Release notes for DIPY version 1.12#

GitHub stats for 2025/03/16 - 2026/03/13 (tag: 1.11.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 187 authors contributed 15284 commits.

  • Adam Richie-Halford

  • Adam Rybinski

  • Alberto Di Biase

  • Alex Rockhill

  • Alexandre Gauvin

  • Aman Arya

  • Aman Srivastava

  • Andrew Lawrence

  • Ankur Sinha (Ankur Sinha Gmail)

  • Antoine Theberge

  • Antonio Ossa

  • Areesha Tariq

  • Ariel Rokem

  • ArjitJ

  • Aryansh Omray

  • Asa Gilmore

  • Atharva Shah

  • Bago Amirbekian

  • Baran Aydogan

  • Basile Pinsard

  • Bennet Fauber

  • Bishakh Ghosh

  • Bramsh Qamar

  • Chandan Gangwar

  • Chantal Tax

  • Charles Poirier

  • Chris Filo Gorgolewski

  • Christopher Nguyen

  • Clint Greene

  • Clément Zotti

  • Conor Corbin

  • Copilot

  • Dan Bullock

  • Daniel Enrico Cahall

  • Daniel McCloy

  • David Hunt

  • David Qixiang Chen

  • David Reagan

  • David Romero-Bascones

  • Demian Wassermann

  • Deneb Boito

  • Derek Pisner

  • Dimitri Papadopoulos

  • Dimitris Rozakis

  • Ebrahim Ebrahim

  • Eleftherios Garyfallidis

  • Emanuele Olivetti

  • Emmanuel Caruyer

  • Emmanuelle Renauld

  • Enes Albay

  • Eric Larson

  • Eric Peterson

  • Erik Ziegler

  • Etienne St-Onge

  • Fabio Nery

  • Felix Liu

  • Florent Wijanto

  • Francis Jerome

  • Francois Rheault

  • Gabriel Girard

  • Giulia Bertò

  • Gnaneswar Lopinti

  • Gonzalo Sanguinetti

  • Gregory Lee

  • Gregory R. Lee

  • Guillaume Theaud

  • Himanshu Mishra

  • Ian Nimmo-Smith

  • Inigo Tellaetxe

  • Jacob Roberts

  • Jaewon Chung

  • Jakob Wasserthal

  • Javier Guaje

  • Jean-Christophe Houde

  • Jirka Borovec

  • John Kruper

  • John Shen

  • Jon Haitz Legarreta Gorroño

  • Jon Mendoza

  • Jong Sung Park

  • Joshua Newton

  • Julio Villalon

  • Kaibo Tang

  • Karan

  • Katrin Leinweber

  • Kaustav Deka

  • Kenji Marshall

  • Kesshi Jordan

  • Kevin Sitek

  • Kimberly Chan

  • Kumar Ashutosh

  • Leevi Kerkela

  • Leon Weninger

  • Liberty

  • Lucas Da Costa

  • Maharshi Gor

  • Malinda Dilhara

  • Manu Tej Sharma

  • Marc-Alexandre Côté

  • Maria Luisa Mandelli

  • Martijn Nagtegaal

  • Martin Kozár

  • Martino Pilia

  • Matt Cieslak

  • Matthew Brett

  • Matthew Feickert

  • Matthias Ekman

  • Matthieu Dumont

  • Mauro Zucchelli

  • Maxime Descoteaux

  • Michael Paquette

  • Michael R. Crusoe

  • Mitesh Gulecha

  • Mohamed Abouagour

  • Mrinal Chaturvedi

  • Nasim Anousheh

  • Naveen Kumarmarri

  • Nicolas Delinte

  • Nil Goyette

  • Nishant Singh

  • Omar Ocegueda

  • Oscar Esteban

  • Parichit Sharma

  • Paul Camacho

  • Philippe Karan

  • Pradeep Reddy Raamana

  • Praitayini Kanakaraj

  • Prajwal Reddy

  • Qiyuan Tian

  • Rafael Neto Henriques

  • Rahul Ubale

  • Ranveer Aggarwal

  • Ricci Woo

  • Riddhish Bhalodia

  • Rohan Prinja

  • Ross Lawrence

  • Rutger Fick

  • Saber Sheybani

  • Sagun Pai

  • Sam Coveney

  • Samuel St-Jean

  • Sandro Turriate

  • Santiago Vila

  • Sarath Chandra

  • Scott Trinkle

  • Serge Koudoro

  • Shahnawaz Ahmed

  • Shilpi Prasad

  • Shreyas Fadnavis

  • Shrishti Hore

  • Shubham Shaswat

  • Siddharth Kapoor

  • Siddhesh Thakur

  • Sourav Singh

  • Sreekar Chigurupati

  • Stefan van der Walt

  • Stephan Meesters

  • Sven Dorkenwald

  • Sylvain Merlet

  • Takis Panagopoulos

  • Tashrif Billah

  • Theodore Ni

  • Tingyi Wanyan

  • Tom Dela Haije

  • Tom Wright

  • Umesh Gupta

  • Vara Lakshmi Bayanagari

  • Vatsala Swaroop

  • Vibhatha Abeykoon

  • Yaroslav Halchenko

  • Yash Sherry

  • Yijun Liu

  • aziza

  • dependabot[bot]

