Public release 1.12.1

=====================================

 Release notes for DIPY version 1.12
=====================================

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
:file:`tools/github_stats.py`):

Pull Requests (173):

* :ghpull:`3844`: NF: FORCE recon model
* :ghpull:`3617`: NF: add dipy_fit_msmtcsd cli with its tests
* :ghpull:`3687`: BUAN Bundle Profiles Lite Version
* :ghpull:`3850`: DOC: Fix broken and outdated links in gitwash documentation
* :ghpull:`3679`: Build aarch64 natively
* :ghpull:`3847`: BF: Updated sherbrooke-3shell.
* :ghpull:`3845`: BF: improve output file management of BiasField correction CLI
* :ghpull:`3841`: DOC: Complete missing parameters in save_polydata docstring
* :ghpull:`3689`: NF: Parallel Eudx
* :ghpull:`3836`: DOC: Documentation fix
* :ghpull:`3808`: RF: improve trx support for recobundles CLI
* :ghpull:`3825`: DOC: Modernize and complete benchmarks/README.rst - closes #3824
* :ghpull:`3813`: Fix #3811: reset warning filters in test_io_peaks_deprecated
* :ghpull:`3833`: DOC: Improve docstrings for SimilarityMetric in align.metrics
* :ghpull:`3795`: Added docs for nn and io
* :ghpull:`3812`: Fix #3810: use warnings.warn() for empty tractogram
* :ghpull:`3700`: RF: Simplify non-negative code in anisotropic_power
* :ghpull:`3783`: Fix figure canvas not cleared in simulation tutorials
* :ghpull:`3699`: Qti robust
* :ghpull:`3834`: Bump docker/setup-qemu-action from 3 to 4 in the actions group
* :ghpull:`3831`: DOC: Fix docstring errors in dipy/io/pickles.py
* :ghpull:`3820`: BF: improve rumba performance
* :ghpull:`3818`: BF: fix future errors/warnings from the future Numpy 2.5
* :ghpull:`3816`: RF: relax precision for affine_registration / motion_correction
* :ghpull:`3823`: DOC: Fix lowercase 'returns' section header in _make_fetcher docstring
* :ghpull:`3805`: Bump the actions group with 2 updates
* :ghpull:`3791`: NF: update biasfield correction method.
* :ghpull:`3793`: DOC: Add documentation for the PAM5 file format
* :ghpull:`3752`: CI: Update secrets management
* :ghpull:`3796`: updated the docstring for ls_fit_dki and cls_fit_dki
* :ghpull:`3790`: ENH: Cythonize AK, RK, and KFA kurtosis computations
* :ghpull:`3789`: BF: handle `force` option when using symlink and hardlink
* :ghpull:`3784`: Fix typo in test_template.yml input description (closes #3774)
* :ghpull:`3765`: NF: add cli dipy_cluster_streamlines
* :ghpull:`3766`: RF: improve CLI help formatting
* :ghpull:`3767`: RF: Fix multiple cli
* :ghpull:`3780`: Fix `numpydoc` validation issues in `fetcher.py`
* :ghpull:`3781`: Fix epsilon docstring mismatch
* :ghpull:`3771`: docs: Add a pull request template to standardize PR submissions.
* :ghpull:`3762`: NF: add new CLI dipy_brain_mask with its associated test
* :ghpull:`3761`:  [DOC] Fix grammatical errors and typos across documentation and codebase
* :ghpull:`3754`: DOC: Typo in gitwash development_workflow guide
* :ghpull:`3758`: DOC: Fix missing space in `load_peaks` deprecation message
* :ghpull:`3756`: DOC: Remove Gitter link
* :ghpull:`3704`: Fix get simplified backward transform
* :ghpull:`3746`: TST: Replace legacy nose-style `yield assert_raises` with `pytest.raises`
* :ghpull:`3750`: Update setuptools requirement from ~=69.5 to >=69.5,<83.0 in the python-dependencies group
* :ghpull:`3739`: CI: Add top-level permissions for least-privilege security
* :ghpull:`3733`: CI: Add pip ecosystem tracking to Dependabot configuration
* :ghpull:`3729`: CI: Fix threading env vars not persisting across steps in benchmark.yml
* :ghpull:`3722`: CI: Pin actions/first-interaction by commit SHA in first_interaction.yml
* :ghpull:`3721`: CI: Pin srvaroa/labeler action by commit SHA in label-pr.yml
* :ghpull:`3719`:  DOC: Update outdated Travis CI reference to GitHub Actions in CONTRIBUTING.md
* :ghpull:`3716`: CI: Fix invalid cron schedule in test.yml
* :ghpull:`3715`: CI: Add missing timeout-minutes to workflow jobs
* :ghpull:`3749`: RF: Updated the list provide a table of dataset names.
* :ghpull:`3740`: Bump srvaroa/labeler from 1.13.0 to 1.14.0 in the actions group
* :ghpull:`3737`:  DOC: Migrate remaining `http://` URLs to `https://`
* :ghpull:`3711`: CI: Fix incorrect Cython file glob patterns in labeler.yml
* :ghpull:`3709`: STYLE: Fix spelling mistakes in docstrings and comments
* :ghpull:`3713`: CI: Remove duplicate .mailmap entry in labeler.yml
* :ghpull:`3706`: RF: Add alternative to symlink for some  CLI
* :ghpull:`3696`: BF: Handle empty tractograms gracefully in horizon
* :ghpull:`3694`: DOC: Fix numpydoc PR03 parameter order in path_length
* :ghpull:`3692`: DOC: Fixed DOC CI Issue
* :ghpull:`3675`: Adding synthseg pytorch model
* :ghpull:`3686`: BF: Handle empty streamlines in slr_with_qbx after length filtering
* :ghpull:`3684`: RF: address some edge cases in multiple workflows
* :ghpull:`3681`: Examples for IRLS (robust fitting)
* :ghpull:`3685`: DOC: fix some missing `:footcite:p` in documentation
* :ghpull:`3671`: Increased speed and lisibility of connectivity matrix, added weights
* :ghpull:`3680`: RF: Added max_version option to optional_package api.
* :ghpull:`3677`: DOC: Fix file path in many tutorials.
* :ghpull:`3676`: RF: Allow reslice to automatically determines isotropic resolution
* :ghpull:`3678`: Build 3.14 nightly wheels
* :ghpull:`3664`: DOC: Improve Horizon class docstring for clarity
* :ghpull:`3665`: FIX: Correct path construction logic in fetcher data loader, Resolve path construction errors in read_bundles_2_subjects
* :ghpull:`3673`: RF: Allow bvals file for medianOtsu workflow
* :ghpull:`3674`: Bump scientific-python/upload-nightly-action from 0.6.2 to 0.6.3 in the actions group
* :ghpull:`3542`: RF: Editing tranform_img in dipy.nn.utils
* :ghpull:`3670`: Test: Add regression test for median_otsu autocrop deprecation
* :ghpull:`3668`: MNT: Replace deprecated autocrop in brain_extraction_dwi.py, reconst_csa.py, reconst_csa_parallel.py, reconst_dti.py tutorial examples
* :ghpull:`3672`: Bump the actions group with 3 updates
* :ghpull:`3669`: DOC: Prefer BibTeX reference in GQSI example documentation
* :ghpull:`3657`: Document pre-commit setup for developers
* :ghpull:`3667`: MNT: Replace deprecated autocrop in reconst_dti.py
* :ghpull:`3659`: NF: Intermediate map for symmetric diffeomorphic registration
* :ghpull:`3660`: DOC: Programmatic DIPY Horizon usage (non-CLI)
* :ghpull:`3623`: RF: refactoring of ``nlmeans`` to allow the selection our classic version and the blockwise version
* :ghpull:`3661`: CI: simplify cache, too many data was cached
* :ghpull:`3662`: Bump actions/checkout from 5 to 6 in the actions group
* :ghpull:`3552`: BF: Discards streamlines by size
* :ghpull:`3652`: NF:  Reduce default iteration counts and make level_iters configurable in motion correction
* :ghpull:`3618`: BF: manage empty file in dipy_slr cli to avoid enigmatic crash
* :ghpull:`3655`: CI: remove fetch-data job
* :ghpull:`3658`: Added interpolation parameter to dipy_apply_transform
* :ghpull:`3648`: Revert split extension (for SFT and SFS)
* :ghpull:`3654`: RF: fix warnings introduced by the future Numpy version 2.4
* :ghpull:`3651`: RF: handle bingham tests warnings
* :ghpull:`3650`: BF: update first interaction Github action parameters
* :ghpull:`3649`: Bump the actions group with 2 updates
* :ghpull:`3635`: BF: Fix CVXPY warning
* :ghpull:`3646`: [BF] Fix fwdti
* :ghpull:`3639`: fix: BUG: fix UnboundLocalError in _single_sf_to_bingham when no valid peaks found
* :ghpull:`3610`: NF: add dipy_fit_powermap workflows with its associated tests
* :ghpull:`3634`: BF: expand requirements during its generation
* :ghpull:`3425`: NF: add FWDTI Workflow
* :ghpull:`3631`: RF: Fixed weird volumes instead of denoised volumes in Patch2Self 3
* :ghpull:`3629`: Bump actions/setup-python from 5 to 6 in the actions group
* :ghpull:`3625`: docs: remove NeuroFedora
* :ghpull:`3424`: NF: Automate requirement files
* :ghpull:`3624`: Bump the actions group with 3 updates
* :ghpull:`3605`: RF: Parallel `quantize_evecs`
* :ghpull:`3613`: BF: Allow `length` to work with float16 streamlines
* :ghpull:`3612`: BF: fix lower triangular bug introduced in #3563
* :ghpull:`1617`: NF: added streamline clipping function to utils
* :ghpull:`3606`: RF: Address cvxpy 1.7.0 warnings.
* :ghpull:`3609`: Bump actions/first-interaction from 1 to 2 in the actions group
* :ghpull:`3560`: Doc: explicit ``finalize_mask`` information in CLI tutorial
* :ghpull:`3602`: ENH: Adopt `pathlib` for workflows
* :ghpull:`3604`: RF: replace old LocalTracking by our new tracking interface
* :ghpull:`3587`: RF: from TRK to TRX as default file format for tracks
* :ghpull:`3603`: DOC: Fix workflows test utils parameter name in docstring
* :ghpull:`3601`: DOC: Record API changes after `pathlib` adoption
* :ghpull:`3593`: STYLE: Adopt `pathlib` for path manipulation
* :ghpull:`3599`: TEST: Restore removed test case in io workflows
* :ghpull:`3600`: MNT: Fix miscellaneous labeler regexes
* :ghpull:`3597`: STYLE: Miscellaneous style fixes
* :ghpull:`3598`: BF: Miscellaneous fixes to surfaces
* :ghpull:`3592`: STYLE: Adopt a unified logger across the code base
* :ghpull:`3429`: StatefulSurface - Class to handle surfaces
* :ghpull:`3595`: DOC: Remove default arguments from docstrings
* :ghpull:`3594`: STYLE: Miscellaneous style fixes
* :ghpull:`3591`: STYLE: Apply `ruff` manually to all files
* :ghpull:`3582`: NF: Add PR labeler workflow
* :ghpull:`3586`: MNT: Change issue template file extensions
* :ghpull:`3584`: MNT: Add GitHub issue templates
* :ghpull:`3583`: DOC: Change unused commit prefixes to some other more useful ones
* :ghpull:`3581`: SciPy deprecation of "disp" in optimizer
* :ghpull:`3556`: RF: allow the saving of S0 estimate for dti workflow
* :ghpull:`3563`: RF: Address some Zero division warnings
* :ghpull:`3565`: RF: use multi_voxel_fit for rumba
* :ghpull:`3541`: RF: Deprecate autocrop in median_otsu
* :ghpull:`3580`: TEST: uncomment and update test_cross
* :ghpull:`3515`: RF: Improve `dipy_info` printed output
* :ghpull:`3562`: DOC: Add missing opening backtick to reference syntax.
* :ghpull:`3561`: STYLE: Make affine variable naming consistent
* :ghpull:`3557`: DOC: fix streamline-tools tutorial by avoiding the use of identity affine
* :ghpull:`3559`: [RF]: Patch2self in denoising CLI tutorial
* :ghpull:`3555`: ENH: improve dipy_info message when no reference for some streamline files.
* :ghpull:`3554`: Doc: Fix typo in multiple tutorial
* :ghpull:`3546`: BF: Make `StoppingCriterion` reproducible for multi-thread execution
* :ghpull:`3548`: RF: fix typo in hcp fetcher function argument name
* :ghpull:`3549`: BF: Improves Cython enum management.
* :ghpull:`3520`: ENH: Opacity slider turned off on hide
* :ghpull:`3493`: NF: allow broadcasting in dipy_math
* :ghpull:`3488`: RF - changed min/max len from nbr pts to mm
* :ghpull:`3538`: RF: Fixed the latex
* :ghpull:`3519`: ENH: Horizon peaks fname support
* :ghpull:`3455`: Fix Bugs in #3453: Ensure Correct Weight Reshaping & Consistent Extra Output in iter_fit_tensor
* :ghpull:`3535`: CI: Ignore fork() warnings.
* :ghpull:`3528`: DOC: Changed documentation errors in dipy.sims.voxel
* :ghpull:`3533`: CI: introduce cached Data.
* :ghpull:`3531`: CI: Ignore specific cvxpy warnings to avoid CI failure.
* :ghpull:`3527`: BF: Search bar should come bigger in the center.
* :ghpull:`3530`: STYLE: Add additional emojis to first interaction message
* :ghpull:`3526`: Bump scientific-python/upload-nightly-action from 0.6.1 to 0.6.2 in the actions group
* :ghpull:`3522`: FIX: Avoid division by zero on single-CPU systems (issue #3521)
* :ghpull:`3510`: [RF]: Saving the figure in the example.
* :ghpull:`3512`: STYLE: Call `warning` instead of the deprecated `warn` function
* :ghpull:`3514`: DOC: Miscellaneous doc improvements
* :ghpull:`3495`: BF: Fixing minor issue in dipy_classify_tissue dam option
* :ghpull:`3481`: UPCOMING:  Release 1.11.0

