dipy/dipy: 1.12.0

What's Changed BF: Fixing minor issue in dipy_classify_tissue dam option by @pjsjongsung in https://github.com/dipy/dipy/pull/3495 DOC: Miscellaneous doc improvements by @jhlegarreta in https://github.com/dipy/dipy/pull/3514 STYLE: Call warning instead of the deprecated warn function by @jhlegarreta in https://github.com/dipy/dipy/pull/3512 [RF]: Saving the figure in the example. by @Atharva-Shah-2298 in https://github.com/dipy/dipy/pull/3510 FIX: Avoid division by zero on single-CPU systems (issue #3521) by @sanvila in https://github.com/dipy/dipy/pull/3522 Bump scientific-python/upload-nightly-action from 0.6.1 to 0.6.2 in the actions group by @dependabot[bot] in https://github.com/dipy/dipy/pull/3526 STYLE: Add additional emojis to first interaction message by @jhlegarreta in https://github.com/dipy/dipy/pull/3530 BF: Search bar should come bigger in the center. by @maharshi-gor in https://github.com/dipy/dipy/pull/3527 CI: Ignore specific cvxpy warnings to avoid CI failure. by @skoudoro in https://github.com/dipy/dipy/pull/3531 CI: introduce cached Data. by @skoudoro in https://github.com/dipy/dipy/pull/3533 DOC: Changed documentation errors in dipy.sims.voxel by @Atharva-Shah-2298 in https://github.com/dipy/dipy/pull/3528 CI: Ignore fork() warnings. by @maharshi-gor in https://github.com/dipy/dipy/pull/3535 Fix Bugs in #3453: Ensure Correct Weight Reshaping & Consistent Extra Output in iter_fit_tensor by @tito21 in https://github.com/dipy/dipy/pull/3455 ENH: Horizon peaks fname support by @maharshi-gor in https://github.com/dipy/dipy/pull/3519 RF: Fixed the latex by @deka27 in https://github.com/dipy/dipy/pull/3538 RF - changed min/max len from nbr pts to mm by @gabknight in https://github.com/dipy/dipy/pull/3488 NF: allow broadcasting in dipy_math by @skoudoro in https://github.com/dipy/dipy/pull/3493 ENH: Opacity slider turned off on hide by @maharshi-gor in https://github.com/dipy/dipy/pull/3520 BF: Improves Cython enum management. by @skoudoro in https://github.com/dipy/dipy/pull/3549 RF: fix typo in hcp fetcher function argument name by @skoudoro in https://github.com/dipy/dipy/pull/3548 BF: Make StoppingCriterion reproducible for multi-thread execution by @jhlegarreta in https://github.com/dipy/dipy/pull/3546 Doc: Fix typo in multiple tutorial by @skoudoro in https://github.com/dipy/dipy/pull/3554 ENH: improve dipy_info message when no reference for some streamline files. by @skoudoro in https://github.com/dipy/dipy/pull/3555 [RF]: Patch2self in denoising CLI tutorial by @iprajwalreddy in https://github.com/dipy/dipy/pull/3559 DOC: fix streamline-tools tutorial by avoiding the use of identity affine by @skoudoro in https://github.com/dipy/dipy/pull/3557 STYLE: Make affine variable naming consistent by @jhlegarreta in https://github.com/dipy/dipy/pull/3561 DOC: Add missing opening backtick to reference syntax. by @jhlegarreta in https://github.com/dipy/dipy/pull/3562 RF: Improve dipy_info printed output by @jhlegarreta in https://github.com/dipy/dipy/pull/3515 TEST: uncomment and update test_cross by @skoudoro in https://github.com/dipy/dipy/pull/3580 RF: Deprecate autocrop in median_otsu by @skoudoro in https://github.com/dipy/dipy/pull/3541 RF: use multi_voxel_fit for rumba by @skoudoro in https://github.com/dipy/dipy/pull/3565 RF: Address some Zero division warnings by @skoudoro in https://github.com/dipy/dipy/pull/3563 RF: allow the saving of S0 estimate for dti workflow by @skoudoro in https://github.com/dipy/dipy/pull/3556 SciPy deprecation of "disp" in optimizer by @drammock in https://github.com/dipy/dipy/pull/3581 DOC: Change unused commit prefixes to some other more useful ones by @jhlegarreta in https://github.com/dipy/dipy/pull/3583 MNT: Add GitHub issue templates by @jhlegarreta in https://github.com/dipy/dipy/pull/3584 MNT: Change issue template file extensions by @jhlegarreta in https://github.com/dipy/dipy/pull/3586 NF: Add PR labeler workflow by @jhlegarreta in https://github.com/dipy/dipy/pull/3582 STYLE: Apply ruff manually to all files by @jhlegarreta in https://github.com/dipy/dipy/pull/3591 STYLE: Miscellaneous style fixes by @jhlegarreta in https://github.com/dipy/dipy/pull/3594 DOC: Remove default arguments from docstrings by @jhlegarreta in https://github.com/dipy/dipy/pull/3595 StatefulSurface - Class to handle surfaces by @frheault in https://github.com/dipy/dipy/pull/3429 STYLE: Adopt a unified logger across the code base by @jhlegarreta in https://github.com/dipy/dipy/pull/3592 BF: Miscellaneous fixes to surfaces by @jhlegarreta in https://github.com/dipy/dipy/pull/3598 STYLE: Miscellaneous style fixes by @jhlegarreta in https://github.com/dipy/dipy/pull/3597 MNT: Fix miscellaneous labeler regexes by @jhlegarreta in https://github.com/dipy/dipy/pull/3600 TEST: Restore removed test case in io workflows by @jhlegarreta in https://github.com/dipy/dipy/pull/3599 STYLE: Adopt pathlib for path manipulation by @jhlegarreta