jaxDecomp: JAX Library for 3D Domain Decomposition and Parallel FFTs - v0.3.1

What's Changed

Support nested sharding by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/113
Doc and isntallation updates by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/114
update JaxTimer and jax hpc profiler dependencies by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/115
Update paper plots by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/117
Update figures by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/118
update guidelines by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/119
JOSS review by @diehlpk in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/120
Bump to v0.3.1 by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/123

New Contributors

@diehlpk made their first contribution in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/120

Full Changelog: https://github.com/DifferentiableUniverseInitiative/jaxDecomp/compare/v0.3.0...v0.3.1

- Python
Published by ASKabalan 13 days ago

GaPFlow: Gap-averaged flow simulations with Gaussian process regression - v1.1.0

What's Changed

Fix Some Docstring Typos by @DanWaxman in https://github.com/hannes-holey/GaPFlow/pull/59
CI: pin jax version by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/61
JOSS review ch by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/62
JOSS review by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/60
JOSS: editorial suggestions by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/65
JOSS: fix JAX and tinygp bibtex entries by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/66
JOSS: fix software urls by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/67
Fine-tuning of active learning for molecular system by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/64

New Contributors

@DanWaxman made their first contribution in https://github.com/hannes-holey/GaPFlow/pull/59

Full Changelog: https://github.com/hannes-holey/GaPFlow/compare/v1.0.2...v1.1.0

- Python
Published by hannes-holey 24 days ago

DeepCausalMMM: A Deep Learning Framework for Marketing Mix Modeling with Causal Structure Learning - v1.0.20 Release

What's Changed

Release v1.0.19: Dependent Variable Mean Regional Scaling, Media and Seasonal Attribution Priors, and JOSS Publication Update by @adityapt in https://github.com/adityapt/deepcausalmmm/pull/9
Add Python 3.13 to test matrix by @adityapt in https://github.com/adityapt/deepcausalmmm/pull/10
FIX: Restore benchmark loader on Pandas 3 by @tomzhengy in https://github.com/adityapt/deepcausalmmm/pull/12
FIX: Align inference outputs with model contract by @tomzhengy in https://github.com/adityapt/deepcausalmmm/pull/11

New Contributors

@tomzhengy made their first contribution in https://github.com/adityapt/deepcausalmmm/pull/12

Full Changelog: https://github.com/adityapt/deepcausalmmm/compare/v1.0.17...v1.0.20

- Python
Published by adityapt about 1 month ago

Nexarag: Democratizing Reproducible Knowledge Graph Contexts for LLM Research - Automated Testing and Documentation

Nexarag Automated Testing and Documentation

Release

Version: 1.1.0
Release type: Testing and documentation
Scope: Extended automated test coverage and enhanced documentation for onboarding and contribution

Highlights

Frontend and backend automated testing
Detailed video guides for deployment and usage
Contribution standards and steps
Tightened paper language to conform to JOSS standards

- Jupyter Notebook
Published by ben-n-fuller about 1 month ago

DataBallPy: Load, synchronize, and Analyse your Soccer Data - Version 0.7.3

What's Changed

Added way to get frame of tracking data based on team possession or event data team by @Alek050 in https://github.com/Alek050/databallpy/pull/251
Added easier way of getting filters on column ids by @Alek050 in https://github.com/Alek050/databallpy/pull/252
WIP: Bundesliga open data by @Alek050 in https://github.com/Alek050/databallpy/pull/253
Added ruff as linting manager by @Alek050 in https://github.com/Alek050/databallpy/pull/255
Logging wrapper by @Alek050 in https://github.com/Alek050/databallpy/pull/257
release for v0.5.2 by @Alek050 in https://github.com/Alek050/databallpy/pull/259
Statsbomb event parser by @DaanGro in https://github.com/Alek050/databallpy/pull/254
fixed bug opta positions by @Alek050 in https://github.com/Alek050/databallpy/pull/265
Add JSON parser for tracab metadata by @jan-swiatek in https://github.com/Alek050/databallpy/pull/266
Fixed some small bugs in synchronise, read tracab xml, and aligning players from tracking and event metadata by @Alek050 in https://github.com/Alek050/databallpy/pull/269
Release 0.5.3 by @Alek050 in https://github.com/Alek050/databallpy/pull/271
Support for python 3.13 by @Alek050 in https://github.com/Alek050/databallpy/pull/256
Added statsbomb event id by @Alek050 in https://github.com/Alek050/databallpy/pull/273
Specify min max pitch dimensions to be between logical values by @Alek050 in https://github.com/Alek050/databallpy/pull/275
fixed scisports parser bug in shot events by @Alek050 in https://github.com/Alek050/databallpy/pull/284
Sportec remove assumption that first player frame is first frame of second half by @Alek050 in https://github.com/Alek050/databallpy/pull/290
V0.5.4 by @Alek050 in https://github.com/Alek050/databallpy/pull/292
Version 0.6.0 by @Alek050 in https://github.com/Alek050/databallpy/pull/297
Main by @Alek050 in https://github.com/Alek050/databallpy/pull/298
Add allow_overwrite kwarg to add_velocity and add_acceleration by @Alek050 in https://github.com/Alek050/databallpy/pull/303
Fixed scisports new format v1 by @Alek050 in https://github.com/Alek050/databallpy/pull/304
V0.6.1 release by @Alek050 in https://github.com/Alek050/databallpy/pull/306
308 bug dfl download link by @Alek050 in https://github.com/Alek050/databallpy/pull/309
Version 0.6.2 by @Alek050 in https://github.com/Alek050/databallpy/pull/310
bug in player possession calculation by @Alek050 in https://github.com/Alek050/databallpy/pull/311
small changes by @Alek050 in https://github.com/Alek050/databallpy/pull/314
support for frame_rate as float by @Alek050 in https://github.com/Alek050/databallpy/pull/315
Kloppy Support by @UnravelSports in https://github.com/Alek050/databallpy/pull/307
V0.7.0 release by @Alek050 in https://github.com/Alek050/databallpy/pull/317
Added offside logic by @Alek050 in https://github.com/Alek050/databallpy/pull/319
318 enh offside filter by @Alek050 in https://github.com/Alek050/databallpy/pull/320
updated logo by @Alek050 in https://github.com/Alek050/databallpy/pull/322
Better color selection of text in plot_tracking_data by @Alek050 in https://github.com/Alek050/databallpy/pull/324
Add dangerous accessible space and expected completion. by @jonas-bischofberger in https://github.com/Alek050/databallpy/pull/321
Updated changelog for DAS functionality by @Alek050 in https://github.com/Alek050/databallpy/pull/325
tkinter fix in git actions by @Alek050 in https://github.com/Alek050/databallpy/pull/326
bug fixes in validation of tracking and event data schemas by @Alek050 in https://github.com/Alek050/databallpy/pull/328
Version0.7.2rc by @Alek050 in https://github.com/Alek050/databallpy/pull/329
Bug in get column ids when end frame is smaller than start frame by @Alek050 in https://github.com/Alek050/databallpy/pull/334
From kloppy skillcorner fix by @Alek050 in https://github.com/Alek050/databallpy/pull/335
Fix for IDSSE download link from FigShare by @Alek050 in https://github.com/Alek050/databallpy/pull/342
Change default caching behavior by @Alek050 in https://github.com/Alek050/databallpy/pull/343
Changed event unasigned error to warning by @Alek050 in https://github.com/Alek050/databallpy/pull/345
Added platformdirs & python3.14 by @Alek050 in https://github.com/Alek050/databallpy/pull/347
fix for pandera & pandas integration python 3.14 by @Alek050 in https://github.com/Alek050/databallpy/pull/348
Enh to xml by @Alek050 in https://github.com/Alek050/databallpy/pull/353
Added CONTRIBUTING.md file by @Alek050 in https://github.com/Alek050/databallpy/pull/364
Remove bs4 as dependency by @Alek050 in https://github.com/Alek050/databallpy/pull/355
Added references to DataBallPy Discussions in ReadMe and docs by @Alek050 in https://github.com/Alek050/databallpy/pull/371
Updated get open game docstrings and added synchronisation to visualisation documentation page by @Alek050 in https://github.com/Alek050/databallpy/pull/372
More elaborate API docs by @Alek050 in https://github.com/Alek050/databallpy/pull/373
Fifa parser by @Alek050 in https://github.com/Alek050/databallpy/pull/374

New Contributors

@jan-swiatek made their first contribution in https://github.com/Alek050/databallpy/pull/266
@UnravelSports made their first contribution in https://github.com/Alek050/databallpy/pull/307
@jonas-bischofberger made their first contribution in https://github.com/Alek050/databallpy/pull/321

Full Changelog: https://github.com/Alek050/databallpy/compare/v0.5.1...v0.7.3

Make ready for Zenodo

- Python
Published by Alek050 about 1 month ago

Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging - Release v1.1.8

Full Changelog: https://github.com/JosephBrunet/cardiotensor/compare/v1.1.7...v1.1.8

- Python
Published by github-actions[bot] about 2 months ago

Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging - Release v1.1.7

What's Changed

Limit handlers for processing in windows by @lchestnutt in https://github.com/JosephBrunet/cardiotensor/pull/26
fix: Update cardio-analysis command to use --N-slice flag in documentation by @by22Jy in https://github.com/JosephBrunet/cardiotensor/pull/29
Fix typos and enhance documentation with advanced section and images by @JosephBrunet in https://github.com/JosephBrunet/cardiotensor/pull/30
Add metadata example by @JosephBrunet in https://github.com/JosephBrunet/cardiotensor/pull/32
Improve slurm launcher by @JosephBrunet in https://github.com/JosephBrunet/cardiotensor/pull/33
Improve slurm launcher by @JosephBrunet in https://github.com/JosephBrunet/cardiotensor/pull/34

New Contributors

@by22Jy made their first contribution in https://github.com/JosephBrunet/cardiotensor/pull/29

Full Changelog: https://github.com/JosephBrunet/cardiotensor/compare/v1.1.6...v1.1.7

- Python
Published by github-actions[bot] about 2 months ago

Felino: Extension of an open-source phase-field framework to geomaterial fracture - v1.0.2

- SWIG
Published by DanielChou0916 2 months ago

flodym: A Python package for dynamic material flow analysis - v0.7.0

Empty version increment for Zenodo syncing.

What's Changed

increment version by @JakobBD in https://github.com/pik-piam/flodym/pull/148

Full Changelog: https://github.com/pik-piam/flodym/compare/v0.6.0...v0.7.0

- Python
Published by JakobBD 2 months ago

flodym: A Python package for dynamic material flow analysis - v0.6.0

What's Changed

Enable MFA systems without stocks by @JakobBD in https://github.com/pik-piam/flodym/pull/142
Notebooks workflow by @JakobBD in https://github.com/pik-piam/flodym/pull/143
Update notebooks by @JakobBD in https://github.com/pik-piam/flodym/pull/144
update readme with information on how to contribute and reach out by @JakobBD in https://github.com/pik-piam/flodym/pull/145
increment version by @JakobBD in https://github.com/pik-piam/flodym/pull/147

Full Changelog: https://github.com/pik-piam/flodym/compare/v0.5.4...v0.6.0

- Python
Published by JakobBD 2 months ago

baysc: An R package for Bayesian survey clustering - v0.1.2 - JOSS manuscript updated

Shortened JOSS manuscript and updated package vignette.

- R
Published by smwu 3 months ago

SkyRank: a unified toolkit for Skyline ranking, benchmarking, and visualization - SkyRank v1.1.1

This release includes several improvements and fixes based on the JOSS review process.