Issues (324):

* :ghissue:`3844`: NF: FORCE recon model
* :ghissue:`3503`: Create new interface for MTMS CSD and standard CSD that use Ray properly
* :ghissue:`3617`: NF: add dipy_fit_msmtcsd cli with its tests
* :ghissue:`3687`: BUAN Bundle Profiles Lite Version
* :ghissue:`3849`: DOC: Fix broken and outdated links in gitwash documentation
* :ghissue:`3850`: DOC: Fix broken and outdated links in gitwash documentation
* :ghissue:`2766`: WIP Issue 2738 click cli refactor
* :ghissue:`2738`: Replace our custom Argparse CLI api by Click ?
* :ghissue:`2547`: [WIP][FIX] option to disable multithreading while multiprocessing
* :ghissue:`3143`: [WIP][NF] Add `dipy_gtable` cli
* :ghissue:`3679`: Build aarch64 natively
* :ghissue:`3847`: BF: Updated sherbrooke-3shell.
* :ghissue:`3845`: BF: improve output file management of BiasField correction CLI
* :ghissue:`3628`: iter_fit_tensor returns {} instead of None causing KeyError in nlls_fit_tensor when return_leverages=False
* :ghissue:`3840`: DOC: Complete missing parameters in save_polydata docstring
* :ghissue:`3841`: DOC: Complete missing parameters in save_polydata docstring
* :ghissue:`3689`: NF: Parallel Eudx
* :ghissue:`3836`: DOC: Documentation fix
* :ghissue:`3808`: RF: improve trx support for recobundles CLI
* :ghissue:`3693`: QTI issues - lack of MIN_POSITIVE_SIGNAL and issue with constrained solver and WLS is wrong anyway
* :ghissue:`3824`: DOC: Modernize and complete benchmarks/README.rst (and developer docs)
* :ghissue:`3825`: DOC: Modernize and complete benchmarks/README.rst - closes #3824
* :ghissue:`3835`: ENH: add ASV continuous benchmarking workflow
* :ghissue:`3811`: test_io_peaks_deprecated fails - ACTUAL: 82 warnings, DESIRED: 2
* :ghissue:`3813`: Fix #3811: reset warning filters in test_io_peaks_deprecated
* :ghissue:`3833`: DOC: Improve docstrings for SimilarityMetric in align.metrics
* :ghissue:`3795`: Added docs for nn and io
* :ghissue:`3827`: Enh asv continuous benchmarks
* :ghissue:`3814`: ENH: Ray-aware CSD and MSMT-CSD workflows (#3503, #3617)
* :ghissue:`3807`: Fix #3502: Add ODF and Tensor visualization to dipy_horizon
* :ghissue:`3810`: test_horizon_empty_tractogram fails - logger.warning() not caught by warnings.catch_warnings()
* :ghissue:`3812`: Fix #3810: use warnings.warn() for empty tractogram
* :ghissue:`3700`: RF: Simplify non-negative code in anisotropic_power
* :ghissue:`3656`: Some tutorials do not clear the figure canvas
* :ghissue:`3783`: Fix figure canvas not cleared in simulation tutorials
* :ghissue:`3645`: Powermap contains negative intensities
* :ghissue:`3699`: Qti robust
* :ghissue:`3834`: Bump docker/setup-qemu-action from 3 to 4 in the actions group
* :ghissue:`3830`: DOC: Fix docstring errors in dipy/io/pickles.py
* :ghissue:`3831`: DOC: Fix docstring errors in dipy/io/pickles.py
* :ghissue:`3820`: BF: improve rumba performance
* :ghissue:`3818`: BF: fix future errors/warnings from the future Numpy 2.5
* :ghissue:`3816`: RF: relax precision for affine_registration / motion_correction
* :ghissue:`3822`: DOC: Fix lowercase 'returns' section header in _make_fetcher docstring
* :ghissue:`3823`: DOC: Fix lowercase 'returns' section header in _make_fetcher docstring
* :ghissue:`3805`: Bump the actions group with 2 updates
* :ghissue:`3647`: Biasfield Correction b0 method not working correctly
* :ghissue:`3791`: NF: update biasfield correction method.
* :ghissue:`2427`: Document the PAM file format
* :ghissue:`3793`: DOC: Add documentation for the PAM5 file format
* :ghissue:`3752`: CI: Update secrets management
* :ghissue:`3785`: Weights parameter documented twice
* :ghissue:`3796`: updated the docstring for ls_fit_dki and cls_fit_dki
* :ghissue:`3790`: ENH: Cythonize AK, RK, and KFA kurtosis computations
* :ghissue:`3799`: DOC: Add tutorial for saving and loading QuickBundles clustering results
* :ghissue:`3789`: BF: handle `force` option when using symlink and hardlink
* :ghissue:`3774`: CI: Fix typo in test_template.yml workflow input description
* :ghissue:`3784`: Fix typo in test_template.yml input description (closes #3774)
* :ghissue:`3765`: NF: add cli dipy_cluster_streamlines
* :ghissue:`3766`: RF: improve CLI help formatting
* :ghissue:`3767`: RF: Fix multiple cli
* :ghissue:`3759`: DOC: Standardize docstring format across modules using numpydoc conventions
* :ghissue:`3780`: Fix `numpydoc` validation issues in `fetcher.py`
* :ghissue:`3764`: epsilon docstring mismatch
* :ghissue:`3781`: Fix epsilon docstring mismatch
* :ghissue:`3778`: CI: Add manual workflow trigger (workflow_dispatch) to test.yml
* :ghissue:`3779`: CI: Add manual workflow trigger (workflow_dispatch) to test.yml
* :ghissue:`3775`: CI: Add pip caching to build_docs.yml
* :ghissue:`3776`: CI: Add pip caching to build_docs.yml
* :ghissue:`3772`: CI: Add concurrency group to build_docs.yml
* :ghissue:`3773`: CI: Add concurrency group to build_docs.yml
* :ghissue:`3770`: Add a Pull Request template to standardize PR descriptions
* :ghissue:`3771`: docs: Add a pull request template to standardize PR submissions.
* :ghissue:`3768`: CI: Add workflow to clean up GitHub Actions caches on closed PRs
* :ghissue:`3769`: CI: Add workflow to clean up GitHub Actions caches on closed PRs
* :ghissue:`3777`:  CI: Add manual workflow trigger (workflow_dispatch) to test.yml
* :ghissue:`3762`: NF: add new CLI dipy_brain_mask with its associated test
* :ghissue:`3760`: [DOC] Fix typos and grammatical errors in documentation and code
* :ghissue:`3761`:  [DOC] Fix grammatical errors and typos across documentation and codebase
* :ghissue:`3753`: DOC: Typo in gitwash development_workflow guide
* :ghissue:`3754`: DOC: Typo in gitwash development_workflow guide
* :ghissue:`3757`: DOC: Fix missing space in `load_peaks` deprecation message
* :ghissue:`3758`: DOC: Fix missing space in `load_peaks` deprecation message
* :ghissue:`3755`: DOC: Update Gitter link to Matrix invite link
* :ghissue:`3756`: DOC: Remove Gitter link
* :ghissue:`3704`: Fix get simplified backward transform
* :ghissue:`3751`: Fixed Github Workflow Issues
* :ghissue:`3745`: Replace legacy nose-style `yield assert_raises` with `pytest.raises`
* :ghissue:`3746`: TST: Replace legacy nose-style `yield assert_raises` with `pytest.raises`
* :ghissue:`3750`: Update setuptools requirement from ~=69.5 to >=69.5,<83.0 in the python-dependencies group
* :ghissue:`3738`: CI: Missing top-level permissions in CI workflow files
* :ghissue:`3739`: CI: Add top-level permissions for least-privilege security
* :ghissue:`3734`: CI: Benchmark workflow triggers on all pushes/PRs instead of master only
* :ghissue:`3735`: CI: Restrict benchmark workflow triggers to master branch
* :ghissue:`3732`: CI: Dependabot only monitors GitHub Actions, not pip dependencies
* :ghissue:`3733`: CI: Add pip ecosystem tracking to Dependabot configuration
* :ghissue:`3731`: MNT: Remove dead install type code paths from install.sh
* :ghissue:`3728`: CI: Benchmark threading env vars don't persist to the benchmarking step
* :ghissue:`3729`: CI: Fix threading env vars not persisting across steps in benchmark.yml
* :ghissue:`3727`: CI: Update stale dependency pins in CI configuration
* :ghissue:`3723`: CI: first_interaction.yml action pinned by tag instead of SHA on pull_request_target trigger
* :ghissue:`3722`: CI: Pin actions/first-interaction by commit SHA in first_interaction.yml
* :ghissue:`3720`: CI: label-pr.yml uses third-party action pinned by tag on pull_request_target trigger
* :ghissue:`3721`: CI: Pin srvaroa/labeler action by commit SHA in label-pr.yml
* :ghissue:`3718`: DOC: CONTRIBUTING.md references Travis CI instead of GitHub Actions
* :ghissue:`3719`:  DOC: Update outdated Travis CI reference to GitHub Actions in CONTRIBUTING.md
* :ghissue:`3717`: CI: Invalid cron schedule in test.yml runs ~1-2x/year instead of monthly
* :ghissue:`3716`: CI: Fix invalid cron schedule in test.yml
* :ghissue:`3714`: CI: Add missing timeout-minutes to workflow jobs
* :ghissue:`3715`: CI: Add missing timeout-minutes to workflow jobs
* :ghissue:`3749`: RF: Updated the list provide a table of dataset names.
* :ghissue:`3724`: CI: Duplicate step names in nightly.yml upload_anaconda job make logs confusing
* :ghissue:`3725`: CI: Rename duplicate 'Upload wheel' steps in nightly.yml for clarity
* :ghissue:`3747`: Missing `__all__` exports in subpackage `__init__.py` files
* :ghissue:`3748`: STY: Add missing `__all__` exports to subpackage `__init__.py` files
* :ghissue:`3740`: Bump srvaroa/labeler from 1.13.0 to 1.14.0 in the actions group
* :ghissue:`3741`: Replace deprecated `numpy.testing.assert_()` with plain `assert`
* :ghissue:`3742`: TST: Replace deprecated `npt.assert_()` with plain `assert`
* :ghissue:`3743`: Replace deprecated `assert_almost_equal` / `assert_array_almost_equal` with `assert_allclose`
* :ghissue:`3744`: TST: Replace deprecated `assert_almost_equal` / `assert_array_almost_equal` with `assert_allclose`
* :ghissue:`3736`: DOC: Remaining insecure `http://` URLs should be migrated to `https://`
* :ghissue:`3737`:  DOC: Migrate remaining `http://` URLs to `https://`
* :ghissue:`3710`: CI: Fix incorrect Cython file glob patterns in labeler.yml
* :ghissue:`3711`: CI: Fix incorrect Cython file glob patterns in labeler.yml
* :ghissue:`3708`: STYLE: Fix spelling mistakes in docstrings and comments
* :ghissue:`3709`: STYLE: Fix spelling mistakes in docstrings and comments
* :ghissue:`3712`: #CI: Remove duplicate `.mailmap` entry in labeler.yml
* :ghissue:`3713`: CI: Remove duplicate .mailmap entry in labeler.yml
* :ghissue:`3706`: RF: Add alternative to symlink for some  CLI
* :ghissue:`3688`: dipy_horizon with Empty Streamline File
* :ghissue:`3696`: BF: Handle empty tractograms gracefully in horizon
* :ghissue:`3701`: Revert temporary suppression of SCS CSC conversion warning
* :ghissue:`3697`: Fix dipy_horizon crash on empty tractogram files
* :ghissue:`3694`: DOC: Fix numpydoc PR03 parameter order in path_length
* :ghissue:`2760`: TRX integration
* :ghissue:`3692`: DOC: Fixed DOC CI Issue
* :ghissue:`3675`: Adding synthseg pytorch model
* :ghissue:`3683`: DIPY_SLR Breaking with Wrong Error
* :ghissue:`3686`: BF: Handle empty streamlines in slr_with_qbx after length filtering
* :ghissue:`3684`: RF: address some edge cases in multiple workflows
* :ghissue:`3222`: Issue with CWLS in dki
* :ghissue:`3405`: Follow up for the Iteratively reweighted least squares
* :ghissue:`3681`: Examples for IRLS (robust fitting)
* :ghissue:`3516`: Do not require FURY to show information from a VTK/VTP tractography files
* :ghissue:`2538`: [WIP] Registration public API for multi-slice 2D data
* :ghissue:`3685`: DOC: fix some missing `:footcite:p` in documentation
* :ghissue:`3671`: Increased speed and lisibility of connectivity matrix, added weights
* :ghissue:`3680`: RF: Added max_version option to optional_package api.
* :ghissue:`3682`: TST: Add interface tests for pure Python DirectionGetter implementations
* :ghissue:`3677`: DOC: Fix file path in many tutorials.
* :ghissue:`3676`: RF: Allow reslice to automatically determines isotropic resolution
* :ghissue:`3678`: Build 3.14 nightly wheels
* :ghissue:`3664`: DOC: Improve Horizon class docstring for clarity
* :ghissue:`3665`: FIX: Correct path construction logic in fetcher data loader, Resolve path construction errors in read_bundles_2_subjects
