Underworld3 — Peer-reviewed • Rank 2.6 • Science 89%

Underworld3: Mathematically Self-Describing Modelling in Python for Desktop, HPC and Cloud - Published in JOSS (2025)

Ferrite • Rank 14.6 • Science 77%

Finite element toolbox for Julia

parpe • Rank 6.6 • Science 85%

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

decaylanguage • Rank 14.6 • Science 77%

Package to parse decay files, describe and convert particle decays between digital representations.

kernel-tuner • Rank 14.6 • Science 77%

Kernel Tuner

srai • Rank 14.6 • Science 77%

Spatial Representations for Artificial Intelligence - a Python library toolkit for geospatial machine learning focused on creating embeddings for downstream tasks

pythainlp • Rank 24.6 • Science 67%

Thai natural language processing in Python

venco.py — Peer-reviewed • Rank 2.6 • Science 89%

venco.py: A Python model to represent the charging flexibility and vehicle-to-grid potential of electric vehicles in energy system models - Published in JOSS (2025)

RHEA — Peer-reviewed • Rank 2.6 • Science 89%

RHEA: an open-source Reproducible Hybrid-architecture flow solver Engineered for Academia - Published in JOSS (2023)

gpullama3.java • Rank 6.6 • Science 85%

GPU-accelerated Llama3.java inference in pure Java using TornadoVM.

mep-django • Rank 6.5 • Science 85%

Shakespeare and Company Project - Python/Django web application

KielMAT: Kiel Motion Analysis Toolbox - An Open-Source Python Toolbox for Analyzing Neurological Motion Data from Various Recording Modalities • Rank 4.5 • Science 87%

KielMAT: Kiel Motion Analysis Toolbox - An Open-Source Python Toolbox for Analyzing Neurological Motion Data from Various Recording Modalities - Published in JOSS (2024)

ManipulaPy: A GPU-Accelerated Python Framework for Robotic Manipulation, Perception, and Control • Rank 4.5 • Science 87%

ManipulaPy: A GPU-Accelerated Python Framework for Robotic Manipulation, Perception, and Control - Published in JOSS (2025)

Sunny.jl: A Julia Package for Spin Dynamics • Rank 4.5 • Science 87%

Sunny.jl: A Julia Package for Spin Dynamics - Published in JOSS (2025)

grizli • Rank 14.4 • Science 77%

Grizli: The "Grism redshift and line" analysis software

bmi-geotiff • Rank 6.4 • Science 85%

Access data (and metadata) from a GeoTIFF file through a BMI

Metatheory.jl — Peer-reviewed • Rank 14.3 • Science 77%

Metatheory.jl: Fast and Elegant Algebraic Computation in Julia with Extensible Equality Saturation - Published in JOSS (2021)

geniza • Rank 6.3 • Science 85%

version 4.x of the Princeton Geniza Project

plotly.net • Rank 24.3 • Science 67%

Interactive graphing library for .NET programming languages :chart_with_upwards_trend:

pyleoclim • Rank 14.3 • Science 77%

Python Package for the Analysis of Paleoclimate Data. Documentation at

HiClimR • Rank 14.3 • Science 77%

Hierarchical Climate Regionalization

Interface to high-performance periodic coupled-cluster theory calculations with atom-centered, localized basis functions — Peer-reviewed • Rank 2.3 • Science 89%

Interface to high-performance periodic coupled-cluster theory calculations with atom-centered, localized basis functions - Published in JOSS (2022)

linien • Rank 14.3 • Science 77%

Spectroscopy lock application using RedPitaya

@openhands/ui • Rank 27.3 • Science 64%

🙌 OpenHands: Code Less, Make More

clap • Rank 37.3 • Science 54%

A full featured, fast Command Line Argument Parser for Rust

pyrealm • Rank 14.3 • Science 77%

Development of the pyrealm package, providing an integrated toolbox for modelling plant productivity, growth and demography using Python.

grnsight • Rank 14.3 • Science 77%

Web app and service for modeling and visualizing gene regulatory networks.