  • endolith

  • kunal mehta

  • lb-97

  • prathameshfuke

  • pre-commit-ci[bot]

  • rishav

  • root

  • samarmaharaj

  • satyam kumar

  • shadow1409

  • svabhishek29

  • ujjwal-shekhar

  • Étienne Mollier

We closed a total of 497 issues, 173 pull requests and 324 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (173):

  • PR #3844: NF: FORCE recon model

  • PR #3617: NF: add dipy_fit_msmtcsd cli with its tests

  • PR #3687: BUAN Bundle Profiles Lite Version

  • PR #3850: DOC: Fix broken and outdated links in gitwash documentation

  • PR #3679: Build aarch64 natively

  • PR #3847: BF: Updated sherbrooke-3shell.

  • PR #3845: BF: improve output file management of BiasField correction CLI

  • PR #3841: DOC: Complete missing parameters in save_polydata docstring

  • PR #3689: NF: Parallel Eudx

  • PR #3836: DOC: Documentation fix

  • PR #3808: RF: improve trx support for recobundles CLI

  • PR #3825: DOC: Modernize and complete benchmarks/README.rst - closes #3824

  • PR #3813: Fix #3811: reset warning filters in test_io_peaks_deprecated

  • PR #3833: DOC: Improve docstrings for SimilarityMetric in align.metrics

  • PR #3795: Added docs for nn and io

  • PR #3812: Fix #3810: use warnings.warn() for empty tractogram

  • PR #3700: RF: Simplify non-negative code in anisotropic_power

  • PR #3783: Fix figure canvas not cleared in simulation tutorials

  • PR #3699: Qti robust

  • PR #3834: Bump docker/setup-qemu-action from 3 to 4 in the actions group

  • PR #3831: DOC: Fix docstring errors in dipy/io/pickles.py

  • PR #3820: BF: improve rumba performance

  • PR #3818: BF: fix future errors/warnings from the future Numpy 2.5

  • PR #3816: RF: relax precision for affine_registration / motion_correction

  • PR #3823: DOC: Fix lowercase ‘returns’ section header in _make_fetcher docstring

  • PR #3805: Bump the actions group with 2 updates

  • PR #3791: NF: update biasfield correction method.

  • PR #3793: DOC: Add documentation for the PAM5 file format

  • PR #3752: CI: Update secrets management

  • PR #3796: updated the docstring for ls_fit_dki and cls_fit_dki

  • PR #3790: ENH: Cythonize AK, RK, and KFA kurtosis computations

  • PR #3789: BF: handle force option when using symlink and hardlink

  • PR #3784: Fix typo in test_template.yml input description (closes #3774)

  • PR #3765: NF: add cli dipy_cluster_streamlines

  • PR #3766: RF: improve CLI help formatting

  • PR #3767: RF: Fix multiple cli

  • PR #3780: Fix numpydoc validation issues in fetcher.py

  • PR #3781: Fix epsilon docstring mismatch

  • PR #3771: docs: Add a pull request template to standardize PR submissions.

  • PR #3762: NF: add new CLI dipy_brain_mask with its associated test

  • PR #3761: [DOC] Fix grammatical errors and typos across documentation and codebase

  • PR #3754: DOC: Typo in gitwash development_workflow guide

  • PR #3758: DOC: Fix missing space in load_peaks deprecation message

  • PR #3756: DOC: Remove Gitter link

  • PR #3704: Fix get simplified backward transform

  • PR #3746: TST: Replace legacy nose-style yield assert_raises with pytest.raises

  • PR #3750: Update setuptools requirement from ~=69.5 to >=69.5,<83.0 in the python-dependencies group

  • PR #3739: CI: Add top-level permissions for least-privilege security

  • PR #3733: CI: Add pip ecosystem tracking to Dependabot configuration

  • PR #3729: CI: Fix threading env vars not persisting across steps in benchmark.yml

  • PR #3722: CI: Pin actions/first-interaction by commit SHA in first_interaction.yml

  • PR #3721: CI: Pin srvaroa/labeler action by commit SHA in label-pr.yml

  • PR #3719: DOC: Update outdated Travis CI reference to GitHub Actions in CONTRIBUTING.md

  • PR #3716: CI: Fix invalid cron schedule in test.yml

  • PR #3715: CI: Add missing timeout-minutes to workflow jobs

  • PR #3749: RF: Updated the list provide a table of dataset names.

