niworkflows - 1.13.5

Release Notes

Patch release in the 1.13.x series.

Changes

• Allow optional/None filters to be overridden (#956)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.13.4...1.13.5

- Python
Published by effigies 8 months ago

niworkflows - 1.13.4

Release notes

Patch release in the 1.13.x series.

This release includes: - A fix to avoid filters overwriting BIDS subject and session entities when collecting data - Additional PET paths for the default BIDS configuration - New file with PET-specific registration options

Changes

• ENH: Update nipreps.json (#950)
• ENH: Add petref-mniregistrationprecise_000.json (#949)
• FIX: Do not allow filters to overwrite participant / session (#952)
• MNT: Fix coverage config for parallel runners (#945)
• MNT: Accept main where master is used (#943)

- Python
Published by mgxd 9 months ago

niworkflows - 1.13.3

Release Notes

Patch release in the 1.13.x series.

This release resolves import errors introduced by excluding excess files in the previous release. Only test modules were affected.

Changes

• ENH: Add PET info to nipreps.json (#942)

- Python
Published by effigies 10 months ago

niworkflows - 1.13.2

Release Notes

Patch release in the 1.13.x series.

This release adjusts the build process to reduce the size of the installed package.

- Python
Published by effigies 10 months ago

niworkflows - 1.13.1

Release Notes

Patch release in the 1.13.x series.

This release adds the niworkflows.engine.splicer module, to facilitate sugery on wworkflows.

Changes

• FIX: Allow passing arguments through tag decorator (#939)
• ENH: Workflow splicer module (#938)
• MNT: Bump astral-sh/setup-uv from 5 to 6 (#937)

- Python
Published by effigies 10 months ago

niworkflows - 1.13.0

Release Notes

First release in the 1.13.x series.

This release restructures the ANTs brain extraction workflow. This should be a backwards compatible change, but a minor release is used out of caution.

Changes

• FIX: Remove duplicated code, problematic deviation from antsBrainExtraction (#931)
• FIX: Listify numbers (#925)
• ENH: Allow + symbol in label entities (#926, #927)
• STY: Apply various ruff checks (#913, #915, #917, #918, #919, #930)

- Python
Published by mgxd 10 months ago

niworkflows - 1.12.2

Release Notes

Patch release that includes a new keyword argument to BIDSDataGrabber to bypass requiring a T1w image

Changes

• ENH: Parse kwargs to allow no T1w (https://github.com/nipreps/niworkflows/pull/922)
• MNT: Bump astral-sh/setup-uv from 4 to 5 (https://github.com/nipreps/niworkflows/pull/920)
• STY: Format + add git blame ignore file (https://github.com/nipreps/niworkflows/pull/923)
• STY: Apply ruff/Pylint rule PLR0402 (https://github.com/nipreps/niworkflows/pull/916)
• STY: Apply ruff/flake8-pie rules (PIE) (https://github.com/nipreps/niworkflows/pull/914)
• STY: Apply ruff/flake8-comprehensions preview rule C409 (https://github.com/nipreps/niworkflows/pull/912)
• STY: Use f-strings where possible (https://github.com/nipreps/niworkflows/pull/836)

- Python
Published by mgxd about 1 year ago

niworkflows - 1.12.1

Release Notes

Patch release that adds a new input to SpatialNormalization, but remains backwards compatible.

Changes

• ENH: Allow adjusting histogram matching of configuration files (https://github.com/nipreps/niworkflows/pull/911)

- Python
Published by mgxd about 1 year ago

niworkflows - 1.12.0

Release notes

New minor release in the 1.12.x series.

This release includes support for Python 3.13, Numpy 2.0 and Nipype 1.9.

Note that using Python 3.13 requires building traits from the development branch.

Changes

• FIX: Pandas deprecations (#906)
• FIX: Numpy 2 compatibility (#905)
• FIX: Check 2D spaces against list from templateflow (#888)
• ENH: Add boldmap suffix to filename patterns. (#899)
• ENH: Add dir entity to T2starmap pattern. (#898)
• TEST: CIFTI2 expected checksum has changed (#895)
• STY: Replace black+flake8 with ruff, add pre-commit (#904)
• STY: use f-string within normalization interface (#892)
• MNT: Enable 3.13 tests (#909)
• MNT: Switch to tox for testing and CI (#900)
• MNT: Drop Python 3.8, update dependencies (#896)
• CI: Fix get_data job on CircleCI (#897)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.11.0...1.12.0

- Python
Published by effigies about 1 year ago

niworkflows - 1.10.2

Release notes

Bug-fix release in the 1.10.x series

Changes

• 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 deprectation error in CI (#866)

- Python
Published by effigies over 1 year ago

niworkflows - 1.10.1

Release notes

Bug-fix release in the 1.10.x series.

