Niworkflows

======================
New minor release to start the 1.11.x series.

The major changes include:
- a deprecation to T1w-only based template processing
- addition of a new dependency ``acres`` for accessing package data

However, this is still backwards compatible with the 1.10.x series.

* MAINT: Depend on acres for data access
* ENH: Add PrepareDerivative/SaveDerivative interfaces (885)
* ENH: Make template dimensions support T2w as well (879)
* ENH: Modify FSSource to output T2 (868)
* FIX: Set cal_max in the NIfTI header for visualization after ``IntensityClip`` (878)
* FIX: Remove accidental MRIQC dependency, allow app config to be passed to workflow plugin (876)
* TEST: Fix plugin invocation, use an initializer that can be verified (880)

======================
Bug-fix release in the 1.10.x series

* ENH: Modify FSSource to output T2 (868)
* STY: Apply ruff/flake8-implicit-str-concat rule ISC001 (870)
* STY: Remove extraneous quotes (859)
* STY: Apply assorted ruff/refurb rules (867)
* MNT: update vendored docs files (834)
* MNT: Fix deprecation error in CI (866)

=======================
Bug-fix release in the 1.10.x series

* ENH: Allow alternative ``extensions`` when creating a BIDS skeleton (858)
* ENH: Parsing for ``space+cohort`` structure (857)

==========================
New feature release in the 1.10.x series.

This release has several improvements targeting ASLPrep and MRIQC, particularly
around BIDS tooling and workflow plugins.
We also drop our use of Convert3D in favor of nitransforms, allowing downstream
projects to remove this non-Python dependency as needed.

Some fixes change workflow structure, so please test before upgrading.

* FIX: Copy header to ensure mask is really aligned (844)
* FIX: Correctly use ``ignore_initial_volumes`` in ``ConfoundsCorrelationPlot`` (846)
* FIX: Add DWI to the default queries of BIDS querying (833)
* ENH: Add ``ignore_initial_volumes`` param to ``ConfoundsCorrelationPlot`` (843)
* ENH: Add MRIQC's custom multiproc runner that allows passing the pool (841)
* ENH: Upstream debugging hook from MRIQC (842)
* ENH: Add ASL support in BIDS utilities (839)
* ENH: Add hemi entity to transform path patterns (832)
* RF: Replace Convert3d with nitransforms in MCFLIRT2ITK (835)
* DOC: fix typo in refmap.py (837)
* STY: Assorted refurb suggestions (831)
* MNT: http:// → https:// (#828)
* CI: Bump actions/setup-python from 4 to 5 (845)
* CI: Bump conda-incubator/setup-miniconda from 2 to 3 (840)

========================
New feature release in the 1.9.x series.

This release should be mostly compatible with 1.8.x.
The most significant addition is the :class:`niworkflows.data.Loader`,
which provides some wrapping around :mod:`importlib.resources` to make
accessing resources more convenient.

* FIX: Build config and CI (826)
* FIX: Compatibility with matplotlib 3.8.0 (825)
* FIX: Save boldrefs as float32 (821)
* FIX: Replace deprecated Matplotlib functionality (820)
* FIX: Test names of paths when calling path.iterdir() (818)
* ENH: Add PET support to niworkflows (823)
* ENH: Add data loader class, install at root and data modules (816)
* MNT: Pyupgrade suggestions (817)
* MNT: update vendored docs files (813)
* CI: Bump actions/checkout from 3 to 4 (824)

=====================
Patch release in the 1.8.x series.

This release includes a fix to CIFTI volume structure indices, and adds additional Workbench interfaces.

* ENH: Port GIFTI/CIFTI interfaces from fMRIPrep (811)
* FIX: Generate CIFTI volume structure indices in column-major order (815)