Changes: - Unit tests were added and updated to improve reliability. - The UI layer was refactored to correctly handle Skyline point mapping, including edge cases (e.g., single-point skylines). - Fixed documentation issues and broken links (e.g., the CONTRIBUTING reference). - General code cleanup and minor improvements.

These updates improve the toolkit's stability, documentation consistency, and overall usability.

- Python
Published by Turlure-Nael-23018992 3 months ago

SkyRank: a unified toolkit for Skyline ranking, benchmarking, and visualization - SkyRank v1.1.0

This release includes several improvements and fixes based on the JOSS review process.

Changes: - Unit tests were added and updated to improve reliability. - The UI layer was refactored to correctly handle Skyline point mapping, including edge cases (e.g., single-point skylines). - Fixed documentation issues and broken links (e.g., the CONTRIBUTING reference). - General code cleanup and minor improvements.

These updates improve the toolkit's stability, documentation consistency, and overall usability.

- Python
Published by Turlure-Nael-23018992 3 months ago

HierarchyCraft: A Benchmark Builder for Hierarchical Reasoning - JOSS Paper release

What's Changed

Fix missing/incorrect references; cite published versions of preprints by @logological in https://github.com/IRLL/HierarchyCraft/pull/49
Fix: add missing DOIs for citations by @liyuxuan-academic in https://github.com/IRLL/HierarchyCraft/pull/50
Remove invalid DOIs by @logological in https://github.com/IRLL/HierarchyCraft/pull/51

New Contributors

@logological made their first contribution in https://github.com/IRLL/HierarchyCraft/pull/49
@liyuxuan-academic made their first contribution in https://github.com/IRLL/HierarchyCraft/pull/50

Full Changelog: https://github.com/IRLL/HierarchyCraft/compare/v2.0.0...v2.0.1

- Python
Published by MathisFederico 3 months ago

TransiFlow: A Python package for performing bifurcation analysis on fluid flow problems - v1.0.1

This release only contains some minor updates to the documentation.

- Python
Published by Sbte 3 months ago

multimodars: A Rust-powered toolkit for multi-modality cardiac image fusion and registration - Ground Truth

This release synchronizes all documentation and examples with the current API. No functional changes -> all features from v0.2.0/v0.2.1 remain:

Read in contour data from intravascular images (lumen, eem, calcium, sidebranch) and create a pseudo 3D model
Rotate/Translate neighbouring frames to minimize Hausdorff distance (parallelized)
Fill holes/smooth and other fixes
Align between different pullbacks with automated spacing adjustment (different heartrate)
Save one (or several interpolated) pseudo 3D models to .obj files (with a calculated deformation map)
Create adventitia (or intramural aortic wall for AAOCA) and catheter .obj files
Read in CCTA data and label different regions based on the centerlines (aorta, rca, lca)
Align intravascular images with the CCTA centerline based on landmark points (and Hausdorff distances)
Label the CCTA region to be replaced and scale different regions to match the intravascular segment

Changed in this release:

Updated all documentation tutorials to match the current API (fromfilesinglepair, fromarraysinglepair, PyInputData, alignthreepoint, updated numpytogeometry parameters)
Updated README quickstart example and added figures for centerline alignment, CCTA labeling and scaling
Fixed broken image links and removed stale references

Additional files:

examples.zip includes updated csv files from different intravascular imaging cases, a CCTA .stl file, and a Jupyter notebook (ivus_to_centerline.ipynb) teaching the usage of multimodars and now fully in sync with the documentation.

Next Release will include the full fusion functionality of intravascular and CCTA geometries.

- Rust
Published by yungselm 3 months ago

DSWL package: a Python implementation of the Debiased Spatial Whittle Likelihood - v2.1.3 - JOSS paper release

What's Changed

Update paper to account for new structure of package by @arthurBarthe in https://github.com/arthurBarthe/debiased-spatial-whittle/pull/39

Full Changelog: https://github.com/arthurBarthe/debiased-spatial-whittle/compare/v2.1.2...v2.1.3

- Python
Published by arthurBarthe 3 months ago

FastTanhSinhQuadrature.jl: High-performance Tanh-Sinh numerical integration in Julia - v1.0.1

FastTanhSinhQuadrature v1.0.1

Diff since v1.0.0

v1.0.1 (patch release)

Summary

This release focuses on quality and maintenance improvements (no API-breaking changes).

Changes

Improved and clarified documentation across README and docs pages.
Expanded test coverage, including complementary-form integrands and stronger 3D cases.
Added a cross-library benchmark workflow and published benchmark result tables.
Fixed package metadata for registration by correcting the Test stdlib UUID in Project.toml.

Breaking changes

None.

Merged pull requests: - Move export block after includes to avoid Julia 1.12+ world-age warnings (#5) (@svretina) - Fix quad_cmpl complementary coordinate handling and docs (#6) (@svretina) - Gate JET type-stability tests by Julia version and JET API line (#7) (@svretina) - CI: test Julia 1.9–1.13 + nightly; make nightly non-blocking and tolerate AVX failures on 1.13+ (#8) (@svretina) - Improve quadrature tests (1D/3D families), split test suite, and fix bounded 3D plane mapping (#9) (@svretina) - Fix/precomputed nodes bound types (#10) (@svretina) - Docs/readme refresh, updated Benchmarks (#11) (@svretina) - Follow-up to #11: Multi-library benchmark harness and published timing tables (#12) (@svretina)

Closed issues: - TagBot trigger issue (#1) - package installation (#2) - code coverage (#3) - README examples: quad_cmpl gives wrong value and precomputed-nodes snippet fails with type mismatch (#4)

- Julia
Published by github-actions[bot] 3 months ago

Nexarag: Democratizing Reproducible Knowledge Graph Contexts for LLM Research - Nexarag Initial Release

Nexarag Initial Release Notes

Release

Version: 1.0.0
Release type: Initial public release
Scope: End-to-end local platform for research knowledge-graph construction, exploration, and AI-assisted querying

Highlights

Build knowledge graphs from Semantic Scholar search results and BibTeX imports.
Expand graph context by adding paper citations and references.
Upload PDF/Markdown/Text documents as graph-linked artifacts; PDF uploads are converted to markdown for downstream embedding.
Query graph context through integrated chat (RAG-style responses over papers, metadata, and uploaded documents).
Generate embedding-based 2D visualizations (PCA) with label-based grouping.
Export, import, list, switch, and delete saved knowledge graphs.
Integrate external AI clients via MCP over HTTP (/mcp).

Included Components

Frontend: Angular UI with interactive Cytoscape graph exploration and Plotly visualizations.
API service: FastAPI endpoints for papers, graph operations, documents, chat, visualization requests, health checks, model listing, and KG management.
KG worker service: asynchronous graph-building, embedding, and chat response workflows.
MCP service: tools for paper search/addition and language-to-Cypher query execution.
Data services: Neo4j (graph store), RabbitMQ (event bus), Ollama (local model runtime).

Deployment and Runtime

Deployment model: Docker Compose (Mac, Linux/WSL CPU, Linux/WSL GPU profiles).
Default local endpoints:
- Frontend: http://localhost:5000 (or 5100 on Mac profile)
- API: http://localhost:8000
- MCP: http://localhost:9000/mcp
- Ollama: http://localhost:11434
Core runtime requirements:
- Docker (plus WSL2 on Windows)
- Ollama models for embedding/chat/MCP flows (defaults: nomic-embed-text:v1.5, gemma3:1b, qwen3:8b)

Configuration

Environment-variable driven runtime configuration for ports, credentials, model selection, and embedding chunking.
Graph export artifacts and metadata are persisted under kg_dumps (mapped Docker volume/path).

Known Limitations

Semantic Scholar ingestion is rate-limited and can delay graph updates.
Knowledge graph import/export operations are designed around one active graph context at a time.
API CORS is currently permissive and service authentication is not enabled by default in this release.

Test Coverage

Backend test suite present for key utility and messaging paths, including:
- API upload and socket utility behavior
- RabbitMQ message serialization/publish/connection logic
- Semantic Scholar retry logic

- Jupyter Notebook
Published by ben-n-fuller 3 months ago

FastTanhSinhQuadrature.jl: High-performance Tanh-Sinh numerical integration in Julia - v1.0.0

FastTanhSinhQuadrature.jl v1.0.0

First stable release of FastTanhSinhQuadrature.jl: fast, high-accuracy numerical integration with Tanh-Sinh (double-exponential) quadrature.

Highlights

High-level adaptive interface: quad
Support for 1D/2D/3D integration
Precomputed-node workflows for repeated integrations
SIMD-accelerated paths (integrate*_avx) via LoopVectorization.jl
Utilities for difficult endpoint behavior (quad_split, complementary-coordinate interface)

Installation

julia import Pkg Pkg.add("FastTanhSinhQuadrature")

Compatibility (v1.0.0): Julia: 1.10, 1.11

- Julia
Published by svretina 3 months ago

times_model - TIMES Version 4.9.3

TIMES Version 4.9.3

Date: 23-Feb-2026 [AL]: Minor release 1) Added support for auto-generation of singleton GR_GENMAP 2) Updated Climate Module default parameters 3) Added support for OCOM flows from retirements, subject to age 4) Added support for reporting value flows under stochastics 5) Cosmetic improvements

Modified files: (reason) initsys.mod : Increased version number to 4.9.3 setglobs.gms : (3) coefnio.mod : (3) coefshp.mod : (3) calcap.mod : (3) calcaps.mod : (5) initmty.vda : (3) initext.vda : (3) prepext.vda : (3) powerflo.vda : (1) initmty.cli : (2) ppmext.cli : (2) coefext.cli : (5) prepret.dsc : (3) solputta.ans : (5) rptlite.rpt : (4) rptobj.rpt : (5) costann.rpt : (5) rptmisc.rpt : (4) pextlevs.stc : (4)

- GAMS
Published by Antti-L 3 months ago

pypsa - v1.1.2

Revised release notes are available in the documentation.

What's Changed

fix serentica user doc entry by @pz-max in https://github.com/PyPSA/PyPSA/pull/1571
docs: Fix a couple of typos by @mgrabovsky in https://github.com/PyPSA/PyPSA/pull/1572
fix(statistics): allow at_port to be specified manually by @coroa in https://github.com/PyPSA/PyPSA/pull/1386
fix: log_to_console breaking cplex by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1575
fix: release pipeline committing to wrong branch by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1577

Full Changelog: https://github.com/PyPSA/PyPSA/compare/v1.1.0...v1.1.2

- Python
Published by github-actions[bot] 3 months ago

pypsa - v1.1.1

Revised release notes are available in the documentation.

What's Changed

fix serentica user doc entry by @pz-max in https://github.com/PyPSA/PyPSA/pull/1571
docs: Fix a couple of typos by @mgrabovsky in https://github.com/PyPSA/PyPSA/pull/1572
fix(statistics): allow at_port to be specified manually by @coroa in https://github.com/PyPSA/PyPSA/pull/1386
fix: log_to_console breaking cplex by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1575

Full Changelog: https://github.com/PyPSA/PyPSA/compare/v1.1.0...v1.1.1

- Python
Published by github-actions[bot] 3 months ago

pypsa - v1.1.0

Revised release notes are available in the documentation.