Changes

• ADD: Parsing for space+cohort structure by @mgxd in https://github.com/nipreps/niworkflows/pull/857
• ENH: Allow alternative extensions when creating a BIDS skeleton by @mgxd in https://github.com/nipreps/niworkflows/pull/858

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.10.0...1.10.1

- Python
Published by effigies almost 2 years ago

niworkflows - 1.10.0

Release notes

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.

Changes

• 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 Contributors

• @acionca made their first contribution in https://github.com/nipreps/niworkflows/pull/837

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.9.0...1.10.0

- Python
Published by effigies about 2 years ago

niworkflows - 1.9.0

Release notes

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.

Changes

• 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)

New Contributors

• @mnoergaard made their first contribution in https://github.com/nipreps/niworkflows/pull/823

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.8.1...1.9.0

- Python
Published by effigies over 2 years ago

niworkflows - 1.8.1

Release Notes

Patch release in the 1.8.x series.

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

Changes

• ENH: Port GIFTI/CIFTI interfaces from fMRIPrep (https://github.com/nipreps/niworkflows/pull/811)
• FIX: Generate CIFTI volume structure indices in column-major order (https://github.com/nipreps/niworkflows/pull/815)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.8.0...1.8.1

- Python
Published by effigies over 2 years ago

niworkflows - 1.8.0

Release notes

New feature release in the 1.8.x series.

This includes only bug-fixes, however the reselection of "white" surfaces as the default gray/white boundary instead of "smoothwm" justifies a minor release.

Changes

• FIX: Add desc entity to all path patterns (https://github.com/nipreps/niworkflows/pull/808)
• FIX: Inspect if template has resolution instead of assuming (https://github.com/nipreps/niworkflows/pull/803)
• FIX: Add missing dir-{direction} pattern for data sinking DWI reportlets (https://github.com/nipreps/niworkflows/pull/807)
• FIX: Move from smoothwm to white (https://github.com/nipreps/niworkflows/pull/806)
• FIX: Add option to bypass twopass in AFNI RobustAverage (https://github.com/nipreps/niworkflows/pull/801)
• FIX: Use len(segments) to avoid nsegments becoming wrong (https://github.com/nipreps/niworkflows/pull/795)
• MNT: Add PendingDeprecationWarning to nireports modules (https://github.com/nipreps/niworkflows/pull/810)
• MNT: Configure dependabot to upgrade actions (https://github.com/nipreps/niworkflows/pull/796)
• MNT: Drop Python 3.7 support, test 3.11 (https://github.com/nipreps/niworkflows/pull/793)
• MNT: Update build system and CI invocations (https://github.com/nipreps/niworkflows/pull/792)
• CI: Do not run scheduled builds on forks (https://github.com/nipreps/niworkflows/pull/800)
• CI: Bump codespell-project/actions-codespell from 1 to 2 (https://github.com/nipreps/niworkflows/pull/805)
• CI: Bump actions/checkout from 2 to 3 (https://github.com/nipreps/niworkflows/pull/797)
• CI: Build and upload wheels (https://github.com/nipreps/niworkflows/pull/791)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.7.9...1.8.0

- Python
Published by effigies over 2 years ago

niworkflows - 1.7.9

Release notes

Patch release in the 1.7.x series.

This release contains a minor fix for degenerate cases that arise on very low resolution datasets, such as used for CI testing.

Changes

• FIX: Use len(segments) to avoid nsegments becoming wrong (https://github.com/nipreps/niworkflows/pull/795)

- Python
Published by effigies almost 3 years ago

niworkflows - 1.7.8

Release Notes

Patch release in the 1.7.x series.

This release combines the fixes in 1.7.6 and 1.7.7, which were accidentally separately branched from 1.7.5.

- Python
Published by effigies almost 3 years ago

niworkflows - 1.7.7

What's Changed

• ENH: Allow passing a database_path to create a BIDSLayout by @oesteban in https://github.com/nipreps/niworkflows/pull/788

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.7.6...1.7.7

- Python
Published by oesteban almost 3 years ago

niworkflows - 1.7.6

What's Changed

• FIX: Use correct image for contour plotting by @effigies in https://github.com/nipreps/niworkflows/pull/785

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.7.5...1.7.6

- Python
Published by oesteban almost 3 years ago

niworkflows - 1.7.5

What's Changed

• FIX: Use a more reliable test of NIfTIness by @effigies in https://github.com/nipreps/niworkflows/pull/784

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.7.4...1.7.5

- Python
Published by oesteban almost 3 years ago

niworkflows - 1.7.4

What's Changed

• FIX: Use keyword sep for pandas.read_csv by @effigies in https://github.com/nipreps/niworkflows/pull/781
• codespell: config, action + some typo fixups by @yarikoptic in https://github.com/nipreps/niworkflows/pull/782
• FIX: Check for empty segments in plot_carpet by @effigies in https://github.com/nipreps/niworkflows/pull/783

New Contributors

• @yarikoptic made their first contribution in https://github.com/nipreps/niworkflows/pull/782

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.7.3...1.7.4

- Python
Published by oesteban almost 3 years ago

niworkflows - 1.7.3

Release Notes

Patch release in the 1.7.x series.