  • PR #3740: Bump srvaroa/labeler from 1.13.0 to 1.14.0 in the actions group

  • PR #3737: DOC: Migrate remaining http:// URLs to https://

  • PR #3711: CI: Fix incorrect Cython file glob patterns in labeler.yml

  • PR #3709: STYLE: Fix spelling mistakes in docstrings and comments

  • PR #3713: CI: Remove duplicate .mailmap entry in labeler.yml

  • PR #3706: RF: Add alternative to symlink for some CLI

  • PR #3696: BF: Handle empty tractograms gracefully in horizon

  • PR #3694: DOC: Fix numpydoc PR03 parameter order in path_length

  • PR #3692: DOC: Fixed DOC CI Issue

  • PR #3675: Adding synthseg pytorch model

  • PR #3686: BF: Handle empty streamlines in slr_with_qbx after length filtering

  • PR #3684: RF: address some edge cases in multiple workflows

  • PR #3681: Examples for IRLS (robust fitting)

  • PR #3685: DOC: fix some missing :footcite:p in documentation

  • PR #3671: Increased speed and lisibility of connectivity matrix, added weights

  • PR #3680: RF: Added max_version option to optional_package api.

  • PR #3677: DOC: Fix file path in many tutorials.

  • PR #3676: RF: Allow reslice to automatically determines isotropic resolution

  • PR #3678: Build 3.14 nightly wheels

  • PR #3664: DOC: Improve Horizon class docstring for clarity

  • PR #3665: FIX: Correct path construction logic in fetcher data loader, Resolve path construction errors in read_bundles_2_subjects

  • PR #3673: RF: Allow bvals file for medianOtsu workflow

  • PR #3674: Bump scientific-python/upload-nightly-action from 0.6.2 to 0.6.3 in the actions group

  • PR #3542: RF: Editing tranform_img in dipy.nn.utils

  • PR #3670: Test: Add regression test for median_otsu autocrop deprecation

  • PR #3668: MNT: Replace deprecated autocrop in brain_extraction_dwi.py, reconst_csa.py, reconst_csa_parallel.py, reconst_dti.py tutorial examples

  • PR #3672: Bump the actions group with 3 updates

  • PR #3669: DOC: Prefer BibTeX reference in GQSI example documentation

  • PR #3657: Document pre-commit setup for developers

  • PR #3667: MNT: Replace deprecated autocrop in reconst_dti.py

  • PR #3659: NF: Intermediate map for symmetric diffeomorphic registration

  • PR #3660: DOC: Programmatic DIPY Horizon usage (non-CLI)

  • PR #3623: RF: refactoring of nlmeans to allow the selection our classic version and the blockwise version

  • PR #3661: CI: simplify cache, too many data was cached

  • PR #3662: Bump actions/checkout from 5 to 6 in the actions group

  • PR #3552: BF: Discards streamlines by size

  • PR #3652: NF: Reduce default iteration counts and make level_iters configurable in motion correction

  • PR #3618: BF: manage empty file in dipy_slr cli to avoid enigmatic crash

  • PR #3655: CI: remove fetch-data job

  • PR #3658: Added interpolation parameter to dipy_apply_transform

  • PR #3648: Revert split extension (for SFT and SFS)

  • PR #3654: RF: fix warnings introduced by the future Numpy version 2.4

  • PR #3651: RF: handle bingham tests warnings

  • PR #3650: BF: update first interaction Github action parameters

  • PR #3649: Bump the actions group with 2 updates

  • PR #3635: BF: Fix CVXPY warning

  • PR #3646: [BF] Fix fwdti

  • PR #3639: fix: BUG: fix UnboundLocalError in _single_sf_to_bingham when no valid peaks found

  • PR #3610: NF: add dipy_fit_powermap workflows with its associated tests

  • PR #3634: BF: expand requirements during its generation

  • PR #3425: NF: add FWDTI Workflow

  • PR #3631: RF: Fixed weird volumes instead of denoised volumes in Patch2Self 3

  • PR #3629: Bump actions/setup-python from 5 to 6 in the actions group

  • PR #3625: docs: remove NeuroFedora

  • PR #3424: NF: Automate requirement files

  • PR #3624: Bump the actions group with 3 updates

  • PR #3605: RF: Parallel quantize_evecs

  • PR #3613: BF: Allow length to work with float16 streamlines

  • PR #3612: BF: fix lower triangular bug introduced in #3563

  • PR #1617: NF: added streamline clipping function to utils

  • PR #3606: RF: Address cvxpy 1.7.0 warnings.

