# Release notes for DIPY version 1.10

GitHub stats for 2024/03/08 - 2024/12/09 (tag: 1.9.0)

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

The following 25 authors contributed 871 commits.

- Alex Rockhill

- Ariel Rokem

- Asa Gilmore

- Atharva Shah

- Bramsh Qamar

- Charles Poirier

- Eleftherios Garyfallidis

- Eric Larson

- Florent Wijanto

- Gabriel Girard

- Jon Haitz Legarreta Gorroño

- Jong Sung Park

- Julio Villalon

- Kaibo Tang

- Kaustav Deka

- Maharshi Gor

- Martin Kozár

- Matt Cieslak

- Matthew Feickert

- Michael R. Crusoe

- Prajwal Reddy

- Rafael Neto Henriques

- Sam Coveney

- Sandro Turriate

- Serge Koudoro

We closed a total of 445 issues, 187 pull requests and 258 regular issues; this is the full list (generated with the script `tools/github_stats.py`):

Pull Requests (187):

- PR #3420: CI: define output path for coverage

- PR #3415: tests: leave no trace behind

- PR #3417: MAINT: Address changes to API with new (1.6) version of cvxpy.

- PR #3414: Bump codecov/codecov-action from 4 to 5 in the actions group

- PR #3412: BF: Fixing single-slice data error in Patch2Self

- PR #3409: [RF] Cleanup deprecated functions and remove some old legacy scripts

- PR #3407: CI: unpin cvxpy

- PR #3408: RF: fix step argument in DTI NLLS model

- PR #3402: DOC: Add Exporting and importing Mapping field information in recipes and registration tutorial

- PR #3403: Robust split idea rebase tidy

- PR #3404: RF: Improve and Simplify version management

- PR #3395: RF: Refactor nn module and deprecate tensorflow module

- PR #1957: niftis2pam, pam2niftis Workflow

- PR #3396: DOC: Adopt sphinxcontrib-bibtex for reconst model list refs

- PR #3399: STYLE: Remove empty quoted paragraph in developer guide index

- PR #3398: DOC: Improve first interaction GitHub Actions config file

- PR #2826: [ENH] Compute fiber density and fiber spread from ODF using Bingham distributions

- PR #3303: NF: Patch2Self3

- PR #3392: [WIP] NF: Adding pytorch versions

- PR #3368: [NF] DAM implementation for tissue classification using DMRI signal properties.

- PR #3390: DOC: Update DTI tutorial title

- PR #3391: STYLE: removing pep8speaks conf file in favor of pre-commit action

- PR #3393: RF: fix API generation

- PR #3387: DOC: Add first interaction GHA workflow file

- PR #3386: DOC: Update the CI tool to GHA in CONTRIBUTING file

- PR #3384: BF: Updated non_local_means

- PR #3140: NF: Adding correct_mask to median_otsu

- PR #3345: DOC: Skip element in documentation generation

- PR #3372: BugFix: New Atlas OMM not working with Horizon

- PR #3381: RF: Add support for sequential processing in Gibbs unringing

- PR #3380: ensure all calls to a python executable are to python3

- PR #3376: DOC: Use placeholder for unused variable in streamline_tools

- PR #3373: DOC: Consider warnings as errors in documentation CI build

- PR #3379: DOC: Remove example files labels

- PR #3378: doc: Link reconstruction model list to multiple pages

- PR #3377: DOC: Miscellaneous improvements to PeakActor docstring

- PR #3375: DOC: Reference footnote in streamline_tools

- PR #3348: DOC: Address remaining some warnings

- PR #3369: ci: Bump scientific-python/upload-nightly-action from 0.6.0 to 0.6.1

- PR #3367: Bump scientific-python/upload-nightly-action from 0.5.0 to 0.6.0 in the actions group

- PR #3366: DOC: Make rng optional parameter docstrings consistent

- PR #3365: DOC: Fix some cites.