This release fixes a minor bug in carpet plot generation and resolves remaining issues with using custom configurations in DerivativesDataSink.

Changes

• FIX: Avoid sorting carpetplot rows when decimated ROIs have one voxel by @effigies in https://github.com/nipreps/niworkflows/pull/780
• ENH:Pass custom configuration into DerivativesDataSink entity parser by @tsalo in https://github.com/nipreps/niworkflows/pull/777

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.7.2...1.7.3

- Python
Published by effigies about 3 years ago

niworkflows - 1.7.2

What's Changed

• FIX: Handle plotting only one MELODIC component by @effigies in https://github.com/nipreps/niworkflows/pull/775
• FIX: Restore confound order in correlation plot by @effigies in https://github.com/nipreps/niworkflows/pull/779

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.7.1...1.7.2

- Python
Published by effigies about 3 years ago

niworkflows - 1.7.1

Release Notes

Patch release in the 1.7.x series.

This release includes updates to the Docker image environment, and a fix for a plotting bug.

Changes

• CI: Update GitHub actions frdom master (https://github.com/nipreps/niworkflows/pull/766)
• CI: Drop set-output (https://github.com/nipreps/niworkflows/pull/763)
• FIX: Remove unused ANTs parameter that was removed in 2.4.1 (https://github.com/nipreps/niworkflows/pull/771)
• FIX: Coerce MGHImage to Nifti1Image when plotting (https://github.com/nipreps/niworkflows/pull/769)
• FIX: Create test label images with realistic dtypes (https://github.com/nipreps/niworkflows/pull/767)
• FIX: error for np.bool with numpy 1.24.0 (https://github.com/nipreps/niworkflows/pull/764)
• MNT: Try bumping docker base to latest nipreps/miniconda (https://github.com/nipreps/niworkflows/pull/773)
• MNT: Use org-level context (https://github.com/nipreps/niworkflows/pull/770)
• REF: Store global variables as DerivativesDataSink attributes (https://github.com/nipreps/niworkflows/pull/762)

- Python
Published by mgxd about 3 years ago

niworkflows - 1.7.0

Release Notes

New feature release in the 1.7.x series. This series will support sMRIPrep 0.10, fMRIPrep 22.1, and NiBabies 22.2.

This will be the last minor release series to support Python 3.7.

Changes

• FIX: Use np.bool_ instead of deprecated np.bool (#760)
• FIX: Use nilearn plot_surf over surfplot (#745)
• ENH: Allow DerivativesDataSink to handle output==input (#758)
• ENH: Add Resolution field to metadata if data has res entity (#754)
• ENH: Add morphometric suffixes to pattern matching (#753)
• RF: GenerateCifti interface (#756)
• MNT: Loosen dependency versions (#759)
• MNT: Remove non-compliant dtseries.json metadata (#750)
• MNT: Build FreeSurfer 7.2 (#751)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.6.4...1.7.0

- Python
Published by effigies about 3 years ago

niworkflows - 1.6.4

What's Changed

• FIX: TSV2JSON should convert empty TSV files to empty JSON files by @effigies in https://github.com/nipreps/niworkflows/pull/746

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.6.3...1.6.4

- Python
Published by effigies over 3 years ago

niworkflows - 1.6.3

Release Notes

This release includes a new interface and improvements to existing interfaces.

Changes

• CI: Fix commit check (https://github.com/nipreps/niworkflows/pull/744)
• CI: Extract pip pre checks into separate, skippable job (https://github.com/nipreps/niworkflows/pull/743)
• FIX: Missing outputs in RobustAverage (https://github.com/nipreps/niworkflows/pull/741)
• ENH: ReorientImage interface (https://github.com/nipreps/niworkflows/pull/736)
• ENH: Add minimumfsversion input to BIDSFreeSurferDir (https://github.com/nipreps/niworkflows/pull/739)
• MNT: Pin traits < 6.4 (https://github.com/nipreps/niworkflows/pull/738)
• MNT: Upgrade versioneer (https://github.com/nipreps/niworkflows/pull/737)
• MAINT: Remove pins that broke prerelease tests (https://github.com/nipreps/niworkflows/pull/735)

- Python
Published by mgxd over 3 years ago

niworkflows - 1.6.2

Bug-fix release in the 1.6.x series.

This release fixes a bug where BIDS data collection would fail if using session as a BIDS filter.

