Scilpy

What's Changed
* [ENH] Upload frozen python requirements aside of release assets by AlexVCaron in https://github.com/scilus/scilpy/pull/695
* (WIP) Adding script to apply transform to bvecs by karanphil in https://github.com/scilus/scilpy/pull/696
* Fix warnings in distortion correction by arnaudbore in https://github.com/scilus/scilpy/pull/700


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.5.0-rc2...1.5.0-rc3

OMG A Big congratulation to karanphil for his 2y+ PR
That's a guinness scilpy record :+1:

We will keep rc-2 for a week or so and if everything adds up we'll release 1.5.0 !!!

What's Changed
* Fixing warning always showing up. by EmmaRenauld in https://github.com/scilus/scilpy/pull/693
* Fix default sphere tracking by arnaudbore in https://github.com/scilus/scilpy/pull/692
* Update to hotdipy + fix load empty sft by arnaudbore in https://github.com/scilus/scilpy/pull/694
* [WIP] Adding b-tensor encoding scripts like compute_fodf/frf and metrics by karanphil in https://github.com/scilus/scilpy/pull/425


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.5.0-rc1...1.5.0-rc2

:partying_face: :tada: :tada: :partying_face:
First of all congratulations to all of you and especially gagnonanthony who made his first contribution.
This is a big step for scilpy and the scilus since we moved from python 3.7 to 3.10.

Mostly new features and a couple of bug fixes.

What's Changed
* Testing 3 10 upgrade by frheault in https://github.com/scilus/scilpy/pull/662
* Fixing unique in dev branch by frheault in https://github.com/scilus/scilpy/pull/668
* Python3 10 readme by frheault in https://github.com/scilus/scilpy/pull/666
* [ENH] scilpy and python3.10 by arnaudbore in https://github.com/scilus/scilpy/pull/678
* Parallelise remove_loops_and_sharp_turns by arnaudbore in https://github.com/scilus/scilpy/pull/677
* Change version number by frheault in https://github.com/scilus/scilpy/pull/681
* Project streamlines from/to wm/gm by frheault in https://github.com/scilus/scilpy/pull/640
* Coloring connectomics by frheault in https://github.com/scilus/scilpy/pull/636
* Added OLO to reorder_connectivity by frheault in https://github.com/scilus/scilpy/pull/630
* New script: Plot dipy sphere by EmmaRenauld in https://github.com/scilus/scilpy/pull/679
* Fix multiprocess in dev tracking by EmmaRenauld in https://github.com/scilus/scilpy/pull/676
* Add python3.10-venv to packages to install by CHrlS98 in https://github.com/scilus/scilpy/pull/682
* skip __init__ in search_keyword. by frheault in https://github.com/scilus/scilpy/pull/683
* Fixing uniform_coloring in scil_visualize_bunldes.py by karanphil in https://github.com/scilus/scilpy/pull/672
* Reactivate md5sum in fetcher by frheault in https://github.com/scilus/scilpy/pull/684
* uint8 in compute_density when possible by frheault in https://github.com/scilus/scilpy/pull/685
* Fix validate bids by arnaudbore in https://github.com/scilus/scilpy/pull/674
* Switch to kdtree for uniformize --target by frheault in https://github.com/scilus/scilpy/pull/686
* Adding variance to scil_visualize_fodf by karanphil in https://github.com/scilus/scilpy/pull/671
* Add check_bbox argument management by EmmaRenauld in https://github.com/scilus/scilpy/pull/641
* Adding PCA script for dimension reduction of metrics by gagnonanthony in https://github.com/scilus/scilpy/pull/673
* Module tractogram operations by EmmaRenauld in https://github.com/scilus/scilpy/pull/658
* fix seed mask empty by arnaudbore in https://github.com/scilus/scilpy/pull/687
* Adding small_dims option to scil_compute_fodf_max_in_ventricles by karanphil in https://github.com/scilus/scilpy/pull/688
* Adding explanations to scil_compute_fodf_max_in_ventricles by karanphil in https://github.com/scilus/scilpy/pull/689
* Fix some deprecated import and fix some tests by arnaudbore in https://github.com/scilus/scilpy/pull/690

New Contributors
* gagnonanthony made their first contribution in https://github.com/scilus/scilpy/pull/673

**Full Changelog**: https://github.com/scilus/scilpy/compare/1.4.2...1.5.0-rc1

scilpy 1.4.1 was supposed to be the last release working on python3.7 but we now have another last version before python 3.10 :+1:

What's Changed
* Fix the unique len issue by frheault in https://github.com/scilus/scilpy/pull/665
* [BF] bids_validate by arnaudbore in https://github.com/scilus/scilpy/pull/669


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.4.1...1.4.2

A minor release for a major issue fixed when using scil_validate_bids with phase and mag data.

