydemic.svg
    :target: https://badge.fury.io/py/epydemic

.. image:: https://readthedocs.org/projects/pyepydemic/badge/?version=latest
    :target: https://pyepydemic.readthedocs.io/en/latest/index.html

.. image:: https://github.com/simoninireland/epydemic/actions/workflows/ci.yaml/badge.svg
    :target: https://github.com/simoninireland/epydemic/actions/workflows/ci.yaml

.. image:: https://pepy.tech/badge/epydemic
    :target: https://pepy.tech/project/epydemic

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6875267.svg
   :target: https://doi.org/10.5281/zenodo.6875267

.. image:: https://www.gnu.org/graphics/gplv3-88x31.png
    :target: https://www.gnu.org/licenses/gpl-3.0.en.html


Overview
--------

``epydemic`` is a Python library that implements simulations of
epidemic (and other) processes on networks. Epidemic processes are
very important in both network science and its applications. The most
common application is to study the ways in which diseases progress in
different network conditions, depending on their infectiousness and
other properties, but ``epydemic`` can be used to study any network
processes of interest.

``epydemic`` provides simulation under synchronous and stochastic
(Gillespie) dynamics, using the well-known ``networkx`` package to
represent and manipulate networks. It supports a generic model for
compartmented models of disease with several standard models provided
and which can be extended to other, more complex, diseases. It also
supports other network processes such as addition-deletion networks
and pulse-coupled synchronisation, generators for several different
ensembles of random networks, and a library for handling generating
functions used in network analysis.

``epydemic`` is built on top of the ``epyc`` experiment management
library, allowing simulations to be conducted at scale on individual
machines, multicore machines, and parallel computing clusters.


Installation
------------

You can install ``epydemic`` directly from PyPi using ``pip``:

::

   pip install epydemic

The master distribution of ``epydemic`` is hosted on GitHub. To obtain a
copy, just clone the repo:

::

    git clone git@github.com:simoninireland/epydemic.git
    cd epydemic
    pip install .



Documentation
-------------

API documentation for `epydemic` is available on `ReadTheDocs `_
(please note the slightly different project name).



Author and license
------------------

Copyright (c) 2017-2024, Simon Dobson 

Licensed under the `GNU General Public Licence v3 `_.

Owner

  • Name: Simon Dobson
  • Login: simoninireland
  • Kind: user
  • Location: St Andrews, UK
  • Company: University of St Andrews

I'm a computer scientist interested in complex systems, where chains of cause and effect can be difficult to establish. #python #emacs #lisp

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software and want to cite it, please reference the following."
title: "epdemic: Epidemic simulation on networks in Python"
authors:
  - family-names: "Dobson"
    given-names: "Simon"
    orcid: "https://orcid.org/0000-0001-9633-2103"
identifiers:
  - description: "DOI for code"
    type: doi
    value: "10.5281/zenodo.6912247"
date-released: 2022-07-27
license: GPL-3.0
repository-code: "https://github.com/simoninireland/epydemic"

GitHub Events

Total
  • Watch event: 6
  • Push event: 6
  • Fork event: 1
  • Create event: 1
Last Year
  • Watch event: 6
  • Push event: 6
  • Fork event: 1
  • Create event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 832
  • Total Committers: 4
  • Avg Commits per committer: 208.0
  • Development Distribution Score (DDS): 0.006
Top Committers
Name Email Commits
Simon Dobson s****n@c****g 827
Alexander Konovalov a****k@m****k 3
liberty-askew l****1@g****m 1
Alexander Konovalov a****v@u****m 1
Committer Domains (Top 20 + Academic)
mcs.st-andrews.ac.uk: 1 computer.org: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 5
  • Total pull requests: 7
  • Average time to close issues: 22 days
  • Average time to close pull requests: about 1 month
  • Total issue authors: 4
  • Total pull request authors: 5
  • Average comments per issue: 4.4
  • Average comments per pull request: 1.14
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ElanOcher (2)
  • jzicker (1)
  • FeynmanDNA (1)
  • gaianoseworthy (1)
Pull Request Authors
  • dependabot[bot] (2)
  • olexandr-konovalov (2)
  • VanBantam (1)
  • liberty-askew (1)
  • Vitineth (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 146 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 4
  • Total versions: 38
  • Total maintainers: 1
pypi.org: epydemic

Epidemic network simulations in Python

  • Versions: 38
  • Dependent Packages: 0
  • Dependent Repositories: 4
  • Downloads: 146 Last month
Rankings
Dependent repos count: 7.5%
Stargazers count: 10.0%
Dependent packages count: 10.1%
Average: 10.7%
Forks count: 10.9%
Downloads: 15.1%
Maintainers (1)
simoninireland
Last synced: 7 months ago

Dependencies

dev-requirements.txt pypi
  • coverage * development
  • doc8 * development
  • jedi * development
  • jedi-language-server * development
  • matplotlib * development
  • mypy * development
  • pylint * development
  • rope * development
  • seaborn * development
  • sphinx * development
  • sphinx-autodoc-typehints * development
  • sphinx_rtd_theme * development
  • sphinxcontrib-bibtex * development
  • tox * development
  • twine * development
  • wheel * development
requirements.txt pypi
  • epyc >=1.7.2
  • epydemicarchive_client *
  • mpmath *
  • networkx >=2.4
  • numpy >=1.18
  • pandas *
  • python-dotenv *
  • scipy *
  • typing_extensions *
setup.py pypi
  • networkx *
.github/workflows/ci.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/release.yaml actions
  • actions/checkout v3 composite
  • ncipollo/release-action v1 composite