* :ghissue:`3673`: RF: Allow bvals file for medianOtsu workflow
* :ghissue:`3674`: Bump scientific-python/upload-nightly-action from 0.6.2 to 0.6.3 in the actions group
* :ghissue:`3542`: RF: Editing tranform_img in dipy.nn.utils
* :ghissue:`3670`: Test: Add regression test for median_otsu autocrop deprecation
* :ghissue:`3668`: MNT: Replace deprecated autocrop in brain_extraction_dwi.py, reconst_csa.py, reconst_csa_parallel.py, reconst_dti.py tutorial examples
* :ghissue:`3672`: Bump the actions group with 3 updates
* :ghissue:`3669`: DOC: Prefer BibTeX reference in GQSI example documentation
* :ghissue:`3643`: Document pre-commit setup
* :ghissue:`3657`: Document pre-commit setup for developers
* :ghissue:`3667`: MNT: Replace deprecated autocrop in reconst_dti.py
* :ghissue:`3439`: data fetching: problem with UW server ?
* :ghissue:`3659`: NF: Intermediate map for symmetric diffeomorphic registration
* :ghissue:`3397`: Adding Python Code Example for DIPY Horizon in Tutorials
* :ghissue:`3660`: DOC: Programmatic DIPY Horizon usage (non-CLI)
* :ghissue:`2950`: Clean up the non-local means denoising modules
* :ghissue:`1259`: nlmeans does not respect boundaries
* :ghissue:`1224`: Memory issue
* :ghissue:`1131`: new non_local_means module seems to disregard 3D array of noise standard deviation
* :ghissue:`1178`: Recheck indexing with nlmeans as some of it is indexing wrong positions
* :ghissue:`3623`: RF: refactoring of ``nlmeans`` to allow the selection our classic version and the blockwise version
* :ghissue:`3661`: CI: simplify cache, too many data was cached
* :ghissue:`3662`: Bump actions/checkout from 5 to 6 in the actions group
* :ghissue:`3552`: BF: Discards streamlines by size
* :ghissue:`3652`: NF:  Reduce default iteration counts and make level_iters configurable in motion correction
* :ghissue:`3618`: BF: manage empty file in dipy_slr cli to avoid enigmatic crash
* :ghissue:`3655`: CI: remove fetch-data job
* :ghissue:`3658`: Added interpolation parameter to dipy_apply_transform
* :ghissue:`3621`: filename for statefulsurface and statefultractogram cannot have period in them anymore
* :ghissue:`3648`: Revert split extension (for SFT and SFS)
* :ghissue:`3636`: Bug with use of where
* :ghissue:`3654`: RF: fix warnings introduced by the future Numpy version 2.4
* :ghissue:`3651`: RF: handle bingham tests warnings
* :ghissue:`3653`: RF: Fix imports in reconst
* :ghissue:`3640`: First interaction workflow doesn't work
* :ghissue:`3650`: BF: update first interaction Github action parameters
* :ghissue:`3649`: Bump the actions group with 2 updates
* :ghissue:`3638`: UnboundLocalError: local variable 'fits' referenced before assignment
* :ghissue:`3635`: BF: Fix CVXPY warning
* :ghissue:`3646`: [BF] Fix fwdti
* :ghissue:`3639`: fix: BUG: fix UnboundLocalError in _single_sf_to_bingham when no valid peaks found
* :ghissue:`3610`: NF: add dipy_fit_powermap workflows with its associated tests
* :ghissue:`2087`: Single-shell Free Water DTI (Object Oriented)
* :ghissue:`3634`: BF: expand requirements during its generation
* :ghissue:`3425`: NF: add FWDTI Workflow
* :ghissue:`2137`: Deep-learning-based registration example
* :ghissue:`3631`: RF: Fixed weird volumes instead of denoised volumes in Patch2Self 3
* :ghissue:`3633`: Patch2Self CLI provides wrong doc string for version
* :ghissue:`3539`: FOSR implementation in Python for tractometry
* :ghissue:`3629`: Bump actions/setup-python from 5 to 6 in the actions group
* :ghissue:`3625`: docs: remove NeuroFedora
* :ghissue:`3424`: NF: Automate requirement files
* :ghissue:`3624`: Bump the actions group with 3 updates
* :ghissue:`3605`: RF: Parallel `quantize_evecs`
* :ghissue:`3613`: BF: Allow `length` to work with float16 streamlines
* :ghissue:`3608`: Predicting from a fitted DTI model is broken?
* :ghissue:`3612`: BF: fix lower triangular bug introduced in #3563
* :ghissue:`3588`: In-house QP solver using numba for fitting MSMT
* :ghissue:`1617`: NF: added streamline clipping function to utils
* :ghissue:`3606`: RF: Address cvxpy 1.7.0 warnings.
* :ghissue:`3609`: Bump actions/first-interaction from 1 to 2 in the actions group
* :ghissue:`3551`: Shutting down the gitter live chat ?
* :ghissue:`1164`: Parallel quantize_evecs + PEP8
* :ghissue:`3124`: ENH: Add commentary on median otsu tutorial/change default parameters
* :ghissue:`3560`: Doc: explicit ``finalize_mask`` information in CLI tutorial
* :ghissue:`3602`: ENH: Adopt `pathlib` for workflows
* :ghissue:`3604`: RF: replace old LocalTracking by our new tracking interface
* :ghissue:`3506`: Make sure .trx is default everywhere
* :ghissue:`3587`: RF: from TRK to TRX as default file format for tracks
* :ghissue:`3603`: DOC: Fix workflows test utils parameter name in docstring
* :ghissue:`3601`: DOC: Record API changes after `pathlib` adoption
* :ghissue:`3593`: STYLE: Adopt `pathlib` for path manipulation
* :ghissue:`3599`: TEST: Restore removed test case in io workflows
* :ghissue:`3600`: MNT: Fix miscellaneous labeler regexes
* :ghissue:`3597`: STYLE: Miscellaneous style fixes
* :ghissue:`3598`: BF: Miscellaneous fixes to surfaces
* :ghissue:`3592`: STYLE: Adopt a unified logger across the code base
* :ghissue:`3596`: NF - Add DirectionGetter for Flocking Tractography
* :ghissue:`3429`: StatefulSurface - Class to handle surfaces
* :ghissue:`3595`: DOC: Remove default arguments from docstrings
* :ghissue:`3594`: STYLE: Miscellaneous style fixes
* :ghissue:`3513`: STYLE: Log message instead of printing orphan string
* :ghissue:`3591`: STYLE: Apply `ruff` manually to all files
* :ghissue:`3582`: NF: Add PR labeler workflow
* :ghissue:`3586`: MNT: Change issue template file extensions
* :ghissue:`3584`: MNT: Add GitHub issue templates
* :ghissue:`3583`: DOC: Change unused commit prefixes to some other more useful ones
* :ghissue:`3581`: SciPy deprecation of "disp" in optimizer
* :ghissue:`3556`: RF: allow the saving of S0 estimate for dti workflow
* :ghissue:`3497`: dipy_fit_dti does not return S0 estimate
* :ghissue:`3418`: Division by 0 warning
* :ghissue:`3563`: RF: Address some Zero division warnings
* :ghissue:`3352`: Rumba and multivoxel fit decorator
* :ghissue:`3565`: RF: use multi_voxel_fit for rumba
* :ghissue:`3537`: Remove autocrop from median_otsu
* :ghissue:`3541`: RF: Deprecate autocrop in median_otsu
* :ghissue:`2866`: arm64 test failure with numpy 1.24.2
* :ghissue:`3580`: TEST: uncomment and update test_cross
* :ghissue:`1776`: make it really easy for DiPy to call graspy functions
* :ghissue:`2269`: Allow dipy_fit_dti Workflow to Use Native Orientation of Provided Mask Image
* :ghissue:`2682`: DIPY Free-Water Corrected DTI (FA output quality)
* :ghissue:`2428`: dipy.align.reslice
* :ghissue:`2399`: fitting free water mapping out of iterations
* :ghissue:`2319`: Reconstruction with MSMT CSD example resulted in Nan values
* :ghissue:`2329`: Slice to volume registration
* :ghissue:`1974`: MAP-MRI optimization & validation errors
* :ghissue:`2612`: Mean Diffusivity turns out low in CSF when reconstructing using ReconstDtiFlow
* :ghissue:`687`: Refactor imaffine class structure.
* :ghissue:`706`: Thoughts about using the SyN algorithm
* :ghissue:`2184`: discussion: continuous integration using GPUs
* :ghissue:`1991`: [DISCUSSION] b-tensor encoding gradient table format
* :ghissue:`2186`: Pure-python implementation of boundary-based registration (BBR)?
* :ghissue:`1852`: Telemetry
* :ghissue:`2338`: Team DIPY Citations
* :ghissue:`2663`: Plotting tensors in Fury: issue with right-handed coordinate system?
* :ghissue:`3515`: RF: Improve `dipy_info` printed output
* :ghissue:`2850`: Orthogonal Tensor Parameter (Moment) Maps
* :ghissue:`1886`: NF - add the option to save the last point of streamlines
* :ghissue:`3562`: DOC: Add missing opening backtick to reference syntax.
* :ghissue:`3561`: STYLE: Make affine variable naming consistent
* :ghissue:`3382`: Check use of affine in `streamline_tools` example
* :ghissue:`3557`: DOC: fix streamline-tools tutorial by avoiding the use of identity affine
* :ghissue:`2473`: Add Patch2self in our denoising CLI tutorial
* :ghissue:`3559`: [RF]: Patch2self in denoising CLI tutorial
* :ghissue:`2695`: Replace CENIR multishell with HBN POD2 data
* :ghissue:`2728`: Do we have multi_processes method for streamline extraction
* :ghissue:`2848`: Noise estimation of T1 brain MR images
* :ghissue:`3500`: dipy_fit_csa does not use num_processes
* :ghissue:`3517`: `dipy_info` provides misleading message when no reference is provided
* :ghissue:`3555`: ENH: improve dipy_info message when no reference for some streamline files.
* :ghissue:`3554`: Doc: Fix typo in multiple tutorial
* :ghissue:`3413`: Tutorial Typos
* :ghissue:`3492`: BF: Peaks working with world coordinates.
* :ghissue:`1249`: Bias correction for local pca
* :ghissue:`823`: WIP: "Out-of-core" LiFE
* :ghissue:`3540`: Tractography with GFA as stopping criterion is not reproducible across runs
* :ghissue:`3546`: BF: Make `StoppingCriterion` reproducible for multi-thread execution
* :ghissue:`3545`: ENH: Add `StopingCriterion` reproducibility test
* :ghissue:`3548`: RF: fix typo in hcp fetcher function argument name
* :ghissue:`3549`: BF: Improves Cython enum management.
* :ghissue:`3507`: Extract b0 interface throws value error with HCP 7T (MGH) - subject 1007
* :ghissue:`3474`: Filenames missing in horizon for peaks objects
* :ghissue:`3520`: ENH: Opacity slider turned off on hide
* :ghissue:`3544`: ENH: Add `StopingCriterion` reproducibility test
* :ghissue:`3493`: NF: allow broadcasting in dipy_math
* :ghissue:`3488`: RF - changed min/max len from nbr pts to mm
* :ghissue:`3536`: FA latex formula does not show correctly on DTI tutorial
* :ghissue:`3538`: RF: Fixed the latex
* :ghissue:`3519`: ENH: Horizon peaks fname support
* :ghissue:`1404`: RF - DirectionGetter.get_direction function return
* :ghissue:`3453`: Inconistancy between documentation and implementation on dipy.reconst.dti.nlls_fit_tensor
* :ghissue:`3455`: Fix Bugs in #3453: Ensure Correct Weight Reshaping & Consistent Extra Output in iter_fit_tensor
* :ghissue:`3535`: CI: Ignore fork() warnings.
* :ghissue:`3501`: Probabilistic reference in docs seems incorrect
* :ghissue:`3336`: Simplify CIs
* :ghissue:`3528`: DOC: Changed documentation errors in dipy.sims.voxel
* :ghissue:`3533`: CI: introduce cached Data.
* :ghissue:`3531`: CI: Ignore specific cvxpy warnings to avoid CI failure.
* :ghissue:`2494`: Potential speed up for the data fetchers
* :ghissue:`3527`: BF: Search bar should come bigger in the center.
* :ghissue:`3530`: STYLE: Add additional emojis to first interaction message
* :ghissue:`3526`: Bump scientific-python/upload-nightly-action from 0.6.1 to 0.6.2 in the actions group
* :ghissue:`3521`: Division by zero when machine has a single CPU
* :ghissue:`3522`: FIX: Avoid division by zero on single-CPU systems (issue #3521)
* :ghissue:`3510`: [RF]: Saving the figure in the example.
* :ghissue:`3512`: STYLE: Call `warning` instead of the deprecated `warn` function
* :ghissue:`3514`: DOC: Miscellaneous doc improvements
* :ghissue:`3508`: New disco tracking tutorial not available in docs
* :ghissue:`3495`: BF: Fixing minor issue in dipy_classify_tissue dam option
* :ghissue:`3494`: publish wheels
* :ghissue:`3481`: UPCOMING:  Release 1.11.0

