nipreps/nibabies: 22.0.0

The first NiBabies release of the year!

The first entry of the 22.0.x series, this release includes a number of new features, as well as various bug fixes. Some of the most notable changes include:

• A new flag --derivatives to allow passing in precomputed derivatives. For more information on how to use this, see the FAQs.
  • Users can now leverage a precomputed brain mask and/or discrete anatomical segmentations.
• A new flag --me-output-echoes to output individual corrected echo time series.
  • This is useful when doing additional multi-echo processing.
• Refinements to CIFTI generation, improve subcortical structure labeling.

If you encounter any issues with this release, please let us know by posting an issue on our GitHub page!

A full list of changes can be found below.

• CI: Add workflow smoke tests (https://github.com/nipreps/nibabies/pull/100)
• DOC: Add FAQs page (https://github.com/nipreps/nibabies/pull/164)
• DOCKER: Upgrade to FSL6, use niprep miniconda base layer (https://github.com/nipreps/nibabies/pull/191)
• ENH: Add major/minor version prefix to base workflow name (https://github.com/nipreps/nibabies/pull/202)
• ENH: Add --me-output-echos CLI flag (https://github.com/nipreps/nibabies/pull/174)
• ENH: Precomputed derivatives (https://github.com/nipreps/nibabies/pull/173)
• ENH: Validate files passed with --derivatives (https://github.com/nipreps/nibabies/pull/182)
• FIX: Clean up generated boilerplate (https://github.com/nipreps/nibabies/pull/200)
• FIX: Various Configuration module touch-ups (https://github.com/nipreps/nibabies/pull/197)
• FIX: Clean up default output space handling (https://github.com/nipreps/nibabies/pull/196)
• FIX: Pandoc citeproc API incompatibility (https://github.com/nipreps/nibabies/pull/195)
• FIX: Check if segmentation directory exists (https://github.com/nipreps/nibabies/pull/165)
• FIX: Update report spec to reflect infant_recon_all (https://github.com/nipreps/nibabies/pull/167)
• FIX: ICA Aroma imports (https://github.com/nipreps/nibabies/pull/170)
• FIX: Relabel sub-structures before discarding (https://github.com/nipreps/nibabies/pull/186)
• FIX: Use precomputed aseg within infant_recon_all (https://github.com/nipreps/nibabies/pull/184)
• FIX: Remove excess arguments on wrapper tests (https://github.com/nipreps/nibabies/pull/181)
• MAINT: Update versioneer, allow static versioning (https://github.com/nipreps/nibabies/pull/190)
• MAINT: Ensure version is written to version file (https://github.com/nipreps/nibabies/pull/189)
• MAINT: Add missing toml dependency
• MAINT: Add pre-commit checks (https://github.com/nipreps/nibabies/pull/178)
• MAINT: Add RTD config (https://github.com/nipreps/nibabies/pull/173)
• MAINT: Freeze black version (https://github.com/nipreps/nibabies/pull/185)
• RF: Wrapper usage logic (https://github.com/nipreps/nibabies/pull/183)
• STY/TEST: Set global style and doctest options (https://github.com/nipreps/nibabies/pull/162)