From 5df76ded773a6913418b71bab24724ace6ff0a23 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Sun, 17 Nov 2024 11:11:28 -0500 Subject: [PATCH] Prepare for 0.10.0 release (#1324) --- CITATION.cff | 4 ++-- docs/changes.md | 49 ++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 50 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index ab5b58007..5b9376c4a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -83,5 +83,5 @@ keywords: - BIDS-App - Neuroimaging license: BSD-3-Clause -version: 0.9.1 -date-released: '2024-09-13' +version: 0.10.0 +date-released: '2024-11-17' diff --git a/docs/changes.md b/docs/changes.md index cb4f8c4b6..999d93bd3 100644 --- a/docs/changes.md +++ b/docs/changes.md @@ -1,5 +1,52 @@ # What's New +## 0.10.0 + +This backwards-incompatible release brings XCP-D further in line with the fMRIPost workflows in the NiPreps ecosystem. +We have added the ability to provide custom confound sets defined as YAML config files, +ingress derivatives from fMRIPost BIDS Apps (for example, fMRIPost-AROMA), +and provide external atlases organized as BIDS-Atlas datasets. + +Please note that the BIDS-Atlas extension proposal has not been merged into BIDS yet, +so the expected organization of these external atlas datasets may change over time. + +### 🛠 Breaking Changes + +* Replace restricted confound sets with config files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1255 +* Rename `--derivatives` parameter to `--datasets` by @tsalo in https://github.com/PennLINC/xcp_d/pull/1276 +* Accept external atlases by searching BIDS-Atlas datasets by @tsalo in https://github.com/PennLINC/xcp_d/pull/1265 +* Move hemi entity before space by @tsalo in https://github.com/PennLINC/xcp_d/pull/1287 + +### 🎉 Exciting New Features + +* Remove Freesurfer node from surface normalization workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/1273 +* Track Sources with BIDSURI interface by @tsalo in https://github.com/PennLINC/xcp_d/pull/1283 +* Add nichart mode by @tsalo in https://github.com/PennLINC/xcp_d/pull/1320 + +### 🐛 Bug Fixes + +* Patch task_id into bids_filters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1271 +* Fix NIfTI-surface connection by @tsalo in https://github.com/PennLINC/xcp_d/pull/1284 +* Update build image version by @tsalo in https://github.com/PennLINC/xcp_d/pull/1293 +* Fix bug with surfaces and external atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/1304 +* Apply notch filter appropriate number of times based on `--motion-filter-order` by @tsalo in https://github.com/PennLINC/xcp_d/pull/1300 +* Fix ingression of standard-space mesh files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1309 +* Fix init_qc_report_wf connections when linc-qc and abcc-qc are disabled by @tsalo in https://github.com/PennLINC/xcp_d/pull/1314 + +### Other Changes + +* Don't rerun alff if num threads changes by @mattcieslak in https://github.com/PennLINC/xcp_d/pull/1263 +* Remove xcp_d_dir and clean datasinks by @tsalo in https://github.com/PennLINC/xcp_d/pull/1262 +* Add dataset links to config object by @tsalo in https://github.com/PennLINC/xcp_d/pull/1266 +* Document minimal required inputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1270 +* Correct documentation regarding Freesurfer by @tsalo in https://github.com/PennLINC/xcp_d/pull/1277 +* Improve custom confound documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1280 +* Improve documentation of new features by @tsalo in https://github.com/PennLINC/xcp_d/pull/1281 +* Use ruff for linting by @tsalo in https://github.com/PennLINC/xcp_d/pull/1312 +* Fix links to documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1323 + +**Full Changelog**: https://github.com/PennLINC/xcp_d/compare/0.9.1...0.10.0 + ## 0.9.1 @@ -18,7 +65,7 @@ This release improves performance with multi-core processing. ## 0.9.0 This backwards-incompatible release makes two important breaking changes. -First, we changd the default file format for 'linc' mode from NIfTI to CIFTI. +First, we changed the default file format for 'linc' mode from NIfTI to CIFTI. Second, XCP-D no longer ingresses and warps the anatomical tissue segmentation file (`*_dseg.nii.gz`), since no one was using it and it's easy enough to collect separately.