msprime | Python Package Wiki

Based on how often these packages appear together in public requirements.txt files on GitHub.

blacken-docs	Run `black` on python code blocks in documentation files
sparse	Sparse n-dimensional arrays
tskit	The tree sequence toolkit.
hepbasestack	Collection of tools/snippets useful for working with the python data analysis stack. Provides logging, matplotlibstyles, etc.
PyDriller	Framework for MSR
gptools	Gaussian process regression with derivative constraints and predictions.
twclassify	.
pydata-sphinx-theme	Bootstrap-based Sphinx theme from the PyData community
dask-ml	A library for distributed and parallel machine learning
py-heat-magic	py-heat as IPython magic
ijroi	Reads ImageJ ROIs.
arviz	Exploratory analysis of Bayesian models
louvain	louvain is a general algorithm for methods of community detection in large networks.
qpsolvers	Quadratic Programming solvers for Python with a unified API
pysd	System Dynamics Modeling in Python
scikit-misc	Miscellaneous tools for scientific computing.
linearmodels	Instrumental Variable and Linear Panel models for Python
stltimelogger	cli time logger
ctbBio	scripts for working with sequencing data

Proportion of downloaded versions in the last 3 months (only versions over 1%).

pip install msprime==1.0.2