What's Changed

Update users.md / d-fine & Fraunhofer ISI by @gincrement in https://github.com/PyPSA/PyPSA/pull/1524
Update models.md / add PyPSA-IEI by @gincrement in https://github.com/PyPSA/PyPSA/pull/1523
feat: add environment variable support for options by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1513
Networks statistics (i)plot refactor and new sanitize functions by @FabianHofmann in https://github.com/PyPSA/PyPSA/pull/1401
fix: pin linopy >= v0.6.1, add tests for log free import, pin pandas < v3.0.0 by @FabianHofmann in https://github.com/PyPSA/PyPSA/pull/1532
fix: update and simplify docs deps & temporary remove demand elasticity example by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1459
fix: ramp limit contstraints failing because of mismatched index by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1537
Add includeobjectiveconstant parameter to optimize by @FabianHofmann in https://github.com/PyPSA/PyPSA/pull/1509
fix: allow passing True to aggregate time which maps to default by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1538
fix: pathlib paths in collections by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1530
feat: Add temporal clustering functionality by @FabianHofmann in https://github.com/PyPSA/PyPSA/pull/1508
feat: split capital_cost into investment and FOM costs by @FabianHofmann in https://github.com/PyPSA/PyPSA/pull/1507
build(deps): bump prefix-dev/setup-pixi from 0.9.3 to 0.9.4 in the github-actions group by @dependabot[bot] in https://github.com/PyPSA/PyPSA/pull/1545
feat: set pypsa options via .env file by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1531
Feat: allow p_set for StorageUnit components by @Irieo in https://github.com/PyPSA/PyPSA/pull/1549
ci: configure Gurobi as default solver for docs build by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1548
Add SALib global sensitivity analysis example by @fneum in https://github.com/PyPSA/PyPSA/pull/1318
Revert "docs: temporary remove demand elasticity example" by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1539
add water values example by @fneum in https://github.com/PyPSA/PyPSA/pull/1492
import series only if not empty for oneport components by @yerbol-akhmetov in https://github.com/PyPSA/PyPSA/pull/1528
docs: notebook cleanup by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1551
docs: add partial elastic demand and log-log approximation by @flxlchr in https://github.com/PyPSA/PyPSA/pull/1519
docs: add demand and supply bid market example by @flxlchr in https://github.com/PyPSA/PyPSA/pull/1536
Update models.md by @gincrement in https://github.com/PyPSA/PyPSA/pull/1554
fix: align dimensions to not rely on transpose in linopy by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1557
feat: pandas v3 support by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1556
Line losses with error control by @lindnemi in https://github.com/PyPSA/PyPSA/pull/1495
docs: better transmission stats docs by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1560
fix: docs version selector on readthedocs by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1563
docs: new docs page for pypsa warnings by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1562
fix: follow up on #1562 by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1564
ramp limit consolidation and fix by @FabianHofmann in https://github.com/PyPSA/PyPSA/pull/1553
Rebased and updated version of #1431. Applies nicename to buscarrier grouping in statistics. by @lukasschirren in https://github.com/PyPSA/PyPSA/pull/1565
clustering api change and better docs by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1567
Make extendability and committability compatible, when modularity is on by @enricogiglio in https://github.com/PyPSA/PyPSA/pull/1007

New Contributors

@lukasschirren made their first contribution in https://github.com/PyPSA/PyPSA/pull/1565

Full Changelog: https://github.com/PyPSA/PyPSA/compare/v1.0.7...v1.1.0

- Python
Published by github-actions[bot] 3 months ago

Graphorge: An open-source forge of graph neural networks - Graphorge 1.0.1

New Features and Improvements

JOSS publication: this release follows the review process of the Journal of Open Source Software. See: https://github.com/openjournals/joss-reviews/issues/9453
MeshGraphNet (MGN) benchmark release: https://github.com/bessagroup/graphorge/pull/35

Bug Fixes

None

Full Changelog: https://github.com/bessagroup/graphorge/compare/1.0.0...1.0.1

- Jupyter Notebook
Published by GuillaumeBroggi 3 months ago

IdentityByDescentDispersal.jl: Inferring dispersal rates with identity-by-descent blocks - v1.0.0+docs

Add citation file

- Julia
Published by currocam 3 months ago

IdentityByDescentDispersal.jl: Inferring dispersal rates with identity-by-descent blocks - v1.0.0

IdentityByDescentDispersal v1.0.0

Diff since v0.1.4

Breaking changes

Automatically fallback to quadrature rules for large bins. This will produce more accurate predictions but might produce discrepancies with the trapezoidal rule used in previous versions.

Minor changes

Improved documentation Improved nested integration

Merged pull requests: - Bump actions/upload-artifact from 5 to 6 (#29) (@dependabot[bot]) - Bump actions/cache from 4 to 5 (#30) (@dependabot[bot]) - Bump peter-evans/create-pull-request from 7 to 8 (#31) (@dependabot[bot]) - [AUTO] pre-commit update (#32) (@github-actions[bot]) - Dev (#34) (@currocam) - Review feedback (#37) (@currocam) - Update README.md (#38) (@arzwa) - Update README.md (#39) (@arzwa)

Closed issues: - JOSS Review Comments: Package only (#35) - JOSS Review Comments: Paper (#36)

- Julia
Published by github-actions[bot] 3 months ago

biodiscvr: Biomarker Discovery Using Composite Value Ratios - v1.3.0: JOSS Review Completion Release

Update addressing peer‑review feedback. This release adds new validation checks, more user‑friendly vignettes with executable synthetic‑data examples, and expanded documentation detailing the software architecture.

- R
Published by isaac-6 3 months ago

Copernicus Seasonal Forecast Tools Package: Bridging Seasonal Climate Predictions and Impact Models for Operational Risk Assessment - copernicus-seasonal-forecast-tools v0.1.1 — JOSS submission

This repository hosts the copernicus-seasonal-forecast-tools, a Python package developed to manage seasonal forecast data from the Copernicus Climate Data Store (CDS) as part of the U-CLIMADAPT project.

It offers comprehensive tools for downloading, processing, computing climate indices, and generating hazard objects based on seasonal forecast datasets, particularly Seasonal forecast daily and subdaily data on single levels. The package is tailored to integrate seamlessly with the CLIMADA (CLIMate ADAptation) platform, supporting climate risk assessment and the development of effective adaptation strategies.

Users can:

Automatically download of high-resolution seasonal forecast data via the CDS API
Preprocess sub-daily fields into daily aggregates
Compute heat-related indices (e.g., heatwave days, tropical nights, TX30)
Generate CLIMADA hazard objects
Benefit from the modular design for extending to new indices or forecast products

- Python
Published by DahyannAraya 4 months ago

pyfive: A pure-Python HDF5 reader - Release v1.1.0

What's Changed

Timing + Optimisations + Minor fixes by @bnlawrence in https://github.com/NCAS-CMS/pyfive/pull/191 - an excellent contribution towards serious optimization!
Add support for pre-commit with mypy and Ruff and start adding type hints by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/173
[JOSS REVIEW PR] Harmonize depenedncies from environment.yml and pyproject.toml by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/174
pep639 license by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/180
add CONTRIBUTING.md file (and contributing guidelines, of course) by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/181
Documentation consistency fixes by @Zeitsperre in https://github.com/NCAS-CMS/pyfive/pull/175
Allow negative slices when indexing chunked data by @davidhassell in https://github.com/NCAS-CMS/pyfive/pull/170
Overhaul .gitignore file by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/179
add link to Pyfive GitHub repository on doc landing page by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/185
Skip tests if ceda-jasmin s3 storage is offline by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/187
Add orthogonal_indexing flag by @davidhassell in https://github.com/NCAS-CMS/pyfive/pull/182
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/NCAS-CMS/pyfive/pull/188
Replace python-lzf with python-neo-lzf by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/189

New Contributors

@Zeitsperre made their first contribution in https://github.com/NCAS-CMS/pyfive/pull/175 as part of the JOSS review, also @dostuffthatmatters contributed towards the JOSS paper review, and gave us good advice on how to improve bits - thank you, gents :beers:
@pre-commit-ci[bot] made their first contribution in https://github.com/NCAS-CMS/pyfive/pull/188 as auto-updater for the pre-commit versions

Full Changelog: https://github.com/NCAS-CMS/pyfive/compare/v1.0.1...v1.1.0

- Python
Published by valeriupredoi 4 months ago

Tissue Data Explorer: a website template for presenting tissue sample research findings - Tissue Data Explorer v1.0.0

The first release of Tissue Data Explorer

- Python
Published by james-labyer 4 months ago

Dyad: a binary-star dynamics and statistics library for Python - Dyad 0.1.0

Initial release with accompanying paper published in The Journal of Open Source Software.

- Python
Published by AmeryGration 4 months ago

jaxDecomp: JAX Library for 3D Domain Decomposition and Parallel FFTs - v0.3.0

What's Changed

Update for joss review 2 by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/98
refactor: improve validation and error handling in cuDecomp backend by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/102
Update cudecomp cpp by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/103
update docs and README to use AxisType.Auto in mesh creation by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/104
Migrating to ffi by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/105
Update docs by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/106
Fix bug with transpose and halo exchange lowering by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/107
Add a better benchmark script by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/108
jax.tools.colabtpu.setuptpu() no longer needed by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/109
Update CITATION by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/110
Bump version to 0.3.0 by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/111
Fix build wheel action by @ASKabalan in https://github.com/DifferentiableUniverseInitiative/jaxDecomp/pull/112

Full Changelog: https://github.com/DifferentiableUniverseInitiative/jaxDecomp/compare/v0.2.9...v0.3.0

- Python
Published by ASKabalan 4 months ago

ParaDigMa: a Python toolbox for extracting Parkinson's disease digital biomarkers from daily life wrist sensor data - v1.1.0 - Add entrypoint, add orchestration, and expand documentation

Features

Orchestrator Pipeline: Added orchestrator.py with run_paradigma() function for complete end-to-end ParaDigMa analysis pipeline from data loading to aggregated results.
Data Preparation: Added prepare_data.py with automatic data preparation capabilities, including column mapping for flexible column names, watch orientation adjustment, and comprehensive validation.
Centralized Loading: Added load.py to centralize data loading capabilities across all pipelines.
High-Level Pipeline Functions: Added run_gait_pipeline(), run_tremor_pipeline(), and run_pulse_rate_pipeline() for simplified pipeline execution.
Segment Distinction: Added GAIT_SEGMENT_NR and DATA_SEGMENT_NR constants to distinguish between temporal gaps and gait bouts. SEGMENT_NR kept as deprecated alias for backward compatibility.
Test Data: Added Physilog Gait-Up test data to LFS.

Improvements

Logging System: Replaced verbose parameter with standard Python logging using logginglevel and customlogger parameters across all pipeline functions for better control and traceability.
Data Segment Preservation: Modified quantify_arm_swing() to preserve datasegmentnr when present in input data.
Bug Fixes: Fixed NaN propagation in resampling by interpolating NaN values before resampling (scipy cannot handle NaN in non-contiguous data).

Documentation

New Tutorials: Added pipeline_orchestrator.ipynb tutorial demonstrating end-to-end processing with logging control examples.
New Guides: Added comprehensive guides for datainput, installation, sensorrequirements, supported_devices, and validation.
Readme: Shortened README.md for readability and expanded detailed guides.
PEP Standards: Updated all docstrings and function signatures to PEP standards.
Build System: Added single-notebook build support with --notebook argument; automated style tag removal in documentation build pipeline.

Testing

Added minimal testing for new pipeline functionalities.
Added tests for segment column naming and backward compatibility.
Added tests to verify data segment tracking preservation.

Backward Compatibility

All existing code using SEGMENT_NR continues to work.
Previously used pipeline code remains functional.

- Python
Published by github-actions[bot] 4 months ago

SOFIA: A Python Library for High-Quality 2D Triangular Mesh Adaptation - v0.1.0

SOFIA is a pure Python library for 2D triangular mesh modification and remeshing. It provides robust, high-quality local operations to edit, refine, and optimize meshes while maintaining mesh conformity and quality.