- PR #3356: BF: fix s390x compatibility

- PR #3360: DOC: Remove unnecessary leading whitespace in rst doc paragraph

- PR #3357: FIX: remove keyword only warning on examples (part2)

- PR #3343: BF Fixing transformation function

- PR #3355: FIX: missing keyword only arguments on example

- PR #3221: Updating BundleWarp default value of alpha

- PR #3323: BF: Allow passing kwargs in fit method, by moving parallelization kwargs elsewhere, including PEP 3102

- PR #3351: DOC: Fix miscellaneous documentation build warnings (part 3)

- PR #3306: NF: Update to examples

- PR #3293: BF: Fix attempting to delete frame local symbol table variable

- PR #3257: NF: Applying Decorators in Module (Reconst)

- PR #3254: NF: Applying Decorators in Module (Direction)

- PR #3317: DOC: Miscellaneous documentation improvements

- PR #3350: DOC: Do not use the scale option for URL-based images

- PR #3344: DOC: Fix miscellaneous documentation build warnings (part 2)

- PR #3346: RF: Removal of keyword form Cython files

- PR #3341: DOC: Host MNI template note references in references file

- PR #3333: RF: Decorator fix

- PR #3335: RF: Allow parallel processing for sphinx extension

- PR #3342: RF: Doctest warnings

- PR #3337: DOC: Fix miscellaneous documentation build warnings

- PR #3338: DOC: Cite examples references using sphinxcontrib-bibtex

- PR #3319: DOC: Use references bibliography file for DIPY citation file

- PR #3321: BF: Set the superclass fit_method param value to the one provided

- PR #3324: RF: Refactored for keyword arguments

- PR #3340: CI: pin cvxpy to 1.4.4 until 1.5.x issues are solved

- PR #3316: DOC: Cite code base references using sphinxcontrib-bibtex

- PR #3332: BF: Set the Diso parameter value to the one provided

- PR #3325: DOC: Fix warnings related to displayed math expressions

- PR #3331: DOC: Miscellaneous documentation improvements (part 3)

- PR #3329: STYLE: Use a leading underscore to name private methods

- PR #3330: DOC: Do not use unfinished double backticks

- PR #3320: DOC: Miscellaneous documentation improvements (part 2)

- PR #3318: RF: Remove unused parameters from method signature

- PR #3310: DOC: Cite nn references through sphinxcontrib-bibtex

- PR #3315: RF: remove legacy numpydoc

- PR #2810: [DOC] introducing sphinxcontrib-Bibtex to improve reference management

- PR #3312: DOC: Use misc for other types of BibTeX entries

- PR #3309: DOC: Miscellaneous doc formatting fixes (part 4)

- PR #3308: DOC: Rework the BibTeX bibliography file

- PR #3275: FIX: remove sagital from codespellrc ignore list .

- PR #3304: DOC: Miscellaneous doc formatting fixes (part 3)

- PR #3295: ENH: Add a GHA workflow file to build docs

- PR #3302: DOC: Miscellaneous doc formatting fixes (part 2)

- PR #3301: FIX: explicit keyword argument for Horizon

- PR #3297: DOC: Miscellaneous doc formatting fixes

- PR #3291: FIX: nightly wheels for macOS arm64

- PR #3262: NF: Applying Decorators in Module (Visualization)

- PR #3263: NF: Applying Decorators in Module (Workflow)

- PR #3287: NF: Add __len__ to GradientTable

- PR #3260: NF: Applying Decorators in Module (Tracking)

- PR #3256: NF: Applying Decorators in Module (NeuralNetwork)

- PR #3258: NF: Applying Decorators in Module (Segment)

- PR #3249: NF: Applying Decorators in Module (Align)

- PR #3251: NF: Applying Decorators in Module (Core)

- PR #3279: FIX: Explicit type origin for long to solve the cython error during compilation

- PR #3259: NF: Applying Decorators in Module (Sims)

- PR #3252: NF: Applying Decorators in Module (Denoise)

- PR #3261: NF: Applying Decorators in Module (Utils)

- PR #3255: NF: Applying Decorators in Module (Io)

- PR #3253: NF: Applying Decorators in Module (Data)

- PR #3233: STYLE: Set stacklevel argument explicitly to warning messages

- PR #3239: NF: Decorator for keyword-only argument

- PR #2593: Embed parallelization into the multi_voxel_fit decorator.

- PR #3274: RF: Update pyproject.toml for numpy 2.0

- PR #3273: STYLE: Make statement dwell on a single line

- PR #3237: Add support for tensor-valued spherical functions in interp_rbf

- PR #3245: RF: Switch from using sparse *_matrix to *_array.

