SunPy
SunPy: A Python package for Solar Physics - Published in JOSS (2020)
SALib
SALib: An open-source Python library for Sensitivity Analysis - Published in JOSS (2017)
tqdm
tqdm: A Fast, Extensible Progress Meter for Python and CLI - Published in JOSS (2019)
xclim
xclim: xarray-based climate data analytics - Published in JOSS (2023)
sourmash v4
sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets - Published in JOSS (2024)
SpiceyPy
SpiceyPy: a Pythonic Wrapper for the SPICE Toolkit - Published in JOSS (2020)
scikit-fem
scikit-fem: A Python package for finite element assembly - Published in JOSS (2020)
matchms - processing and similarity evaluation of mass spectrometry data.
matchms - processing and similarity evaluation of mass spectrometry data. - Published in JOSS (2020)
pyhf
pyhf: pure-Python implementation of HistFactory statistical models - Published in JOSS (2021)
TextDescriptives
TextDescriptives: A Python package for calculating a large variety of metrics from text - Published in JOSS (2023)
SkyPy
SkyPy: A package for modelling the Universe - Published in JOSS (2021)
A Module for Calibrating Impact Functions in the Climate Risk Modeling Platform CLIMADA
A Module for Calibrating Impact Functions in the Climate Risk Modeling Platform CLIMADA - Published in JOSS (2024)
GCM-Filters
GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data - Published in JOSS (2022)
scores
scores: A Python package for verifying and evaluating models and predictions with xarray - Published in JOSS (2024)
PsychroLib
PsychroLib: a library of psychrometric functions to calculate thermodynamic properties of air - Published in JOSS (2019)
NOMAD CAMELS
NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems - Published in JOSS (2024)
TE-dependent analysis of multi-echo fMRI with tedana
TE-dependent analysis of multi-echo fMRI with tedana - Published in JOSS (2021)
pynucastro
pynucastro: an interface to nuclear reaction rates and code generator for reaction network equations - Published in JOSS (2018)
New developments in PySDM and PySDM-examples v2
New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol initialization, and adaptive time-stepping - Published in JOSS (2023)
pyro
pyro: a framework for hydrodynamics explorations and prototyping - Published in JOSS (2019)
DelaunayTriangulation.jl
DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane - Published in JOSS (2024)
Generating synthetic star catalogs from simulated data for next-gen observatories with py-ananke
Generating synthetic star catalogs from simulated data for next-gen observatories with py-ananke - Published in JOSS (2024)
Gibbs Sea Water Oceanographic Toolbox of TEOS-10 implemented in Rust
Gibbs Sea Water Oceanographic Toolbox of TEOS-10 implemented in Rust - Published in JOSS (2024)
pentapy
pentapy: A Python toolbox for pentadiagonal linear systems - Published in JOSS (2019)
otoole
otoole: OSeMOSYS Tools for Energy Work - Published in JOSS (2023)
AMReX
AMReX: a framework for block-structured adaptive mesh refinement - Published in JOSS (2019)
The pdb2sql Python Package
The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queries - Published in JOSS (2020)
Pyglmnet
Pyglmnet: Python implementation of elastic-net regularized generalized linear models - Published in JOSS (2020)
DeepRank2
DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning - Published in JOSS (2024)
Manopt.jl
Manopt.jl: Optimization on Manifolds in Julia - Published in JOSS (2022)
kuibit
kuibit: Analyzing Einstein Toolkit simulations with Python - Published in JOSS (2021)
Open OnDemand
Open OnDemand: A web-based client portal for HPC centers - Published in JOSS (2018)
Nanoq
Nanoq: ultra-fast quality control for nanopore reads - Published in JOSS (2022)
Speakerbox
Speakerbox: Few-Shot Learning for Speaker Identification with Transformers - Published in JOSS (2023)
OSTIR
OSTIR: open source translation initiation rate prediction - Published in JOSS (2021)
uravu
uravu: Making Bayesian modelling easy(er) - Published in JOSS (2020)
py-sc-fermi
py-sc-fermi: self-consistent Fermi energies and defect concentrations from electronic structure calculations - Published in JOSS (2023)
CASTRO
CASTRO: A Massively Parallel Compressible Astrophysics Simulation Code - Published in JOSS (2020)
A Framework to Quality Control Oceanographic Data
A Framework to Quality Control Oceanographic Data - Published in JOSS (2020)
physical_validation
physical_validation: A Python package to assess the physical validity of molecular simulation results - Published in JOSS (2022)
mosartwmpy
mosartwmpy: A Python implementation of the MOSART-WM coupled hydrologic routing and water management model - Published in JOSS (2021)
HydroMT
HydroMT: Automated and reproducible model building and analysis - Published in JOSS (2023)
sorn
sorn: A Python package for Self Organizing Recurrent Neural Network - Published in JOSS (2021)
NiBetaSeries
NiBetaSeries: task related correlations in fMRI - Published in JOSS (2019)
The MTPy software package for magnetotelluric data analysis and visualisation
The MTPy software package for magnetotelluric data analysis and visualisation - Published in JOSS (2019)
timeseriesflattener