Perfect for: - Computational scientists working with 2D simulations - Computer graphics professionals needing mesh processing - Numerical analysis requiring adaptive mesh refinement - Researchers in mesh generation and optimization

- Python
Published by youssef-mesri 4 months ago

MieSimulatorGUI: A user-friendly tool to compute and visualize light scattering by spherical dielectric particles - Version 2.0

Mie Simulator GUI 2.0

Downloads

Installers
- Windows Installer: MieSimulatorGUIv20.exe
- MacOS Installer: MieSimulatorGUIv20.app.zip
Stand-alone Packages
- Windows Compressed Application Package: MieSimulatorGUIv20.zip
- MacOS Disk Image: MieSimulatorGUIv20.dmg
- Linux AppImage: MieSimulatorGUIv20.AppImage

Getting Started

Release Notes

New Features & Enhancements

Updated Libraries: We have upgraded the core framework from Qt 5 to Qt 6 (Version 6.2.4) and updated the plotting library QCustomPlot from version 2.0.1 to 2.1.1, which eliminates the need for the Qwt library.
Enhanced Plotting: The old Qwt library has been replaced with QCustomPlot for polar plots. Users can now zoom and hover over polar plots to view specific curve values. The Qwtslider has also been replaced with standard QSlider widget.
Exportable Plots: Users can now save individual plots as .png, .jpg, .bmp, or .pdf files using new, dedicated buttons.
Expanded Data Support: We have updated the "Custom" selection to include a new column for reading medium refractive indices for different scatterers. Two new sample files, CustomSample3.txt and CustomSample4.txt, have been included to demonstrate this feature.
Dependent Scattering Check: A new validation layer has been added to check for dependent scattering. If the input parameters deviate from the independent scattering approximation, the application will now provide a detailed warning message to ensure physical accuracy.
Flexible Visualization: Replaced radio buttons with checkboxes for phase functions. Users can now overlay and compare Average, Parallel, and Perpendicular plots simultaneously.
Increased the Upper Limit of Number of Sphere Sizes: Doubled the upper limit for the number of sphere sizes from 101 to 201.
Dynamic UI Scaling: The application now automatically detects your screen resolution and scales the window size proportionally.
Dark Mode Optimization: Colors have been adjusted to ensure legibility and contrast when using dark system themes.
UI Consistency: The addition of the "Fusion" style and OS-specific font logic ensures the app looks native and professional whether you are on Windows, macOS, or Linux.

Stability & Bug Fixes

Improved Stability: The application is now more stable and reliable. We have implemented unit tests for all C++ computational functions and restructured the project with separate app/ and test/ directories for more efficient builds.
Automated Testing (CI/CD): Implemented a GitHub Actions workflow to automatically run unit tests on every push and pull request.
Corrected Scattering Calculations: A bug in the calculation of forward and backward scattering percentages has been fixed. The angle range is now correctly defined as 0 to 180 degrees, resolving a previous discrepancy.
Fixed Data Formatting: An issue with incorrect tab spacing in saved phase function data has been resolved.

Changes

Coefficient Notation: The power law coefficient was changed from 'a' to 'A' to align with common literature.
Refined Distributions: Optimized Log-Normal and Gaussian calculations to ensure smooth computation of radii and accurate number density allocations.
Volume Fraction Limit: Changed the upper limit of the volume fraction from 1 to $\frac{\pi}{3\sqrt{2}}$ (~0.74). This ensures the volume fraction does not exceed the maximum packing factor for monodisperse spheres (hexagonal close-packed cubic).

- C++
Published by janakarana 4 months ago

Copernicus Seasonal Forecast Tools Package: Bridging Seasonal Climate Predictions and Impact Models for Operational Risk Assessment - Zenodo release

Release to be published in Zenodo

- Python
Published by ValentinGebhart 4 months ago

MieSimulatorGUI: A user-friendly tool to compute and visualize light scattering by spherical dielectric particles - Version 2.0-beta

Mie Simulator GUI 2.0-beta

Downloads

Installers
- Windows Installer: MieSimulatorGUIv20.exe
- MacOS Installer: MieSimulatorGUIv20.app.zip
Stand-alone Packages
- Windows Compressed Application Package: MieSimulatorGUIv20.zip
- MacOS Disk Image: MieSimulatorGUIv20.dmg
- Linux AppImage: MieSimulatorGUIv20.AppImage

Getting Started

Release Notes

New Features & Enhancements

Updated Libraries: We have upgraded the core framework from Qt 5 to Qt 6 (Version 6.2.4) and updated the plotting library QCustomPlot from version 2.0.1 to 2.1.1, which eliminates the need for the Qwt library.
Enhanced Plotting: The old Qwt library has been replaced with QCustomPlot for polar plots. Users can now zoom and hover over polar plots to view specific curve values. The Qwtslider has also been replaced with standard QSlider widget.
Exportable Plots: Users can now save individual plots as .png, .jpg, .bmp, or .pdf files using new, dedicated buttons.
Expanded Data Support: We have updated the "Custom" selection to include a new column for reading medium refractive indices for different scatterers. Two new sample files, CustomSample3.txt and CustomSample4.txt, have been included to demonstrate this feature.
Dependent Scattering Check: A new validation layer has been added to check for dependent scattering. If the input parameters deviate from the independent scattering approximation, the application will now provide a warning message to ensure physical accuracy.
Flexible Visualization: Replaced radio buttons with checkboxes for phase functions. Users can now overlay and compare Average, Parallel, and Perpendicular plots simultaneously.
Increased the Upper Limit of Number of Sphere Sizes: Doubled the upper limit for the number of sphere sizes from 101 to 201.
Dynamic UI Scaling: The application now automatically detects your screen resolution and scales the window size proportionally.
Dark Mode Optimization: Colors have been adjusted to ensure legibility and contrast when using dark system themes.
UI Consistency: The addition of the "Fusion" style and OS-specific font logic ensures the app looks native and professional whether you are on Windows, macOS, or Linux.

Stability & Bug Fixes

Improved Stability: The application is now more stable and reliable. We have implemented unit tests for all C++ computational functions and restructured the project with separate app/ and test/ directories for more efficient builds.
Automated Testing (CI/CD): Implemented a GitHub Actions workflow to automatically run unit tests on every push and pull request.
Corrected Scattering Calculations: A bug in the calculation of forward and backward scattering percentages has been fixed. The angle range is now correctly defined as 0 to 180 degrees, resolving a previous discrepancy.
Fixed Data Formatting: An issue with incorrect tab spacing in saved phase function data has been resolved.

Changes

Coefficient Notation: The power law coefficient was changed from 'a' to 'A' to align with common literature.
Refined Distributions: Optimized Log-Normal and Gaussian calculations to ensure smooth computation of radii and accurate number density allocations.
Volume Fraction Limit: Changed the upper limit of the volume fraction from 1 to $\frac{\pi}{3\sqrt{2}}$ (~0.74). This ensures the volume fraction does not exceed the maximum packing factor for monodisperse spheres (hexagonal close-packed cubic).

- C++
Published by janakarana 4 months ago

chatAI4R: Interactive Artificial Intelligence toolkit for Data Science in R - chatAI4R - v1.3.2

title: chatAI4R: Interactive Artificial Intelligence toolkit for Data Science in R tags: R, artificial intelligence, large language models, data analysis, software development authors: Satoshi Kume (orcid: 0000-0001-7481-2843, corresponding) affiliations: Bio"Pack"athon, Osaka, Japan

date: 14 January 2026

Summary

Large Language Models (LLMs) have revolutionized natural language processing (NLP), data mining, and program coding. The chatAI4R package provides a comprehensive toolkit for seamlessly integrating LLMs within R environments. Beyond basic text generation and conversation capabilities, it supports text embeddings and delivers sophisticated LLM assistance through simple function calls, significantly extending R-based data analysis and knowledge discovery processes. Unlike existing R packages, the chatAI4R package offers unique R package development support features. Rather than functioning as a multi-functional API wrapper, it provides comprehensive development automation and AI-assisted data mining capabilities. The package combines command-line and graphical operations, offering flexibility for users across all skill levels. Available on both GitHub and the Comprehensive R Archive Network (CRAN), chatAI4R ensures stability, reliability, and broad community accessibility.

Originally a development aid for R packages since 2023, chatAI4R has evolved into a data-analysis companion by adding interpretation, knowledge extraction, and multi-LLM capabilities. It serves R package developers (automating Roxygen2 docs, function generation, code quality) and data analysts (statistical interpretation, literature processing, insight extraction) with a four-layer architecture that goes beyond multi-functional API wrappers.

- HTML
Published by kumeS 4 months ago

HiMAP: Hidden Markov for Advanced Prognostics - HiMAP v1.3.0

Added testing, changed imports to relative, updated documentation, paper and readme to comply with JOSS review.

- Python
Published by thanoskont 4 months ago

Bloch: a strongly typed, hardware-agnostic, hybrid quantum programming language - v1.0.3

What's Changed

docs: adjust figure size for JOSS PDF rendering by @HectorMozo3110 in https://github.com/bloch-labs/bloch/pull/216

New Contributors

@HectorMozo3110 made their first contribution in https://github.com/bloch-labs/bloch/pull/216

Full Changelog: https://github.com/bloch-labs/bloch/compare/v1.0.2...v1.0.3

- C++
Published by github-actions[bot] 4 months ago

GaPFlow: Gap-averaged flow simulations with Gaussian process regression - v1.0.2

What's Changed

Docstrings by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/45
MAINT: remove wrong sphinx references by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/46
MAINT: added getrealfield wrapper and slice access for setting .p by @ChristophHuber25 in https://github.com/hannes-holey/GaPFlow/pull/49
Switch build system to sckit-build-core by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/50
MAINT: fix typo in install instructions by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/52
Simplify multi output GP by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/47
Windows wheels by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/53
Fix variance output by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/54
Temporarily use tinygp fork by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/56
CI: Upgrade OS runner by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/57
Deploy with latest tinygp instead of own fork by @hannes-holey in https://github.com/hannes-holey/GaPFlow/pull/58

Full Changelog: https://github.com/hannes-holey/GaPFlow/compare/v1.0.1...v1.0.2

- Python
Published by hannes-holey 4 months ago

DeepCausalMMM: A Deep Learning Framework for Marketing Mix Modeling with Causal Structure Learning - version v1.0.19

Full Changelog: https://github.com/adityapt/deepcausalmmm/compare/v1.0.17...v1.0.19

RELEASENOTES1.0.19.md

- Python
Published by adityapt 4 months ago

diffsol: Rust crate for solving differential equations - v0.10.3

What's Changed

doc: correct dataset and improved docs for neural ode example by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/235

Full Changelog: https://github.com/martinjrobins/diffsol/compare/v0.10.2...v0.10.3

- Rust
Published by martinjrobins 4 months ago

diffsol: Rust crate for solving differential equations - v0.10.2

What's Changed

fix: adapt onnx example for ort rc.10 by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/232
fix: solve and solve_dense respect roots in problem by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/231
doc: adjust line numbers in pred-prey fitting example by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/234
Expose nonlinear solver tolerance and timestep growth/shrink options by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/233
avoid Jacobian resets for endpoint checkpoints by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/237
dep: update diffsl 0.9.0 by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/238
fix: update diffsl, make sure densesolve writes out all teval before root by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/239

Full Changelog: https://github.com/martinjrobins/diffsol/compare/v0.10.1...v0.10.2

- Rust
Published by martinjrobins 4 months ago

baysc: An R package for Bayesian survey clustering - v0.1.1 - JOSS release updated

DOIs updated in package

- R
Published by smwu 4 months ago

KinOpt: A Python package for chemical kinetics analysis and optimization - JOSS release

This release of the KinOpt project contains all the modification following the JOSS review.