• FIX: Ensure we do not clobber entities from bids filters (https://github.com/nipreps/niworkflows/pull/731)

- Python
Published by mgxd over 3 years ago

niworkflows - 1.6.1

Release Notes

Bug-fix release in the 1.6.x series.

This release allows downstream tools to use nitransforms 22.0.

Changes

• MNT: Relax nitransforms dependency by @effigies in https://github.com/nipreps/niworkflows/pull/727

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.6.0...1.6.1

- Python
Published by effigies almost 4 years ago

niworkflows - 1.6.0

Release Notes

New feature release in the 1.6.x series. This series will support sMRIPrep 0.9, fMRIPrep 22.0., and nibabies 22.1.

Changes

• FIX: Address some reliability issues of the functional masking workflow (#714)
• FIX: Improve reliability of BOLD masking workflow (#712)
• FIX: Account for potential lists of lists in multi-echo cases (#719)
• ENH: Added MRtrix3 gradients to derivative path patterns (#724)
• ENH: Add T2starmap as a functional derivative (#720)
• MAINT: Replace distutils use, upgrade versioneer (#725)
• CI: Let datalad handle git-annex installation (#721)
• CI: Bump environment cache version (#717)
• CI: Fallback to maintenance branch first (#716)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.5.4...1.6.0

- Python
Published by effigies almost 4 years ago

niworkflows - 1.4.9

Release Notes

This release includes improvements to the reliability of the BOLD masking workflow, as well as an fMRIPrep bug-fix when reusing multi-echo anatomicals.

Changes

• FIX: Account for potential lists of lists in multi-echo cases (#719)
• FIX: Improve reliability of BOLD masking workflow (#712)

- Python
Published by mgxd almost 4 years ago

niworkflows - 1.4.8

Release Notes

This change enables a bug-fix in sdcflows where images with slightly different affines were unable to be concatenated for use with TOPUP.

Changes

• ENH: Add affine_tolerance flag to MergeSeries (https://github.com/nipreps/niworkflows/pull/706)

- Python
Published by mgxd almost 4 years ago

niworkflows - 1.5.2

Release Notes

Bug-fix release in 1.5.x series.

Changes

• FIX: Add unlink() with missing_ok for Python 3.7 by @effigies in https://github.com/nipreps/niworkflows/pull/695

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.5.1...1.5.2

- Python
Published by effigies almost 4 years ago

niworkflows - 1.4.7

Release Notes

Bug-fix release in the 1.4.x series.

Changes

• FIX: Use copy function that does not preserve mtime when creating fsaverage directories (#703)
• FIX: Add unlink() with missing_ok for Python 3.7 (#695)
• ENH: Select magnitude images in collect_data for BIDS 1.5.0 (#594)
• CI: Install package across Python versions and run pytest (#697)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.4.6...1.4.7

- Python
Published by effigies almost 4 years ago

niworkflows - 1.3.7

What's Changed

• FIX: Use copy function that does not preserve mtime when creating fsaverage directories by @effigies in https://github.com/nipreps/niworkflows/pull/703

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.3.6...1.3.7

- Python
Published by effigies almost 4 years ago

niworkflows - 1.5.1

What's Changed

• ENH: Reorder within-segment rows of carpetplot with hierarchical clustering by @celprov in https://github.com/nipreps/niworkflows/pull/686
• ENH: Initiate a module of nipype interfaces for mathematical morphology by @celprov in https://github.com/nipreps/niworkflows/pull/651
• ENH: Refactor carpetplot reasigning responsibilities by @oesteban in https://github.com/nipreps/niworkflows/pull/687
• ENH: Miscellaneous improvements to carpetplot by @oesteban in https://github.com/nipreps/niworkflows/pull/688
• FIX: Error handling the segmentation in NIfTI extraction by @oesteban in https://github.com/nipreps/niworkflows/pull/689
• ENH: Add a legend to carpet plots with more than one segment by @oesteban in https://github.com/nipreps/niworkflows/pull/690
• FIX: Smarter decision to remap input segmentation to carpetplot by @oesteban in https://github.com/nipreps/niworkflows/pull/691
• DOC: Fix doc builds in maint/1.3.x by @effigies in https://github.com/nipreps/niworkflows/pull/692
• FIX: Unlink destination files before saving derivative by @effigies in https://github.com/nipreps/niworkflows/pull/683
• FIX: Set pixdim[4] to match RepetitionTime by @effigies in https://github.com/nipreps/niworkflows/pull/679

New Contributors

• @celprov made their first contribution in https://github.com/nipreps/niworkflows/pull/651

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.5.0...1.5.1

- Python
Published by oesteban almost 4 years ago

niworkflows - 1.4.6

What's Changed

• FIX: Unlink destination files before saving derivative by @effigies in https://github.com/nipreps/niworkflows/pull/683
• FIX: Set pixdim[4] to match RepetitionTime by @effigies in https://github.com/nipreps/niworkflows/pull/679