- PR #3267: STYLE: Avoid deprecated NumPy types and methods for NumPy 2.0 compat

- PR #3264: TEST: avoid direct comparison of floating point numbers

- PR #3268: STYLE: Prefer using np.asarray to avoid copy while creating an array

- PR #3271: RF: Do not use np.any for checking optional array parameters

- PR #3250: DOC: Fix param order

- PR #3269: STYLE: Prefer using isin over in1d

- PR #3238: NF - add affine to peaks_from_position

- PR #3247: STYLE: Add imported symbols to __all__ in direction module

- PR #3246: STYLE: Import explicitly direction.peaks symbols

- PR #3241: RF: Codespell fix for CI

- PR #3228: STYLE: Fix unused loop control variable warning

- PR #3235: STYLE: Do not allow running unintended modules as scripts

- PR #3230: STYLE: Fix function definition loop variable binding warning

- PR #3232: STYLE: Simplify implicitly concatenated strings

- PR #3229: STYLE: Prefer using f-strings

- PR #3224: BF: Rewrite list creation as list() instead of []

- PR #3216: STYLE: Format code using ruff

- PR #3178: DOC: Fixes the AFQ tract profile tutorial.

- PR #3218: STYLE: Fix codespell issues

- PR #3209: [CI] Move filterwarnings from pyproject to conftest

- PR #3220: [RF] from os.fork to spawn for multiprocessing

- PR #3214: RF - remove buffer argument in pmf_gen.get_pmf_value(.)

- PR #3219: [ENH] Prefer CLARABEL over ECOS as the CVXPY solver

- PR #3215: tests: correct module-level setup

- PR #3211: [RF] PMF Gen: from memoryview to pointer

- PR #3210: Python 3.13: Fix tests for next Python release

- PR #3212: STYLE: Relocate pre-commit and ruff packages to style requirements

- PR #3205: BF: Declare variables holding integers as cnp.npy_intp over double

- PR #3174: NF - initial directions from seed positions

- PR #3207: DOC: Fix Cython method parameter type description

- PR #3206: BF: Use cnp.npy_intp instead of int as counter

- PR #3204: DOC: Fix documentation typos

- PR #3202: [TEST] Add flag to turn warnings into errors for pytest

- PR #3158: ENH: Remove filtering UserWarning warnings in test config file

- PR #3194: MAINT: fix warning

- PR #3199: Bump pre-commit/action from 3.0.0 to 3.0.1 in the actions group

- PR #3182: [NF] Add DiSCo challenge data fetcher

- PR #3197: ENH: Fix miscellaneous warnings in dki reconstruction module

- PR #3198: ENH: Ensure that arccos argument is in the [-1,1] range

- PR #3191: [RF] allow float and double for trilinear_interpolate4d_c

- PR #3151: DKI Updates: (new radial tensor kurtosis metric, updated documentation and missing tests)

- PR #3189: Update affine_registration to clarify returns and make them consistent with docstring

- PR #3176: ENH: allow vol_idx in align workflow

- PR #3188: ENH: Add pre-commit to project dev dependencies

- PR #3183: ENH: Specify the solver for the MAP-MRI positivity constraint test

- PR #3184: STYLE: Sort import statements using ruff

- PR #3181: [PEP8] fix pep8 and docstring style in dti.py file

- PR #3177: Loading Peaks faster with complete range and synchronization functionality.