- Python
Published by alan-tabore 4 months ago

A Python API for OTTER - v1.0.2

v1.0.2 (2026-01-19)

Bug Fixes

Catch and handle documents that don't have the telescope column when cleaning the phot (11a9475)

Detailed Changes: v1.0.1...v1.0.2

- Python
Published by noahfranz13 4 months ago

A Python API for OTTER - v1.0.1

v1.0.1 (2026-01-19)

Bug Fixes

A bug in the photometry deduplication code (0227fb0)
Add argument to clean photometry that allows users to drop not host subtracted data (ea1fe31)
Allow users to pass additional kwargs to Transient.cleanphotometry from Otter.getphot (3ef876c)
Bug in filter name cleanup (6066926)
Ensure the datemin/datemax cols are in the photometry df before filtering on them (dfc7229)
This is a patch for when datemin and datemax are null rather than NaN (83ec951)

Detailed Changes: v1.0.0...v1.0.1

- Python
Published by noahfranz13 4 months ago

flodym: A Python package for dynamic material flow analysis - v0.5.4

What's Changed

Add (np-like) convenience helper functions to DimensionSet and FlodymArray by @bennet21 in https://github.com/pik-piam/flodym/pull/135
fix numpy indexing error in SubArrayHandler by @JakobBD in https://github.com/pik-piam/flodym/pull/136
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/pik-piam/flodym/pull/132

Full Changelog: https://github.com/pik-piam/flodym/compare/v0.5.3...v0.5.4

- Python
Published by JakobBD 4 months ago

gkwreg: An R Package for Generalized Kumaraswamy Regression Models for Bounded Data - JOSS submission - Reviewed version [Zenodo]

JOSS Submission - Reviewed Version [After with Zenodo]

This release corresponds to the reviewed version of the gkwreg package submitted to the Journal of Open Source Software (JOSS).

Review issue: openjournals/joss-reviews#8991

This version contains all changes requested during the peer review process and represents the state of the software at the time of acceptance for publication.

- R
Published by evandeilton 4 months ago

gkwreg: An R Package for Generalized Kumaraswamy Regression Models for Bounded Data - JOSS submission - reviewed version

JOSS Submission - Reviewed Version

This release corresponds to the reviewed version of the gkwreg package submitted to the Journal of Open Source Software (JOSS).

Review issue: openjournals/joss-reviews#8991

This version contains all changes requested during the peer review process and represents the state of the software at the time of acceptance for publication.

Full Changelog: https://github.com/evandeilton/gkwreg/compare/v2.1.15...v2.1.15

- R
Published by evandeilton 4 months ago

PyIRD: A Python-Based Data Reduction Pipeline for Subaru/IRD and REACH - Release version 1.2.1

This release exists to enable Zenodo archiving and DOI assignment. No code changes since v1.2.0.

- Jupyter Notebook
Published by YuiKasagi 4 months ago

QMCPy: A Python Framework for (Quasi-)Monte Carlo Algorithms - QMCPy v2.2

What's Changed

Make sure CI tests failed with detailed error stack when there are testbook failures by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/438
Change Lookback to include start price by @fjhickernell in https://github.com/QMCSoftware/QMCSoftware/pull/440
Release Documentation by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/439
Added Booktests for Windows and combined all tests in 1 workflow by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/444
Revert "Speedup" commit from booktests_choi branch by @Copilot in https://github.com/QMCSoftware/QMCSoftware/pull/447
Coverage Reports and Badge of CI Tests in GitHub Actions by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/445
Add seed values and coverage percentage to 100% by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/448
Add and Enhance Test Documenation by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/450
Speedup CI Test Workflow with Injection (In-Memory Replacements) by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/452
Test Python 3.5 to 3.14 for 3 OS by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/454
update license by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/459
Add dependent and custom distribution support to SciPyWrapper (issue #406) by @Laasya-73 in https://github.com/QMCSoftware/QMCSoftware/pull/427
Clarify unit-test coverage workflow and improve DigitalNetB2 coverage by @algo-hawk in https://github.com/QMCSoftware/QMCSoftware/pull/456
Enhance documentation by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/461
Add Paper folder with first paper submitted to JOSS by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/460
Geometric brownian motion by @larissensium in https://github.com/QMCSoftware/QMCSoftware/pull/477
Digital nets with arbitrary bases by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/451
QMCPy v2.2 by @rvare in https://github.com/QMCSoftware/QMCSoftware/pull/481

New Contributors

@Laasya-73 made their first contribution in https://github.com/QMCSoftware/QMCSoftware/pull/427
@algo-hawk made their first contribution in https://github.com/QMCSoftware/QMCSoftware/pull/456
@rvare made their first contribution in https://github.com/QMCSoftware/QMCSoftware/pull/481

Full Changelog: https://github.com/QMCSoftware/QMCSoftware/compare/v2.1...v2.2

- Python
Published by rvare 4 months ago

<strong>geospaNN</strong>: A Python package for geospatial neural networks - geospaNN

- Python
Published by WentaoZhan1998 4 months ago

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization - OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization

Peer-reviewed software and manuscript. See the JOSS review issue for details: https://github.com/openjournals/joss-reviews/issues/9293

Non-negative Matrix Factorization (NMF) is a widely used dimensionality reduction technique for identifying a small number of non-negative components that minimize the reconstruction error when applied to high-dimensional data. NMF has been applied across various fields of data science, including face recognition, audio signal processing, recommender system, natural language processing (also known as a "topic model"), population genetics (also known as "admixture analysis"), and omics studies.

Despite its broad applicability, NMF becomes computationally prohibitive for large data matrices, making it difficult to apply in practice. In particular, recent advances in single-cell omics have led to datasets with millions of cells, for which standard NMF implementations often fail to scale. To meet this requirement, I present OnlineNMF.jl, which is a Julia package to perform some NMF algorithms (https://github.com/rikenbit/OnlineNMF.jl).

Zenodo doi: 10.5281/zenodo.18250632

- Julia
Published by kokitsuyuzaki 4 months ago

pyDARTdiags: A Python package for manipulating observation sequences and calculating observation-space diagnostics for the Data Assimilation Research Testbed (DART) - 0.6.3

What's Changed

Dart workflow example by @mjs2369 in https://github.com/NCAR/pyDARTdiags/pull/121
Packaging and example data download module by @hkershaw-brown in https://github.com/NCAR/pyDARTdiags/pull/119

Full Changelog: https://github.com/NCAR/pyDARTdiags/compare/0.6.2...0.6.3

- Python
Published by hkershaw-brown 4 months ago

PyIRD: A Python-Based Data Reduction Pipeline for Subaru/IRD and REACH - Release version 1.2.0

Release Note version 1.2.0

This release includes revisions addressing comments from the JOSS review.

What's Changed

Add instruction to run tests by @YuiKasagi in https://github.com/prvjapan/pyird/pull/124
Clarify output messages and rename parameters by @YuiKasagi in https://github.com/prvjapan/pyird/pull/129
Fix fitsid issue in IRD_stream.py by @YuiKasagi in https://github.com/prvjapan/pyird/pull/128
Update documents by @YuiKasagi in https://github.com/prvjapan/pyird/pull/127
Revise the paper by @YuiKasagi in https://github.com/prvjapan/pyird/pull/130
Merge JOSS review fixes into master by @YuiKasagi in https://github.com/prvjapan/pyird/pull/131
minor fix of documents by @YuiKasagi in https://github.com/prvjapan/pyird/pull/132
Final revisions for JOSS review by @YuiKasagi in https://github.com/prvjapan/pyird/pull/133
update pyproject.toml and setup.cfg for PyPI upload by @YuiKasagi in https://github.com/prvjapan/pyird/pull/134

Full Changelog: https://github.com/prvjapan/pyird/compare/v1.1.0...v1.2.0

- Jupyter Notebook
Published by YuiKasagi 4 months ago

diffsol: Rust crate for solving differential equations - v0.10.1

What's Changed

feat: use average convergence rate, eta persists across solves by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/222
fix: build pred-prey fit example, fix compile errors by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/225
doc: improve API docs by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/229
deps: diffsl 0.8.3 by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/230

Full Changelog: https://github.com/martinjrobins/diffsol/compare/v0.9.1...v0.10.1

- Rust
Published by martinjrobins 4 months ago

baysc: An R package for Bayesian survey clustering - v0.1.0 - JOSS paper release

- R
Published by smwu 4 months ago

pypsa - v1.0.7

Revised release notes are available in the documentation.

What's Changed

build(deps): bump the github-actions group with 3 updates by @dependabot[bot] in https://github.com/PyPSA/PyPSA/pull/1505
docs: add security policy by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1506
fix: pin netcdf!=1.7.4 by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1510
revert pypsa.common.annuity change 58c7a0e by @fneum in https://github.com/PyPSA/PyPSA/pull/1512
chore: support for python 3.14 by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1511
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/PyPSA/PyPSA/pull/1514
Skip the subset check in as_index() (in some cases) by @chriselion in https://github.com/PyPSA/PyPSA/pull/1515
fix: update pydeck min version to 0.6 by @coroa in https://github.com/PyPSA/PyPSA/pull/1518
fix: netcdf export corrupting dynamic attributes when directly assigning df by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1522

New Contributors

@chriselion made their first contribution in https://github.com/PyPSA/PyPSA/pull/1515

Full Changelog: https://github.com/PyPSA/PyPSA/compare/v1.0.6...v1.0.7

- Python
Published by github-actions[bot] 4 months ago

multimodars: A Rust-powered toolkit for multi-modality cardiac image fusion and registration - Initial release

This realease includes the following final implementations of functionalities for multimodars: - Read in contour data from intravascular images (lumen, eem, calcium, sidebranch) and create a pseudo 3D model: - - Rotate/Translate neighbouring frames to minimize Hausdorff distance (parallelized) - - Fill holes/smooth and other fixes - - Align between different pullbacks with automated spacing adjustment between them (different heartrate) - - Save one (or several interpolated) of these pseudo 3D models to .obj files (with a calculated deformation map) - - Create adventitia (or intramural aortic wall for AAOCA) and catheter .obj files - Read in CCTA data and label different regions based on the centerlines (aorta, rca, lca) - Align intravascular images with the CCTA centerline based on landmark points (and Hausdorff distances) - Label the CCTA region to be replaced and scale different regions to match the intravascular segment

Additional files: - multimodars_examples.zip includes several csv files from different intravascular images, a ccta stl file and several example scripts (including jupyter notebook) teaching the usage of multimodars

Next release will include: - The full fusion functionality

- Rust
Published by yungselm 5 months ago

Htool-DDM: A C++ library for parallel solvers and compressed linear systems. - Release v1.0.0-joss-paper

This release is based on v1.0.0 and includes the final, reviewed JOSS paper.

- C++
Published by PierreMarchand20 5 months ago

<strong>geospaNN</strong>: A Python package for geospatial neural networks - geospaNN

A stable version for joss submission.

- Python
Published by WentaoZhan1998 5 months ago

gkwreg: An R Package for Generalized Kumaraswamy Regression Models for Bounded Data - gkwreg 2.1.14

CRAN Resubmission

Addresses all remaining issues for CRAN acceptance after archival on 2025-11-30.