=====================================

 Release notes for DIPY version 1.11
=====================================

GitHub stats for 2024/12/12 - 2025/03/14 (tag: 1.10.0)

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

The following 11 authors contributed 175 commits.

* Ariel Rokem
* Atharva Shah
* Eleftherios Garyfallidis
* Gabriel Girard
* Jon Haitz Legarreta Gorroño
* Jong Sung Park
* Maharshi Gor
* Michael R. Crusoe
* Prajwal Reddy
* Sam Coveney
* Serge Koudoro

We closed a total of 120 issues, 47 pull requests and 73 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (47):

* :ghpull:`3487`: RF: update tracking cli
* :ghpull:`3490`: ENH: Updated the logging info
* :ghpull:`3489`: DOC - Renamed fast tracking example
* :ghpull:`3475`: NF: add workflow for N4 biasfield
* :ghpull:`3485`: DOC: remove modulo in dipy_math docstring
* :ghpull:`3486`: RF: Fixed Warnings of Patch2self3
* :ghpull:`3483`: ENH: Add use_cuda option to torch models
* :ghpull:`3471`: Patch2Self3 skipping b0_denoising error fixed.
* :ghpull:`3477`: NF: Add dipy_classify_tissue CLI
* :ghpull:`3461`: BF: Handling binary and small intensity value range and Volume slider not be shown if single channel provided.
* :ghpull:`3479`: DOC - Updated tracking examples to use the fast tracking framework
* :ghpull:`3482`: RF: Avoid crash of `optional_package` when dirty install
* :ghpull:`3480`: RF: Allow hcp and hcp in dipy_fetch CLI
* :ghpull:`3476`: BF - generate_tractogram needs seed coordinate in image space
* :ghpull:`3478`: RF: Small variable mismatch in the tutorial for DAM classifier
* :ghpull:`3458`: NF: Add optional fetcher
* :ghpull:`3438`: NF: Add 7 new `dipy_fit_*` workflows
* :ghpull:`3462`: NF: Reset of visualization introduced.
* :ghpull:`3470`: RF: Enforce bvecs for the cli extract_b0
* :ghpull:`3472`: RF: Rename and Deprecate dipy_sh_convert_mrtrix CLI
* :ghpull:`3449`: Adding DeepN4 PyTorch model
* :ghpull:`3465`: RF: Import fixes
* :ghpull:`3459`: NF: Add default value to docstring for the CLI
* :ghpull:`3446`: Dki constraints
* :ghpull:`3467`: RF: Changed the matrix
* :ghpull:`3457`: DOC: fix markup issues with tracking tutorial
* :ghpull:`3456`: Added tissue classification with DAM example
* :ghpull:`3444`: NF: Add 3 new ``dipy_extract_*`` workflows
* :ghpull:`3089`: Parallel Tracking Framework
* :ghpull:`3448`: Spelling error in the deprecation warning
* :ghpull:`3442`: RF: update of peak_directions to allow nogil
* :ghpull:`3445`: DOC: removed title
* :ghpull:`3400`: CI: Add python 3.13
* :ghpull:`3440`: RF - add pmf_gen argument to peaks_from_positions
* :ghpull:`3441`: ENH: Add GitHub CI workflow file to run benchmarks using `asv`
* :ghpull:`3427`: NF: add dipy_math workflow
* :ghpull:`3432`: RF: bump tensorflow minimal version to 2.18.0.
* :ghpull:`3436`: RF: Update ``scipy.special`` deprecated functions
* :ghpull:`3433`: TEST: remove skip if not have_delaunay
* :ghpull:`3434`: ENH: Transition remaining `NumPy` `RandomState` instances to `Generator`
* :ghpull:`3430`: ENH: Add type annotation information
* :ghpull:`3428`: DOC: Add implemented tractography method table to tracking example index
* :ghpull:`3426`: RF: from relative import to absolute import
* :ghpull:`3423`: Make the docs more reproducible
* :ghpull:`3421`: CI: remove python3.9 support
* :ghpull:`3422`: RF: fix joblib warning in sfm
* :ghpull:`3364`: UPCOMING:  Release 1.10.0

Issues (73):

* :ghissue:`3487`: RF: update tracking cli
* :ghissue:`3490`: ENH: Updated the logging info
* :ghissue:`3489`: DOC - Renamed fast tracking example
* :ghissue:`3475`: NF: add workflow for N4 biasfield
* :ghissue:`3485`: DOC: remove modulo in dipy_math docstring
* :ghissue:`3486`: RF: Fixed Warnings of Patch2self3
* :ghissue:`3483`: ENH: Add use_cuda option to torch models
* :ghissue:`3471`: Patch2Self3 skipping b0_denoising error fixed.
* :ghissue:`3477`: NF: Add dipy_classify_tissue CLI
* :ghissue:`3484`: Default parameter values not shown on DIPY's CLIs
* :ghissue:`3371`: Horizon miscalculating contrast when returning to previous volume
* :ghissue:`3112`: Horizon fails with a single channel 4D volume
* :ghissue:`3461`: BF: Handling binary and small intensity value range and Volume slider not be shown if single channel provided.
* :ghissue:`3479`: DOC - Updated tracking examples to use the fast tracking framework
* :ghissue:`3482`: RF: Avoid crash of `optional_package` when dirty install
* :ghissue:`3480`: RF: Allow hcp and hcp in dipy_fetch CLI
* :ghissue:`3476`: BF - generate_tractogram needs seed coordinate in image space
* :ghissue:`3478`: RF: Small variable mismatch in the tutorial for DAM classifier
* :ghissue:`3190`: Allow to define optional file to fetch
* :ghissue:`3458`: NF: Add optional fetcher
* :ghissue:`3438`: NF: Add 7 new `dipy_fit_*` workflows
* :ghissue:`3469`: horizon - SSLCertVerificationError
* :ghissue:`3152`: Horizon needs a home button which realigns the view to the z slice we are at.
* :ghissue:`2421`: DIPY Horizon Menu
* :ghissue:`3462`: NF: Reset of visualization introduced.
* :ghissue:`3470`: RF: Enforce bvecs for the cli extract_b0
* :ghissue:`3472`: RF: Rename and Deprecate dipy_sh_convert_mrtrix CLI
* :ghissue:`3449`: Adding DeepN4 PyTorch model
* :ghissue:`3164`: Simplify or remove the use of mpl_tri in viz module
* :ghissue:`3465`: RF: Import fixes
* :ghissue:`3454`: Default Value in Workflows docstring
* :ghissue:`3459`: NF: Add default value to docstring for the CLI
* :ghissue:`3446`: Dki constraints
* :ghissue:`3467`: RF: Changed the matrix
* :ghissue:`3466`: Theory for b and q values represent incorrect b matrix
* :ghissue:`3457`: DOC: fix markup issues with tracking tutorial
* :ghissue:`3463`: Remove the warnings from doc build in DIPY docs
* :ghissue:`3451`: How can be the drawing background changed from black to white using `actor.odf_slicer`
* :ghissue:`3179`: Need specific area zooming for horizon
* :ghissue:`3359`: Bug: Horizon throws errors when changing intensity range and then changing volumes
* :ghissue:`3460`: [WIP] RF: force use of header for fetcher
* :ghissue:`3394`: Create a tutorial for DAM classifier
* :ghissue:`3456`: Added tissue classification with DAM example
* :ghissue:`3444`: NF: Add 3 new ``dipy_extract_*`` workflows
* :ghissue:`1501`: Refactoring tracking and checking tutorials and workflows - high priority for next release.
* :ghissue:`834`: Multiprocessing the local tracking?
* :ghissue:`3089`: Parallel Tracking Framework
* :ghissue:`3448`: Spelling error in the deprecation warning
* :ghissue:`3442`: RF: update of peak_directions to allow nogil
* :ghissue:`3445`: DOC: removed title
* :ghissue:`3443`: NF: Replace urllib by requests to improve fetcher stability.
* :ghissue:`3400`: CI: Add python 3.13
* :ghissue:`3440`: RF - add pmf_gen argument to peaks_from_positions
* :ghissue:`3441`: ENH: Add GitHub CI workflow file to run benchmarks using `asv`
* :ghissue:`3427`: NF: add dipy_math workflow
* :ghissue:`3432`: RF: bump tensorflow minimal version to 2.18.0.
* :ghissue:`3436`: RF: Update ``scipy.special`` deprecated functions
* :ghissue:`3431`: Tests with scipy.spatial.Delaunay being skipped
* :ghissue:`3433`: TEST: remove skip if not have_delaunay
* :ghissue:`3434`: ENH: Transition remaining `NumPy` `RandomState` instances to `Generator`
* :ghissue:`3430`: ENH: Add type annotation information
* :ghissue:`3428`: DOC: Add implemented tractography method table to tracking example index
* :ghissue:`3426`: RF: from relative import to absolute import
* :ghissue:`3423`: Make the docs more reproducible
* :ghissue:`3421`: CI: remove python3.9 support
* :ghissue:`3422`: RF: fix joblib warning in sfm
* :ghissue:`2364`: Streamlines get negative coordinates in voxel space
* :ghissue:`3016`: [WIP] NF: Wigner-D Rotation Functions
* :ghissue:`3276`: [Feature] Multithreading support for reading and opening files.
* :ghissue:`2304`: [WIP] DKI ODF redux
* :ghissue:`2705`: WIP: Single-shell FWDTI
* :ghissue:`3416`: support for numpy 2.0 seems missing
* :ghissue:`3364`: UPCOMING:  Release 1.10.0

**DIPY 1.10.0** is now available. New features include:

- NF: Patch2Self3 - Large improvements of self-supervised denoising method added.
- NF: Fiber density and spread from ODF using Bingham distributions method added.
- NF: Iteratively reweighted least squares for robust fitting of diffusion models added.
- NF: NDC - Neighboring DWI Correlation quality metric added.
- NF: DAM - tissue classification method added.
- NF: New Parallel Backends (Ray, joblib, Dask) for fitting reconstruction methods added.
- RF: Deprecation of Tensorflow support. PyTorch support is now the default.
- Transition to Keyword-only arguments (PEP 3102).
- Zero-warnings policy (CIs, Compilation, doc generation) adopted.
- Adoption of ruff for automatic style enforcement.
- Transition to using f-strings.
- Citation system updated. It is more uniform and robust.
- Multiple Workflows updated.
- Multiple DIPY Horizon features updated.
- Large documentation update.
- Closed 250 issues and merged 185 pull requests.