- PR #3180: BF: Fix bug in mode for isotropic tensors

- PR #3172: [ENH] Enable range for dipy_median_otsu workflow

- PR #3171: Clean up for tabs and tab manager

- PR #3168: Feature/peaks tab revamp

- PR #3128: NF: Fibonacci Hemisphere

- PR #3153: ENH: add save peaks to dipy_fit_dti, dki

- PR #3156: ENH: Implement NDC from Yeh2019

- PR #3161: DOC: Fix tri parameter docstring in viz.projections.sph_project

- PR #3163: STYLE: Make fury and matplotlib presence message in test consistent

- PR #3162: ENH: Fix variable potentially being referenced before assignment

- PR #3144: ROI tab revamped

- PR #2982: [FIX] Force the use of pre-wheels

- PR #3134: Feature/cluster revamp

- PR #3146: [NF] Add 30 Bundle brain atlas fetcher

- PR #3150: BUG: Fix bug with nightly wheel build

- PR #3149: ENH: Miscellaneous cleanup

- PR #3148: ENH: Fix HDF5 key warning when saving BUAN profile data

- PR #3138: [CI] update CI’s script

- PR #3126: Bugfix for ROI images updates

- PR #3141: ENH: Fix miscellaneous warnings

- PR #3139: BF: Removing Error/Warning from Tensorflow 2.16

- PR #3132: BF: Removed allow_break

- PR #3135: DOC: Fix documentation URLs

- PR #3133: grg-sphinx-theme added as dependency

- PR #3127: Feature/viz interface tutorials

- PR #3120: DOC - Removed unnecessary line from tracking example

- PR #3110: Viz cli tutorial updated

- PR #3086: [RF] Fix spherical harmonic terminology swap

- PR #3095: [UPCOMING] Release preparation for 1.9.0

Issues (258):

- #3420: CI: define output path for coverage

- #3415: tests: leave no trace behind

- #3417: MAINT: Address changes to API with new (1.6) version of cvxpy.

- #3414: Bump codecov/codecov-action from 4 to 5 in the actions group

- #2469: Error in patch2self for single-slice data

- #3412: BF: Fixing single-slice data error in Patch2Self

- #1531: Test suite fails with errors regarding the ConvexHull of scipy.spatial.qhull objects

- #3409: [RF] Cleanup deprecated functions and remove some old legacy scripts

- #3410: radial_scale parameter of actor.odf_slicer has some issues

- #3407: CI: unpin cvxpy

- #3030: I do not see a way to change step as used by reconst.dti.TensorModel.fit()

- #3408: RF: fix step argument in DTI NLLS model

- #3361: Exporting and importing SymmetricDiffeomorphicRegistration outputs

- #3402: DOC: Add Exporting and importing Mapping field information in recipes and registration tutorial

- #3170: Iteratively reweighted least squares for robust fitting

- #3358: robust algorithm REBASE

- #3403: Robust split idea rebase tidy

- #3115: Fix get_info for release package

- #3404: RF: Improve and Simplify version management

- #3401: Robust split idea rebase arokem

- #3395: RF: Refactor nn module and deprecate tensorflow module

- #1957: niftis2pam, pam2niftis Workflow

- #3396: DOC: Adopt sphinxcontrib-bibtex for reconst model list refs

- #3399: STYLE: Remove empty quoted paragraph in developer guide index

- #3398: DOC: Improve first interaction GitHub Actions config file

- #2826: [ENH] Compute fiber density and fiber spread from ODF using Bingham distributions

- #3169: [RF] Add peaks generation to reconst workflows

- #3303: NF: Patch2Self3

- #3392: [WIP] NF: Adding pytorch versions

- #3368: [NF] DAM implementation for tissue classification using DMRI signal properties.

- #3389: Single tensor tutorial - hard to find

- #3390: DOC: Update DTI tutorial title

- #3391: STYLE: removing pep8speaks conf file in favor of pre-commit action

- #3393: RF: fix API generation

- #3387: DOC: Add first interaction GHA workflow file

- #3386: DOC: Update the CI tool to GHA in CONTRIBUTING file

- #3384: BF: Updated non_local_means

- #3285: Awkward interaction of dipy.denoise.non_local_means.non_local_means and dipy.denoise.noise_estimate.estimate_sigma

- #3140: NF: Adding correct_mask to median_otsu

- #3345: DOC: Skip element in documentation generation

- #3372: BugFix: New Atlas OMM not working with Horizon

- #2757: Use for loop when num_processes=1 in gibbs_removal()

- #3381: RF: Add support for sequential processing in Gibbs unringing

- #3380: ensure all calls to a python executable are to python3

- #3376: DOC: Use placeholder for unused variable in streamline_tools

- #3373: DOC: Consider warnings as errors in documentation CI build

- #3379: DOC: Remove example files labels

- #3374: DOC: Remove tracking_introduction_eudx from quick start

- #3347: Reconstruction model list not linked in documentation since it cannot be located

- #3378: doc: Link reconstruction model list to multiple pages

- #2665: DOC: Improve the CLI documentation rendering

- #3377: DOC: Miscellaneous improvements to PeakActor docstring

- #3375: DOC: Reference footnote in streamline_tools

- #3326: Avoid Sphinx warnings from inherited third-party method documentation

- #3348: DOC: Address remaining some warnings

- #3349: DOC: Fix footbibliography-related errors in workflow help doc

- #3370: dipy_buan_profiles CLI IndexError

- #3369: ci: Bump scientific-python/upload-nightly-action from 0.6.0 to 0.6.1

- #3367: Bump scientific-python/upload-nightly-action from 0.5.0 to 0.6.0 in the actions group

- #3366: DOC: Make rng optional parameter docstrings consistent

- #3248: [NF] Multicompartment DWI simulation technique implementation

- #3365: DOC: Fix some cites.