  • PR #3609: Bump actions/first-interaction from 1 to 2 in the actions group

  • PR #3560: Doc: explicit finalize_mask information in CLI tutorial

  • PR #3602: ENH: Adopt pathlib for workflows

  • PR #3604: RF: replace old LocalTracking by our new tracking interface

  • PR #3587: RF: from TRK to TRX as default file format for tracks

  • PR #3603: DOC: Fix workflows test utils parameter name in docstring

  • PR #3601: DOC: Record API changes after pathlib adoption

  • PR #3593: STYLE: Adopt pathlib for path manipulation

  • PR #3599: TEST: Restore removed test case in io workflows

  • PR #3600: MNT: Fix miscellaneous labeler regexes

  • PR #3597: STYLE: Miscellaneous style fixes

  • PR #3598: BF: Miscellaneous fixes to surfaces

  • PR #3592: STYLE: Adopt a unified logger across the code base

  • PR #3429: StatefulSurface - Class to handle surfaces

  • PR #3595: DOC: Remove default arguments from docstrings

  • PR #3594: STYLE: Miscellaneous style fixes

  • PR #3591: STYLE: Apply ruff manually to all files

  • PR #3582: NF: Add PR labeler workflow

  • PR #3586: MNT: Change issue template file extensions

  • PR #3584: MNT: Add GitHub issue templates

  • PR #3583: DOC: Change unused commit prefixes to some other more useful ones

  • PR #3581: SciPy deprecation of “disp” in optimizer

  • PR #3556: RF: allow the saving of S0 estimate for dti workflow

  • PR #3563: RF: Address some Zero division warnings

  • PR #3565: RF: use multi_voxel_fit for rumba

  • PR #3541: RF: Deprecate autocrop in median_otsu

  • PR #3580: TEST: uncomment and update test_cross

  • PR #3515: RF: Improve dipy_info printed output

  • PR #3562: DOC: Add missing opening backtick to reference syntax.

  • PR #3561: STYLE: Make affine variable naming consistent

  • PR #3557: DOC: fix streamline-tools tutorial by avoiding the use of identity affine

  • PR #3559: [RF]: Patch2self in denoising CLI tutorial

  • PR #3555: ENH: improve dipy_info message when no reference for some streamline files.

  • PR #3554: Doc: Fix typo in multiple tutorial

  • PR #3546: BF: Make StoppingCriterion reproducible for multi-thread execution

  • PR #3548: RF: fix typo in hcp fetcher function argument name

  • PR #3549: BF: Improves Cython enum management.

  • PR #3520: ENH: Opacity slider turned off on hide

  • PR #3493: NF: allow broadcasting in dipy_math

  • PR #3488: RF - changed min/max len from nbr pts to mm

  • PR #3538: RF: Fixed the latex

  • PR #3519: ENH: Horizon peaks fname support

  • PR #3455: Fix Bugs in #3453: Ensure Correct Weight Reshaping & Consistent Extra Output in iter_fit_tensor

  • PR #3535: CI: Ignore fork() warnings.

  • PR #3528: DOC: Changed documentation errors in dipy.sims.voxel

  • PR #3533: CI: introduce cached Data.

  • PR #3531: CI: Ignore specific cvxpy warnings to avoid CI failure.

  • PR #3527: BF: Search bar should come bigger in the center.

  • PR #3530: STYLE: Add additional emojis to first interaction message

  • PR #3526: Bump scientific-python/upload-nightly-action from 0.6.1 to 0.6.2 in the actions group

  • PR #3522: FIX: Avoid division by zero on single-CPU systems (issue #3521)

  • PR #3510: [RF]: Saving the figure in the example.

  • PR #3512: STYLE: Call warning instead of the deprecated warn function

  • PR #3514: DOC: Miscellaneous doc improvements

  • PR #3495: BF: Fixing minor issue in dipy_classify_tissue dam option

  • PR #3481: UPCOMING: Release 1.11.0

Issues (324):

  • #3844: NF: FORCE recon model

  • #3503: Create new interface for MTMS CSD and standard CSD that use Ray properly

  • #3617: NF: add dipy_fit_msmtcsd cli with its tests

  • #3687: BUAN Bundle Profiles Lite Version

  • #3849: DOC: Fix broken and outdated links in gitwash documentation

  • #3850: DOC: Fix broken and outdated links in gitwash documentation

  • #2766: WIP Issue 2738 click cli refactor

  • #2738: Replace our custom Argparse CLI api by Click ?

  • #2547: [WIP][FIX] option to disable multithreading while multiprocessing

  • #3143: [WIP][NF] Add dipy_gtable cli

  • #3679: Build aarch64 natively

  • #3847: BF: Updated sherbrooke-3shell.

  • #3845: BF: improve output file management of BiasField correction CLI

  • #3628: iter_fit_tensor returns {} instead of None causing KeyError in nlls_fit_tensor when return_leverages=False

  • #3840: DOC: Complete missing parameters in save_polydata docstring

  • #3841: DOC: Complete missing parameters in save_polydata docstring

  • #3689: NF: Parallel Eudx

  • #3836: DOC: Documentation fix

  • #3808: RF: improve trx support for recobundles CLI

  • #3693: QTI issues - lack of MIN_POSITIVE_SIGNAL and issue with constrained solver and WLS is wrong anyway

  • #3824: DOC: Modernize and complete benchmarks/README.rst (and developer docs)

  • #3825: DOC: Modernize and complete benchmarks/README.rst - closes #3824

  • #3835: ENH: add ASV continuous benchmarking workflow

  • #3811: test_io_peaks_deprecated fails - ACTUAL: 82 warnings, DESIRED: 2

  • #3813: Fix #3811: reset warning filters in test_io_peaks_deprecated

  • #3833: DOC: Improve docstrings for SimilarityMetric in align.metrics

  • #3795: Added docs for nn and io

  • #3827: Enh asv continuous benchmarks

  • #3814: ENH: Ray-aware CSD and MSMT-CSD workflows (#3503, #3617)