**DIPY 1.9.0** is now available. New features include:

- Numpy 2.0.0 support.
- DeepN4 novel DL-based N4 Bias Correction method added.
- Multiple Workflows added.
- Large update of DIPY Horizon features.
- Pytest for Cython files(*.pyx) added.
- Large documentation update.
- Support of Python 3.8 removed.
- Closed 142 issues and merged 60 pull requests.

====================================
 Release notes for DIPY version 1.9
====================================

GitHub stats for 2023/12/14 - 2024/03/07 (tag: 1.8.0)

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

The following 17 authors contributed 175 commits.

* Ariel Rokem
* Atharva Shah
* Ebrahim Ebrahim
* Eleftherios Garyfallidis
* Gabriel Girard
* John Shen
* Jon Haitz Legarreta Gorroño
* Jong Sung Park
* Maharshi Gor
* Matthew Feickert
* Philippe Karan
* Praitayini Kanakaraj
* Sam Coveney
* Sandro
* Serge Koudoro
* dependabot[bot]
* Étienne Mollier

We closed a total of 139 issues, 60 pull requests and 81 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (60):

* :ghpull:`3095`: [UPCOMING] Release preparation for 1.9.0
* :ghpull:`3086`: [RF] Fix spherical harmonic terminology swap
* :ghpull:`3105`: [doc] improve some tutorials rendering
* :ghpull:`3109`: [BF] convert_tractogram fix
* :ghpull:`3108`: enabled trx support with correct header
* :ghpull:`3107`: enabled trx support for viz
* :ghpull:`3033`: [RF] fix dki mask for nlls
* :ghpull:`3104`: Dkimaskfix
* :ghpull:`3106`: volume slices visibility fixed
* :ghpull:`3102`: Bugfix for peaks slices and synchronization.
* :ghpull:`3078`: return S0 from dki fit
* :ghpull:`3101`: [BF] Uniformize cython version
* :ghpull:`3097`: Feature/surface
* :ghpull:`3048`: [TEST] Adds support of cython for pytest
* :ghpull:`3053`: [NF] Add workflow to convert tensors in different formats
* :ghpull:`3073`: [NF] Add DSI workflow
* :ghpull:`3099`: [DOC] fix some typo [ci skip]
* :ghpull:`3098`: Removing tensorflow addon from DL models
* :ghpull:`2973`: Tab names for slice tabs as file names.
* :ghpull:`3081`: NF: Adding N4 bias correction deep learning model
* :ghpull:`3092`: Feature: volume synchronizing
* :ghpull:`3059`: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors
* :ghpull:`3090`: RF - changed memory view to double* trilinear_interpolation_4d
* :ghpull:`3080`: Adding SH basis legacy option support to peaks_from_model
* :ghpull:`3087`: backward compatibility fixed
* :ghpull:`3088`: [TEST] Pin pytest
* :ghpull:`3084`: fixed 4d slice issue
* :ghpull:`3083`: Np.unique check removed.
* :ghpull:`3082`: Add Fedora installation instructions [ci skip]
* :ghpull:`3076`: [CI] Update scientific-python/upload-nightly-action to 0.5.0
* :ghpull:`3070`: [DOC] Fix installation link in README  [ci skip]
* :ghpull:`3069`: [DOC] Fix DTI Tutorial [ci skip]
* :ghpull:`3063`: [RF] remove cpdef in PmfGen
* :ghpull:`3054`: [DOC] Fix some links [ci skip]
* :ghpull:`3060`: Bump codecov/codecov-action from 3 to 4
* :ghpull:`3061`: [OPT] Enable openmp for macOS wheel and CI's
* :ghpull:`3049`: [MTN] code cleaning: remove some dependencies version checking
* :ghpull:`3050`: [RF] Move ``dipy.boots.resampling`` to  ``dipy.stats.resampling``
* :ghpull:`3051`: [RF] Remove dipy.io.bvectxt module
* :ghpull:`3052`: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874
* :ghpull:`3045`: [DOC] fix `multi_shell_fiber_response` docstring array dims [ci skip]
* :ghpull:`3041`: [NF] Add convert tractograms flow
* :ghpull:`3040`: [BW] Remove some python2 reference
* :ghpull:`3039`: [TEST] Add setup_module and teardown_module
* :ghpull:`3038`: [NF] Update `dipy_info`: allow tractogram files format
* :ghpull:`3043`: d/d/t/test_data.py: endian independent dtype.
* :ghpull:`3042`: pyproject.toml: no cython at run time.
* :ghpull:`3027`: [NF] Add Concatenate tracks workflows
* :ghpull:`3008`: NF: add SH basis conversion between dipy and mrtrix3
* :ghpull:`3025`: [TEST] Manage http errors for stateful tractograms
* :ghpull:`3031`: Bugfix: Horizon image's dtype validation
* :ghpull:`3021`: [MTN] Remove 3.8 Ci's
* :ghpull:`3026`: [RF] Fix cython 3 warnings
* :ghpull:`3022`: [DOC] Fix logo size and link [ci skip]
* :ghpull:`3013`: Added Fibonacci spiral and test for it
* :ghpull:`3019`: DOC: Fix link to toolchain roadmap page in `README`
* :ghpull:`3012`: DOC: Document observance for Scientific Python min supported versions
* :ghpull:`3018`: Bump actions/download-artifact from 3 to 4
* :ghpull:`3017`: Bump actions/upload-artifact from 3 to 4
* :ghpull:`3014`: Update release1.8.rst

Issues (81):

* :ghissue:`2970`: spherical harmonic degree/order terminology swapped
* :ghissue:`3105`: [doc] improve some tutorials rendering
* :ghissue:`3109`: [BF] convert_tractogram fix
* :ghissue:`3108`: enabled trx support with correct header
* :ghissue:`3107`: enabled trx support for viz
* :ghissue:`2994`: DKI masking
* :ghissue:`3033`: [RF] fix dki mask for nlls
* :ghissue:`3104`: Dkimaskfix
* :ghissue:`3106`: volume slices visibility fixed
* :ghissue:`3102`: Bugfix for peaks slices and synchronization.
* :ghissue:`2281`: Black Output for pam5 file with dipy_horizon
* :ghissue:`3078`: return S0 from dki fit
* :ghissue:`3101`: [BF] Uniformize cython version
* :ghissue:`3097`: Feature/surface
* :ghissue:`2719`: pytest and cdef functions
* :ghissue:`3048`: [TEST] Adds support of cython for pytest
* :ghissue:`3053`: [NF] Add workflow to convert tensors in different formats
* :ghissue:`3073`: [NF] Add DSI workflow
* :ghissue:`3099`: [DOC] fix some typo [ci skip]
* :ghissue:`3098`: Removing tensorflow addon from DL models
* :ghissue:`2973`: Tab names for slice tabs as file names.
* :ghissue:`3081`: NF: Adding N4 bias correction deep learning model
* :ghissue:`3092`: Feature: volume synchronizing
* :ghissue:`3093`: Can I use a different sort of dataset and also what if I don't have a bval , I use . mat images format PATCH2Self
* :ghissue:`3059`: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors
* :ghissue:`3090`: RF - changed memory view to double* trilinear_interpolation_4d
* :ghissue:`3080`: Adding SH basis legacy option support to peaks_from_model
* :ghissue:`3085`: Viz Tests failing
* :ghissue:`3087`: backward compatibility fixed
* :ghissue:`3088`: [TEST] Pin pytest
* :ghissue:`3074`: Horizon for large datasets - concerns regarding np.unique
* :ghissue:`3075`: Horizon - 4D data support - slicing on the 4-th dim
* :ghissue:`3084`: fixed 4d slice issue
* :ghissue:`3083`: Np.unique check removed.
* :ghissue:`3082`: Add Fedora installation instructions [ci skip]
* :ghissue:`3065`: Add s390x test workflow
* :ghissue:`3076`: [CI] Update scientific-python/upload-nightly-action to 0.5.0
* :ghissue:`3070`: [DOC] Fix installation link in README  [ci skip]
* :ghissue:`3069`: [DOC] Fix DTI Tutorial [ci skip]
* :ghissue:`3066`: Dipy website incorrect image
* :ghissue:`3063`: [RF] remove cpdef in PmfGen
* :ghissue:`3054`: [DOC] Fix some links [ci skip]
* :ghissue:`3060`: Bump codecov/codecov-action from 3 to 4
* :ghissue:`3061`: [OPT] Enable openmp for macOS wheel and CI's
* :ghissue:`3057`:   Using the atlas HCP1065 in DIPY
* :ghissue:`3055`: [RF] replace Bunch by Enum
* :ghissue:`3049`: [MTN] code cleaning: remove some dependencies version checking
* :ghissue:`3050`: [RF] Move ``dipy.boots.resampling`` to  ``dipy.stats.resampling``
* :ghissue:`3051`: [RF] Remove dipy.io.bvectxt module
* :ghissue:`3052`: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874
* :ghissue:`2789`: Horizon image's dtype validation
* :ghissue:`3047`: "Editable" installation broken
* :ghissue:`3045`: [DOC] fix `multi_shell_fiber_response` docstring array dims [ci skip]
* :ghissue:`3041`: [NF] Add convert tractograms flow
* :ghissue:`3040`: [BW] Remove some python2 reference
* :ghissue:`3039`: [TEST] Add setup_module and teardown_module
* :ghissue:`3038`: [NF] Update `dipy_info`: allow tractogram files format
* :ghissue:`3043`: d/d/t/test_data.py: endian independent dtype.
* :ghissue:`3042`: pyproject.toml: no cython at run time.
* :ghissue:`3027`: [NF] Add Concatenate tracks workflows
* :ghissue:`3035`: If I want to use  6D array in "actor.odf_slicer", how can i do?
* :ghissue:`2993`: Add conversion utility between DIPY and MRtrix3 spherical harmonic basis
* :ghissue:`3008`: NF: add SH basis conversion between dipy and mrtrix3
* :ghissue:`3025`: [TEST] Manage http errors for stateful tractograms
* :ghissue:`3031`: Bugfix: Horizon image's dtype validation
* :ghissue:`3032`: Consider moving your nightly wheel away from the scipy-wheel-nightly (old location) to scientific-python-nightly-wheels
* :ghissue:`3021`: [MTN] Remove 3.8 Ci's
* :ghissue:`3003`: DIPY installation raises Cython warnings
* :ghissue:`3026`: [RF] Fix cython 3 warnings
* :ghissue:`2852`: Different behavior regarding color channels of horizon
* :ghissue:`2378`: A novice's request for advice on loading very large tractograms (.tck)
* :ghissue:`2064`: How to register MR to CT of the same person?
* :ghissue:`2601`: read_bvals_bvecs can't read double volume dwi
* :ghissue:`3022`: [DOC] Fix logo size and link [ci skip]
* :ghissue:`3013`: Added Fibonacci spiral and test for it
* :ghissue:`3020`: load_nifti import doesn't work if using submodule directly
* :ghissue:`3019`: DOC: Fix link to toolchain roadmap page in `README`
* :ghissue:`3012`: DOC: Document observance for Scientific Python min supported versions
* :ghissue:`3018`: Bump actions/download-artifact from 3 to 4
* :ghissue:`3017`: Bump actions/upload-artifact from 3 to 4
* :ghissue:`3014`: Update release1.8.rst
* :ghissue:`1525`: Clang-omp moved to boneyard on brew

**DIPY 1.8.0** is now available. New features include:

- Python 3.12.0 support.
- Cython 3.0.0 compatibility.
- Migrated to Meson build system. Setuptools is no more.
- EVAC+ novel DL-based brain extraction method added.
- Parallel Transport Tractography (PTT) 10X faster.
- Many Horizon updates. Fast overlays of many images.
- New Correlation Tensor Imaging (CTI) method added.
- Improved warnings for optional dependencies.
- Large documentation update. New theme/design integration.
- Closed 197 issues and merged 130 pull requests.

====================================

 Release notes for DIPY version 1.7
====================================

**DIPY 1.7.0** is now available. New features include:

- NF: BundleWarp - Streamline-based nonlinear registration method for bundles added.
- NF: DKI+ - Diffusion Kurtosis modeling with advanced constraints added.
- NF: Synb0 - Synthetic b0 creation added using deep learning added.
- NF: New Parallel Transport Tractography (PTT) added.
- NF: Fast Streamline Search algorithm added.
- NF: New denoising methods based on 1D CNN added.
- Handle Asymmetric Spherical Functions.
- Large update of DIPY Horizon features.
- Multiple Workflows updated
- Large codebase cleaning.
- Large documentation update. Integration of Sphinx-Gallery.
- Closed 53 issues and merged 34 pull requests.