- #3363: Avoid SyntaxWarnings due to embedded LaTeX

- #2886: test_streamwarp.py: Little-endian buffer not supported on big-endian compiler

- #3356: BF: fix s390x compatibility

- #3360: DOC: Remove unnecessary leading whitespace in rst doc paragraph

- #3357: FIX: remove keyword only warning on examples (part2)

- #3343: BF Fixing transformation function

- #3355: FIX: missing keyword only arguments on example

- #2143: Build template CLI

- #3221: Updating BundleWarp default value of alpha

- #3286: BF: Allow passing kwargs in fit method, by moving parallelization kwargs elsewhere

- #3323: BF: Allow passing kwargs in fit method, by moving parallelization kwargs elsewhere, including PEP 3102

- #3351: DOC: Fix miscellaneous documentation build warnings (part 3)

- #3306: NF: Update to examples

- #3292: Python 3.13: TypeError: cannot remove variables from FrameLocalsProxy in tests

- #3293: BF: Fix attempting to delete frame local symbol table variable

- #3257: NF: Applying Decorators in Module (Reconst)

- #3254: NF: Applying Decorators in Module (Direction)

- #3317: DOC: Miscellaneous documentation improvements

- #3350: DOC: Do not use the scale option for URL-based images

- #3344: DOC: Fix miscellaneous documentation build warnings (part 2)

- #3346: RF: Removal of keyword form Cython files

- #2394: Documentation References - Remove (1, 2, …)

- #3341: DOC: Host MNI template note references in references file

- #3333: RF: Decorator fix

- #3335: RF: Allow parallel processing for sphinx extension

- #3342: RF: Doctest warnings

- #3337: DOC: Fix miscellaneous documentation build warnings

- #3338: DOC: Cite examples references using sphinxcontrib-bibtex

- #3319: DOC: Use references bibliography file for DIPY citation file

- #3321: BF: Set the superclass fit_method param value to the one provided

- #3339: BUG: Bug with params

- #3324: RF: Refactored for keyword arguments

- #3340: CI: pin cvxpy to 1.4.4 until 1.5.x issues are solved

- #3316: DOC: Cite code base references using sphinxcontrib-bibtex

- #3332: BF: Set the Diso parameter value to the one provided

- #3325: DOC: Fix warnings related to displayed math expressions

- #3331: DOC: Miscellaneous documentation improvements (part 3)

- #3329: STYLE: Use a leading underscore to name private methods

- #3330: DOC: Do not use unfinished double backticks

- #3320: DOC: Miscellaneous documentation improvements (part 2)

- #3318: RF: Remove unused parameters from method signature

- #3310: DOC: Cite nn references through sphinxcontrib-bibtex

- #3315: RF: remove legacy numpydoc

- #1026: Multprocessing the multivoxel fit

- #2810: [DOC] introducing sphinxcontrib-Bibtex to improve reference management

- #3312: DOC: Use misc for other types of BibTeX entries

- #3309: DOC: Miscellaneous doc formatting fixes (part 4)

- #3308: DOC: Rework the BibTeX bibliography file

- #3223: Remove`sagital` from de codespell ignore list .

- #3275: FIX: remove sagital from codespellrc ignore list .

- #3298: Inaccurate docstring in omp.pyx::determine_num_threads

- #3304: DOC: Miscellaneous doc formatting fixes (part 3)

- #3305: How to apply NODDI sequence in dipy

- #3295: ENH: Add a GHA workflow file to build docs

- #3056: [WIP][RF] Use lazy loading

- #3302: DOC: Miscellaneous doc formatting fixes (part 2)

- #3301: FIX: explicit keyword argument for Horizon

- #3231: Coverage build failing on and off in to a numpy-related statement

- #3297: DOC: Miscellaneous doc formatting fixes

- #3300: BF: Title Fix

- #3299: Numpy compatibility issue

- #3291: FIX: nightly wheels for macOS arm64

- #3262: NF: Applying Decorators in Module (Visualization)

- #3263: NF: Applying Decorators in Module (Workflow)

- #3283: BUG: Gradient table requires at least 2 orientations

- #3287: NF: Add __len__ to GradientTable

- #3282: Define `__len__` within `GradientTable`?

