Research Software Python Packages

datajoint

Relational Workflows: where database schemas define executable data pipelines.

qs-dmss

QS-DMSS Studio: evidence-first simulation lab for reproducible runs, evidence bundles, campaign comparison, and research-object exports.

howfairis

Command line tool to analyze a GitHub or GitLab repository's compliance with the fair-software.eu recommendations

rrdoctor

Artifact Evaluation readiness checker for research code: static scan, safe fixes, verify ladder, appendix, and agent-ready gates. Local-first, no API key.

pii-codex

A research python package for detecting, categorizing, and assessing the severity of personal identifiable information (PII)

papercheck

A reproducible audit harness for mathematical LaTeX papers: deterministic scanner, schema-validated issue ledgers with mechanical quote verification, and a stage-gated final gate — driven by any MCP agent or the CLI.

galaxy-cli

Agent-native CLI for Galaxy bioinformatics. pip install galaxy-cli. Use from terminal, subprocess, or as a Python library

synthpopcan

Canadian synthetic population tooling for StatCan margin tables and Census microdata.

datazimmer

sscu-budapest utilities for scientific data engineering

heatrapy

Python library for simulating heat transfer processes

iga

The InvenioRDM GitHub Archiver (IGA) automatically archives GitHub releases in an InvenioRDM repository.

codontrace

CodonTrace Genesis — deterministic research software for digital evolution, causal mechanism auditing, replayable ALife experiments, and evidence-gated AI/evolution studies.

critiplot

Critiplot: A Python Package for Visualizing Risk-of-Bias Data in Systematic Reviews and Meta-Analyses

hera-matlab

HERA: Hierarchical-Compensatory, Effect-Size Driven Ranking Algorithm.

crossverify

A six-phase verification harness for statistical analysis, with Python-vs-R cross-tool triangulation.

rse

tools for assessment and categorization of research software

simpa

The Simulation and Image Processing for Photonics and Acoustics (SIMPA) toolkit.

relationalstats

Practical and statistical social network analysis tools for Python.

quaternion-monoid-algebra

Compositional algebra over fixed-width quaternionic-symbolic state packets. A monoid (closed, associative, with two-sided identity) plus empirical topology preservation. MIT licensed.

inverse-projections

Inverse projection techniques for dimensionality reduction

echotime

Explainable structural similarity for time series and time-series datasets.

pyfunctionhood

Local computation of immediate neighbours of a given monotone non-degenerate Boolean function

ingestforge

Auditable AI content ingestion: safe fetch, extraction, evidence gates, provenance ledgers, RAG datasets, and configurable provider/API exports.

seismic-linter

A static analysis tool for preventing temporal causality leaks in seismology ML.