timeseriesflattener: A Python package for summarizing features from (medical) time series - Published in JOSS (2023)
antimeridian
antimeridian: A Python package for correcting geometries that cross the 180th meridian - Published in JOSS (2025)
CGC
CGC: a Scalable Python Package for Co- and Tri-Clustering of Geodata Cubes - Published in JOSS (2022)
Underworld2
Underworld2: Python Geodynamics Modelling for Desktop, HPC and Cloud - Published in JOSS (2020)
SysIdentPy
SysIdentPy: A Python package for System Identification using NARMAX models - Published in JOSS (2020)
biopeaks
biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals - Published in JOSS (2020)
Pyafscgap.org
Pyafscgap.org: Open source multi-modal Python-based tools for NOAA AFSC RACE GAP - Published in JOSS (2023)
PlanetMapper
PlanetMapper: A Python package for visualising, navigating and mapping Solar System observations - Published in JOSS (2023)
NodePy
NodePy: A package for the analysis of numerical ODE solvers - Published in JOSS (2020)
Pooltool
Pooltool: A Python package for realistic billiards simulation - Published in JOSS (2024)
pyOptSparse
pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems - Published in JOSS (2020)
CADET-Core 5.0
CADET-Core 5.0: High-Performance Solver for Advanced Biotechnology Process Modeling - Published in JOSS (2025)
DeepReg
DeepReg: a deep learning toolkit for medical image registration - Published in JOSS (2020)
msmhelper
msmhelper: A Python package for Markov state modeling of protein dynamics - Published in JOSS (2023)
diyepw
diyepw: A Python package for Do-It-Yourself EnergyPlus weather file generation - Published in JOSS (2021)
xCDAT
xCDAT: A Python Package for Simple and Robust Analysis of Climate Data - Published in JOSS (2024)
CLOVER
CLOVER: A modelling framework for sustainable community-scale energy systems - Published in JOSS (2023)
MAESTROeX
MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver - Published in JOSS (2019)
SHARPy
SHARPy: A dynamic aeroelastic simulation toolbox for very flexible aircraft and wind turbines - Published in JOSS (2019)
AddaxAI
AddaxAI: A no-code platform to train and deploy custom YOLOv5 object detection models - Published in JOSS (2023)
TrixiParticles.jl
TrixiParticles.jl: Particle-based multiphysics simulation in Julia - Published in JOSS (2025)
Clouddrift
Clouddrift: a Python package to accelerate the use of Lagrangian data for atmospheric, oceanic, and climate sciences - Published in JOSS (2024)
SummationByPartsOperators.jl
SummationByPartsOperators.jl: A Julia library of provably stable discretization techniques with mimetic properties - Published in JOSS (2021)
CoastSeg
CoastSeg: an accessible and extendable hub for satellite-derived-shoreline (SDS) detection and mapping - Published in JOSS (2024)
PyFstat
PyFstat: a Python package for continuous gravitational-wave data analysis - Published in JOSS (2021)
portalr
portalr: an R package for summarizing and using the Portal Project Data - Published in JOSS (2019)
MetSim
MetSim: A Python package for estimation and disaggregation of meteorological data - Published in JOSS (2020)
GrainLearning
GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials - Published in JOSS (2024)
HOHQMesh
HOHQMesh: An All Quadrilateral/Hexahedral Unstructured Mesh Generator for High Order Elements - Published in JOSS (2024)
OfflineMOT
OfflineMOT: A Python package for multiple objects detection and tracking from bird view stationary drone videos - Published in JOSS (2022)
PII-Codex
PII-Codex: a Python library for PII detection, categorization, and severity assessment - Published in JOSS (2023)
PyProBE
PyProBE: Python Processing for Battery Experiments - Published in JOSS (2025)
byteparsing
byteparsing: a functional parser combinator for mixed ASCII/binary data - Published in JOSS (2023)
ewstools
ewstools: A Python package for early warning signals of bifurcations in time series data - Published in JOSS (2023)
pyndl
pyndl: Naïve Discriminative Learning in Python - Published in JOSS (2022)
Connectome Mapper 3
Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping - Published in JOSS (2022)
AIBECS.jl
AIBECS.jl: A tool for exploring global marine biogeochemical cycles. - Published in JOSS (2022)
BlueCelluLab
BlueCelluLab: Biologically Detailed Neural Network Experimentation API - Published in JOSS (2024)
bsym
bsym: A basic symmetry module - Published in JOSS (2017)
scribl
scribl: A system for the semantic capture of relationships in biological literature - Published in JOSS (2024)
Cacatoo
Cacatoo: building, exploring, and sharing spatially structured models of biological systems - Published in JOSS (2022)
WrightTools
WrightTools: a Python package for multidimensional spectroscopy - Published in JOSS (2019)
Chips-n-Salsa
Chips-n-Salsa: A Java Library of Customizable, Hybridizable, Iterative, Parallel, Stochastic, and Self-Adaptive Local Search Algorithms - Published in JOSS (2020)
SMITE
SMITE: Single Molecule Imaging Toolbox Extraordinaire (MATLAB) - Published in JOSS (2023)
HRV
HRV: a Pythonic package for Heart Rate Variability Analysis - Published in JOSS (2020)
PolarToolkit
PolarToolkit: Python Tools for Convenient, Reproducible, and Open Polar Science - Published in JOSS (2024)