  • #3807: Fix #3502: Add ODF and Tensor visualization to dipy_horizon

  • #3810: test_horizon_empty_tractogram fails - logger.warning() not caught by warnings.catch_warnings()

  • #3812: Fix #3810: use warnings.warn() for empty tractogram

  • #3700: RF: Simplify non-negative code in anisotropic_power

  • #3656: Some tutorials do not clear the figure canvas

  • #3783: Fix figure canvas not cleared in simulation tutorials

  • #3645: Powermap contains negative intensities

  • #3699: Qti robust

  • #3834: Bump docker/setup-qemu-action from 3 to 4 in the actions group

  • #3830: DOC: Fix docstring errors in dipy/io/pickles.py

  • #3831: DOC: Fix docstring errors in dipy/io/pickles.py

  • #3820: BF: improve rumba performance

  • #3818: BF: fix future errors/warnings from the future Numpy 2.5

  • #3816: RF: relax precision for affine_registration / motion_correction

  • #3822: DOC: Fix lowercase ‘returns’ section header in _make_fetcher docstring

  • #3823: DOC: Fix lowercase ‘returns’ section header in _make_fetcher docstring

  • #3805: Bump the actions group with 2 updates

  • #3647: Biasfield Correction b0 method not working correctly

  • #3791: NF: update biasfield correction method.

  • #2427: Document the PAM file format

  • #3793: DOC: Add documentation for the PAM5 file format

  • #3752: CI: Update secrets management

  • #3785: Weights parameter documented twice

  • #3796: updated the docstring for ls_fit_dki and cls_fit_dki

  • #3790: ENH: Cythonize AK, RK, and KFA kurtosis computations

  • #3799: DOC: Add tutorial for saving and loading QuickBundles clustering results

  • #3789: BF: handle force option when using symlink and hardlink

  • #3774: CI: Fix typo in test_template.yml workflow input description

  • #3784: Fix typo in test_template.yml input description (closes #3774)

  • #3765: NF: add cli dipy_cluster_streamlines

  • #3766: RF: improve CLI help formatting

  • #3767: RF: Fix multiple cli

  • #3759: DOC: Standardize docstring format across modules using numpydoc conventions

  • #3780: Fix numpydoc validation issues in fetcher.py

  • #3764: epsilon docstring mismatch

  • #3781: Fix epsilon docstring mismatch

  • #3778: CI: Add manual workflow trigger (workflow_dispatch) to test.yml

  • #3779: CI: Add manual workflow trigger (workflow_dispatch) to test.yml

  • #3775: CI: Add pip caching to build_docs.yml

  • #3776: CI: Add pip caching to build_docs.yml

  • #3772: CI: Add concurrency group to build_docs.yml

  • #3773: CI: Add concurrency group to build_docs.yml

  • #3770: Add a Pull Request template to standardize PR descriptions

  • #3771: docs: Add a pull request template to standardize PR submissions.

  • #3768: CI: Add workflow to clean up GitHub Actions caches on closed PRs

  • #3769: CI: Add workflow to clean up GitHub Actions caches on closed PRs

  • #3777: CI: Add manual workflow trigger (workflow_dispatch) to test.yml

  • #3762: NF: add new CLI dipy_brain_mask with its associated test

  • #3760: [DOC] Fix typos and grammatical errors in documentation and code

  • #3761: [DOC] Fix grammatical errors and typos across documentation and codebase

  • #3753: DOC: Typo in gitwash development_workflow guide

  • #3754: DOC: Typo in gitwash development_workflow guide

  • #3757: DOC: Fix missing space in load_peaks deprecation message

  • #3758: DOC: Fix missing space in load_peaks deprecation message

  • #3755: DOC: Update Gitter link to Matrix invite link

  • #3756: DOC: Remove Gitter link

  • #3704: Fix get simplified backward transform

  • #3751: Fixed Github Workflow Issues

  • #3745: Replace legacy nose-style yield assert_raises with pytest.raises

  • #3746: TST: Replace legacy nose-style yield assert_raises with pytest.raises

  • #3750: Update setuptools requirement from ~=69.5 to >=69.5,<83.0 in the python-dependencies group

  • #3738: CI: Missing top-level permissions in CI workflow files

  • #3739: CI: Add top-level permissions for least-privilege security

  • #3734: CI: Benchmark workflow triggers on all pushes/PRs instead of master only

  • #3735: CI: Restrict benchmark workflow triggers to master branch

  • #3732: CI: Dependabot only monitors GitHub Actions, not pip dependencies

  • #3733: CI: Add pip ecosystem tracking to Dependabot configuration

  • #3731: MNT: Remove dead install type code paths from install.sh

  • #3728: CI: Benchmark threading env vars don’t persist to the benchmarking step

  • #3729: CI: Fix threading env vars not persisting across steps in benchmark.yml

  • #3727: CI: Update stale dependency pins in CI configuration

  • #3723: CI: first_interaction.yml action pinned by tag instead of SHA on pull_request_target trigger