GitHub stats for 2023/01/16 - 2023/04/23 (tag: 1.6.0)

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

The following 21 authors contributed 496 commits.

* Ariel Rokem
* Bramsh Qamar
* Charles Poirier
* Dogu Baran Aydogan
* Eleftherios Garyfallidis
* Etienne St-Onge
* Francois Rheault
* Gabriel Girard
* Javier Guaje
* Jong Sung Park
* Martino Pilia
* Mitesh Gulecha
* Rahul Ubale
* Sam Coveney
* Serge Koudoro
* Shilpi
* Tom Dela Haije
* Yaroslav Halchenko
* karp2601
* lb-97
* ujjwal-shekhar

We closed a total of 87 issues, 34 pull requests and 53 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (34):

* :ghpull:`2765`: Sphinx-gallery integration
* :ghpull:`2788`: Remove NoseTester
* :ghpull:`2768`: BundleWarp, streamline-based nonlinear registration of white matter tracts
* :ghpull:`2749`: adding a new getitem method
* :ghpull:`2744`: Horizon Tabs
* :ghpull:`2785`: EVAC+ workflow
* :ghpull:`2540`: Updates the default value of rm_small_clusters variable in slr_with_qbx function
* :ghpull:`2609`: NF: DKI+ constraints
* :ghpull:`2596`: NF - Parallel Transport Tractography (PTT)
* :ghpull:`2740`: Integration of Denoising Method for DWI with 1D CNN
* :ghpull:`2773`: Including EVAC+ and util function
* :ghpull:`2783`: Fix test_roi_images
* :ghpull:`2782`: [MTN] Fix CI codecov upload
* :ghpull:`2780`: Added option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff
* :ghpull:`2778`: BF: QBX and merge clusters should return streamlines
* :ghpull:`2767`: NF - add utility functions to fast_numpy
* :ghpull:`2626`: Adding Synb0
* :ghpull:`2763`: Update dki.py
* :ghpull:`2751`: [ENH] Asymmetric peak_directions
* :ghpull:`2762`: Remove Python 3.7 from CI
* :ghpull:`2753`: Update adaptive_soft_matching.py
* :ghpull:`2722`: fixed pca for features > samples, and fixed pca_noise_estimate
* :ghpull:`2741`: Fixing solve_qp error
* :ghpull:`2739`: codespell: config, workflow, typos fixed
* :ghpull:`2590`: Fast Streamline Search algorithm implementation
* :ghpull:`2733`: Update SynRegistrationFlow for #2648
* :ghpull:`2723`: TRX integration, requires new attributes for SFT
* :ghpull:`2727`: Fix EXTRAS_REQUIRE
* :ghpull:`2725`: DOC - Update RUMBA-SD data requirement
* :ghpull:`2716`: NF - Added cython utility functions
* :ghpull:`2717`: fixed bug for non-linear fitting with masks
* :ghpull:`2628`: resolve some CI's script typo
* :ghpull:`2713`: Empty vtk support
* :ghpull:`2625`: [Upcoming] Release 1.6.0

Issues (53):

* :ghissue:`2537`: Importing an example in another example - doc
* :ghissue:`1778`: jupyter notebooks from examples
* :ghissue:`720`: Auto-convert the examples into IPython notebooks
* :ghissue:`1990`: [WIP] Sphinx-Gallery integration
* :ghissue:`2765`: Sphinx-gallery integration
* :ghissue:`2788`: Remove NoseTester
* :ghissue:`2768`: BundleWarp, streamline-based nonlinear registration of white matter tracts
* :ghissue:`1073`: Add a method to slice gtab using bvals (Eg : gtab[bvals>200])
* :ghissue:`2749`: adding a new getitem method
* :ghissue:`2744`: Horizon Tabs
* :ghissue:`2785`: EVAC+ workflow
* :ghissue:`2530`: slr_with_qbx breaks when bundle has only one streamline
* :ghissue:`2540`: Updates the default value of rm_small_clusters variable in slr_with_qbx function
* :ghissue:`2609`: NF: DKI+ constraints
* :ghissue:`2596`: NF - Parallel Transport Tractography (PTT)
* :ghissue:`2756`: Remove unused inplace param from gibbs_removal()
* :ghissue:`2754`: [Question] dipy/denoise/gibbs.py
* :ghissue:`2740`: Integration of Denoising Method for DWI with 1D CNN
* :ghissue:`2773`: Including EVAC+ and util function
* :ghissue:`2783`: Fix test_roi_images
* :ghissue:`2782`: [MTN] Fix CI codecov upload
* :ghissue:`2775`: NF - Add option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff(.)
* :ghissue:`2780`: Added option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff
* :ghissue:`2778`: BF: QBX and merge clusters should return streamlines
* :ghissue:`2767`: NF - add utility functions to fast_numpy
* :ghissue:`2626`: Adding Synb0
* :ghissue:`2770`: BF - update viz.py
* :ghissue:`2763`: Update dki.py
* :ghissue:`2751`: [ENH] Asymmetric peak_directions
* :ghissue:`2762`: Remove Python 3.7 from CI
* :ghissue:`2753`: Update adaptive_soft_matching.py
* :ghissue:`2722`: fixed pca for features > samples, and fixed pca_noise_estimate
* :ghissue:`2750`: Adding tests for gradient.py.
* :ghissue:`2741`: Fixing solve_qp error
* :ghissue:`2745`: Dipy Segmentation Core Dumped - Windows.Record
* :ghissue:`2742`: ValueError: slice step cannot be zero
* :ghissue:`2739`: codespell: config, workflow, typos fixed
* :ghissue:`2590`: Fast Streamline Search algorithm implementation
* :ghissue:`2733`: Update SynRegistrationFlow for #2648
* :ghissue:`2723`: TRX integration, requires new attributes for SFT
* :ghissue:`2729`: Numpy Version Incompatibility, AttributeError in dipy.align
* :ghissue:`2726`: Setup broken on Python 3.10.9 setuptools 67.2.0
* :ghissue:`2727`: Fix EXTRAS_REQUIRE
* :ghissue:`2725`: DOC - Update RUMBA-SD data requirement
* :ghissue:`2707`: Fixdenoise
* :ghissue:`2575`: [WIP]  Define curvature and stepsize as default parameter instead of max_angle for tractography
* :ghissue:`2414`: AffineMap.transform with option: interpolation='nearest' returns: "TypeError: No matching signature found"
* :ghissue:`2716`: NF - Added cython utility functions
* :ghissue:`2717`: fixed bug for non-linear fitting with masks
* :ghissue:`2628`: resolve some CI's script typo
* :ghissue:`2713`: Empty vtk support
* :ghissue:`2599`: Support empty ArraySequence in transform_streamlines
* :ghissue:`2625`: [Upcoming] Release 1.6.0

====================================

 Release notes for DIPY version 1.6
====================================

- NF: Unbiased groupwise linear bundle registration added.
- NF: MAP+ constraints added.
- Generalized PCA to less than 3 spatial dims.
- Add positivity constraints to QTI.
- Ability to apply Symmetric Diffeomorphic Registration to points/streamlines.
- New Human Connectome Project (HCP) data fetcher added.
- New Healthy Brain Network (HBN) data fetcher added.
- Multiple Workflows updated (DTIFlow, LPCAFlow, MPPCA) and added (RUMBAFlow).
- Ability to handle VTP files.
- Large codebase cleaning.
- Large documentation update.
- Closed 75 issues and merged 41 pull requests.

GitHub stats for 2022/03/11 - 2023/01/12 (tag: 1.5.0)

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

The following 15 authors contributed 242 commits.

* Ariel Rokem
* David Romero-Bascones
* Deneb Boito
* Eleftherios Garyfallidis
* Emmanuelle Renauld
* Eric Larson
* Francois Rheault
* Jacob Roberts
* Jon Haitz Legarreta Gorroño
* Malinda Dilhara
* Omar Ocegueda
* Sam Coveney
* Serge Koudoro
* Shreyas Fadnavis
* Tom Dela Haije

We closed a total of 116 issues, 41 pull requests and 75 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (41):

* :ghpull:`2710`: small fixes for tutorials
* :ghpull:`2711`: [FIX] use tempfile module instead of nibabel for TemporaryDirectory
* :ghpull:`2702`: One more small fix to the hcp fetcher.
* :ghpull:`2704`: MAINT: Fixes for 3.11 and sdist
* :ghpull:`2701`: FIX: Don't print a progbar for downloading unless you need to.
* :ghpull:`2700`: [FIX] incompatible type in numpy array
* :ghpull:`2694`: NF: Add RUMBA-SD reconstruction workflow
* :ghpull:`2697`: NF: Adds a fetcher for HCP data.
* :ghpull:`2692`: RF: Improve multi-shell RUMBA test WM response parameterization
* :ghpull:`2693`: TEST: Fix `Node.js` warnings linked to GitHub actions
* :ghpull:`2687`: DOC: Fix typos in SH theory documentation page
* :ghpull:`2690`: STYLE: Remove unnecessary b-val print in CSD reconstruction flow
* :ghpull:`2688`: DOC: Document Dirac delta generation method missing member
* :ghpull:`2683`: DOC: Adds missing documentation for a kwarg.
* :ghpull:`2668`: ENH: Make the DTI fit CLI metric saving message accurate
* :ghpull:`2674`: Improve doc (tensor values' order)
* :ghpull:`2670`: ENH: Allow non-default parameters to `Patch2Self` CLI
* :ghpull:`2672`: DOC: Miscellaneous docstring fixes
* :ghpull:`2669`: DOC: Remove inaccurate `patch2self` docstring default values
* :ghpull:`2664`: DOC: Fix DTI fit CLI docstring
* :ghpull:`2553`: NF: Unbiased groupwise linear bundle registration
* :ghpull:`2369`: Transform points with DiffeormorphicMap
* :ghpull:`2631`: [FIX] Allow patch size parameter to be an int on denoise Workflow
* :ghpull:`2630`: [DOC] Remove search index
* :ghpull:`2629`: [FIX ] Handle save VTP
* :ghpull:`2618`: Use np.linalg.multi_dot instead of multiple np.dot routines
* :ghpull:`2606`: STYLE: Fix miscellaneous Python warnings
* :ghpull:`2600`: Pin Ray
* :ghpull:`2531`: NF: MAP+ constraints
* :ghpull:`2589`: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module
* :ghpull:`2577`: Add positivity constraints to QTI
* :ghpull:`2595`: Temporary skip Cython 0.29.29
* :ghpull:`2591`: STYLE: Avoid array-like mutable default argument values
* :ghpull:`2592`: STYLE: Fix miscellaneous Python warnings
* :ghpull:`2579`: Generalized PCA to less than 3 spatial dims
* :ghpull:`2584`: transform_streamlines changes dtype to float64
* :ghpull:`2566`: [FIX] Update tests for the deprecated `dipy.io.bvectxt` module
* :ghpull:`2581`: Fix logger in SFT
* :ghpull:`2580`: DOC: Fix typos and grammar
* :ghpull:`2576`: DOC: Documentation fixes
* :ghpull:`2568`: DOC: Fix the docstring of `write_mapping`

Issues (75):