Fixed

Added inst/WORDLIST with 'Kumaraswamy' to resolve spelling NOTE
Added skip_on_cran() to all test files to reduce check time from 18min to ~9min
Added cran-comments.md documenting changes since archival (excluded from build via .Rbuildignore)

Confirmed

Cache policy now fully compliant: uses only tempdir() for session-specific TMB DLL cache
All ~/.cache/gkwreg usage completely removed (fixed in v2.1.11)
Check time now under 10 minutes

- R
Published by evandeilton 5 months ago

A Python API for OTTER - v1.0.0

Release version 1 of the software. There are now breaking changes in this release but

the initial OTTER catalog paper was recently accepted
The JOSS reviewers have approved the corresponding submission for this API and we need to re-version it anyways!

Given this, I find this an appropriate time to bump the v0 to v1!

- Python
Published by noahfranz13 5 months ago

diffsol: Rust crate for solving differential equations - v0.9.1

What's Changed

feat: expose more solver options by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/219
feat: expose DiffSlScalar by @alexallmont in https://github.com/martinjrobins/diffsol/pull/213

New Contributors

@alexallmont made their first contribution in https://github.com/martinjrobins/diffsol/pull/213

Full Changelog: https://github.com/martinjrobins/diffsol/compare/v0.9.0...v0.9.1

- Rust
Published by martinjrobins 5 months ago

pyDARTdiags: A Python package for manipulating observation sequences and calculating observation-space diagnostics for the Data Assimilation Research Testbed (DART) - 0.6.2

What's Changed

Draft of JOSS Paper by @hkershaw-brown in https://github.com/NCAR/pyDARTdiags/pull/101
Fix plot rh for ocean obs by @hkershaw-brown in https://github.com/NCAR/pyDARTdiags/pull/106
API documentation for obs_sequence.py by @hkershaw-brown in https://github.com/NCAR/pyDARTdiags/pull/118 separate public and private methods

Full Changelog: https://github.com/NCAR/pyDARTdiags/compare/0.6.1...0.6.2

- Python
Published by hkershaw-brown 5 months ago

Htool-DDM: A C++ library for parallel solvers and compressed linear systems. - Release v1.0.0

Added

HMatrix recompression with SVD.
Generic recompressed low-rank compression with RecompressedLowRankGenerator.
Checks about UPLO for hmatrix factorization.
HMatrixBuilder for easier HMatrix creation (especially when using only the HMatrix component of Htool-DDM).
add_hmatrix_vector_product and add_hmatrix_matrix_product for working in user numbering.
For C++17 and onward, interfaces supporting execution policies (default being sequential execution) has been added for these functions:
- HMatrixTreeBuilder::build
- add_hmatrix_matrix_product
- add_hmatrix_vector_product
- lu_factorization
- cholesky_factorization
Mocking execution policies have been added when compiler does not define std::execution. See exec_compat.
task_dependencies.hpp for miscellaneous functions used for task based approach.
hmatrix_output_dot.hpp for L0 and block tree visualization.
Task based parallelism support has been added via
- HMatrixTreeBuilder::task_based_build for task based assembly.
- task_based_internal_add_hmatrix_vector_product for task based alternative to {sequential,openmp}_internal_add_hmatrix_vector_product.
- task_based_internal_add_hmatrix_hmatrix_product for task based alternative to {sequential,openmp}_internal_add_hmatrix_hmatrix_product.
- task_based_internal_triangular_hmatrix_hmatrix_solve for task based alternative to internal_triangular_hmatrix_hmatrix_solve.
- task_based_lu_factorization and task_based_cholesky_factorization for task based alternatives to {sequential,openmp}_lu_factorization and {sequential,openmp}_cholesky_factorization.
- test_task_based_hmatrix_*.hpp for testing various task based features.
internal_add_lrmat_hmatrix is now overloaded to handle the case where the HMatrix is larger than the LowRankMatrix.
get_leaves_from is overloaded to return non const arguments.
get_false_positive in a tree builder.
left_hmatrix_ancestor_of_right_hmatrix and left_hmatrix_descendant_of_right_hmatrix for returning parent and children of a hmatrix.
Partition_N is an alternative to Partition for defining the partition of a cluster. The latter only splits along the principal axis of the cluster, while the former tries to be smarter.

Changed

VirtualInternalLowRankGenerator and VirtualLowRankGenerator's copy_low_rank_approximation function takes a LowRankMatrix as input to populate it and returns a boolean. The return value is true if the compression succeded, false otherwise.
LowRankMatrix constructors changed. It only takes sizes and an epsilon or a required rank. Then, it is expected to call a VirtualInternalLowRankGenerator to populate it.
ClusterTreeBuilder has now one strategy as VirtualPartitioning. Usual implementations are still available, for example using Partitioning<double,ComputeLargestExtent,RegularSplitting>.
ClusterTreeBuilder parameter minclustersize was removed, and a parameter maximal_leaf_size has been added.
DistributedOperator supports now both "global-to-local" and "local-to-local" operators, using respectively VirtualGlobalToLocalOperator and VirtualLocalToLocalOperator interfaces. The linear algebra associated has been updated to follow a more Blas-like interface.
MatrixView has been added to ease the use of matrix product. Most public functions for matrix products have also new template arguments to accept, Matrix, MatrixView or any other type following the same interface.

Fixed

Fix inline definition of logging_level_to_string.
Fix error when resizing Matrix.
Fix error due to using int instead of size_t, thanks to @vdubos.
Fix warnings with -Wold-style-cast.

- C++
Published by PierreMarchand20 5 months ago

Htool-DDM: A C++ library for parallel solvers and compressed linear systems. - Release v1.0.1

Fixed

Fix wrong boolean tests in triangularmatrixmatrix_solve, PR #75 from @ABoisneault
Avoid empty-sized gemv, PR #64 from @prj-

- C++
Published by github-actions[bot] 5 months ago

Ellip: An Elliptic Integral Library for Rust - v1.0.2

What's Changed

Ellip is no_std by default.
Deprecate no_std feature flag.

Full Changelog: https://github.com/p-sira/ellip/compare/v1.0.1...v1.0.2

- Rust
Published by p-sira 5 months ago

diffsol: Rust crate for solving differential equations - v0.9.0

What's Changed

feat: move solver config to problem by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/210
fix: line search by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/211
doc: broken link by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/217
feat: pybamm dfn bench, use diffsl symbolic sparsity by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/218

Full Changelog: https://github.com/martinjrobins/diffsol/compare/v0.8.4...v0.9.0

- Rust
Published by martinjrobins 5 months ago

qlass: A Python Package for Variational Quantum Algorithms on Photonic Devices - v0.2.1

What's Changed

Modernize and clean up package setup by @burgholzer in https://github.com/unitaryfoundation/qlass/pull/140
Update README.md by @FarLab in https://github.com/unitaryfoundation/qlass/pull/144
Add CD workflow for automatic PyPI deployment by @FarLab in https://github.com/unitaryfoundation/qlass/pull/149
Type checking by @FarLab in https://github.com/unitaryfoundation/qlass/pull/153
add linter to ci by @FarLab in https://github.com/unitaryfoundation/qlass/pull/154
add relevant references in the documentation by @FarLab in https://github.com/unitaryfoundation/qlass/pull/164
Updating WFT Hamiltonian for Hchain by @Akilan-QC in https://github.com/unitaryfoundation/qlass/pull/163
Bump actions/checkout from 4 to 6 by @dependabot[bot] in https://github.com/unitaryfoundation/qlass/pull/157
Bump actions/setup-python from 5 to 6 by @dependabot[bot] in https://github.com/unitaryfoundation/qlass/pull/158
Bump codecov/codecov-action from 4 to 5 by @dependabot[bot] in https://github.com/unitaryfoundation/qlass/pull/159
Bump actions/download-artifact from 4 to 6 by @dependabot[bot] in https://github.com/unitaryfoundation/qlass/pull/160
Bump actions/upload-artifact from 4 to 5 by @dependabot[bot] in https://github.com/unitaryfoundation/qlass/pull/161
add Makefile to verify all example scripts by @FarLab in https://github.com/unitaryfoundation/qlass/pull/165
Update installation instructions to use uv instead of pip by @FarLab in https://github.com/unitaryfoundation/qlass/pull/167
adding CONTRIBUTING.md for a guide to a PR by @FarLab in https://github.com/unitaryfoundation/qlass/pull/166
hfansatz seperated as Bitstringinitialstates and CSFinitial_states by @Akilan-QC in https://github.com/unitaryfoundation/qlass/pull/168
Update vqe.py by @Akilan-QC in https://github.com/unitaryfoundation/qlass/pull/169
add Piquasso example by @Kolarovszki in https://github.com/unitaryfoundation/qlass/pull/170
Statement of need in the introduction by @FarLab in https://github.com/unitaryfoundation/qlass/pull/174

New Contributors

@burgholzer made their first contribution in https://github.com/unitaryfoundation/qlass/pull/140
@Kolarovszki made their first contribution in https://github.com/unitaryfoundation/qlass/pull/170

Full Changelog: https://github.com/unitaryfoundation/qlass/compare/v0.2.0...v0.2.1

- Python
Published by FarLab 5 months ago

pypsa - v1.0.6

Revised release notes are available in the documentation.

What's Changed

feat: add stats accessor as alternative to statistics by @FabianHofmann in https://github.com/PyPSA/PyPSA/pull/1448
Update models.md / add PyPSA-AT, AGGM by @gincrement in https://github.com/PyPSA/PyPSA/pull/1466
Update users.md / AGGM add repository reference by @gincrement in https://github.com/PyPSA/PyPSA/pull/1465
Update users.md / fix typo in AGGM reference by @gincrement in https://github.com/PyPSA/PyPSA/pull/1467
fix: type checks by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1468
Update models.md / add agoenergy/PyPSA-SPICE by @gincrement in https://github.com/PyPSA/PyPSA/pull/1469
Add user SFU and model PyPSA-BC by @gincrement in https://github.com/PyPSA/PyPSA/pull/1471
Bug Fix: rolling horizon with linearized UC and ramp limits by @Irieo in https://github.com/PyPSA/PyPSA/pull/1489
Fix masking of ramp constraints for assets with NaN ramp limits by @sasa821 in https://github.com/PyPSA/PyPSA/pull/1494
fix: assign duals back to stochastic network by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1498
updated users.md by @SanghyunPLANiT in https://github.com/PyPSA/PyPSA/pull/1501
fix: user warning on missing out when using mask with numpy 2.4 by @lkstrp in https://github.com/PyPSA/PyPSA/pull/1503
Feature: enable modular expansion in stochastic problems by @Irieo in https://github.com/PyPSA/PyPSA/pull/1500
Fix bug: Transformer type handling in stochastic networks by @Irieo in https://github.com/PyPSA/PyPSA/pull/1499

New Contributors

@sasa821 made their first contribution in https://github.com/PyPSA/PyPSA/pull/1494
@SanghyunPLANiT made their first contribution in https://github.com/PyPSA/PyPSA/pull/1501

Full Changelog: https://github.com/PyPSA/PyPSA/compare/v1.0.5...v1.0.6

- Python
Published by github-actions[bot] 5 months ago

SeqIKPy: a Python package for inverse kinematics in insects - v1.1.0 - JOSS publication

SeqIKPy v1.1.0 — Parallel processing and new examples

This is the JOSS publication release of SeqIKPy. It introduces parallel execution to accelerate inverse and forward kinematics, along with new examples, benchmarks, and updated documentation.