- #3260: NF: Applying Decorators in Module (Tracking)

- #3256: NF: Applying Decorators in Module (NeuralNetwork)

- #3258: NF: Applying Decorators in Module (Segment)

- #3249: NF: Applying Decorators in Module (Align)

- #3251: NF: Applying Decorators in Module (Core)

- #3279: FIX: Explicit type origin for long to solve the cython error during compilation

- #3242: Broken source installation

- #3259: NF: Applying Decorators in Module (Sims)

- #3252: NF: Applying Decorators in Module (Denoise)

- #3280: numpy.core.multiarray failed when importing dipy.io.streamline (dipy.tracking.streamlinespeed)

- #3261: NF: Applying Decorators in Module (Utils)

- #3255: NF: Applying Decorators in Module (Io)

- #3253: NF: Applying Decorators in Module (Data)

- #3233: STYLE: Set stacklevel argument explicitly to warning messages

- #3277: can’t find dipy_buan_profiles!!!

- #3029: Migrating to Keyword Only arguments (PEP 3102)

- #3239: NF: Decorator for keyword-only argument

- #2593: Embed parallelization into the multi_voxel_fit decorator.

- #3274: RF: Update pyproject.toml for numpy 2.0

- #3265: NumPy 2.0 incompatibility

- #3266: NF: Call cnp.import_array() explicitly to use the NumPy C API

- #3273: STYLE: Make statement dwell on a single line

- #3236: Allow interp_rbf to accept tensor-valued spherical functions

- #3237: Add support for tensor-valued spherical functions in interp_rbf

- #3245: RF: Switch from using sparse *_matrix to *_array.

- #3267: STYLE: Avoid deprecated NumPy types and methods for NumPy 2.0 compat

- #3264: TEST: avoid direct comparison of floating point numbers

- #3268: STYLE: Prefer using np.asarray to avoid copy while creating an array

- #3271: RF: Do not use np.any for checking optional array parameters

- #3243: Create DiffeomorphicMap object with saved nifti forward warp data

- #3250: DOC: Fix param order

- #3269: STYLE: Prefer using isin over in1d

- #3238: NF - add affine to peaks_from_position

- #3247: STYLE: Add imported symbols to __all__ in direction module

- #3246: STYLE: Import explicitly direction.peaks symbols

- #3241: RF: Codespell fix for CI

- #3228: STYLE: Fix unused loop control variable warning

- #3235: STYLE: Do not allow running unintended modules as scripts

- #3230: STYLE: Fix function definition loop variable binding warning

- #3232: STYLE: Simplify implicitly concatenated strings

- #3229: STYLE: Prefer using f-strings

- #3224: BF: Rewrite list creation as list() instead of []

- #3216: STYLE: Format code using ruff

- #3175: Tract profiles in afq example look all wrong

- #3178: DOC: Fixes the AFQ tract profile tutorial.

- #3218: STYLE: Fix codespell issues

- #3209: [CI] Move filterwarnings from pyproject to conftest

- #3220: [RF] from os.fork to spawn for multiprocessing

- #3214: RF - remove buffer argument in pmf_gen.get_pmf_value(.)

- #3196: Enhancing Gradient Approximation in DTI Tests #3155

- #3203: [WIP][CI] warning as error at compilation level

- #3219: [ENH] Prefer CLARABEL over ECOS as the CVXPY solver

- #3165: 1.9.0 system test failures

- #3215: tests: correct module-level setup

- #3217: ENH: Prefer CLARABEL over ECOS as the CVXPY solver

- #3211: [RF] PMF Gen: from memoryview to pointer

- #3210: Python 3.13: Fix tests for next Python release

- #3212: STYLE: Relocate pre-commit and ruff packages to style requirements

- #3205: BF: Declare variables holding integers as cnp.npy_intp over double

- #3174: NF - initial directions from seed positions

- #3207: DOC: Fix Cython method parameter type description

- #3206: BF: Use cnp.npy_intp instead of int as counter

- #3204: DOC: Fix documentation typos

- #3208: BF: Cast operation explicitly to cnp.npy_intp in denoising Cython

- #3202: [TEST] Add flag to turn warnings into errors for pytest

- #3201: TEST: Turn warnings into errors when calling pytest in CI testing

- #3158: ENH: Remove filtering UserWarning warnings in test config file

- #3200: Check relevant warnings raised (DO NOT MERGE)

