Research Software Python Packages

datajoint

Relational Workflows: where database schemas define executable data pipelines.

pii-codex

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

codontrace

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

surf-agentic-base

Run provenance, comparison validity, and the shared primitives for agentic work on research infrastructure. A base layer, not an agent framework.

cpdatakit

Schema-first Python toolkit for validating, normalizing, inspecting, and visualizing scientific and engineering datasets.

attestation

Auditable research provenance as local-first MCP tools. The claim checker, paper feed, knowledge graph and symbolic math assume nothing about your field — any results JSON or CSV works, from any instrument. The experiment ledger adds W&B/MLflow/Sacred/DVC/Hydra for computational work. Nothing leaves the machine.

cmeta

Common Meta Framework (cMeta/cX): code, data, models, scripts, workflows, agents and notes as uniform artifacts behind one CLI and one Python API - for R&D that is collaborative, reproducible, reusable, scalable, portable and sustainable. Plain files, minimal dependencies, and context an AI agent can read.

plumb-line-provenance

Stop uncertain data becoming confident-looking results. plumb-line carries provenance, confidence and mock-taint with values through JavaScript and Python, and its review-time checks and GitHub Action catch uncertainty laundered into a claim in AI-assisted code.

openomicsbench

Traceable omics benchmarks with multi-method matrices, regression gates, portable bundles and sequence tools.

howfairis

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

pageledger

Auditable page-level run ledger for OCR and document extraction

horus-runtime

Run reproducible scientific workflows anywhere (laptop, remote, or HPC cluster) from a single YAML file. The open-source runtime behind Temple Compute.

gpbiometricspy

Scientific Python infrastructure for Gazepoint EDA/SCR, PPG/HRV, pupil, gaze, AOI, QC and multimodal psychophysiology.

cfad

Research software for empirical characteristic-function analysis of distributional change in financial return series

aegis-qec

Aegis QEC — Open-source quantum error correction for surface codes: Stim/PyMatching MWPM decoding, noise simulation, benchmarking, and reproducible research.

citations

Command-line tools and a Claude Code plugin bundling preregistration, citation verification, and results provenance for reproducible science workflows

provenance-core

Command-line tools and a Claude Code plugin bundling preregistration, citation verification, and results provenance for reproducible science workflows

prereg

Command-line tools and a Claude Code plugin bundling preregistration, citation verification, and results provenance for reproducible science workflows

pyfracessa

Exact computation of evolutionarily stable strategies (ESS) / strict local maximizers for rational standard quadratic optimization problems (StQP).

results-cli

Command-line tools and a Claude Code plugin bundling preregistration, citation verification, and results provenance for reproducible science workflows

reproducible-science

Command-line tools and a Claude Code plugin bundling preregistration, citation verification, and results provenance for reproducible science workflows

detime-toolkit

Unified Python/CLI time-series decomposition library with native acceleration, multivariate workflows, and machine-readable outputs.

adduce

Local research-artifact auditor for tracing paper claims to code, configurations, data, runs, and reported results.

askwol

OWL ontology review and validation for quality and publication readiness, with automated checks, visualisation, and guidance.