Sdcflows

=====================
Feature release in the 2.9.x series.

The main change is that B0FieldIdentifiers with special characters
are now sanitized and exposed through a ``FieldmapEstimator.sanitized_id``
attribute.

Workflow names and input/output connections will use ``sanitized_id``,
to ensure compatibility with filenames and workflow graph generation.
Internal lookup tables will continue to use the the unsanitized ``bids_id``.

* FIX: Update suffix only when finding related fieldmap files (436)
* FIX: Remove unused ANTs parameter that was removed in 2.4.1 (431)
* RF: Add sanitized_id field to FieldmapEstimation (444)
* DOC: Un-mock the already-imported numpy (440)
* CI: Bump actions/cache from 3 to 4 (429)

========================
Bug-fix release in the 2.8.x series.

Fixes doc builds and CLI support for fieldmapless workflows.
Introduces support for BIDS-URIs.

* FIX: Enable fieldmapless by default in CLI (426)
* FIX: Pandoc requires Texlive to render LaTeX in notebook (427)
* FIX: New test ``test_wrangler_URIs`` had the wrong oracle (425)
* ENH: Resolve BIDS-URIs (349)
* TEST: Use less confusing function name for testing CLI with --dry-run (424)
* MNT: Bump actions/download-artifact from 3 to 4 (418)
* MNT: Bump actions/upload-artifact from 3 to 4 (417)
* CI: Move PR doc build into main doc build, add texlive to build dependencies (428)

========================
New feature release in the 2.8.x series.

This release fixes a bug in converting SyN-SDC displacements to fieldmaps,
resulting in exaggerated corrections. As this makes changes to the structure
of a workflow and the expected inputs of a workflow node, this release is
considered a minor release.

* FIX: Derive field from SyN displacements using EPI affine (421)
* FIX: Change ``os.basename`` to ``os.path.basename`` (419)
* DOC: Add smeisler to contributors (420)

=========================
New feature release in the 2.7.0 series.

This release includes an updated CLI, which allows ``sdcflows`` to be
run as a BIDS App. To achieve the previous behavior of ``sdcflows-find-estimators``,
use the ``-n`` flag.

Addtional bug fixes and enhancements are included.

* FIX: Drop header before resampling image to avoid unsafe cast (415)
* FIX: Wrangler now ignores ``part-phase`` EPI files (407)
* ENH: Standalone CLI now estimates fieldmaps (408)
* ENH: Add support for ASL data (411)
* ENH: Enable rendering of the Jupyter notebooks (409)
* MNT: Migrate to PEP517/518 packaging (410)
* CI: bump actions/setup-python from 4 to 5 (412)
* CI: bump conda-incubator/setup-miniconda from 2 to 3 (406)

=========================
New feature release in the 2.6.0 series.

This release resolves a number of issues with fieldmaps inducing distortions
during correction. Phase difference and direct fieldmaps are now masked correctly,
preventing the overestimation of distortions outside the brain. Additionally,
we now implement Jacobian weighting during unwarping, which corrects for compression
and expansion effects on signal intensity.

* FIX: Mask fieldmap before fitting spline field (396)
* FIX: Interpolate to floating point values (394)
* FIX: Refactoring the ``B0FieldTransform`` implementation (346)
* FIX: Nipype workflows like to be passed absolute paths (phasediff fieldmap) (374)
* ENH: Implement Jacobian weighting during unwarp (391)
* ENH: Output target2fmap_xfm from coeff2epi_wf (381)
* ENH: Add data loader to sdcflows.data, drop pkg_resources (379)
* RF: Use scipy.interpolate.BSpline to construct spline basis (393)
* DOC: Use latest sphinx to fix bad sphinx/furo interaction (390)
* DOC: Fix missing dependency when merging new data loader (380)
* MNT: Update emprical values in test to allow transition to new scipy's BSpline (387)
* MNT: Add pre-commit config (375)
* MNT: Add a seed to random generator of coefficients (368)

=========================
Bug-fix release in the 2.5.x series.

This release includes a fix for phasediff/direct fieldmaps that were previously
producing distortions outside the brain due to an incorrect masking of the fieldmap.

* FIX: Mask fieldmap before fitting spline field [backport gh-396] (398)
* DOC: Fix doc build for 2.5.x branch (399)
* MAINT: Make call to scipy.stats.mode compatible with scipy 1.11.0 (371)