simuPOP 1.1.18

Forward-time population genetics simulation environment

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. Please refer to the simuPOP homepage https://bopeng.github.io/simuPOP/ for details.

Installation

simuPOP is distributed under a GPL3 license. Starting from simuPOP 1.1.8, it supports only Python 3 (3.9 and up) on Windows, macOS and Linux systems.

Install from conda-forge

simuPOP is part of the conda-forge. If you use Anaconda Python 3, you can install simuPOP with command

conda install -c conda-forge simuPOP

Install from PyPI

pip install simuPOP

Install from source

If you are working with a development version of simuPOP or an unsupported platform, you can install from source:

git clone https://github.com/BoPeng/simuPOP.git
cd simuPOP
pip install .

Please refer to INSTALL for detailed instructions and platform-specific requirements.

Documentation

The user guide and reference manual of simuPOP is available at http://bopeng.github.io/simuPOP/. simuPOP is also introduced in the following two books:

1. Forward-Time Population Genetics Simulations: Methods, Implementation, and Applications by Bo Peng, Marek Kimmel and Christopher I Amos, published by Wiley & Sons Inc, and available at Amazon and other bookstores.
2. Bioinformatics with Python Cookbook by Tiago Antao, available at Amazon

Change Log since 1.1.7

simuPOP 1.1.18

• Modernize build system: migrate from setup.py to CMake + scikit-build-core (PEP 517 compliant)
• Add multi-platform CI testing (Linux, macOS, Windows)
• Move simuOpt module into the simuPOP package. Use from simuPOP.simuOpt import setOptions instead of from simuOpt import setOptions. The old import path still works but is deprecated.

simuPOP 1.1.17

• Fix compatibility with Python 3.13 and latest version of Xcode on mac.

simuPOP 1.1.16

• #103 Fix compatibility with recent compilers with c++17 support, and fix conda-forge release.

simuPOP 1.1.15

• #122 Fix compatibility with Visual Studio 2022 under windows.

simuPOP 1.1.14

• #114 Fix compatibility with Python 3.11.

simuPOP 1.1.13

• #114 Allow negative weight of a heterogeneous mating scheme to generate less individuals than calculated.

simuPOP 1.1.12

• #102: Fix compatibility issues with Python 3.11
• #98: Write banner messaged to stderr insted of stdout

simuPOP 1.1.11

• #94: Fix HeteroMating when being used in a ConditionalMating mating scheme.
• #93: Add function form of selection operators such as maSelect (for MapSelector) and mlSelect (for MlSelector).

simuPOP 1.1.10

• #70: Fix compatibility with Mac OS using libc++ instead of libstdc++.

simuPOP 1.1.9

• #28: Fix a segmentation fault when providing a non-existent VSP index
• #31: Allow operator DiscardIf to accept a probability in addition to True/False
• #35: Add a weightBy parameter to allow HeteroMating to produce offspring subpopulation with weights determined by not only the size of the parental subpopulation, but also by for example number of mating pairs.
• #49: Fix output of loci positions in MS and other formats.