- #2299: NF: Add array parsing capabilities to the CLIs

- #2880: improve test_io_fetch_fetcher_datanames

- #3194: MAINT: fix warning

- #3199: Bump pre-commit/action from 3.0.0 to 3.0.1 in the actions group

- #3182: [NF] Add DiSCo challenge data fetcher

- #3197: ENH: Fix miscellaneous warnings in dki reconstruction module

- #3198: ENH: Ensure that arccos argument is in the [-1,1] range

- #3186: Update trilinear_interpolate4d to accept float and double

- #3191: [RF] allow float and double for trilinear_interpolate4d_c

- #3151: DKI Updates: (new radial tensor kurtosis metric, updated documentation and missing tests)

- #3185: Improve consistency of affine_registration docstring

- #3189: Update affine_registration to clarify returns and make them consistent with docstring

- #3187: Setting Legacy=True SH basis is not possible for SH models

- #3176: ENH: allow vol_idx in align workflow

- #3188: ENH: Add pre-commit to project dev dependencies

- #3183: ENH: Specify the solver for the MAP-MRI positivity constraint test

- #3184: STYLE: Sort import statements using ruff

- #3181: [PEP8] fix pep8 and docstring style in dti.py file

- #3177: Loading Peaks faster with complete range and synchronization functionality.

- #3145: dki_fit errors from divide by zero

- #3180: BF: Fix bug in mode for isotropic tensors

- #3172: [ENH] Enable range for dipy_median_otsu workflow

- #3171: Clean up for tabs and tab manager

- #2796: Tract profiles in the afq_profile example look terrible

- #1985: Something is wonky with the AFQ tracts profile example

- #3168: Feature/peaks tab revamp

- #2036: [WIP] NF - Add Closest Peak direction getter from peaks array

- #3128: NF: Fibonacci Hemisphere

- #3122: Add peaks_from_model to dipy_fit_dti CLI

- #3153: ENH: add save peaks to dipy_fit_dti, dki

- #3113: [FIX] Nlmeans Algorithm Enhancement #2950

- #3111: Add support for sequential processing in Gibbs unringing #2757

- #3154: ENH: Add neighboring DWI correlation QC metric

- #3156: ENH: Implement NDC from Yeh2019

- #3161: DOC: Fix tri parameter docstring in viz.projections.sph_project

- #3163: STYLE: Make fury and matplotlib presence message in test consistent

- #3162: ENH: Fix variable potentially being referenced before assignment

- #3144: ROI tab revamped

- #2982: [FIX] Force the use of pre-wheels

- #3134: Feature/cluster revamp

- #3146: [NF] Add 30 Bundle brain atlas fetcher

- #3150: BUG: Fix bug with nightly wheel build

- #3149: ENH: Miscellaneous cleanup

- #3148: ENH: Fix HDF5 key warning when saving BUAN profile data

- #3138: [CI] update CI’s script

- #3142: Horizon slider does not show proper 0-1 range images such as FA

- #3126: Bugfix for ROI images updates

- #3141: ENH: Fix miscellaneous warnings

- #3139: BF: Removing Error/Warning from Tensorflow 2.16

- #3096: TissueClassifierHMRF has some argument logic error

- #3132: BF: Removed allow_break

- #3136: conversion of cudipy.align.imwarp.DiffeomorphicMap to dipy.align.imwarp.DiffeomorphicMap

- #3135: DOC: Fix documentation URLs

- #3133: grg-sphinx-theme added as dependency

- #3127: Feature/viz interface tutorials

- #3120: DOC - Removed unnecessary line from tracking example

- #3116: diffusion gradient nonlinearity correction

- #3110: Viz cli tutorial updated

- #2970: spherical harmonic degree/order terminology swapped

- #3086: [RF] Fix spherical harmonic terminology swap

- #3095: [UPCOMING] Release preparation for 1.9.0