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.4.5...1.4.6

- Python
Published by effigies almost 4 years ago

niworkflows - 1.3.6

What's Changed

• DOC: Fix doc builds in maint/1.3.x by @effigies in https://github.com/nipreps/niworkflows/pull/692
• FIX: Set pixdim[4] to match RepetitionTime by @effigies in https://github.com/nipreps/niworkflows/pull/679

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.3.5...1.3.6

- Python
Published by effigies almost 4 years ago

niworkflows - 1.5.0

What's Changed

• ENH: Add utility function to generate sample BIDS directory by @mgxd in https://github.com/nipreps/niworkflows/pull/677
• ENH: Additional nibabel interfaces by @mgxd in https://github.com/nipreps/niworkflows/pull/680
• FIX: Scipy docs path by @mgxd in https://github.com/nipreps/niworkflows/pull/681
• TST: Update to FSL6 by @mgxd in https://github.com/nipreps/niworkflows/pull/675
• TEST: Drop excessively long interface equivalence tests by @effigies in https://github.com/nipreps/niworkflows/pull/674

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.4.5...1.5.0

- Python
Published by effigies about 4 years ago

niworkflows - 1.4.5

Patch release in the 1.4.x series.

In preparation for fMRIPrep 21.0.0 release.

• FIX: Conform entity ordering to BIDS specification for derivatives (#676)
• ENH: Add CIFTI surface plot (#663)

- Python
Published by mgxd about 4 years ago

niworkflows - 1.4.4

Release Notes

Patch release in the 1.4.x series.

This release enables better multi-echo handling in fMRIPrep.

CHANGES

• ENH: Return all bold files from initboldreference_wf (#673)

- Python
Published by effigies about 4 years ago

niworkflows - 1.4.3

Patch Notes

Patch release in the 1.4.x series, including improvements to the carpetplot figure. With thanks to Zaki A. for the contributions.

Changes

• ENH: Carpet plot tweaks (#617)
• FIX: Patch ants.Registration interface temporarily (#654)
• MAINT: Revise Docker image building and dependencies (#655)
• MAINT: Relax matplotlib constraint (#668)
• MAINT: Configure black to avoid excessive rewriting (#666)

- Python
Published by mgxd over 4 years ago

niworkflows - 1.4.2

Release Notes

Bug-fix release in the 1.4.x series revising dependencies and including minor improvements to the Docker image, a complete overhaul of the documentation skin, building and deployment & archival.

CHANGES

• DOC: Overhaul - new skin, new deployment & multiversion archival (#656, #657, #658)
• MAINT: Revise Docker image building and dependencies (#655)

Full Changelog: https://github.com/nipreps/niworkflows/compare/1.4.1...1.4.2

Maintainers

@mgxd, @effigies, @oesteban

- Python
Published by oesteban over 4 years ago

niworkflows - 1.4.1

Release Notes

Bug-fix release in the 1.4.x series.

This depends on the latest nitransforms, enabling downstream tools to upgrade.

CHANGES

• FIX: Patch ants.Registration interface temporarily (#654)

- Python
Published by effigies over 4 years ago

niworkflows - 1.3.5

Release Notes

Bug-fix release in the 1.3.x series

Changes

• FIX: Set slope and intercept to 1/0 if not otherwise provided (#649)
• FIX: DerivativesDataSink warning when it has multiple source files backport #573
• FIX: FSDetectInputs mutually exclusive options for ReconAll (#646)
• MNT: Update some version pinning and correct for pandas warning about keyword arguments (#645)
• CI: Use datalad-managed test data BACKPORT

- Python
Published by effigies over 4 years ago

niworkflows - 1.4.0

Release Notes

First release in the 1.4.x series. This release includes enhancements and bug-fixes towards the release of the first beta version of dMRIPrep. It also contains new features that are necessary for the API overhaul that has happened within the new SDCFlows 2.x series. The new series include a cross-cutting (modalities, species) workflow to generate EPI references. Finally other NiPreps will also have a first release with specific support for them: NiRodents and NiBabies (and their corresponding fMRIPrep extensions).

⚠️ NiWorkflows has been relicensed! ⚠️ As of the first release candidate of the 1.4 series, the license has changed from BSD 3-clause to the Apache License 2.0. Amongst several terms that are changing, the following two premises are relevant if you derive code from the new series: * You must give any other recipients of the Work or Derivative Works a copy of this License; and * You must cause any modified files to carry prominent notices stating that You changed the files.

