1.3.2 (May 31, 2024)

This release adds the ability to do tractography in parallel using ray.
It also adds Pydra integration into GroupAFQ (ParallelGroupAFQ).
We also added RUMBA-SD from DIPY and made other minor changes.

• Streamlines task in parallel using ray (#1136)
• Check bvals on dki (#1139)
• [FIX] different CST ROI 2 for L/R (#1138)
• Adds ParallelGroupAFQ (#1124)
• [DOC] Update kwargs.rst (#1135)
• [ENH] Added RUMBA-SD to data.py (#1129)
• [DOC] Update baby_afq.py (#1131)
• Add conversion dictionary for old acronyms (#1107)
• [ENH] small change to viz utils panel code (#1123)
• Make altair required (#1130)
• [DOC] Some improvements to the documentation based on conversations during the hackathon (#1126)
• [ENH] expose FA thresh param for autoresponse ssst for csd (#1127)

Adds the mean signal diffusion kurtosis model as an option.
Adds more information in JSON sidecars. Adds an explanation
of our current bundle orientation system to the documentation.

• [ENH] add mean signal diffusion kurtosis model (#1121)
• [ENH] make source field relative in json sidecars (#1118)
• [ENH] add more information from bundle dict into jsons (#1117)
• [DOC] add bundle orientation explanation (#1120)

1.3 (March 25, 2024)

All bundles are now ordered according to LPI and
are output as full names instead of abbreviations.
Only the lowest shell is now used in the calculation of
the CSD response function. Corrects typos in babyAFQ and
GPU tracking, pARC/VOF cleaning parameters updated,
along with other minor improvements.

• Adds an example to plot stages of tractometry. (#1073)
• [FIX] fix bundle colors (#1116)
• Fix gpu tracking (#1115)
• Move s3 BIDS to separate repo (#1109)
• [DOC] try to reproduce and fix nightly test (#1113)
• [FIX] Set parc/vof cleaning params to default (#1111)
• [DOC] make altair example (#1108)
• [ENH] allow random seeds in gpu tracking (#1105)
• [FIX] force upgraded joblib (#1104)
• [ENH/FIX] Smarter file finding (#1103)
• Upgrade python versions supported, and drop 3.8. (#1102)
• (#1101)
• [ENH] add anisotropic kurtosis, make dki default? (#1097)
• [ENH] Make the cleaning easier to interact with (#1100)
• [ENH] Order all bundles according to LPI (#1099)
• [FIX] update this nightly test (#1095)
• [ENH] Some segmentation speed-ups (#1094)
• Use only the lowest shell in calculation of the CSD response function. (#1089)
• [FIX] Fix GPU Tractography (#1091)
• [ENH] Begin removing confusing abbreviations (#1086)
• [ENH] simplify verbose tracking (#1087)
• [FIX] correct typo in baby bundle dict OR (#1088)
• [ENH] more little tweaks to the AFQ viz utils panelfigure class (#1084)
• (#1085)

Incorporates TRX, a new tractography file format, makes
a new way for organizing bundle dictionaries, extensive
documentation improvements, and many other minor fixes

• DOC: Small fixes to the visualization example. (#1083)
• [WIP/ENH] add AR from endpoint ROIs (#1078)
• Update grant funding (#1076)
• [FIX] Add exclusion ROI to IFOF (#1074)
• Update fury (#1080)
• [ENH] add some utilities for working with altair and pyafq (#1049)
• [FIX] possible fix to pediatric bundle dict; some convenience updates in babyafq example (#1071)
• (#1067)
• fixed bundle prob map order (#1070)
• ENH allow removal of profiles.csv; allow setting n_nodes in profile; make callosal bundles the default (#1052)
• DOC: Extensive documentation improvements (#1051)
• DOC: finish tractometry figure (#1055)
• [doc] make afq tractometry pipeline page, reorganize usage section (#1053)
• [FIX] bf for roi clipping (#1048)
• [ENH] add line width argument to fury (#1046)
• RF: Update call to seaborn plotting. (#1042)
• [ENH,FIX] Integrate more steps into the segmentation pipeline (#1041)
• [ENH] more specific bids entities and fixes to be bids compatible (#1035)
• Removes some of the sphinx gallery ignore patterns. (#1017)
• [enh] set afq home (#1037)
• [FIX] pin astroid (#1038)
• [ENH] Proposal for better bd management (#1014)
• [FIX] download LV1 roi in this example (#1031)
• [FIX] set default back to serial (#1030)
• Adds an option to build the docs without running the examples. (#1025)
• Fence the TRX test by checking whether TRX is installed. (#1020)
• Remove unused MPL import (#1029)
• Update installation_guide.rst (#1026)
• (#1022)
• add "GeneratedBy"s in dataset_description.json for BIDS 1.4 compliance (#1019)
• Incorporate TRX (#1006)

1.1 (September 08, 2023)

Add compatibility with GPU based tractography. Speeds
up the Mahalanobis cleaning step. Removes interface for
loading ITK files and using them as maps in pyAFQ, because
it did not work in all cases. Adds more examples and updates
docs to a new system. Other minor fixes.

