🔀 Merge changes from branch 'feature/check_orientations' into 'many_p…

…ipelines'

CHANGELOG.md

@@ -18,14 +18,54 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- `pyproject.toml` file with `[build-system]` defined.
+- [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/FCP-INDI/C-PAC/main.svg)](https://results.pre-commit.ci/latest/github/FCP-INDI/C-PAC/main) badge to [`README`](./README.md).
+- `desired_orientation` key in participant-level pipeline config under `pipeline_setup`.
+- Required positional parameter "wf" in input and output of `ingress_pipeconfig_paths` function, where a node to reorient templates is added to the `wf`.
+- Required positional parameter "orientation" to `resolve_resolution`.
+- Optional positional argument "cfg" to `create_lesion_preproc`.
+
+### Changed
+
+- Moved `pygraphviz` from requirements to `graphviz` optional dependencies group.
+- Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files.
+- Made orientation configurable (was hard-coded as "RPI").
+
+### Fixed
+
+- A bug in which AWS S3 encryption was looked for in Nipype config instead of pipeline config (only affected uploading logs).
+- Restored `bids-validator` functionality.
+- Fixed empty `shell` variable in cluster run scripts.
+- A bug in which bandpass filters always assumed 1D regressor files have exactly 5 header rows.
+
+### Removed
+
+- Variant image recipes.
+  - `ABCD-HCP`
+  - `fMRIPrep-LTS`
+- Typehinting support for Python < 3.10.
+
+## [1.8.7] - 2024-05-03
+
+### Added
+
 - `Robustfov` feature in `FSL-BET` to crop images ensuring removal of neck regions that may appear in the skull-stripped images.
-- Ability to throttle nodes, estimating all available memory when threading
+- Ability to throttle nodes, estimating all available memory when threading.
+- Ability to configure FreeSurfer ingress from the command line.
 
 ### Changed
 
+- The ABCD-pipeline based surface post-processing workflows have been modularized to be more robust, resolving a running issue with this part of the pipeline stalling or crashing in some runs.
 - Moved autoversioning from CI to pre-commit
 - Updated `FSL-BET` config to default `-mask-boolean` flag as on, and removed all removed `mask-boolean` keys from configs.
-- Added `dvars` as optional output in `cpac_outputs`
+- Added `dvars` as optional output in `cpac_outputs`.
+
+### Fixed
+
+- Fixed a bug where ingressing fmriprep outputs into C-PAC with a blank nuisance confounds field in the C-PAC pipeline configuration file would cause a crash.
+- Fixed a bug where spatial smoothing and z-scoring of final outputs would sometimes fail to run when running a C-PAC pipeline that would ingress fmriprep outputs.
+- Fixed a bug where ingress of distortion correction-related field map metadata would sometimes fail to recognize both echo times, when there were two present, leading to an error message claiming an echo time is missing.
+- Changed an extraneous default pipeline configuration setting - `surface_connectivity` is now disabled in the default configuration as intended.
 
 ## [1.8.6] - 2024-01-15
 
@@ -285,7 +325,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 See [Version 1.8.1 Beta](https://fcp-indi.github.io/docs/user/release_notes/v1.8.1) for release notes for v1.8.1 and [Release Notes](https://fcp-indi.github.io/docs/user/release_notes) for all release notes back to v0.1.1.
 
-[unreleased]: https://github.com/FCP-INDI/C-PAC/compare/v1.8.6...develop
+[unreleased]: https://github.com/FCP-INDI/C-PAC/compare/v1.8.7...develop
+[1.8.7]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.7
 [1.8.6]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.6
 [1.8.5]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.5
 [1.8.4]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.4