Thank you EmmaRenauld frheault AlexVCaron :tada:

What's Changed
* Creating module 'labels' by EmmaRenauld in https://github.com/scilus/scilpy/pull/648
* [ENH] POC : Use mocking to get faster execution of tests by AlexVCaron in https://github.com/scilus/scilpy/pull/639
* Unit tests for the new labels module by frheault in https://github.com/scilus/scilpy/pull/659
* --no_empty in scil_remove invalid streamlines.py by frheault in https://github.com/scilus/scilpy/pull/657
* [ENH][BF] scil_validate_bids by arnaudbore in https://github.com/scilus/scilpy/pull/661
* [BF] Bids validate by arnaudbore in https://github.com/scilus/scilpy/pull/663


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.4.0...1.4.1

Holy :cow: :cow: :cow: !

:rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket:
:rocket: Congrats everybody for this amazing work ! :rocket:
:rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket::rocket:

SCILUS team you rock !! :tada:

:fire: CHrlS98 :fire:
:fire: EmmaRenauld :fire:
:fire: AlexVCaron :fire:
:fire: karanphil :fire:
:fire: frheault :fire:
:fire: AntoineTheb :fire:

What's Changed
* Better docstring for scil_validate_and_correct_bvecs by CHrlS98 in https://github.com/scilus/scilpy/pull/570
* Improve DOC on scil_resample_tractogram.py by frheault in https://github.com/scilus/scilpy/pull/574
* Fix wrong condition for is_voxel_in_bound used in dev tracking by CHrlS98 in https://github.com/scilus/scilpy/pull/569
* Small fixes and improvements in tractogram filtering scripts by EmmaRenauld in https://github.com/scilus/scilpy/pull/567
* Adding new filtering script by orientation by EmmaRenauld in https://github.com/scilus/scilpy/pull/571
* Fix fix dsi studio by frheault in https://github.com/scilus/scilpy/pull/572
* Add mask option for bingham fit and metrics by CHrlS98 in https://github.com/scilus/scilpy/pull/573
* Fixing coordinate type + decreasing test size in dev tracking by EmmaRenauld in https://github.com/scilus/scilpy/pull/581
* Warn user for rk > 1 with prob tracking in dev tracking by CHrlS98 in https://github.com/scilus/scilpy/pull/580
* Clean pep8 in the fetcher file by EmmaRenauld in https://github.com/scilus/scilpy/pull/582
* Modifying scil_score tractogram by EmmaRenauld in https://github.com/scilus/scilpy/pull/568
* Simple GPU tracking by CHrlS98 in https://github.com/scilus/scilpy/pull/576
* Small changes in the dev tracker by EmmaRenauld in https://github.com/scilus/scilpy/pull/585
* Fixing transform_anatomy by karanphil in https://github.com/scilus/scilpy/pull/586
* Add split image script by karanphil in https://github.com/scilus/scilpy/pull/584
* Enhance GPU tracking by CHrlS98 in https://github.com/scilus/scilpy/pull/587
* Upgrading dipy by EmmaRenauld in https://github.com/scilus/scilpy/pull/578
* Fix case with no wpc in scil_score_tractogram by EmmaRenauld in https://github.com/scilus/scilpy/pull/595
* Modify scil_cut_streamlines.py by karanphil in https://github.com/scilus/scilpy/pull/588
* [BF] Fix arg in invalid streamlines + warning in todi by arnaudbore in https://github.com/scilus/scilpy/pull/589
* [BF] Fix bug in scil_concatenate_dwi.py when supplying more than 2 images by CHrlS98 in https://github.com/scilus/scilpy/pull/603
* Fix lazy usage with tck files by EmmaRenauld in https://github.com/scilus/scilpy/pull/598
* Fix F1 score by EmmaRenauld in https://github.com/scilus/scilpy/pull/600
* ENH: Add overlapping volume mosaic screenshot script by jhlegarreta in https://github.com/scilus/scilpy/pull/577
