From d9279dbf5c31b3b73dce5f82d739e2ef08c9cfec Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Fri, 19 Jul 2024 11:22:35 -0400 Subject: [PATCH] Update CHANGES --- CHANGES.rst | 115 +++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 4 +- 2 files changed, 117 insertions(+), 2 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 14d5d5d2..2a8500e9 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,3 +1,118 @@ +0.22.0 (July 19, 2024) +====================== + +Continuing the update to current NiPreps best practices, an update to PyAFQ and a few bugfixes. + + * [ENH] Compress recon derivatives (#787) + * [FIX] Make hsvs workflow work (#784) + * [FIX] Use new bundle names (#783) + * [RF] Drop functions to read sidecar JSONs (#760) + * [FIX] FUGUE bug (#769) + * [ENH] Save SIFT2 mu parameter (#774) + * [FIX] Fix the mif2fib workflow (#778) + * [FIX] CI test file checking + * [CI] Update expected AFQ outputs again + * [CI] add optional bundles (#771) + * [ENH] Update dependencies in docker image (#768) + * [ENH] Upgrade pyAFQ to 1.3.2 (#764) + * [RF] Run integration tests with pytest (#763) + * [FIX] API documentation (#748) + * [ENH] Update to NiPreps-style config file (#745) + + +0.21.4 (May 4, 2024) +==================== + + +## What's Changed +The effort to update to current NiPreps standards has begun, plus another bugfix in the TOPUP workflow. + +### Other Changes +* Remove copy of Niworkflows in favor of dependency by @tsalo in https://github.com/PennLINC/qsiprep/pull/709 +* [FIX] stop bizarre argsort behavior in best b=0 by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/744 + + + +0.21.3 (May 2, 2024) +==================== + +## What's Changed + +This update addresses an important coregistration bug (#740), makes CPU Eddy much more usable and fixes a bug in the PyAFQ workflow. + +### Other Changes +* [FIX] PyAFQ was not being written to derivatives by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/738 +* [FIX] use b0 ref from eddy-processed data by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/739 +* [MAINT] remove pypi by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/742 +* [ENH] add parallel argument for topup by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/741 +* [ENH] Allow multithreading in eddy by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/743 + + + +0.21.1 (Apr 25, 2024) +===================== + +There are important software updates in this release, along with a lot of infrastructure improvements. + +## Important Changes + * FSL version 6.0.7.8 is now in qsiprep. This contains 2 [serious bugfixes](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/development/history/changelog-6.0.7.8.md). One has to do with susceptibility-by-volume correction and the other resulted in incorrect CNR values being calculated. + * DSI Studio has been updated to fix a bug in [Neighboring DWI Correlation](https://github.com/frankyeh/DSI-Studio/issues/84). + * You can use `"mporder"` in your eddy config json file and the slice timings will automatically be created and passed to eddy (even if you're concatenating runs) + * Recon workflows can now include a "bundle mapping" and "scalar mapping", where scalars created in individual workflows can be mapped to a template or summarized inside autotrack bundles. This does not do tract profiles or surface mapping - yet. See `qsiprep/data/pipelines/hbcd_scalar_maps.json` for an example. + * The recon derivatives are written approximately according to BEP-016 + +## New Features + +* [ENH] Add workflow to resample recon scalars to template space by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/688 +* Support complex-valued dwidenoising by @tsalo in https://github.com/PennLINC/qsiprep/pull/679 +* [ENH] Add ReconScalars node to recon workflows by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/683 +* Pin current version of pyAFQ (1.3.1) by @arokem in https://github.com/PennLINC/qsiprep/pull/729 +* [ENH] Add TORTOISE Estimator recon workflows by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/674 +* [ENH] Make Eddy's slice2vol much easier to use by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/710 + +## Other Changes +* Apply stylistic changes to `workflows/base.py` by @tsalo in https://github.com/PennLINC/qsiprep/pull/678 +* Pin Nilearn version by @tsalo in https://github.com/PennLINC/qsiprep/pull/687 +* Add a series of infrastructure files from ASLPrep/XCP-D by @tsalo in https://github.com/PennLINC/qsiprep/pull/684 +* Run isort and remove unused imports by @tsalo in https://github.com/PennLINC/qsiprep/pull/690 +* Apply stylistic changes to `workflows/utils.py` by @tsalo in https://github.com/PennLINC/qsiprep/pull/680 +* Remove unused classes flagged by vulture by @tsalo in https://github.com/PennLINC/qsiprep/pull/693 +* [RF] Use Black to reformat package by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/701 + +## Bugfixes +* [FIX] Prevent undecodable terminal output in calc_connectivity by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/711 +* [FIX] save recon anat files by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/702 +* [FIX] revert citeproc for old pandoc by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/736 +* [FIX] recon workflows when --anat-modality T2w was used by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/734 +* [FIX] remove old nodes from csdsi_3dshore.json by @kjamison in https://github.com/PennLINC/qsiprep/pull/733 +* [ENH] Update TORTOISE for lower cuda memory use by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/730 + + + +0.20.0 (Jan 12, 2024) +====================== +Please note there is no corresponding release on PyPI for this version + +## New features +* [ENH] allow topup+drbuddi for hbcd by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/667 + * Adds a 2-stage distortion correction option `--pepolar-method TOPUP+DRBUDDI`, which will run TOPUP -> Eddy -> DRBUDDI +* [ENH] Use UKB processed data as input for recon workflows by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/651 + * This adds the --recon-input-pipeline, which lets you run recon workflows on UKB data +* [ENH] Update to python 3.10 by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/670 + * Hopefully this will address the hang-after-crashing problem in the recent releases + +## Bugfixes/Docs +* DOC: Add SMeisler and JHLegarreta to contributors list by @jhlegarreta in https://github.com/PennLINC/qsiprep/pull/642 +* Fixes typos on FreeSurfer requirements for ss3t hsvs recon by @pcamach2 in https://github.com/PennLINC/qsiprep/pull/414 +* Fix RTD build by @tsalo in https://github.com/PennLINC/qsiprep/pull/652 +* ENH: conform bvals to shells separated by b0_threshold by @cookpa in https://github.com/PennLINC/qsiprep/pull/660 +* [FIX] remove unneeded "method" from tracking by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/641 +* FIX: allow finding of lesion rois by @psadil in https://github.com/PennLINC/qsiprep/pull/659 +* MISC: Remove outdated dsi_studio tracking parameters by @cookpa in https://github.com/PennLINC/qsiprep/pull/668 +* [DOC] Add documentation for dsi_studio_autotrack reconstruction workflow by @valeriejill in https://github.com/PennLINC/qsiprep/pull/669 +* [ENH] Update BIDS validator to 1.8.4 by @mattcieslak in https://github.com/PennLINC/qsiprep/pull/671 + + 0.19.0 (August 10, 2023) ======================== diff --git a/pyproject.toml b/pyproject.toml index 95891de1..2866e00f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["hatchling", "hatch-vcs", "cython", "numpy"] +requires = ["hatchling", "hatch-vcs", "nipreps-versions", "cython", "numpy"] build-backend = "hatchling.build" [project] @@ -51,7 +51,7 @@ dynamic = ["version"] Homepage = "https://github.com/pennbbl/qsiprep" Documentation = "https://www.qsiprep.readthedocs.io" Paper = "https://doi.org/10.1038/s41592-022-01458-7" -"Docker Images" = "https://hub.docker.com/r/pennlinc/qsiprep/tags/" +"Docker Images" = "https://hub.docker.com/r/pennbbl/qsiprep/tags/" [project.optional-dependencies] doc = [