A list of prominent changes can be found below. (With thanks to Lea Waller for the contributions)

Changes

• DOC: Ensure copyright notice in all headers' comment (#635)
• FIX: Set slope and intercept to 1/0 if not otherwise provided (#649)
• FIX: DerivativesDataSink warning when it has multiple source files (#647)
• FIX: FSDetectInputs mutually exclusive options for ReconAll (#646)
• FIX: Remove pandas warning about use of keyword arguments (#645)
• FIX: Improve SimpleBeforeAfterRPT contour visibility (#643)
• FIX: DerivativesDataSink dismissing entity writing reportlet (#638)
• FIX: Ensure IntensityClip input is a 3D file (#621)
• FIX: Limit memory usage in EstimateReferenceImage (#629)
• FIX: Purge removed --disable flag from svgo call (#626)
• FIX: Readd sbref_file input to reference volume interface (#624)
• FIX: Update svgutils after breaking API changes (#620)
• FIX: Address issues with RobustAverage global signal measurement (#607)
• FIX: NonsteadyStatesDetector wrongly using Nipype's is_outlier (#605)
• FIX: Change in svgutils' API on 0.3.2 breaks reportlets (#599)
• FIX: Check for in_segm input, not seg_file (typo) (#592)
• FIX: Use the mask to calculate FOV rather than the fixed image in GenerateSamplingReference (#583)
• FIX: Allow omission of <res> for template normalization (#582)
• FIX: Include _T2starw _MTw and _TSE-suffixes in build_path options (#584)
• FIX: DerivativesDataSink warning when it has multiple source files (#573)
• ENH: Allow SimpleBeforeAfterRPT plotting of image rotated to cardinal axes (#650)
• ENH: Update visual report specification with fieldmaps (#634)
• ENH: Expose the output of the ValidateImage node as an output in EPI reference workflow (#636)
• ENH: Add an inversion operation to IntensityClip (#616)
• ENH: Cross-cutting (modalities, species) workflow to generate EPI references (#610)
• ENH: Add a RobustAverage interface and split volume selection (#602)
• ENH: Revise some patterns of the BIDSLayout config to aid SDCFlows new API (#585)
• ENH: Upstream fMRIPrep's init_bbreg_wf to integrate it in dMRIPrep (#586)
• MAINT: Pin svgutils to previous versions (#596)
• MAINT: Drop gh-pages history, reducing repository size (#622)
• MAINT: Add DS030 dataset, with clipped (55 timepoints) BOLD data (#609)
• MAINT: Migrate ds003_downsampled to nipreps-data (#608)
• MAINT: Move mask-regressions test-data to datalad + nipreps-data (#606)
• MAINT: Refactor structure of interfaces (#603)
• MAINT: Drop Python 3.6, test setuptools builds, pip installations, and revise Docker pinned versions (#593)
• MAINT: CircleCI housekeeping (#580)
• RF: Write derivatives once, using deterministic gzip settings (#641)

⚠️ API Changes ⚠️ The niworkflows.interfaces submodule has been refactored. To migrate from previous series, please modify the following imports: * images.MatchHeader -> header.MatchHeader * images.ValidateImage -> header.ValidateImage * images.Demean -> nibabel.Demean * images.FilledImageLike -> nibabel.FilledImageLike * images.RegridToZooms -> nibabel.RegridToZooms * masks.ROIsPlot -> reportlets.masks.ROIsPlot * masks.ComputeEPIMask -> nilearn.ComputeEPIMask * mni.RobustMNINormalization -> norm.SpatialNormalization * New niworkflows.interfaces.reportlets submodule * report_base -> reportlets.base * masks -> reportlets.masks * registration -> reportlets.registration * segmentation -> reportlets.segmentation * utils.GenerateSamplingReference -> nibabel.GenerateSamplingReference * utils.CopyXForm -> header.CopyXForm * utils.NormalizeMotionParams -> confounds.NormalizeMotionParams * utils.AddTPMs -> probmaps.AddTPMs * utils.TPM2ROI -> probmaps.TPM2ROI * utils.AddTSVHeader -> utility.AddTSVHeader * utils.JoinTSVColumns -> utility.JoinTSVColumns * utils.DictMerge -> utility.DictMerge * utils.TSV2JSON -> utility.TSV2JSON Beware that interface aliases at the top niworkflows.interfaces level have been removed: * ExpandModel, SpikeRegressors from confounds * BET -> reportlets.masks.BETRPT * FAST -> reportlets.segmentation.FASTRPT * FLIRT, ApplyXFM, RobustMNINormalization, Registration, ApplyTransforms, SimpleBeforeAfter now under reportlets.registration as FLIRTRPT, ApplyXFMRPT, RobustMNINormalizationRPT, ANTSRegistrationRPT, ANTSApplyTransformsRPT, SimpleBeforeAfterRPT. * CopyXForm, CopyHeader, SanitizeImage now under header * NormalizeMotionParams now under confounds. * FMRISummary, CompCorVariancePlot, ConfoundsCorrelationPlot from plotting

- Python
Published by mgxd over 4 years ago

niworkflows - 1.4.0rc6

- Python
Published by oesteban almost 5 years ago

niworkflows - 1.3.3

Release Notes

Bug-fix release in the 1.3.x series.

