Qsiprep

This is a prerelease for the version that will be used by the HBCD project for their first data release.
Starting with this release, QSIPrep is now being deployed to `pennlinc/qsiprep`
on DockerHub instead of `pennbbl/qsiprep`.

We plan to not introduce any backwards-incompatible changes for a while.

🛠 Breaking Changes

* Replace pennbbl with pennlinc in package by tsalo in https://github.com/PennLINC/qsiprep/pull/869
* Move common metadata to top of JSON by tsalo in https://github.com/PennLINC/qsiprep/pull/875

🐛 Bug Fixes

* [FIX] synthstrip extra arg by mattcieslak in https://github.com/PennLINC/qsiprep/pull/881
* Pin nireports version and allow GIFs by tsalo in https://github.com/PennLINC/qsiprep/pull/883

Other Changes

* Restructure documentation and document how to run tests locally by tsalo in https://github.com/PennLINC/qsiprep/pull/879

**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.24.0...1.0.0rc1

This is a major, backwards-incompatible release.
It is also the last release using the `pennbbl` organization on DockerHub.

We recommend that users jump straight to 1.0.0rc1 rather than using 0.24.0.

🛠 Breaking Changes

* Rename `--anat-space-definition` to `--subject-anatomical-reference` by tsalo in https://github.com/PennLINC/qsiprep/pull/855
* Remove underscore versions of all parameters by tsalo in https://github.com/PennLINC/qsiprep/pull/861
* Change T1wACPC to ACPC and T1wNative to anat by tsalo in https://github.com/PennLINC/qsiprep/pull/859
* Change _cnr to stat-cnr_dwimap by tsalo in https://github.com/PennLINC/qsiprep/pull/867
* Rename confounds file to `desc-confounds_timeseries` by tsalo in https://github.com/PennLINC/qsiprep/pull/874

🎉 Exciting New Features

* Infer the appropriate MNIInfant cohort based on the participant's age by tsalo in https://github.com/PennLINC/qsiprep/pull/856
* Make grouping account for acquisition entity by tsalo in https://github.com/PennLINC/qsiprep/pull/862

🐛 Bug Fixes

* [FIX] Change to Linear for upsampling by mattcieslak in https://github.com/PennLINC/qsiprep/pull/820
* Add MNIInfant to template enum by tsalo in https://github.com/PennLINC/qsiprep/pull/824
* Add ability to ignore phase data by tsalo in https://github.com/PennLINC/qsiprep/pull/849
* Use correct base name with `--distortion-group-merge average` by tsalo in https://github.com/PennLINC/qsiprep/pull/863

Other Changes

* [CI] Swap synthstrip for bet when sloppy mode is chosen by mattcieslak in https://github.com/PennLINC/qsiprep/pull/817
* [FIX] Constrain threading for intramodal template by mattcieslak in https://github.com/PennLINC/qsiprep/pull/825
* [FIX] use correct arguments for merging distortion groups by mattcieslak in https://github.com/PennLINC/qsiprep/pull/831
* rf(py314): Replace deprecated pkgutil.find_loader by effigies in https://github.com/PennLINC/qsiprep/pull/828
* [ENH] Enable session selection by mattcieslak in https://github.com/PennLINC/qsiprep/pull/832
* [FIX] Add denoising reportlets back to html by mattcieslak in https://github.com/PennLINC/qsiprep/pull/841
* [ENH] Add derivatives metadata by mattcieslak in https://github.com/PennLINC/qsiprep/pull/844
* Use "Apptainer" instead of "Singularity" by arokem in https://github.com/PennLINC/qsiprep/pull/846
* Document the transforms produced by QSIPrep by tsalo in https://github.com/PennLINC/qsiprep/pull/866
* Add warning for pennbbl Docker image by tsalo in https://github.com/PennLINC/qsiprep/pull/870
* Add QSIPrep paper to boilerplate by tsalo in https://github.com/PennLINC/qsiprep/pull/873
* Remove `aggr_ses_reports` field by tsalo in https://github.com/PennLINC/qsiprep/pull/872

New Contributors

* effigies made their first contribution in https://github.com/PennLINC/qsiprep/pull/828

**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.23.0...0.24.0

* [FIX] CUDA threads for Eddy (788) by araikes
* [FIX] Update bundle list for hbcd_scalar_maps (795) by mattcieslak
* [ENH] Update DSI Studio to Hao (782) by mattcieslak
* Fix bad phase connection when using --denoise-after-combining (781) by tsalo
* [RF] Remove the recon workflows from QSIPrep (802) by mattcieslak
* Drop mentions of the qsiprep-docker wrapper (807) by tsalo
* Collect templates from TemplateFlow instead of package data (809) by tsalo
* Use nireports for HTML reports (808) by tsalo
* [CI] Update CI to be more efficient (814) by mattcieslak
* [CI] add back pypi (816) by mattcieslak

**Full Changelog**: https://github.com/PennLINC/qsiprep/compare/0.22.0...0.23.0

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)

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

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