A friend to fetch your data files

GitHub Action to set up micromamba

Ghost atom bonded term modifications for alchemical free energy simulations

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Streaming analysis from running MD simulations.

PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations

Pydantic Pint Quantities

Materials for the joint demo at the 2025 OMSF Symposium

OpenMM is a toolkit for molecular simulation using high performance GPU code.

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

A free font that is a tribute to LITT.CHR

The Open Free Energy toolkit

Mermaid diagrams in yours sphinx powered docs

Run your GitHub Actions locally 🚀

Simple click-based tools for plugin-based CLIs

Algorithms for various Network Layouts and Tooling for planning FE Calculations

Tools used to generate the SciPy conference proceedings

Community Detection on Higher-Order Networks: Identifying Patterns in US Air Traffic

Parse Jupyter notebook cell outputs and replace user paths "/home/user/..." with links relative to the project root.

strip output from Jupyter and IPython notebooks

Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.

matplotlib: plotting with Python

An open access book on scientific visualization using python and matplotlib

The fundamental package for scientific computing with Python.

A collection of useful .gitignore templates

Loading GTFS data into NetworkX

A Python library for reading, validating, and writing transit schedule information in the GTFS format.

Positively Split Ewald

A HOOMD-blue component for soft matter simulations.