CHANGES

• FIX: Limit memory usage in EstimateReferenceImage (#629)
• FIX: Check for in_segm input, not seg_file (#592)
• FIX: Use the mask to calculate FOV rather than the fixed image in GenerateSamplingReference (#583)
• FIX: Allow omission of for template normalization (#582)
• MAINT: Pin svgutils to 0.3.1 (#596)
• MAINT: Migrate from Travis -> GH Actions (#589)
• CI: CircleCI housekeeping (#580)

- Python
Published by effigies almost 5 years ago

niworkflows - 1.4.0rc5

- Python
Published by oesteban almost 5 years ago

niworkflows - 1.4.0rc4

- Python
Published by oesteban about 5 years ago

niworkflows - 1.4.0rc3

- Python
Published by oesteban about 5 years ago

niworkflows - 1.4.0rc2

- Python
Published by oesteban about 5 years ago

niworkflows - 1.4.0rc1

- Python
Published by oesteban about 5 years ago

niworkflows - 1.4.0rc0

- Python
Published by oesteban about 5 years ago

niworkflows - 1.3.2

Release Notes

Bug-fix release in the 1.3.x series.

CHANGES

• FIX: Cordon off .dtseries.json contents (#578)
• ENH: Add units to qform overwrite report (#577)

- Python
Published by effigies over 5 years ago

niworkflows - 1.3.1

Release Notes

Bug-fix release in the 1.3.x series. Addresses longstanding issues in the anatomical MRI brain extraction workflow.

CHANGES

• FIX: Revision of antsBrainExtraction, better handling edge cases (#567)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.3.0

Release Notes

First release in the 1.3.x series. This release includes enhancements and bug-fixes towards the release of the first LTS (long-term support) version of fMRIPrep. PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces have been deemed ready to upstream into Nipype, and several improvements regarding multi-echo EPI are included. With thanks to Basile Pinsard for contributions.

CHANGES

• FIX: Patch ApplyTransforms spec to permit identity in a chain (#554)
• FIX: Add dots to extensions in PyBIDS' config file (#548)
• FIX: Segmentation plots aligned with cardinal axes (#544)
• FIX: Skip T1w file existence check if anat_derivatives are provided (#545)
• FIX: Avoid diverting CIFTI dtype from original BOLD (#532)
• ENH: Add smooth input to RegridToZooms (#549)
• ENH: Enable DerivativesDataSink to take multiple source files to derive entities (#547)
• ENH: Allow bold_reference_wf to accept multiple EPIs/SBRefs (#408)
• ENH: Numerical stability of EPI brain-masks using probabilistic prior (#485)
• ENH: Add a pure-Python interface to resample to specific resolutions (#511)
• MAINT: Upstream all bug-fixes in the 1.2.9 release
• MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550)
• MAINT: Update to Python +3.6 (#541)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.2.9

Release Notes

Bug-fix release in the 1.2.x series with very minor problems addressed.

CHANGES

• FIX: Reportlets would crash in edge condition (#566)
• FIX: AROMA metadata CsfFraction -> CSFFraction (#563)
• FIX: Add DWI nonstandard spaces (#565)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.3.0rc3

Release Notes

First release in the 1.3.x series. This release includes enhancements and bug-fixes towards the release of the first LTS version of fMRIPrep. PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces have been deemed ready to upstream into Nipype, and several improvements regarding multi-echo EPI are included. With thanks to Basile Pinsard for contributions.

CHANGES

• FIX: Patch ApplyTransforms spec to permit identity in a chain (#554)
• FIX: Add dots to extensions in PyBIDS' config file (#548)
• FIX: Segmentation plots aligned with cardinal axes (#544)
• FIX: Skip T1w file existence check if anat_derivatives are provided (#545)
• FIX: Avoid diverting CIFTI dtype from original BOLD (#532)
• ENH: Add smooth input to RegridToZooms (#549)
• ENH: Enable DerivativesDataSink to take multiple source files to derive entities (#547)
• ENH: Allow bold_reference_wf to accept multiple EPIs/SBRefs (#408)
• ENH: Numerical stability of EPI brain-masks using probabilistic prior (#485)
• ENH: Add a pure-Python interface to resample to specific resolutions (#511)
• MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550)
• MAINT: Update to Python +3.6 (#541)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.2.8

Release Notes

Bug-fix release in the 1.2.x series with a minor improvement of the correlations plot.