* :ghissue:`2710`: small fixes for tutorials
* :ghissue:`2711`: [FIX] use tempfile module instead of nibabel for TemporaryDirectory
* :ghissue:`2709`: DiffeomorphicMap object on github not the same as recent release
* :ghissue:`2708`: Provide the dataset of this code
* :ghissue:`2699`: WIP: Single shell/noreg redux
* :ghissue:`2702`: One more small fix to the hcp fetcher.
* :ghissue:`2704`: MAINT: Fixes for 3.11 and sdist
* :ghissue:`2701`: FIX: Don't print a progbar for downloading unless you need to.
* :ghissue:`2700`: [FIX] incompatible type in numpy array
* :ghissue:`2694`: NF: Add RUMBA-SD reconstruction workflow
* :ghissue:`2696`: Port HCP fetcher from pyAFQ into here
* :ghissue:`2697`: NF: Adds a fetcher for HCP data.
* :ghissue:`2692`: RF: Improve multi-shell RUMBA test WM response parameterization
* :ghissue:`2693`: TEST: Fix `Node.js` warnings linked to GitHub actions
* :ghissue:`1418`: Adding parallel_voxel_fit decorator
* :ghissue:`2687`: DOC: Fix typos in SH theory documentation page
* :ghissue:`2690`: STYLE: Remove unnecessary b-val print in CSD reconstruction flow
* :ghissue:`2688`: DOC: Document Dirac delta generation method missing member
* :ghissue:`2683`: DOC: Adds missing documentation for a kwarg.
* :ghissue:`2679`: Problems with a .nii.gz file when loading and floating
* :ghissue:`2676`: Does ```convert_sh_to_legacy``` work as intended ?
* :ghissue:`2668`: ENH: Make the DTI fit CLI metric saving message accurate
* :ghissue:`2674`: Improve doc (tensor values' order)
* :ghissue:`2670`: ENH: Allow non-default parameters to `Patch2Self` CLI
* :ghissue:`2673`: ENH: Doc: DTI format
* :ghissue:`2667`: Defaults for Patch2Self
* :ghissue:`2672`: DOC: Miscellaneous docstring fixes
* :ghissue:`2669`: DOC: Remove inaccurate `patch2self` docstring default values
* :ghissue:`2662`: Update cmd_line dipy_fit_dti
* :ghissue:`2664`: DOC: Fix DTI fit CLI docstring
* :ghissue:`2658`: Any chance of arm64 wheels for Mac / Python 3.10?
* :ghissue:`2659`: Angle var
* :ghissue:`2649`: IVIM VarPro fitting running error
* :ghissue:`2553`: NF: Unbiased groupwise linear bundle registration
* :ghissue:`2424`: Transforming individual points with SDR
* :ghissue:`2327`: Diffeomorphic transformation of coordinates
* :ghissue:`2313`: deform_streamlines for wholebrain tractogram doesn't function properly
* :ghissue:`936`: WIP: coordinate mapping with DiffeomorphicMap
* :ghissue:`2369`: Transform points with DiffeormorphicMap
* :ghissue:`2616`: dti TensorModel fitting issue
* :ghissue:`2627`: Free-Water Analysis Gradient Table Error
* :ghissue:`2635`: get_flexi_tvis_affine(tvis_hdr, nii_aff)
* :ghissue:`2634`: Fix small difference between pdfs dense 2d/3d
* :ghissue:`2559`: CLI denoise patch_size error
* :ghissue:`2631`: [FIX] Allow patch size parameter to be an int on denoise Workflow
* :ghissue:`2564`: Search, index, module links not working in the doc
* :ghissue:`2630`: [DOC] Remove search index
* :ghissue:`2572`: Saving vtp file error
* :ghissue:`2629`: [FIX ] Handle save VTP
* :ghissue:`2622`: Error with Illustrating Electrostatic Repulsion
* :ghissue:`2618`: Use np.linalg.multi_dot instead of multiple np.dot routines
* :ghissue:`2617`: DKI model fit shape broadcast error
* :ghissue:`2606`: STYLE: Fix miscellaneous Python warnings
* :ghissue:`2602`: Dear experts, how can I set different number of fiber tracks before generating streamlines?
* :ghissue:`2603`: Dear experts, how to save dti_peaks?
* :ghissue:`2600`: Pin Ray
* :ghissue:`2531`: NF: MAP+ constraints
* :ghissue:`2587`: Thread safety concerns with reliance on `nibabel.tmpdirs.InTemporaryDirectory`
* :ghissue:`2589`: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module
* :ghissue:`2577`: Add positivity constraints to QTI
* :ghissue:`2450`: [NF] New tracking Algorithm:  Parallel Transport Tractography (PTT)
* :ghissue:`2594`: DIPY compilation fails with the last release of cython (0.29.29)
* :ghissue:`2595`: Temporary skip Cython 0.29.29
* :ghissue:`2591`: STYLE: Avoid array-like mutable default argument values
* :ghissue:`2592`: STYLE: Fix miscellaneous Python warnings
* :ghissue:`2579`: Generalized PCA to less than 3 spatial dims
* :ghissue:`2584`: transform_streamlines changes dtype to float64
* :ghissue:`2566`: [FIX] Update tests for the deprecated `dipy.io.bvectxt` module
* :ghissue:`2581`: Fix logger in SFT
* :ghissue:`2580`: DOC: Fix typos and grammar
* :ghissue:`2576`: DOC: Documentation fixes
* :ghissue:`2573`: Cannot Import "Feature" From "dipy.segment.metric"
* :ghissue:`2568`: DOC: Fix the docstring of `write_mapping`
* :ghissue:`2567`: This should be a `1`
* :ghissue:`2565`: compress_streamlines() not available anymore

===================================

 Release notes for DIPY version 1.5
===================================

GitHub stats for 2021/05/06 - 2022/03/10 (tag: 1.4.1)

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

The following 22 authors contributed 573 commits.

* Ariel Rokem
* Dan Bullock
* David Romero-Bascones
* Derek Pisner
* Eleftherios Garyfallidis
* Eric Larson
* Francis Jerome
* Francois Rheault
* Gabriel Girard
* Giulia Bertò
* Javier Guaje
* Jon Haitz Legarreta Gorroño
* Joshua Newton
* Kenji Marshall
* Leevi Kerkela
* Leon Weninger
* Lucas Da Costa
* Nasim Anousheh
* Rafael Neto Henriques
* Sam Coveney
* Serge Koudoro
* Shreyas Fadnavis

We closed a total of 200 issues, 72 pull requests and 128 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (72):

* :ghpull:`2561`: [FIX] Motion correction tutorial
* :ghpull:`2520`: Resdnn inference
* :ghpull:`2558`: BUG: Fix errant warning about starting_affine
* :ghpull:`2557`: MAINT: Fix version
* :ghpull:`2556`: [FIX] Update `dipy.segment` tutorials
* :ghpull:`2554`: Support .vtp files
* :ghpull:`2555`: Limit `peaks_from_model` number of processes in examples
* :ghpull:`2539`: Adds utilities for embarassingly parallel loops.
* :ghpull:`2545`: Stateful Tractogram DPS and DPP keys ordering
* :ghpull:`2548`: Add timeout + concurrency to GHA
* :ghpull:`2549`: [ENH] Clarify reconst_sh tutorial
* :ghpull:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow
* :ghpull:`2551`: [MNT] Update mininal dependencies version
* :ghpull:`2536`: Random colors fix in horizon
* :ghpull:`2533`: [FIX] Docstring cleaning: wrong underline length...
* :ghpull:`2342`: NF:  q-space trajectory imaging
* :ghpull:`2512`: Masking for affine registration
* :ghpull:`2526`: TEST: Filter legacy SH bases warnings in tests
* :ghpull:`2534`: TEST: Remove unnecessary `main` method definition in tests
* :ghpull:`2532`: STYLE: Remove unused import statements
* :ghpull:`2529`: STYLE: Remove unused import statements
* :ghpull:`2528`: TEST: Remove legacy `nose`-related dead testing code
* :ghpull:`2527`: TEST: Fix intermittent RUMBA test check failure
* :ghpull:`2493`: Fury dependency resolution
* :ghpull:`2522`: ENH: Miscellaneous cleanup
* :ghpull:`2521`: DOC: Use GitHub actions status badge in README
* :ghpull:`2420`: Documentation corrections
* :ghpull:`2482`: ENH: Improve SH bases warning messages
* :ghpull:`2423`: NF: rumba reconst
* :ghpull:`2518`: Migrations from Azure Pipeline to Github Actions
* :ghpull:`2515`: Default to False output for null streamlines in streamline_near_roi
* :ghpull:`2513`: [MNT] Drop distutils
* :ghpull:`2506`: Horizon FURY update
* :ghpull:`2510`: Optimize sfm (reboot)
* :ghpull:`2487`: ENH: Better error message
* :ghpull:`2442`: [NF] Add Motion correction workflow
* :ghpull:`2470`: Add utilities functions:  radius curvature <--> maximum deviation angle
* :ghpull:`2485`: DOC: Small updates.
* :ghpull:`2481`: ENH: Import ABCs from `collections.abc`
* :ghpull:`2480`: STYLE: Make `sklearn` import warning messages consistent
* :ghpull:`2478`: ENH: Deal appropriately with user warnings
* :ghpull:`2479`: STYLE: Improve style in misc files
* :ghpull:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings
* :ghpull:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning
* :ghpull:`2472`: ENH: Return unique invalid streamline removal indices
* :ghpull:`2471`: DOC: Fix coding style guideline link
* :ghpull:`2468`: [MNT] Use windows-latest on azure pipeline
* :ghpull:`2467`: [ENH] Add fit_method option in DTI and DKI CLI
* :ghpull:`2466`: deprecate dipy.io.bvectxt module
* :ghpull:`2453`: make it compatible when number of volume is 2
* :ghpull:`2413`: Azure pipeline: from ubuntu 1604 to 2004
* :ghpull:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors
* :ghpull:`2444`: [DOC] : Added citation for IVIM dataset
* :ghpull:`2434`: MAINT: Update import from ndimage
* :ghpull:`2435`: BUG: Backward compat support for pipeline
* :ghpull:`2436`: MAINT: Bump tolerance
* :ghpull:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py`
* :ghpull:`2374`: ROIs visualizer
* :ghpull:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling
* :ghpull:`2417`: OPT: Initialize `Shape` struct
* :ghpull:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols'
* :ghpull:`2406`: Manage Approx_polygon_track with repeated points
* :ghpull:`2411`: [FIX] `c_compress_streamline` discard identical points
* :ghpull:`2416`: OPT: Prefer using a typed index to get the PMF value
* :ghpull:`2415`: Implementation multi_voxel_fit progress bar
* :ghpull:`2410`: [ENH] Improve Shore Tests
* :ghpull:`2409`: NF - Sample PMF for an input position and direction
* :ghpull:`2405`: Small correction on KFA
* :ghpull:`2407`: from random to deterministic test for deform_streamlines
* :ghpull:`2392`: Add decomposition
* :ghpull:`2389`: [Fix] bundles_distances_mdf asymmetric values
* :ghpull:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.

Issues (128):