Highlights

Parallel processing: Optional parallelization over kinematic chains and time via n_workers and parallel_over_time, with adaptive task sizing (see the related tutorial here).
New benchmark example: example_leg_inv_kinematics_parallel.py compares serial and parallel execution and reports timing results.
Updated examples: Consolidated pipeline demos for leg, head, and full-body workflows (example_entire_pipeline.py, example_leg_inv_kinematics.py).
New model example: Mouse forelimb kinematics demo (see the related tutorial here).
Documentation: Added a parallel-processing tutorial and updated paper.md with implementation and benchmark details.

Compatibility

Non-breaking release; serial behavior is preserved when n_workers=1.

- Python
Published by gizemozd 5 months ago

Ellip: An Elliptic Integral Library for Rust - v1.0.1

What's Changed

Bug Fixes - Fix integer overflow in ellipk and ellipe.

Full Changelog: https://github.com/p-sira/ellip/compare/v1.0.0...v1.0.1

- Rust
Published by p-sira 5 months ago

JetFuelBurn: A Python package for calculating fuel burn of commercial aircraft - 1.1.1

Release for Zenodo archiving and JOSS publication.

- Python
Published by michaelweinold 5 months ago

Ellip: An Elliptic Integral Library for Rust - v1.0.0

What's Changed

First stable release of Ellip.

Full Changelog: https://github.com/p-sira/ellip/compare/v0.5.9...v1.0.0

- Rust
Published by p-sira 5 months ago

flodym: A Python package for dynamic material flow analysis - v0.5.3

What's Changed

fix error message in FlodymArray.from_df by @JakobBD in https://github.com/pik-piam/flodym/pull/131
Add DimensionSet operators by @JakobBD in https://github.com/pik-piam/flodym/pull/123
skip empty definition lists in MFADefinition df export by @bennet21 in https://github.com/pik-piam/flodym/pull/134

Full Changelog: https://github.com/pik-piam/flodym/compare/v0.5.2...v0.5.3

- Python
Published by JakobBD 5 months ago

pyfive: A pure-Python HDF5 reader - Release v1.0.1

What's Changed

Set __version__ attribute dynamically in __init__.py by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/152
pin numpy>=2 by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/157
add a pip check by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/159
Test case for corner case file (buffer too small) by @kmuehlbauer in https://github.com/NCAS-CMS/pyfive/pull/160
update setuptools pins by @valeriupredoi in https://github.com/NCAS-CMS/pyfive/pull/165
Fix display of p5dump global attributes by @zequihg50 in https://github.com/NCAS-CMS/pyfive/pull/163

Special mentions

With very many thanks to @mo-gill for highlighting to us the corner case, and to @kmuehlbauer for finding an excellent fix to it in #160

Many thanks to all contributors :beers:

Full Changelog: https://github.com/NCAS-CMS/pyfive/compare/v1.0.0...v1.1.0

- Python
Published by valeriupredoi 5 months ago

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - SPAC v0.9.0 Public Release

This release is the public release with efforts to provide better documentations.

- Jupyter Notebook
Published by ruiheesi 5 months ago

A Python API for OTTER - v0.7.0

v0.7.0 (2025-12-16)

Bug Fixes

Allow users to pass numpy arrays of names to Otter.query/Otter.get_meta (Issue #19) (ce89ccc)
Fully address issue #32 (63b7d0d)
Minor bug in photometry de-reddening (c6e5e33)
Modernize test_transient unit tests (81e87e2)
Plotter to use the prod db rather than dev (03351ce)
Redshift is now cast as a float (Issue #20) (7fba7a6)

Features

Add automatic MW dust extinction correction to Transient.clean_photometry (341fd2c)
Standardize UVOIR filter names (Issue #21) (d798bbd)

Detailed Changes: v0.6.2...v0.7.0

- Python
Published by noahfranz13 5 months ago

PyMetric: A Geometry Informed Array Mathematics Package - v0.0.3a1

Hotfix update removing a deprecated import impacting documentation compilation.

- Python
Published by Eliza-Diggins 5 months ago

PyMetric: A Geometry Informed Array Mathematics Package - v0.0.3a

What's Changed

Unit support by @Eliza-Diggins in https://github.com/Pisces-Project/PyMetric/pull/3
Buffer UFUNC bug fixes by @Eliza-Diggins in https://github.com/Pisces-Project/PyMetric/pull/6
Docs by @Eliza-Diggins in https://github.com/Pisces-Project/PyMetric/pull/7
Testing standardization by @Eliza-Diggins in https://github.com/Pisces-Project/PyMetric/pull/8
Add containers module with FieldContainer class and update documentation by @Eliza-Diggins in https://github.com/Pisces-Project/PyMetric/pull/4
Paper by @Eliza-Diggins in https://github.com/Pisces-Project/PyMetric/pull/10

New Contributors

@Eliza-Diggins made their first contribution in https://github.com/Pisces-Project/PyMetric/pull/3

Full Changelog: https://github.com/Pisces-Project/PyMetric/commits/v0.0.3a

- Python
Published by Eliza-Diggins 5 months ago

Scikit-Topt: A Python Library for Algorithm Development in Topology Optimization - v0.3.8 is released

This release finalizes the JOSS submission.

Updated author affiliation to include city and country
Resolved minor documentation issues identified during review

- Python
Published by kevin-tofu 5 months ago

sklearn-migrator: Cross-version migration of scikit-learn models for reproducible MLOps - sklearn-migrator v0.21.1

Added

Cross-version support for AgglomerativeClustering
Improved robustness for sklearn internal changes

Fixed

Edge cases in tree-based model migration

- Python
Published by anvaldes 6 months ago

A Python API for OTTER - v0.6.2

v0.6.2 (2025-12-12)

Bug Fixes

Add specific paths to only run CI unit tests when those files are edited (3b263ab)

Detailed Changes: v0.6.1...v0.6.2

- Python
Published by noahfranz13 6 months ago

A Python API for OTTER - v0.6.1

v0.6.1 (2025-12-12)

Bug Fixes

Ensure we don't run the semver workflow in an infinite loop (ec32d65)

Detailed Changes: v0.6.0...v0.6.1

- Python
Published by noahfranz13 6 months ago

A Python API for OTTER - v0.6.0

v0.6.0 (2025-12-12)

Bug Fixes

A typo in the semver workflow (4666eaa)
Add new semver.yml (cafbe26)
Allow for versions to start with 0 with semantic-versioning (00bb113)
Following python-semantic-version docs add the token argument to actions/checkout (3a02c1f)
Try adding in the repository name explicitly (43deea5)
Try again with the semver workflow (6b7f948)
Try again with the semver workflow (c51e999)
Try to fix the semver workflow file (9bb8bce)
Try using a PAT instead of GITHUB_TOKEN (85deeff)
Update to use more recent versions of github actions (84926d8)

Features

Try to add semantic versioning automatically (33f7664)

Detailed Changes: v0.5.0...v0.6.0

- Python
Published by noahfranz13 6 months ago

BiGSTARS.jl: A Julia package for bi-global stability analysis for rotating stratified flows - v2.0.6

What's Changed

Fix typos and math formatting in docs by @alexfikl in https://github.com/subhk/BiGSTARS.jl/pull/17
Remove unneeded DS_Store files by @alexfikl in https://github.com/subhk/BiGSTARS.jl/pull/18

New Contributors

@alexfikl made their first contribution in https://github.com/subhk/BiGSTARS.jl/pull/17

Full Changelog: https://github.com/subhk/BiGSTARS.jl/compare/v2.0.5...v2.0.6

- Julia
Published by subhk 6 months ago

Bloch: a strongly typed, hardware-agnostic, hybrid quantum programming language - v1.0.2

1.0.2 (2025-12-11)

Bug Fixes

hotfix windows build (#189) (148bb3d)

- C++
Published by github-actions[bot] 6 months ago

Bloch: a strongly typed, hardware-agnostic, hybrid quantum programming language - v1.0.1

1.0.1 (2025-12-11)

Bug Fixes

cx gate works on subspace where ctrl is 1 only (#180) (6938c5d)
fixed bug where arrays could only be initialised by literals (#185) (4c676f3)
initialise m_state to a single amplitude (#177) (b6d59e2)
install scripts migrated to website, added update checker (#184) (fee4115)
optimise qasm logging for better performance (#178) (a2b9cd4)
parenthesised expressions not being evaluated at runtime (#182) (68c6371)
perf: made runtime evaluator single use to prevent state leakage (#170) (87afa42)
reset now clears measured flag (#172) (e07f9fd)

- C++
Published by github-actions[bot] 6 months ago

anvay: A Web-based Tool for Interpretive Topic Modelling in Bengali - Improve topic interpretability, unify visual styling, and update documentation

Implemented multiple usability and interpretability improvements for v1.1.1:

Added top-word hover tooltips across all visualisations for clearer topic interpretation.
Standardised global topic colour scheme across all charts.
Updated documentation to explain that Heatmap and Bar Chart visualise the same topic–word weight matrix.
Reduced number of displayed terms in plots to prevent hidden tick labels; added hover-based x-axis details where needed.
Clarified Topic Evolution axis (document upload order) and added filenames to hover output.
Enhanced hierarchical clustering with BERTopic-style merged-cluster keyword tooltips.
Unified Plotly font styling using Roboto/Noto Bengali; reduced margins for a cleaner layout.
Added missing loading spinner to indicate processing during analysis.

These changes significantly improve clarity, consistency, and user experience in the visualisation interface.

- HTML
Published by vinayakdasgupta 6 months ago

QMCPy: A Python Framework for (Quasi-)Monte Carlo Algorithms - QMCPy v2.1

What's Changed

QMCPy v2.0 release by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/395
sponsor logos by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/396
patch GBM docs by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/397
patch GBM doctests by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/398
rerun JOSS notebook by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/399
Develop by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/400
update acm toms + contributing by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/401
Develop by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/402
Overcome cancelation errors by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/414
Fix parslfest2025.ipynb test failures and verbose output by @Copilot in https://github.com/QMCSoftware/QMCSoftware/pull/421
Parsl presentation from Parslfest 2025 by @zitterbewegung in https://github.com/QMCSoftware/QMCSoftware/pull/419
Booktests: Unit tests for Jupiter Notebooks by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/424
Class install switch for students and instructors using qmcpy in their classes by @fjhickernell in https://github.com/QMCSoftware/QMCSoftware/pull/426
Class install fixing package incompatibilities by @fjhickernell in https://github.com/QMCSoftware/QMCSoftware/pull/429
Move demos/parslfest2025/* to demos/ParslFest2025/ by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/428
Aleksei thesis by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/423
Move demos/parslfest2025/* to demos/Parslfest_2025 by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/430
Doc patch for CONTRIBUTING.md by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/432
Intermittent Doctest Failures in sidsikernels.py by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/431
Geometric brownian motion by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/433
Geometric brownian motion by @larissensium in https://github.com/QMCSoftware/QMCSoftware/pull/434
Fixing Intermittant CI Test Failures by @sou-cheng-choi in https://github.com/QMCSoftware/QMCSoftware/pull/435
v2.1 release by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/436

New Contributors

@Copilot made their first contribution in https://github.com/QMCSoftware/QMCSoftware/pull/421

Full Changelog: https://github.com/QMCSoftware/QMCSoftware/compare/v2.0...v2.1

- Python
Published by alegresor 6 months ago

A Python API for OTTER - v0.5.0

Significant updates including 1. Removing the "negative flux filter" per a discussion with Sjoert 2. improved source documentation 3. Additional examples

Full Changelog: https://github.com/astro-otter/otter/compare/v0.4.1...v0.5.0

- Python
Published by noahfranz13 6 months ago

diffsol: Rust crate for solving differential equations - v0.8.4

What's Changed

version 0.8.3: diffsl version 0.6.3 by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/207
version 0.8.4: diffsl version 0.6.5 by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/208
feat: add optional backtracking line search to newton non-linear solver by @martinjrobins in https://github.com/martinjrobins/diffsol/pull/209