• [FIX] delete folders in AFQ derivatives when clobbering (#1015)
• Update the pypi action so that it runs on latest ubuntu. (#1012)
• NF: Adds fetcher for cerebellar peduncle waypoint ROIs. (#968)
• [ENH] Bundle montage (#994)
• Slf123new (#997)
• (#1011)
• [FIX] fix a small bug in the curvature code (#985)
• added more documentation of dependencies (#1002)
• [Doc] add an example of single subject rois; reduce example time (#999)
• RF: Set dask as the default paralellization engine. (#1009)
• [ENH] add OR pediatric bundle definition, make it easier to add future pediatric bundles (#1007)
• DOC: Myst (#992)
• [ENH] Much faster mahal cleaning (#982)
• [FIX] Remove itk (#981)
• Update setup.cfg with newer pybids (#991)
• Update plot_viz.py (#993)
• Installation with quotes (#988)
• [ENH] update dipy (#986)
• [ENH] Adds export_up_to, adds some minor fixes here and there (#977)
• [ENH] allow the setting of number of voxels for a seed mask (#976)
• [ENH] Calculate new curvature metric manually (#973)
• [FIX] split GPU pyafq docker builds into differnet actions (#975)
• [ENH] add CUDA 12 compat to GPU tractography (#972)
• [ENH] allow GPU docker file to play nice with singularity (#971)
• [ENH/FIX] Improvements for finding the Visual Pathway (#953)
• Adds back reference documentation to reference section. (#964)
• Starting doc overhaul (#948)
• [ENH] add gpu tracking to pyAFQ (#962)

Fixed two bugs, where max streamline length was not being enforced and the
mean b0 was being calculated incorrectly. Small documenation fixes.

• [FIX] Add max length constraint, b0 fix (#955)
• Small documentation fixes, to improve auto-rendering of API docs. (#949)
• MAINT: Upgrade pytest as a start to tackling CI errors. (#945)
• MAINT: pep517 => build. (#947)

This is the first major release of pyAFQ. The API should be stable
from here until the next major release of pyAFQ.
Adds freewater DTI, fiber density maps, VOF and pAF bundles,
and montage and combine bundle visualizations, as well as other
minor additions, fixes, and documentation updates.

• [FIX] Missing underscore in custom tissue property filenames (#944)
• [FIX] finally finish this SLR PR (#937)
• Add fwDTI (#931)
• [FIX] Import tract docs (#936)
• TST: Fixes another failing nightly test by setting the seed. (#932)
• DOC: Fix the random seed for the OR example. (#930)
• TST: Fix a random seed for this test. (#929)
• [FIX] don't resample subject-space ROIs unless user provides something (#919)
• [ENH] Density task (#900)
• Increase inclusion tolerance for pAF; add suffix for cmd_outputs (#921)
• [DOC] add interactive bundle viz to OR example (#861)
• [ENH] Allow pediatric bundledict and template to be accessed from config file. (#923)
• [FIX] Some pediatric bundle dict fixes (#922)
• DOC: Adds an example of visualizations using FURY. (#910)
• [FIX] put afq_metadata.toml in the correct spot (#913)
• [FIX] Updating DIPY tracking params (#911)
• [ENH] VOF endpoints don't include pAF endpoints (#912)
• DOC: Document S3BIDS access examples. (#909)
• [FIX] correctly calculate min / max sl length, update step_size docs (#905)
• Added streamline filtering by primary orientation; other bundle definition fixes (#898)
• [FIX] cmd output only run on our files (#881)
• Set logger levels to INFO (#867)
• [DOC] add pyafq overview desciption (#875)
• Fix nightly tests (#873)
• Upgrade pybids. (#869)
• [ENH] Apply arbitrary command to some/all pyAFQ outputs, more BIDSy names (#853)
• [FIX] only calc subject registration images when necessary (#862)
• RF: Removes key-word argument that is not being used. (#868)
• ENH: add DKI kurtosis fit elements as scalars (#865)
• ENH: add lower triangular scalars from DTI (could be useful for ML)? (#863)
• FIX: Reorder endpoint (#858)
• [FIX] Some ITK map fixes for running with groupAFQ and in CLI (#855)
• [ENH] Add montage and combine bundle to GroupAFQ (#849)
• [DOC] add fatal error when no bundles found at all (#851)
• [ENH] add median bundle len function (#852)

This release fixes a critical bug introduced in version 0.11, which caused exclusion ROIs to be ignored.

• [FIX]: Reorder endpoint (#858)
• [FIX] Some ITK map fixes for running with groupAFQ and in CLI (#855)
• [ENH] Add montage and combine bundle to GroupAFQ (#849)
• [DOC] add fatal error when no bundles found at all (#851)
• [ENH] add median bundle len function (#852)

More informative warnings and errors, minor fixes.

• [FIX] warn user about number of invalid streamlines removed (#850)
• TST: Test the nibabel release candidate. (#842)
• MAINT: Refreshes the zenodo metadata file. (#845)
• [ENH] minor docs updates and qsiprep changes (#847)
• [FIX] Error when file not found should be more informative (#844)
• [ENH] Return path to single viz file if its generated (#839)
• [ENH] Add core_bundle functionality to fury backend (#838)
• [FIX] update to_call in pyAFQ CLI to new API (#836)

This release simplifies the API, in part by merging the
scalar and mask definitions into one image definition.
pyAFQ now must use python >=3.8. Other minor bug fixes.

• [FIX] update nightly tests and fix kwargs (#834)
• [DOC] update track docstring (#833)
• [ENH] Ignore pandas out of date warning / SFT reference warning (#832)
• [ENH] Simplify API system (#825)
• [FIX] always resample when loading from disk, not just first time (#830)
• [FIX] fix ImageFile for scalars, add test (#829)
• [ENH] replace parfor with paramap (#828)
• [FIX] Replace split(.) with splitext() (#827)
• [ENH] Change pyAFQ to use python >=3.8 (#826)
• [ENH] Autogenerate two separate QSIprep pipelines (#816)
• [ENH] Reorganize mask and scalar system into one "Image" system (#817)
• Update DIPY to 1.5 (#814)
• [ENH] Allow user to customize core bundle text indicating nodeID (#815)