* ENH: Adding QBx option in subsampling + cleaning by EmmaRenauld in https://github.com/scilus/scilpy/pull/590
* Clarify vox space by EmmaRenauld in https://github.com/scilus/scilpy/pull/593
* Update prepare eddy by arnaudbore in https://github.com/scilus/scilpy/pull/609
* update jenkins and requirements by arnaudbore in https://github.com/scilus/scilpy/pull/611
* ENH: scil scoring unique streamlines by AntoineTheb in https://github.com/scilus/scilpy/pull/614
* Added a 'must_pass_mask' by EmmaRenauld in https://github.com/scilus/scilpy/pull/599
* [BF] Update bundle metrics - handle NaN by arnaudbore in https://github.com/scilus/scilpy/pull/619
* New assign color options by frheault in https://github.com/scilus/scilpy/pull/566
* Add a function to verify compatibility by arnaudbore in https://github.com/scilus/scilpy/pull/616
* Moving methods by EmmaRenauld in https://github.com/scilus/scilpy/pull/621
* New method to get n seeds at once. by EmmaRenauld in https://github.com/scilus/scilpy/pull/597
* Add arguments for RGB color ODF and RGB background color by karanphil in https://github.com/scilus/scilpy/pull/612
* Change default interpolation for mask by CHrlS98 in https://github.com/scilus/scilpy/pull/625
* Fix jenkins by arnaudbore in https://github.com/scilus/scilpy/pull/635
* [WIP] Correlate dwi QC by frheault in https://github.com/scilus/scilpy/pull/528
* WIP: New labels maps and simplification of tractometry profile scripts by frheault in https://github.com/scilus/scilpy/pull/554
* [ENH] Add multiple ID to filter tractogram with atlas by arnaudbore in https://github.com/scilus/scilpy/pull/627
* `scil_assign_custom_color_to_tractogram.py` optional colorbar image output by CHrlS98 in https://github.com/scilus/scilpy/pull/629
* Trilinear interpolation + sf threshold for GPU tracking by CHrlS98 in https://github.com/scilus/scilpy/pull/613
* ENH: unit test PoC by AntoineTheb in https://github.com/scilus/scilpy/pull/631
* Creating new script to score tractogram that is already segmented. by EmmaRenauld in https://github.com/scilus/scilpy/pull/622
* Bug fix for scil_swap_gradient_axis by CHrlS98 in https://github.com/scilus/scilpy/pull/634
* [ENH] Validate bids by arnaudbore in https://github.com/scilus/scilpy/pull/591
* Fix rare division by 0 in f1 by EmmaRenauld in https://github.com/scilus/scilpy/pull/642
* Gradient sampling ajustment by karanphil in https://github.com/scilus/scilpy/pull/626
* [ENH] Extract gradient scheme from eddy output - for tractoflow by arnaudbore in https://github.com/scilus/scilpy/pull/623
* Tensor format by EmmaRenauld in https://github.com/scilus/scilpy/pull/637
* [BF] validate BIDS by arnaudbore in https://github.com/scilus/scilpy/pull/645
* Fix: names for overreach by EmmaRenauld in https://github.com/scilus/scilpy/pull/643
* Add check_bbox_false (only in scil_score_bundles) by EmmaRenauld in https://github.com/scilus/scilpy/pull/646
* Fix logging across scilpy by frheault in https://github.com/scilus/scilpy/pull/647
* Fix logging for RBx (file handling) by frheault in https://github.com/scilus/scilpy/pull/649
* Fix total count by EmmaRenauld in https://github.com/scilus/scilpy/pull/650
* [BF] BG color as optional function argument by CHrlS98 in https://github.com/scilus/scilpy/pull/651
* Fix fetcher by EmmaRenauld in https://github.com/scilus/scilpy/pull/655
* BF validate_bids when full reverse by arnaudbore in https://github.com/scilus/scilpy/pull/654


**Full Changelog**: https://github.com/scilus/scilpy/compare/1.3.0...1.4.0