* :ghissue:`2561`: [FIX] Motion correction tutorial
* :ghissue:`2123`: WIP: Residual Deep NN
* :ghissue:`2520`: Resdnn inference
* :ghissue:`2558`: BUG: Fix errant warning about starting_affine
* :ghissue:`2557`: MAINT: Fix version
* :ghissue:`2489`: MAINT: Get Python 3.10 binaries up on scipy-wheels-nightly
* :ghissue:`2556`: [FIX] Update `dipy.segment` tutorials
* :ghissue:`2554`: Support .vtp files
* :ghissue:`2525`: Support Opening `.vtp` files
* :ghissue:`2555`: Limit `peaks_from_model` number of processes in examples
* :ghissue:`2539`: Adds utilities for embarassingly parallel loops.
* :ghissue:`2509`: Easy robustness for streamline_near_roi and near_roi for empty streamlines?
* :ghissue:`2543`: StatefulTractogram.are_compatible compare data_per_point keys as list instead of set
* :ghissue:`2545`: Stateful Tractogram DPS and DPP keys ordering
* :ghissue:`2548`: Add timeout + concurrency to GHA
* :ghissue:`2549`: [ENH] Clarify reconst_sh tutorial
* :ghissue:`2546`: Confusing import in 'reconst_sh`
* :ghissue:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow
* :ghissue:`2542`: DTI workflow should allow user-defined fitting method
* :ghissue:`2551`: [MNT] Update mininal dependencies version
* :ghissue:`2477`: Numpy min dependency update
* :ghissue:`2541`: Issue with coverage and pytests for numpy.min()
* :ghissue:`2507`: kernel died when use dipy.viz
* :ghissue:`2536`: Random colors fix in horizon
* :ghissue:`2533`: [FIX] Docstring cleaning: wrong underline length...
* :ghissue:`2422`: WIP-Adding math in SLR tutorial
* :ghissue:`2342`: NF:  q-space trajectory imaging
* :ghissue:`2512`: Masking for affine registration
* :ghissue:`1969`: imaffine mask support
* :ghissue:`2526`: TEST: Filter legacy SH bases warnings in tests
* :ghissue:`2456`: Horizon tests failing
* :ghissue:`2534`: TEST: Remove unnecessary `main` method definition in tests
* :ghissue:`2532`: STYLE: Remove unused import statements
* :ghissue:`2524`: Add concurrency + timeout to Github Actions (GHA)
* :ghissue:`2529`: STYLE: Remove unused import statements
* :ghissue:`2528`: TEST: Remove legacy `nose`-related dead testing code
* :ghissue:`2527`: TEST: Fix intermittent RUMBA test check failure
* :ghissue:`2493`: Fury dependency resolution
* :ghissue:`2522`: ENH: Miscellaneous cleanup
* :ghissue:`2521`: DOC: Use GitHub actions status badge in README
* :ghissue:`2420`: Documentation corrections
* :ghissue:`2482`: ENH: Improve SH bases warning messages
* :ghissue:`2449`: Nonsense deprecation warning
* :ghissue:`2423`: NF: rumba reconst
* :ghissue:`2179`: NF: Complete masking implementation in affine registration with MI
* :ghissue:`2518`: Migrations from Azure Pipeline to Github Actions
* :ghissue:`2492`: Move to GitHub actions / reusable actions
* :ghissue:`2515`: Default to False output for null streamlines in streamline_near_roi
* :ghissue:`2497`: Remove python 3.6 from Azure pipelines
* :ghissue:`2495`: Remove Distutils (deprecated)
* :ghissue:`2513`: [MNT] Drop distutils
* :ghissue:`2506`: Horizon FURY update
* :ghissue:`2305`: [WIP] Brain Tumor Image Segmentation Code
* :ghissue:`2499`: Problem generating Connectivity Matrix: "Slice step cannot be zero"
* :ghissue:`2510`: Optimize sfm (reboot)
* :ghissue:`2488`: Minimize memory footprint whereever possible, add joblib support for …
* :ghissue:`2504`: Why are there many small dots on the fwdwi image?
* :ghissue:`2502`: Can i read specific b-values from my own multishell data?
* :ghissue:`2500`: MAP issue
* :ghissue:`2490`: [BUG] MRI-CT alignment failure
* :ghissue:`2487`: ENH: Better error message
* :ghissue:`2402`: Dipy 1.4.1 breaks nipype.interfaces.dipy.dipy_to_nipype_interface
* :ghissue:`2486`: Wrong doc in interpolation
* :ghissue:`2442`: [NF] Add Motion correction workflow
* :ghissue:`2470`: Add utilities functions:  radius curvature <--> maximum deviation angle
* :ghissue:`2485`: DOC: Small updates.
* :ghissue:`2484`: [ENH] Add grid search to `AffineRegistration.optimize`
* :ghissue:`2483`: [DOC] Stable/Latest Documentation Structure
* :ghissue:`2481`: ENH: Import ABCs from `collections.abc`
* :ghissue:`2480`: STYLE: Make `sklearn` import warning messages consistent
* :ghissue:`2478`: ENH: Deal appropriately with user warnings
* :ghissue:`2479`: STYLE: Improve style in misc files
* :ghissue:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings
* :ghissue:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning
* :ghissue:`2472`: ENH: Return unique invalid streamline removal indices
* :ghissue:`2471`: DOC: Fix coding style guideline link
* :ghissue:`2468`: [MNT] Use windows-latest on azure pipeline
* :ghissue:`2467`: [ENH] Add fit_method option in DTI and DKI CLI
* :ghissue:`2463`: DTI RESTORE on the CLI
* :ghissue:`2466`: deprecate dipy.io.bvectxt module
* :ghissue:`2460`: Deprecate and Remove dipy.io.bvectxt
* :ghissue:`2429`: random_colors flag in dipy_horizon does not work as before
* :ghissue:`2461`: Patch2Self: Less than 10 3D Volumes Bug
* :ghissue:`2464`: Typo on the homepage
* :ghissue:`2453`: make it compatible when number of volume is 2
* :ghissue:`2457`: Choosing sigma_diff and radius parameters for SyN registration
* :ghissue:`2413`: Azure pipeline: from ubuntu 1604 to 2004
* :ghissue:`2454`: Can I show fiber with vtk?
* :ghissue:`2446`: Use of bitwise or with non-bool inputs results in ufunc 'bitwise_or' error
* :ghissue:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors
* :ghissue:`2444`: [DOC] : Added citation for IVIM dataset
* :ghissue:`2443`: Citation for IVIM dataset not present in docs
* :ghissue:`2434`: MAINT: Update import from ndimage
* :ghissue:`2441`: Horizon error - disk position outside the slider line
* :ghissue:`2435`: BUG: Backward compat support for pipeline
* :ghissue:`2436`: MAINT: Bump tolerance
* :ghissue:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py`
* :ghissue:`2430`: dipy.align.reslice
* :ghissue:`2431`: dipy.align.reslice interpolation order for downsampling
* :ghissue:`2432`: How to apply MI metric in dipy？
* :ghissue:`2374`: ROIs visualizer
* :ghissue:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling
* :ghissue:`2417`: OPT: Initialize `Shape` struct
* :ghissue:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols'
* :ghissue:`2406`: Manage Approx_polygon_track with repeated points
* :ghissue:`2314`: Approx_polygon_track with repeated points gives an error
* :ghissue:`2411`: [FIX] `c_compress_streamline` discard identical points
* :ghissue:`1805`: `c_compress_streamline` keeps identical points when it shouldn't
* :ghissue:`2418`: kernel failure when importing mask from dipy.segment
* :ghissue:`2416`: OPT: Prefer using a typed index to get the PMF value
* :ghissue:`2415`: Implementation multi_voxel_fit progress bar
* :ghissue:`2410`: [ENH] Improve Shore Tests
* :ghissue:`365`: Code review items for `dipy.reconst.shore`
* :ghissue:`2409`: NF - Sample PMF for an input position and direction
* :ghissue:`2404`: Change affine in StatefulTractogram
* :ghissue:`2405`: Small correction on KFA
* :ghissue:`2407`: from random to deterministic test for deform_streamlines
* :ghissue:`2392`: Add decomposition
* :ghissue:`717`: Download each shell of the CENIR data separately?
* :ghissue:`2209`: _pytest.pathlib.ImportPathMismatchError:
* :ghissue:`1934`: Random lpca denoise
* :ghissue:`2312`: DIPY open group meetings, Spring 2021
* :ghissue:`2383`: error in mcsd model fitting (DCPError)
* :ghissue:`2391`: error performing cross-validation on diffusion HCP data
* :ghissue:`2393`: Add a function to read streamline from the result generated by the command "probtrackx2" in FMRIB's Diffusion Toolbox
* :ghissue:`2389`: [Fix] bundles_distances_mdf asymmetric values
* :ghissue:`2310`: `bundles_distances_mdf` asymmetric values
* :ghissue:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.

=====================================

 Release notes for DIPY version 1.4.1
=====================================

- Patch2Self and its documentation updated.
- BUAN and Recobundles documentation updated.
- Standardization and improvement of the multiprocessing / multithreading rules.
- Community and governance information added.
- New surface seeding module for tractography named `mesh`.
- Large update of Cython code in respect of the last standard.
- Large documentation update.
- Closed 61 issues and merged 28 pull requests.

GitHub stats for 2021/03/14 - 2021/05/05 (tag: 1.4.0)

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

The following 11 authors contributed 153 commits.

* Ariel Rokem
* Bramsh Qamar Chandio
* David Romero-Bascones
* Eleftherios Garyfallidis
* Etienne St-Onge
* Felix Liu
* Gabriel Girard
* John Kruper
* Nasim Anousheh
* Serge Koudoro
* Shreyas Fadnavis

We closed a total of 89 issues, 28 pull requests and 61 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (28):

* :ghpull:`2367`: [Upcoming] Release 1.4.1
* :ghpull:`2387`: added all examples of CST and updated AFQ file name
* :ghpull:`2386`: Adding CST_L back in Bundle Segmentation Tutorial
* :ghpull:`2375`: Expanding Bundle Segmentation Tutorial
* :ghpull:`2382`: Updated docs for using P2S optimally
* :ghpull:`2385`: RF: Standardize the argument name for the number of threads/cores
* :ghpull:`2384`: RF - Removed deprecated tracking code
* :ghpull:`2351`: Updating Vec2vec_rotmat to deal with numerical issues
* :ghpull:`2381`: Adds the NIPY code of conduct to our repo.
* :ghpull:`2371`: [Fix] Add "None" options in the CLIs
* :ghpull:`2352`: RF: configure num_threads==-1 as the value to use all cores
* :ghpull:`2373`: [FIX] warning if not the same number of points
* :ghpull:`2372`: Expand patch radius if input is int
* :ghpull:`2348`: RF: Use new name for this function.
* :ghpull:`2363`: [ENH] Adding cython file(*.pyx) in documentation
* :ghpull:`2365`: [DOC]: Change defaults in Patch2Self example
* :ghpull:`2349`: [ENH] Allow for other statistics, like median, in afq_profile
* :ghpull:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays
* :ghpull:`2346`: [MNT]  Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible
* :ghpull:`2347`: Replacing Data in NLMeans Tutorial
* :ghpull:`2340`: [FIX] reactivate codecov
* :ghpull:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial
* :ghpull:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int
* :ghpull:`1648`: Mesh seeding (surface)
* :ghpull:`2337`: BF: Change patch2self defaults.
* :ghpull:`2333`: Add __str__ to GradientTable
* :ghpull:`2335`: RF: Replaces deprecated basis by its new name.
* :ghpull:`2332`: [FIX] fix tests for all new deprecated functions

Issues (61):

* :ghissue:`2375`: Expanding Bundle Segmentation Tutorial
* :ghissue:`1973`: Recobundles documentation
* :ghissue:`2382`: Updated docs for using P2S optimally
* :ghissue:`2385`: RF: Standardize the argument name for the number of threads/cores
* :ghissue:`2377`: RF: standardize the argument name for the number of threads/cores
* :ghissue:`2384`: RF - Removed deprecated tracking code
* :ghissue:`2351`: Updating Vec2vec_rotmat to deal with numerical issues
* :ghissue:`2381`: Adds the NIPY code of conduct to our repo.
* :ghissue:`2380`: Community and governance
* :ghissue:`2371`: [Fix] Add "None" options in the CLIs
* :ghissue:`2300`: NF: Add "None" options in the CLIs
* :ghissue:`2352`: RF: configure num_threads==-1 as the value to use all cores
* :ghissue:`2373`: [FIX] warning if not the same number of points
* :ghissue:`2320`: RecoBundles distances
* :ghissue:`2372`: Expand patch radius if input is int
* :ghissue:`2341`: Allow use of all threads in the gibbs ringing workflow
* :ghissue:`2348`: RF: Use new name for this function.
* :ghissue:`2353`: How to create tractogram from a multi-shell data for RecoBundles
* :ghissue:`1311`: Adding cython file(*.pyx) in documentation
* :ghissue:`2363`: [ENH] Adding cython file(*.pyx) in documentation
* :ghissue:`1302`: [DOC] cython (pyx) files are not parsed
* :ghissue:`366`: Some doc missing
* :ghissue:`2365`: [DOC]: Change defaults in Patch2Self example
* :ghissue:`1672`: Dipy Segmentation fault when visualizing
* :ghissue:`1444`: Move general registration tools into own package?
* :ghissue:`562`: Multiprocessing the tensor reconstruction
* :ghissue:`13`: Cordinate maps stuff
* :ghissue:`2324`: Dipy for VR/AR
* :ghissue:`2345`: Saving and/or importing nonlinear warps
* :ghissue:`2349`: [ENH] Allow for other statistics, like median, in afq_profile
* :ghissue:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays
* :ghissue:`423`: Use npy_intp variables instead of int and size_t to iterate over numpy arrays
* :ghissue:`837`: Should we enforce float32 in tractography results?
* :ghissue:`636`: Get a standard interface for the functions using the noise variance
* :ghissue:`861`: open mp defaults to one core, is that a good idea?
* :ghissue:`2346`: [MNT]  Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible
* :ghissue:`1895`: Cython warnings
* :ghissue:`545`: Use cnp.PyArray_DATA wherever possible
* :ghissue:`2347`: Replacing Data in NLMeans Tutorial
* :ghissue:`1847`: Replacing Data in NLMeans Tutorial
* :ghissue:`2340`: [FIX] reactivate codecov
* :ghissue:`1872`: Did we lose our coverage reporting?
* :ghissue:`1646`: Fetcher should not be under coverage
* :ghissue:`1635`: Track from mesh
* :ghissue:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial
* :ghissue:`2309`: Tractogram Header in RecoBundles Tutorial
* :ghissue:`2334`: Aphysical signal after running patch2self
* :ghissue:`1873`: ERROR while import data
* :ghissue:`2343`: Missing Python 3.9 wheels
* :ghissue:`1996`: Documentation not being rendered correctly
* :ghissue:`2311`: Accuracy of DKI measures
* :ghissue:`2274`: DKI metrics' accuracy
* :ghissue:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int
* :ghissue:`1648`: Mesh seeding (surface)
* :ghissue:`1675`: WIP: Integer indices
* :ghissue:`2316`: TranslationTransform2D Exact X-Y Shift
* :ghissue:`2337`: BF: Change patch2self defaults.
* :ghissue:`2333`: Add __str__ to GradientTable
* :ghissue:`2331`: gtab.info does not print anything
* :ghissue:`2335`: RF: Replaces deprecated basis by its new name.
* :ghissue:`2332`: [FIX] fix tests for all new deprecated functions