Full Changelog: https://github.com/martinjrobins/diffsol/compare/v0.8.2...v0.8.4

- Rust
Published by martinjrobins 6 months ago

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization - v0.99.7

What's Changed

Bump julia-actions/setup-julia from 1 to 2 by @dependabot[bot] in https://github.com/rikenbit/OnlineNMF.jl/pull/12
Bump actions/checkout from 3 to 5 by @dependabot[bot] in https://github.com/rikenbit/OnlineNMF.jl/pull/16
JOSS: Update LICENSE file formatting and content by @rahulkhorana in https://github.com/rikenbit/OnlineNMF.jl/pull/17
JOSS: Test Suite and Checks by @rahulkhorana in https://github.com/rikenbit/OnlineNMF.jl/pull/19
JOSS: Extending Test Suite by @rahulkhorana in https://github.com/rikenbit/OnlineNMF.jl/pull/18
Bump actions/checkout from 5 to 6 by @dependabot[bot] in https://github.com/rikenbit/OnlineNMF.jl/pull/20

New Contributors

@dependabot[bot] made their first contribution in https://github.com/rikenbit/OnlineNMF.jl/pull/12
@rahulkhorana made their first contribution in https://github.com/rikenbit/OnlineNMF.jl/pull/17

Full Changelog: https://github.com/rikenbit/OnlineNMF.jl/compare/v0.99.6...v0.99.7

- Julia
Published by kokitsuyuzaki 6 months ago

pyforce: Python Framework for data-driven model Order Reduction of multi-physiCs problEms - 0.1.3

Code implementation after review process from JOSS.

What's Changed

Add joss-paper and related Github Action by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/5
Update License by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/7
Minor Update before JOSS revision by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/11
10 joss submission review reviewer 2 software paper by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/12
Update joss paper by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/13
9 joss submission review reviewer 2 functionality by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/14
8 docs review by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/15
Update docs - review by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/16
8 docs review by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/17
Add tests for most important classes in pyforce - Minor Fixes by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/19
Update Paper and Installation notes by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/21
Add EIM algorithm minor fixes by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/22
New features, new tutorial and minor fix by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/23
Code and paper update following comments from reviewer 2 by @Steriva in https://github.com/ERMETE-Lab/ROSE-pyforce/pull/26

Full Changelog: https://github.com/ERMETE-Lab/ROSE-pyforce/compare/0.1.2...0.1.3

- Jupyter Notebook
Published by Steriva 6 months ago

DataBallPy: Load, synchronize, and Analyse your Soccer Data - Version 0.7.2

What's Changed

Added way to get frame of tracking data based on team possession or event data team by @Alek050 in https://github.com/Alek050/databallpy/pull/251
Added easier way of getting filters on column ids by @Alek050 in https://github.com/Alek050/databallpy/pull/252
WIP: Bundesliga open data by @Alek050 in https://github.com/Alek050/databallpy/pull/253
Added ruff as linting manager by @Alek050 in https://github.com/Alek050/databallpy/pull/255
Logging wrapper by @Alek050 in https://github.com/Alek050/databallpy/pull/257
release for v0.5.2 by @Alek050 in https://github.com/Alek050/databallpy/pull/259
Statsbomb event parser by @DaanGro in https://github.com/Alek050/databallpy/pull/254
fixed bug opta positions by @Alek050 in https://github.com/Alek050/databallpy/pull/265
Add JSON parser for tracab metadata by @jan-swiatek in https://github.com/Alek050/databallpy/pull/266
Fixed some small bugs in synchronise, read tracab xml, and aligning players from tracking and event metadata by @Alek050 in https://github.com/Alek050/databallpy/pull/269
Release 0.5.3 by @Alek050 in https://github.com/Alek050/databallpy/pull/271
Support for python 3.13 by @Alek050 in https://github.com/Alek050/databallpy/pull/256
Added statsbomb event id by @Alek050 in https://github.com/Alek050/databallpy/pull/273
Specify min max pitch dimensions to be between logical values by @Alek050 in https://github.com/Alek050/databallpy/pull/275
fixed scisports parser bug in shot events by @Alek050 in https://github.com/Alek050/databallpy/pull/284
Sportec remove assumption that first player frame is first frame of second half by @Alek050 in https://github.com/Alek050/databallpy/pull/290
V0.5.4 by @Alek050 in https://github.com/Alek050/databallpy/pull/292
Version 0.6.0 by @Alek050 in https://github.com/Alek050/databallpy/pull/297
Main by @Alek050 in https://github.com/Alek050/databallpy/pull/298
Add allow_overwrite kwarg to add_velocity and add_acceleration by @Alek050 in https://github.com/Alek050/databallpy/pull/303
Fixed scisports new format v1 by @Alek050 in https://github.com/Alek050/databallpy/pull/304
V0.6.1 release by @Alek050 in https://github.com/Alek050/databallpy/pull/306
308 bug dfl download link by @Alek050 in https://github.com/Alek050/databallpy/pull/309
Version 0.6.2 by @Alek050 in https://github.com/Alek050/databallpy/pull/310
bug in player possession calculation by @Alek050 in https://github.com/Alek050/databallpy/pull/311
small changes by @Alek050 in https://github.com/Alek050/databallpy/pull/314
support for frame_rate as float by @Alek050 in https://github.com/Alek050/databallpy/pull/315
Kloppy Support by @UnravelSports in https://github.com/Alek050/databallpy/pull/307
V0.7.0 release by @Alek050 in https://github.com/Alek050/databallpy/pull/317
Added offside logic by @Alek050 in https://github.com/Alek050/databallpy/pull/319
318 enh offside filter by @Alek050 in https://github.com/Alek050/databallpy/pull/320
updated logo by @Alek050 in https://github.com/Alek050/databallpy/pull/322
Better color selection of text in plot_tracking_data by @Alek050 in https://github.com/Alek050/databallpy/pull/324
Add dangerous accessible space and expected completion. by @jonas-bischofberger in https://github.com/Alek050/databallpy/pull/321
Updated changelog for DAS functionality by @Alek050 in https://github.com/Alek050/databallpy/pull/325
tkinter fix in git actions by @Alek050 in https://github.com/Alek050/databallpy/pull/326
bug fixes in validation of tracking and event data schemas by @Alek050 in https://github.com/Alek050/databallpy/pull/328

New Contributors

@jan-swiatek made their first contribution in https://github.com/Alek050/databallpy/pull/266
@UnravelSports made their first contribution in https://github.com/Alek050/databallpy/pull/307
@jonas-bischofberger made their first contribution in https://github.com/Alek050/databallpy/pull/321

Full Changelog: https://github.com/Alek050/databallpy/compare/v0.5.1...v0.7.2

- Python
Published by Alek050 6 months ago

DSWL package: a Python implementation of the Debiased Spatial Whittle Likelihood - v2.1.2

What's Changed

Update behaviour of BackendManager by @arthurBarthe in https://github.com/arthurBarthe/debiased-spatial-whittle/pull/24
Change import np to xp in src and docs by @arthurBarthe in https://github.com/arthurBarthe/debiased-spatial-whittle/pull/33
fix import of france.jpg by @arthurBarthe in https://github.com/arthurBarthe/debiased-spatial-whittle/pull/35
fix references by @arthurBarthe in https://github.com/arthurBarthe/debiased-spatial-whittle/pull/37

Full Changelog: https://github.com/arthurBarthe/debiased-spatial-whittle/compare/v2.1.1...v2.1.2

- Python
Published by arthurBarthe 6 months ago

Recent Releases of Open Source Science Software Projects

jaxDecomp: JAX Library for 3D Domain Decomposition and Parallel FFTs - v0.3.1

What's Changed

New Contributors

GaPFlow: Gap-averaged flow simulations with Gaussian process regression - v1.1.0

What's Changed

New Contributors

DeepCausalMMM: A Deep Learning Framework for Marketing Mix Modeling with Causal Structure Learning - v1.0.20 Release

What's Changed

New Contributors

Nexarag: Democratizing Reproducible Knowledge Graph Contexts for LLM Research - Automated Testing and Documentation

Nexarag Automated Testing and Documentation

Release

Highlights

DataBallPy: Load, synchronize, and Analyse your Soccer Data - Version 0.7.3

What's Changed

New Contributors

Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging - Release v1.1.8

Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging - Release v1.1.7

What's Changed

New Contributors

Felino: Extension of an open-source phase-field framework to geomaterial fracture - v1.0.2

flodym: A Python package for dynamic material flow analysis - v0.7.0

What's Changed

flodym: A Python package for dynamic material flow analysis - v0.6.0

What's Changed

baysc: An R package for Bayesian survey clustering - v0.1.2 - JOSS manuscript updated

SkyRank: a unified toolkit for Skyline ranking, benchmarking, and visualization - SkyRank v1.1.1

SkyRank: a unified toolkit for Skyline ranking, benchmarking, and visualization - SkyRank v1.1.0

HierarchyCraft: A Benchmark Builder for Hierarchical Reasoning - JOSS Paper release

What's Changed

New Contributors

TransiFlow: A Python package for performing bifurcation analysis on fluid flow problems - v1.0.1

multimodars: A Rust-powered toolkit for multi-modality cardiac image fusion and registration - Ground Truth

DSWL package: a Python implementation of the Debiased Spatial Whittle Likelihood - v2.1.3 - JOSS paper release

What's Changed

FastTanhSinhQuadrature.jl: High-performance Tanh-Sinh numerical integration in Julia - v1.0.1

FastTanhSinhQuadrature v1.0.1

v1.0.1 (patch release)

Summary

Changes

Breaking changes

Nexarag: Democratizing Reproducible Knowledge Graph Contexts for LLM Research - Nexarag Initial Release

Nexarag Initial Release Notes

Release

Highlights

Included Components

Deployment and Runtime

Configuration

Known Limitations

Test Coverage

FastTanhSinhQuadrature.jl: High-performance Tanh-Sinh numerical integration in Julia - v1.0.0

FastTanhSinhQuadrature.jl v1.0.0

Highlights

Installation

times_model - TIMES Version 4.9.3

TIMES Version 4.9.3

pypsa - v1.1.2

What's Changed

pypsa - v1.1.1

What's Changed

pypsa - v1.1.0

What's Changed

New Contributors

Graphorge: An open-source forge of graph neural networks - Graphorge 1.0.1

New Features and Improvements

Bug Fixes

IdentityByDescentDispersal.jl: Inferring dispersal rates with identity-by-descent blocks - v1.0.0+docs

IdentityByDescentDispersal.jl: Inferring dispersal rates with identity-by-descent blocks - v1.0.0

IdentityByDescentDispersal v1.0.0

Breaking changes

Minor changes

biodiscvr: Biomarker Discovery Using Composite Value Ratios - v1.3.0: JOSS Review Completion Release

Copernicus Seasonal Forecast Tools Package: Bridging Seasonal Climate Predictions and Impact Models for Operational Risk Assessment - copernicus-seasonal-forecast-tools v0.1.1 — JOSS submission

pyfive: A pure-Python HDF5 reader - Release v1.1.0

What's Changed

New Contributors

Tissue Data Explorer: a website template for presenting tissue sample research findings - Tissue Data Explorer v1.0.0

Dyad: a binary-star dynamics and statistics library for Python - Dyad 0.1.0

jaxDecomp: JAX Library for 3D Domain Decomposition and Parallel FFTs - v0.3.0