  • #3722: CI: Pin actions/first-interaction by commit SHA in first_interaction.yml

  • #3720: CI: label-pr.yml uses third-party action pinned by tag on pull_request_target trigger

  • #3721: CI: Pin srvaroa/labeler action by commit SHA in label-pr.yml

  • #3718: DOC: CONTRIBUTING.md references Travis CI instead of GitHub Actions

  • #3719: DOC: Update outdated Travis CI reference to GitHub Actions in CONTRIBUTING.md

  • #3717: CI: Invalid cron schedule in test.yml runs ~1-2x/year instead of monthly

  • #3716: CI: Fix invalid cron schedule in test.yml

  • #3714: CI: Add missing timeout-minutes to workflow jobs

  • #3715: CI: Add missing timeout-minutes to workflow jobs

  • #3749: RF: Updated the list provide a table of dataset names.

  • #3724: CI: Duplicate step names in nightly.yml upload_anaconda job make logs confusing

  • #3725: CI: Rename duplicate ‘Upload wheel’ steps in nightly.yml for clarity

  • #3747: Missing __all__ exports in subpackage __init__.py files

  • #3748: STY: Add missing __all__ exports to subpackage __init__.py files

  • #3740: Bump srvaroa/labeler from 1.13.0 to 1.14.0 in the actions group

  • #3741: Replace deprecated numpy.testing.assert_() with plain assert

  • #3742: TST: Replace deprecated npt.assert_() with plain assert

  • #3743: Replace deprecated assert_almost_equal / assert_array_almost_equal with assert_allclose

  • #3744: TST: Replace deprecated assert_almost_equal / assert_array_almost_equal with assert_allclose

  • #3736: DOC: Remaining insecure http:// URLs should be migrated to https://

  • #3737: DOC: Migrate remaining http:// URLs to https://

  • #3710: CI: Fix incorrect Cython file glob patterns in labeler.yml

  • #3711: CI: Fix incorrect Cython file glob patterns in labeler.yml

  • #3708: STYLE: Fix spelling mistakes in docstrings and comments

  • #3709: STYLE: Fix spelling mistakes in docstrings and comments

  • #3712: #CI: Remove duplicate .mailmap entry in labeler.yml

  • #3713: CI: Remove duplicate .mailmap entry in labeler.yml

  • #3706: RF: Add alternative to symlink for some CLI

  • #3688: dipy_horizon with Empty Streamline File

  • #3696: BF: Handle empty tractograms gracefully in horizon

  • #3701: Revert temporary suppression of SCS CSC conversion warning

  • #3697: Fix dipy_horizon crash on empty tractogram files

  • #3694: DOC: Fix numpydoc PR03 parameter order in path_length

  • #2760: TRX integration

  • #3692: DOC: Fixed DOC CI Issue

  • #3675: Adding synthseg pytorch model

  • #3683: DIPY_SLR Breaking with Wrong Error

  • #3686: BF: Handle empty streamlines in slr_with_qbx after length filtering

  • #3684: RF: address some edge cases in multiple workflows

  • #3222: Issue with CWLS in dki

  • #3405: Follow up for the Iteratively reweighted least squares

  • #3681: Examples for IRLS (robust fitting)

  • #3516: Do not require FURY to show information from a VTK/VTP tractography files

  • #2538: [WIP] Registration public API for multi-slice 2D data

  • #3685: DOC: fix some missing :footcite:p in documentation

  • #3671: Increased speed and lisibility of connectivity matrix, added weights

  • #3680: RF: Added max_version option to optional_package api.

  • #3682: TST: Add interface tests for pure Python DirectionGetter implementations

  • #3677: DOC: Fix file path in many tutorials.

  • #3676: RF: Allow reslice to automatically determines isotropic resolution

  • #3678: Build 3.14 nightly wheels

  • #3664: DOC: Improve Horizon class docstring for clarity

  • #3665: FIX: Correct path construction logic in fetcher data loader, Resolve path construction errors in read_bundles_2_subjects

  • #3673: RF: Allow bvals file for medianOtsu workflow

  • #3674: Bump scientific-python/upload-nightly-action from 0.6.2 to 0.6.3 in the actions group

  • #3542: RF: Editing tranform_img in dipy.nn.utils

  • #3670: Test: Add regression test for median_otsu autocrop deprecation

  • #3668: MNT: Replace deprecated autocrop in brain_extraction_dwi.py, reconst_csa.py, reconst_csa_parallel.py, reconst_dti.py tutorial examples

  • #3672: Bump the actions group with 3 updates

  • #3669: DOC: Prefer BibTeX reference in GQSI example documentation

  • #3643: Document pre-commit setup

  • #3657: Document pre-commit setup for developers

  • #3667: MNT: Replace deprecated autocrop in reconst_dti.py

  • #3439: data fetching: problem with UW server ?

