Version 2.0.1

2.0.1 (May 15, 2025)

Minor Fixes to VOF, ROI dists, baby BD primary axis filtering, import_tract
with trx files. Increase in number of examples in docs.

• [DOC] update broken references (#90)
• Add track, segment, cleaning explanation (#87)
• [DOC] How to Export examples (#86)
• [DOC] Add GPU, clobber docs (#82)
• [DOC] ParticipantAFQ example (#83)
• Small docs/viz tool improvements (#62)
• [ENH] Make Subject Space ROIs Resample By Default (#72)
• Upgrade DIPY dependency. (#76)
• Remove funcargparser dependency, replace with extreme regex (#80)
• RF: Better error handling. (#68)
• update reference in example (#75)
• [FIX] recently added typo in pyAFQ GPU integration (#74)
• DOC: Adds an example of tract profile visualization with "glass brain". (#67)
• remove dependencies; clarify <3.13 for now (#66)
• Loosen skimage dependency pin to be larger than 0.14.2 (#61)
• [FIX] make import_tract work better with TRX files (#54)
• Remove numpy version restrictions (#53)
• Further tweaks to new file system (#50)
• [FIX] change helvetica-bold to helvetica in pyAFQ plotting library (#49)
• (#48)
• [ENH/FIX] Pyafq file outputs more folders, more BIDS (#43)
• [ENH] Include custom ODFs (#33)
• [ENH] update to numpy 2 (#46)
• [ENH] update to 3.12 (#45)
• [FIX] fix VOF (#29)
• [DOC] added singularity build and usage (#28)
• [ENH] Use Distance Transform for Include/Exclude Distance calculation; fix ROI dists (#25)
• DOC: Document the significance of ROIS order in BundleDict (#27)
• [FIX] update baby BD to new primary axis api (#26)

Version 2.0

This is a major version release, which includes support for Python 3.12 and numpy 2.0, as well as major changes to the way that output data are organized.

What's Changed

• [FIX] update baby BD to new primary axis api by @36000 in #26
• DOC: Document the significance of ROIS order in BundleDict by @arokem in #27
• [ENH] Use Distance Transform for Include/Exclude Distance calculation; fix ROI dists by @36000 in #25
• [DOC] added singularity build and usage by @nmuncy in #28
• [FIX] fix VOF by @36000 in #29
• [ENH] update to 3.12 by @36000 in #45
• [ENH] update to numpy 2 by @36000 in #46
• [ENH] Include custom ODFs by @kellychang4 in #33
• [ENH/FIX] Pyafq file outputs more folders, more BIDS by @36000 in #43
• [FIX] fix pft code for new dipy by @36000 in #48
• [FIX] change helvetica-bold to helvetica in pyAFQ plotting library by @36000 in #49
• Further tweaks to new file system by @36000 in #50
• Remove numpy version restrictions by @36000 in #53
• [FIX] make import_tract work better with TRX files by @36000 in #54
• Loosen skimage dependency pin to be larger than 0.14.2 by @arokem in #61
• remove dependencies; clarify <3.13 for now by @36000 in #66

New Contributors

• @nmuncy made their first contribution in #28
• @kellychang4 made their first contribution in #33

Full Changelog: 1.3.6...2.0

Version 1.3.6

1.3.6 (November 17, 2024)

Adds system for recognizing bundles based on other bundles, and implements
it for the VOF. Adds code to work with new GPU tracking which can do
probabilistic tracking. Fixes bugs that arise when working with images
that are not RAS/RPS/LAS/LPS. Other minor fixes.

• [FIX] fix cross_midline when R/L axis not first orientation (#17)
• Too many t's in https (#22)
• Update gpu code (#20)
• [FIX] smarter automatic scalar names (#19)
• [ENH] Update segmentation.py (#15)
• Update tractography default (#13)
• Fixes a small typo (#10)
• [DOC] Update fetch.py (#12)
• Upgrade python (#9)
• Add system for recognizing bundles based on other bundles; implement it for VOF (#7)
• print method for BundleDict class (#5)
• Fixes typo in warning message (#6)
• (#4)
• Replace yeatmanlab with tractometry wherever that appears. (#2)
• New release (#1)