in https://github.com/dipy/dipy/pull/3593 DOC: Record API changes after pathlib adoption by @jhlegarreta in https://github.com/dipy/dipy/pull/3601 DOC: Fix workflows test utils parameter name in docstring by @jhlegarreta in https://github.com/dipy/dipy/pull/3603 RF: from TRK to TRX as default file format for tracks by @skoudoro in https://github.com/dipy/dipy/pull/3587 RF: replace old LocalTracking by our new tracking interface by @skoudoro in https://github.com/dipy/dipy/pull/3604 ENH: Adopt pathlib for workflows by @jhlegarreta in https://github.com/dipy/dipy/pull/3602 Doc: explicit finalize_mask information in CLI tutorial by @skoudoro in https://github.com/dipy/dipy/pull/3560 Bump actions/first-interaction from 1 to 2 in the actions group by @dependabot[bot] in https://github.com/dipy/dipy/pull/3609 RF: Address cvxpy 1.7.0 warnings. by @skoudoro in https://github.com/dipy/dipy/pull/3606 NF: added streamline clipping function to utils by @kesshijordan in https://github.com/dipy/dipy/pull/1617 BF: fix lower triangular bug introduced in #3563 by @skoudoro in https://github.com/dipy/dipy/pull/3612 BF: Allow length to work with float16 streamlines by @skoudoro in https://github.com/dipy/dipy/pull/3613 RF: Parallel quantize_evecs by @skoudoro in https://github.com/dipy/dipy/pull/3605 Bump the actions group with 3 updates by @dependabot[bot] in https://github.com/dipy/dipy/pull/3624 NF: Automate requirement files by @skoudoro in https://github.com/dipy/dipy/pull/3424 docs: remove NeuroFedora by @sanjayankur31 in https://github.com/dipy/dipy/pull/3625 Bump actions/setup-python from 5 to 6 in the actions group by @dependabot[bot] in https://github.com/dipy/dipy/pull/3629 RF: Fixed weird volumes instead of denoised volumes in Patch2Self 3 by @iprajwalreddy in https://github.com/dipy/dipy/pull/3631 NF: add FWDTI Workflow by @skoudoro in https://github.com/dipy/dipy/pull/3425 BF: expand requirements during its generation by @skoudoro in https://github.com/dipy/dipy/pull/3634 NF: add dipy_fit_powermap workflows with its associated tests by @skoudoro in https://github.com/dipy/dipy/pull/3610 fix: BUG: fix UnboundLocalError in _single_sf_to_bingham when no valid peaks found by @Mengyao-Li in https://github.com/dipy/dipy/pull/3639 [BF] Fix fwdti by @skoudoro in https://github.com/dipy/dipy/pull/3646 BF: Fix CVXPY warning by @deka27 in https://github.com/dipy/dipy/pull/3635 Bump the actions group with 2 updates by @dependabot[bot] in https://github.com/dipy/dipy/pull/3649 BF: update first interaction Github action parameters by @skoudoro in https://github.com/dipy/dipy/pull/3650 RF: handle bingham tests warnings by @skoudoro in https://github.com/dipy/dipy/pull/3651 RF: fix warnings introduced by the future Numpy version 2.4 by @skoudoro in https://github.com/dipy/dipy/pull/3654 Revert split extension (for SFT and SFS) by @frheault in https://github.com/dipy/dipy/pull/3648 Added interpolation parameter to dipy_apply_transform by @azizasaber in https://github.com/dipy/dipy/pull/3658 CI: remove fetch-data job by @skoudoro in https://github.com/dipy/dipy/pull/3655 BF: manage empty file in dipy_slr cli to avoid enigmatic crash by @skoudoro in https://github.com/dipy/dipy/pull/3618 NF: Reduce default iteration counts and make level_iters configurable in motion correction by @deka27 in https://github.com/dipy/dipy/pull/3652 BF: Discards streamlines by size by @deka27 in https://github.com/dipy/dipy/pull/3552 Bump actions/checkout from 5 to 6 in the actions group by @dependabot[bot] in https://github.com/dipy/dipy/pull/3662 CI: simplify cache, too many data was cached by @skoudoro in https://github.com/dipy/dipy/pull/3661 RF: refactoring of nlmeans to allow the selection our classic version and the blockwise version by @skoudoro in https://github.com/dipy/dipy/pull/3623 DOC: Programmatic DIPY Horizon usage (non-CLI) by @m-agour in https://github.com/dipy/dipy/pull/3660 NF: Intermediate map for symmetric diffeomorphic registration by @sreekarchigurupati in https://github.com/dipy/dipy/pull/3659 Document pre-commit setup for developers by @Copilot in https://github.com/dipy/dipy/pull/3657 DOC: Prefer BibTeX reference in GQSI example documentation by @jhlegarreta in https://github.com/dipy/dipy/pull/3669 Bump the actions group with 3 updates by @dependabot[bot] in https://github.com/dipy/dipy/pull/3672 MNT: Replace deprecated autocrop in brain_extraction_dwi.py, reconst_csa.py, reconst_csa_parallel.py, reconst_dti.py tutorial examples by @flying-spagetti in https://github.com/dipy/dipy/pull/3668 Test: Add regression test for median_otsu autocrop deprecation by @flying-spagetti in https://github.com/dipy/dipy/pull/3670 RF: Editing tranform_img in dipy.nn.utils by @pjsjongsung in https://github.com/dipy/dipy/pull/3542 Bump scientific-python/upload-nightly-action from 0.6.2 to 0.6.3 in the actions group by @dependabot[bot] in https://github.com/dipy/dipy/pull/3674 RF: Allow bvals file for