  • #3659: NF: Intermediate map for symmetric diffeomorphic registration

  • #3397: Adding Python Code Example for DIPY Horizon in Tutorials

  • #3660: DOC: Programmatic DIPY Horizon usage (non-CLI)

  • #2950: Clean up the non-local means denoising modules

  • #1259: nlmeans does not respect boundaries

  • #1224: Memory issue

  • #1131: new non_local_means module seems to disregard 3D array of noise standard deviation

  • #1178: Recheck indexing with nlmeans as some of it is indexing wrong positions

  • #3623: RF: refactoring of nlmeans to allow the selection our classic version and the blockwise version

  • #3661: CI: simplify cache, too many data was cached

  • #3662: Bump actions/checkout from 5 to 6 in the actions group

  • #3552: BF: Discards streamlines by size

  • #3652: NF: Reduce default iteration counts and make level_iters configurable in motion correction

  • #3618: BF: manage empty file in dipy_slr cli to avoid enigmatic crash

  • #3655: CI: remove fetch-data job

  • #3658: Added interpolation parameter to dipy_apply_transform

  • #3621: filename for statefulsurface and statefultractogram cannot have period in them anymore

  • #3648: Revert split extension (for SFT and SFS)

  • #3636: Bug with use of where

  • #3654: RF: fix warnings introduced by the future Numpy version 2.4

  • #3651: RF: handle bingham tests warnings

  • #3653: RF: Fix imports in reconst

  • #3640: First interaction workflow doesn’t work

  • #3650: BF: update first interaction Github action parameters

  • #3649: Bump the actions group with 2 updates

  • #3638: UnboundLocalError: local variable ‘fits’ referenced before assignment

  • #3635: BF: Fix CVXPY warning

  • #3646: [BF] Fix fwdti

  • #3639: fix: BUG: fix UnboundLocalError in _single_sf_to_bingham when no valid peaks found

  • #3610: NF: add dipy_fit_powermap workflows with its associated tests

  • #2087: Single-shell Free Water DTI (Object Oriented)

  • #3634: BF: expand requirements during its generation

  • #3425: NF: add FWDTI Workflow

  • #2137: Deep-learning-based registration example

  • #3631: RF: Fixed weird volumes instead of denoised volumes in Patch2Self 3

  • #3633: Patch2Self CLI provides wrong doc string for version

  • #3539: FOSR implementation in Python for tractometry

  • #3629: Bump actions/setup-python from 5 to 6 in the actions group

  • #3625: docs: remove NeuroFedora

  • #3424: NF: Automate requirement files

  • #3624: Bump the actions group with 3 updates

  • #3605: RF: Parallel quantize_evecs

  • #3613: BF: Allow length to work with float16 streamlines

  • #3608: Predicting from a fitted DTI model is broken?

  • #3612: BF: fix lower triangular bug introduced in #3563

  • #3588: In-house QP solver using numba for fitting MSMT

  • #1617: NF: added streamline clipping function to utils

  • #3606: RF: Address cvxpy 1.7.0 warnings.

  • #3609: Bump actions/first-interaction from 1 to 2 in the actions group

  • #3551: Shutting down the gitter live chat ?

  • #1164: Parallel quantize_evecs + PEP8

  • #3124: ENH: Add commentary on median otsu tutorial/change default parameters

  • #3560: Doc: explicit finalize_mask information in CLI tutorial

  • #3602: ENH: Adopt pathlib for workflows

  • #3604: RF: replace old LocalTracking by our new tracking interface

  • #3506: Make sure .trx is default everywhere

  • #3587: RF: from TRK to TRX as default file format for tracks

  • #3603: DOC: Fix workflows test utils parameter name in docstring

  • #3601: DOC: Record API changes after pathlib adoption

  • #3593: STYLE: Adopt pathlib for path manipulation

  • #3599: TEST: Restore removed test case in io workflows

  • #3600: MNT: Fix miscellaneous labeler regexes

  • #3597: STYLE: Miscellaneous style fixes

  • #3598: BF: Miscellaneous fixes to surfaces

  • #3592: STYLE: Adopt a unified logger across the code base

  • #3596: NF - Add DirectionGetter for Flocking Tractography

  • #3429: StatefulSurface - Class to handle surfaces

  • #3595: DOC: Remove default arguments from docstrings

  • #3594: STYLE: Miscellaneous style fixes

  • #3513: STYLE: Log message instead of printing orphan string

  • #3591: STYLE: Apply ruff manually to all files

  • #3582: NF: Add PR labeler workflow

  • #3586: MNT: Change issue template file extensions

  • #3584: MNT: Add GitHub issue templates

  • #3583: DOC: Change unused commit prefixes to some other more useful ones

  • #3581: SciPy deprecation of “disp” in optimizer

  • #3556: RF: allow the saving of S0 estimate for dti workflow

  • #3497: dipy_fit_dti does not return S0 estimate

  • #3418: Division by 0 warning

  • #3563: RF: Address some Zero division warnings

  • #3352: Rumba and multivoxel fit decorator

  • #3565: RF: use multi_voxel_fit for rumba

  • #3537: Remove autocrop from median_otsu

  • #3541: RF: Deprecate autocrop in median_otsu

  • #2866: arm64 test failure with numpy 1.24.2

  • #3580: TEST: uncomment and update test_cross

  • #1776: make it really easy for DiPy to call graspy functions

  • #2269: Allow dipy_fit_dti Workflow to Use Native Orientation of Provided Mask Image

