Reproducible Research Python Packages

pystow

👜 Easily pick a place to store data for your Python code.

pynwb

A Python API for working with Neurodata stored in the NWB Format

itk-core

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

itk-numerics

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

itk-filtering

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

itk-io

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

itk

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

itk-segmentation

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

itk-registration

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

pipefunc

Lightweight fast function pipeline (DAG) creation in pure Python for scientific (HPC) workflows 🕸️🧪

sacred

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

sionna

Sionna: An Open-Source Library for Research on Communication Systems

sionna-rt

Sionna RT: The Ray Tracing Package of Sionna

research-os

An AI-native operating system for reproducible research. Features citation-verified analysis, audited provenance, and automated data integrity pipelines.

pen-stack

Open infrastructure for genome writing: the Writable Genome (learned safe+durable insertion-site atlas), the Writer Atlas of 33k genome-writing enzymes, an inverse-design Write Planner, and a bridge-recombinase off-target engine. Consolidates 5 prior repos. Pre-registered, blind-validated, single install.

citevahti

Run unit tests on your manuscript. Check every manuscript claim against its cited evidence. Human-first, AI-second, Zotero-audited, local-first.

itkwidgets

An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.

calkit-python

Integrated, automated, accelerated research projects.

scitrack

library aimed at scientists who want a simple tool to help log research computations

agi-env

Open-source platform for reproducible AI/ML workflows, from local experimentation to distributed workers and long-lived services.

umls-downloader

Don't worry about UMLS, RxNorm, SNOMED, or SemMedDB licensing - write code that knows how to download it automatically

agi-node

Open-source platform for reproducible AI/ML workflows, from local experimentation to distributed workers and long-lived services.

agilab

Open-source platform for reproducible AI/ML workflows, from local experimentation to distributed workers and long-lived services.

kshana

Open, validated, reproducible PNT-resilience simulator spanning the full positioning, navigation & timing stack — orbit, clocks, INS, GNSS, integrity, resilience — plus quantum-vs-classical performance models. Runs as a Rust lib/CLI, Python, in-browser (WASM), an MCP server for AI agents, and a JetBrains plugin.