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