ShakeNBreak — Peer-reviewed • Rank 14.3 • Science 77%

ShakeNBreak: Navigating the defect configurational landscape - Published in JOSS (2022)

rexmex • Rank 14.2 • Science 77%

A general purpose recommender metrics library for fair evaluation.

proxmin • Rank 14.2 • Science 77%

Proximal optimization in pure python

rna-tools • Rank 14.2 • Science 77%

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

comb-spec-searcher • Rank 14.2 • Science 77%

a Python library for combinatorial exploration

ag2 • Rank 27.2 • Science 64%

AG2 (formerly AutoGen): The Open-Source AgentOS. Join us at: https://discord.gg/pAbnFJrkgZ

node-red • Rank 37.2 • Science 54%

Low-code programming for event-driven applications

Ciclope: micro Computed Tomography to Finite Elements • Rank 4.2 • Science 87%

Ciclope: micro Computed Tomography to Finite Elements - Published in JOSS (2023)

madminer • Rank 14.1 • Science 77%

Machine learning–based inference toolkit for particle physics

ERAD: A Graph-Based Tool for Energy Resilience Analysis of Electric Distribution Systems • Rank 4.1 • Science 87%

ERAD: A Graph-Based Tool for Energy Resilience Analysis of Electric Distribution Systems - Published in JOSS (2025)

rust-kmedoids • Rank 14.1 • Science 77%

k-Medoids clustering in Rust with the FasterPAM algorithm

monai • Rank 27.1 • Science 64%

AI Toolkit for Healthcare Imaging

wpextract • Rank 6.1 • Science 85%

Create datasets from WordPress sites for research or archiving

metric-temporal-logic • Rank 14.1 • Science 77%

Python library for working with Metric Temporal Logic (MTL)

dace • Rank 19.1 • Science 72%

DaCe - Data Centric Parallel Programming

variation-normalization • Rank 14.1 • Science 77%

Services and guidelines for normalizing variants

aimsim • Rank 16.0 • Science 75%

A Python toolbox to work with molecular similarity

ampform • Rank 14.0 • Science 77%

Automatically generate symbolic amplitude models for Partial Wave Analysis

movement • Rank 14.0 • Science 77%

A Python toolbox for analysing animal body movements across space and time

eazy • Rank 14.0 • Science 77%

Pythonic photometric redshift tools based on EAZY

SSMSE — Peer-reviewed • Rank 6.0 • Science 85%

SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models - Published in JOSS (2023)

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments • Rank 4.0 • Science 87%

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments - Published in JOSS (2024)

MadNLP • Rank 14.0 • Science 77%

A solver for nonlinear programming with GPU support

pygeohydro • Rank 13.9 • Science 77%

A part of HyRiver software stack for accessing hydrology data through web services

cheminformatics-microservice • Rank 5.9 • Science 85%

This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

numexpr • Rank 31.9 • Science 59%

Fast numerical array expression evaluator for Python, NumPy, Pandas, PyTables and more

bonsai_ipcc - a Python package for the calculation of national greenhouse gas inventories — Peer-reviewed • Rank 3.9 • Science 87%

bonsai_ipcc - a Python package for the calculation of national greenhouse gas inventories - Published in JOSS (2024)

speasy • Rank 13.9 • Science 77%

Space Physics made EASY! A simple Python package to deal with main Space Physics WebServices (CDA,SSC,AMDA,..)

EvoMaster: A Search-Based System Test Generation Tool • Rank 3.9 • Science 87%

EvoMaster: A Search-Based System Test Generation Tool - Published in JOSS (2021)

pyEQL — Peer-reviewed • Rank 13.9 • Science 77%

pyEQL: A Python interface for water chemistry - Published in JOSS (2024)

rosella • Rank 13.9 • Science 77%

Metagenomic Binning Algorithm

ldtk • Rank 13.9 • Science 77%

Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients using the stellar atmosphere spectrum library by Husser et al. (2013). Described in Parviainen & Aigrain, MNRAS 453, 3821–3826 (2015).

deeplabcut-live • Rank 13.9 • Science 77%

SDK for running DeepLabCut on a live video stream

sepia • Rank 5.8 • Science 85%

Simulation-Enabled Prediction, Inference, and Analysis: physics-informed statistical learning.

SEPARATE: Storm Event Partitioning And Rainfall Analytics for Tipping-bucket rain gauge data Evaluation • Rank 3.8 • Science 87%

SEPARATE: Storm Event Partitioning And Rainfall Analytics for Tipping-bucket rain gauge data Evaluation - Published in JOSS (2026)

pylint • Rank 36.8 • Science 54%

It's not just a linter that annoys you!

Clapeyron • Rank 13.8 • Science 77%

Clapeyron provides a framework for the development and use of fluid-thermodynamic models, including SAFT, cubic, activity, multi-parameter, and COSMO-SAC.