  • #2682: DIPY Free-Water Corrected DTI (FA output quality)

  • #2428: dipy.align.reslice

  • #2399: fitting free water mapping out of iterations

  • #2319: Reconstruction with MSMT CSD example resulted in Nan values

  • #2329: Slice to volume registration

  • #1974: MAP-MRI optimization & validation errors

  • #2612: Mean Diffusivity turns out low in CSF when reconstructing using ReconstDtiFlow

  • #687: Refactor imaffine class structure.

  • #706: Thoughts about using the SyN algorithm

  • #2184: discussion: continuous integration using GPUs

  • #1991: [DISCUSSION] b-tensor encoding gradient table format

  • #2186: Pure-python implementation of boundary-based registration (BBR)?

  • #1852: Telemetry

  • #2338: Team DIPY Citations

  • #2663: Plotting tensors in Fury: issue with right-handed coordinate system?

  • #3515: RF: Improve dipy_info printed output

  • #2850: Orthogonal Tensor Parameter (Moment) Maps

  • #1886: NF - add the option to save the last point of streamlines

  • #3562: DOC: Add missing opening backtick to reference syntax.

  • #3561: STYLE: Make affine variable naming consistent

  • #3382: Check use of affine in streamline_tools example

  • #3557: DOC: fix streamline-tools tutorial by avoiding the use of identity affine

  • #2473: Add Patch2self in our denoising CLI tutorial

  • #3559: [RF]: Patch2self in denoising CLI tutorial

  • #2695: Replace CENIR multishell with HBN POD2 data

  • #2728: Do we have multi_processes method for streamline extraction

  • #2848: Noise estimation of T1 brain MR images

  • #3500: dipy_fit_csa does not use num_processes

  • #3517: dipy_info provides misleading message when no reference is provided

  • #3555: ENH: improve dipy_info message when no reference for some streamline files.

  • #3554: Doc: Fix typo in multiple tutorial

  • #3413: Tutorial Typos

  • #3492: BF: Peaks working with world coordinates.

  • #1249: Bias correction for local pca

  • #823: WIP: “Out-of-core” LiFE

  • #3540: Tractography with GFA as stopping criterion is not reproducible across runs

  • #3546: BF: Make StoppingCriterion reproducible for multi-thread execution

  • #3545: ENH: Add StopingCriterion reproducibility test

  • #3548: RF: fix typo in hcp fetcher function argument name

  • #3549: BF: Improves Cython enum management.

  • #3507: Extract b0 interface throws value error with HCP 7T (MGH) - subject 1007

  • #3474: Filenames missing in horizon for peaks objects

  • #3520: ENH: Opacity slider turned off on hide

  • #3544: ENH: Add StopingCriterion reproducibility test

  • #3493: NF: allow broadcasting in dipy_math

  • #3488: RF - changed min/max len from nbr pts to mm

  • #3536: FA latex formula does not show correctly on DTI tutorial

  • #3538: RF: Fixed the latex

  • #3519: ENH: Horizon peaks fname support

  • #1404: RF - DirectionGetter.get_direction function return

  • #3453: Inconistancy between documentation and implementation on dipy.reconst.dti.nlls_fit_tensor

  • #3455: Fix Bugs in #3453: Ensure Correct Weight Reshaping & Consistent Extra Output in iter_fit_tensor

  • #3535: CI: Ignore fork() warnings.

  • #3501: Probabilistic reference in docs seems incorrect

  • #3336: Simplify CIs

  • #3528: DOC: Changed documentation errors in dipy.sims.voxel

  • #3533: CI: introduce cached Data.

  • #3531: CI: Ignore specific cvxpy warnings to avoid CI failure.

  • #2494: Potential speed up for the data fetchers

  • #3527: BF: Search bar should come bigger in the center.

  • #3530: STYLE: Add additional emojis to first interaction message

  • #3526: Bump scientific-python/upload-nightly-action from 0.6.1 to 0.6.2 in the actions group

  • #3521: Division by zero when machine has a single CPU

  • #3522: FIX: Avoid division by zero on single-CPU systems (issue #3521)

  • #3510: [RF]: Saving the figure in the example.

  • #3512: STYLE: Call warning instead of the deprecated warn function

  • #3514: DOC: Miscellaneous doc improvements

  • #3508: New disco tracking tutorial not available in docs

  • #3495: BF: Fixing minor issue in dipy_classify_tissue dam option

  • #3494: publish wheels

  • #3481: UPCOMING: Release 1.11.0