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fwdpy11

Forward-time simulation in Python using fwdpp

https://github.com/molpopgen/fwdpy11

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.1%) to scientific vocabulary

Keywords

genetics genomics population-genetics simulation tree-sequences

Keywords from Contributors

interactive serializer packaging network-simulation shellcodes hacking autograding observability embedded optim
Last synced: 6 months ago · JSON representation

Repository

Forward-time simulation in Python using fwdpp

Basic Info
Statistics
  • Stars: 31
  • Watchers: 4
  • Forks: 6
  • Open Issues: 11
  • Releases: 109
Topics
genetics genomics population-genetics simulation tree-sequences
Created almost 9 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.rst 

fwdpy11
*************************

This is the README for fwdpy11_, which is a Python package for forward-time population genetic simulation.  It uses
fwdpp_ as its C++ back-end.


Build status
-----------------------

Main:

.. image:: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main
    :target: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main

.. image:: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main
    :target: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main

Development: 

.. image:: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev
    :target: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev

.. image:: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev
    :target: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev

Conda status
-----------------------

.. image:: https://anaconda.org/bioconda/fwdpy11/badges/version.svg   
	:target: https://anaconda.org/bioconda/fwdpy11

.. image:: https://anaconda.org/bioconda/fwdpy11/badges/platforms.svg   
        :target: https://anaconda.org/bioconda/fwdpy11

Miscellaneous
-----------------------

Python code style:

.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black

Features
-----------------------

* Pickle-able population objects
* Parallel computation via multiprocessing_ or concurrent.futures_.
* Custom temporal samplers to analyze populations *during* a simulation may be written in pure Python.
* Flexible interface for simulating models with multiple populations.

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

The manual can be found `here `_.

License
-----------------------

GPLv3 or later (See COPYING)

Supported Python version
-------------------------------------------------

fwdpy11 is written for Python 3.
We will not modify the package to be compatible with Python 2.7.


Dependencies and installation
---------------------------------

These topics are covered in the user manual:

* People wishing to run `fwpdy11` should see `this section `_.
* Those who need to build the package from source should look `the developer's guide `_.

Citation
----------------------------------

If you use this software for research, please cite the following publications:

* Kevin R Thornton. Polygenic adaptation to an environmental shift: temporal dynamics of variation under gaussian stabilizing selection and additive effects on a single trait. Genetics, 213(4):1513–1530, December 2019.

* Kevin R Thornton. A c++ template library for efficient forward-time population genetic simulation of large populations. Genetics, 198(1):157–166, September 2014.

This software was developed for the first paper.
The second paper describes a key part of this software's back end.


.. _fwdpy11: https://github.com/molpopgen/fwdpy11
.. _fwdpp: https://github.com/molpopgen/fwdpp
.. _GSL: http://gnu.org/software/gsl
.. _pybind11: https://github.com/pybind/pybind11
.. _multiprocessing: https://docs.python.org/3/library/multiprocessing.html
.. _concurrent.futures: https://docs.python.org/3/library/concurrent.futures.html
.. _bioconda: https://bioconda.github.io/
.. _release: https://github.com/molpopgen/fwdpy11/releases
.. _cmake: https://cmake.org

Owner

  • Name: Kevin R. Thornton
  • Login: molpopgen
  • Kind: user
  • Location: Irvine, CA
  • Company: University of California Irvine

Faculty member in Ecology & Evolutionary Biology at UC Irvine. @ThorntonLab is our group's GitHub account.

GitHub Events

Total
  • Create event: 42
  • Issues event: 7
  • Release event: 4
  • Delete event: 42
  • Issue comment event: 20
  • Push event: 143
  • Pull request event: 85
Last Year
  • Create event: 42
  • Issues event: 7
  • Release event: 4
  • Delete event: 42
  • Issue comment event: 20
  • Push event: 143
  • Pull request event: 85

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 3,206
  • Total Committers: 4
  • Avg Commits per committer: 801.5
  • Development Distribution Score (DDS): 0.013
Past Year
  • Commits: 55
  • Committers: 2
  • Avg Commits per committer: 27.5
  • Development Distribution Score (DDS): 0.218
Top Committers
Name Email Commits
molpopgen k****t@u****u 3,164
dependabot[bot] 4****] 33
Aaron Ragsdale a****e@m****a 5
Kevin Thornton k****n@p****n 4
Committer Domains (Top 20 + Academic)
pop-os.localdomain: 1 mail.mcgill.ca: 1 uci.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 73
  • Total pull requests: 353
  • Average time to close issues: 6 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 1.04
  • Average comments per pull request: 0.2
  • Merged pull requests: 304
  • Bot issues: 0
  • Bot pull requests: 58
Past Year
  • Issues: 5
  • Pull requests: 87
  • Average time to close issues: about 16 hours
  • Average time to close pull requests: about 14 hours
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.8
  • Average comments per pull request: 0.31
  • Merged pull requests: 82
  • Bot issues: 0
  • Bot pull requests: 22
View more stats
Top Authors
Issue Authors
  • molpopgen (70)
  • NW-Anderson (1)
  • hanbin973 (1)
  • hyanwong (1)
Pull Request Authors
  • molpopgen (295)
  • dependabot[bot] (58)
Top Labels
Issue Labels
documentation (15) UI (6) C++ back end (5) pending deprecation (4) bug (4) deployment (4) demographic models (3) testing (3) tree sequences (3) demes integration (2) enhancement (2) tracking issue (2) performance (2) tricky (1) build system (1) tskit (1)
Pull Request Labels
dependencies (58) github_actions (52) bug (1) rust (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 581 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 113
  • Total maintainers: 1
pypi.org: fwdpy11

Forward-time population genetic simulation in Python

  • Versions: 113
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 581 Last month
Rankings
Downloads: 5.7%
Dependent packages count: 10.1%
Stargazers count: 12.1%
Average: 12.5%
Forks count: 13.3%
Dependent repos count: 21.5%
Maintainers (1)
molpopgen
Last synced: 6 months ago

Dependencies

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requirements/conda_minimal_deps_Linux.txt pypi
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requirements/conda_minimal_deps_macOS.txt pypi
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requirements/development.txt pypi
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requirements/wheel_building_workflow.txt pypi
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deployment/docker/Dockerfile docker
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rust/fp11rust/Cargo.lock cargo
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rust/fp11rust/Cargo.toml cargo
pyproject.toml pypi
setup.py pypi