PyMilo: A Python Library for ML I/O • Rank 3.8 • Science 87%

PyMilo: A Python Library for ML I/O - Published in JOSS (2025)

fishStan — Peer-reviewed • Rank 1.8 • Science 89%

fishStan: Hierarchical Bayesian models for fisheries - Published in JOSS (2022)

georasters • Rank 13.8 • Science 77%

GeoRasters is a Python module that provides a fast and flexible tool to work with GIS raster files.

xarrayutils • Rank 13.8 • Science 77%

AdditiveFOAM — Peer-reviewed • Rank 5.7 • Science 85%

AdditiveFOAM: A Continuum Multiphysics Code for Additive Manufacturing - Published in JOSS (2025)

carlos • Rank 5.7 • Science 85%

CARLA Open Simulation Architecture

ELDAM — Peer-reviewed • Rank 3.7 • Science 87%

ELDAM: A Python software for Life Cycle Inventory data management - Published in JOSS (2021)

nobrainer • Rank 13.7 • Science 77%

A framework for developing neural network models for 3D image processing.

gosling.js • Rank 13.7 • Science 77%

Grammar of Scalable Linked Interactive Nucleotide Graphics

python-novice-gdp-penguins • Rank 5.7 • Science 85%

rewrite of inflammation lesson using pandas

yt_astro_analysis • Rank 13.7 • Science 77%

yt astrophysical analysis modules

partseg • Rank 13.7 • Science 77%

Tool for segmentation in bioimaging

great-tables • Rank 23.7 • Science 67%

Make awesome display tables using Python

gimmemotifs • Rank 13.6 • Science 77%

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

pymccrgb: Color- and curvature-based classification of multispectral point clouds in Python • Rank 3.6 • Science 87%

pymccrgb: Color- and curvature-based classification of multispectral point clouds in Python - Published in JOSS (2019)

Predihood — Peer-reviewed • Rank 1.6 • Science 89%

Predihood: an open-source tool for predicting neighbourhoods' information - Published in JOSS (2021)

RxInfer — Peer-reviewed • Rank 13.6 • Science 77%

RxInfer: A Julia package for reactive real-time Bayesian inference - Published in JOSS (2023)

openfermion • Rank 13.6 • Science 77%

Python package for compiling and analyzing quantum algorithms to simulate electronic structures.

LightKrylov: Lightweight implementation of Krylov subspace techniques in modern Fortran • Rank 3.6 • Science 87%

LightKrylov: Lightweight implementation of Krylov subspace techniques in modern Fortran - Published in JOSS (2026)

cppduals — Peer-reviewed • Rank 3.6 • Science 87%

cppduals: a nestable vectorized templated dual number library for C++11 - Published in JOSS (2019)

PEFAP — Peer-reviewed • Rank 3.6 • Science 87%

PEFAP : Estimating the environmental footprint of food products from packaging data - Published in JOSS (2022)

NiaAML — Peer-reviewed • Rank 3.6 • Science 87%

NiaAML: AutoML framework based on stochastic population-based nature-inspired algorithms - Published in JOSS (2021)

cytoscape.js-undo-redo • Rank 15.5 • Science 75%

A Cytoscape.js extension to provide an undo-redo framework

cabinetry • Rank 13.5 • Science 77%

design and steer profile likelihood fits

ChaosTools • Rank 13.5 • Science 77%

Tools for the exploration of chaos and nonlinear dynamics

viresclient • Rank 13.5 • Science 77%

viresclient is a Python package for easy access to Swarm & Aeolus products as xarray.Dataset

t-elf • Rank 5.5 • Science 85%

Tensor Extraction of Latent Features (T-ELF). Within T-ELF's arsenal are non-negative matrix and tensor factorization solutions, equipped with automatic model determination (also known as the estimation of latent factors - rank) for accurate data modeling. Our software suite encompasses cutting-edge data pre-processing and post-processing modules.

nltk • Rank 36.5 • Science 54%

NLTK Source

tuv-x • Rank 5.4 • Science 85%

Photolysis rate constant calculator

pysisyphus • Rank 13.4 • Science 77%

Python suite for optimization of stationary points on ground- and excited states PES and determination of reaction paths.

mail-deduplicate • Rank 13.4 • Science 77%

📧 CLI to deduplicate mails from mail boxes

gesel: a JavaScript package for client-side gene set enrichment • Rank 3.4 • Science 87%

gesel: a JavaScript package for client-side gene set enrichment - Published in JOSS (2023)

ImSwitch: Generalizing microscope control in Python • Rank 3.4 • Science 87%

ImSwitch: Generalizing microscope control in Python - Published in JOSS (2021)

cadquery • Rank 23.4 • Science 67%

A python parametric CAD scripting framework based on OCCT

miet — Peer-reviewed • Rank 1.4 • Science 89%

miet: an R package for region of interest analysis from magnetic reasonance images - Published in JOSS (2020)

mgviz • Rank 5.3 • Science 85%

Multi-Mission Geographic Information System (MMGIS) Global Navigation Satellite System (GNSS) Visualizer