CHANGES

• FIX: Improved control over correlations plot (#561)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.3.0rc2

Release Notes

First release in the 1.3.x series. This release includes enhancements and bug-fixes towards the release of the first LTS version of fMRIPrep. PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces have been deemed ready to upstream into Nipype, and several improvements regarding multi-echo EPI are included.

With thanks to Basile Pinsard for contributions.

CHANGES

• FIX: Patch ApplyTransforms spec to permit identity in a chain (#554)
• FIX: Add dots to extensions in PyBIDS' config file (#548)
• FIX: Segmentation plots aligned with cardinal axes (#544)
• FIX: Skip T1w file existence check if anat_derivatives are provided (#545)
• FIX: Avoid diverting CIFTI dtype from original BOLD (#532)
• ENH: Add smooth input to RegridToZooms (#549)
• ENH: Enable DerivativesDataSink to take multiple source files to derive entities (#547)
• ENH: Allow bold_reference_wf to accept multiple EPIs/SBRefs (#408)
• ENH: Numerical stability of EPI brain-masks using probabilistic prior (#485)
• ENH: Add a pure-Python interface to resample to specific resolutions (#511)
• MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550)
• MAINT: Update to Python +3.6 (#541)

- Python
Published by effigies over 5 years ago

niworkflows - 1.3.0rc1

Release Notes

First release in the 1.3.x series. This release includes enhancements and bug-fixes towards the release of the first LTS version of fMRIPrep. PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces have been deemed ready to upstream into Nipype, and several improvements regarding multi-echo EPI are included. With thanks to Basile Pinsard for contributions.

CHANGES

• FIX: Patch ApplyTransforms spec to permit identity in a chain (#554)
• FIX: Add dots to extensions in PyBIDS' config file (#548)
• FIX: Segmentation plots aligned with cardinal axes (#544)
• FIX: Skip T1w file existence check if anat_derivatives are provided (#545)
• FIX: Avoid diverting CIFTI dtype from original BOLD (#532)
• ENH: Add smooth input to RegridToZooms (#549)
• ENH: Enable DerivativesDataSink to take multiple source files to derive entities (#547)
• ENH: Allow bold_reference_wf to accept multiple EPIs/SBRefs (#408)
• ENH: Numerical stability of EPI brain-masks using probabilistic prior (#485)
• ENH: Add a pure-Python interface to resample to specific resolutions (#511)
• MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550)
• MAINT: Update to Python +3.6 (#541)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.2.7

Release Notes

Bug-fix release in the 1.2.x series with a very minor improvement of the reportlets.

CHANGES

• FIX: Pin PyBIDS < 0.11 (and TemplateFlow < 0.6.3) only on the 1.2.x series. (#552)
• FIX: Use numpy.linspace to calculate mosaic plots' cutting planes (#543)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.2.6

Release Notes

Bug-fix release in the 1.2.x series addressing minor bugs encountered mostly within sMRIPrep. With thanks to Franziskus Liem for contributions.

CHANGES

• FIX: Error conforming T1w images with differing zooms before recon-all (#534)
• FIX: Restore and deprecate license argument to check_valid_fs_license (#538)
• FIX: Allow anatomical derivatives to have run- entity (#539)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.2.5

Release Notes

Bug-fix release that remedies an issue with packaging data

CHANGES

• FIX: Packaging data of FS canary sentinel NIfTI (#535)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.2.4

Release Notes

Bug-fix release improving the FS license checking

CHANGES

• ENH: Improve FS license checking (#533)

- Python
Published by oesteban over 5 years ago

niworkflows - 1.2.3

Release Notes

Bug-fix release addressing some downstream issues in fMRIPrep.

CHANGES

• FIX: MultiLabel interpolations should not use float=True (#530)
• FIX: Do not break figure-datatype derivatives by sessions (#529)
• MNT: Update comments, minimum versions for setup requirements (#512)

- Python
Published by oesteban almost 6 years ago

niworkflows - 1.2.2

Release Notes

A bug-fix release remedying a casting issue in DerivativesDataSink.

Changes

• FIX: Non-integer data coercion initialization (#528)

- Python
Published by mgxd almost 6 years ago

niworkflows - 1.2.1

Release Notes

A bug-fix release in the 1.2.x series. This ensures consistency of datatype (dataobj, header) when casting to a new type in DerivativesDataSink.

Changes

• FIX: Ensure consistency when changing derivative datatype (#527)

- Python
Published by mgxd almost 6 years ago

niworkflows - 1.2.0

Release notes

First release in the 1.2.x series. This release includes a variety of enhancements and bug fixes, including a large scale refactoring of DerivativesDataSink.

CHANGES

• FIX: Purge greedy lstrip from reports (#521)
• FIX: Add DWI default patterns for dMRIPrep's reportlets (#504)
• FIX: Merge/SplitSeries write to path of input image, instead of cwd (#503)
• FIX: Better generalization and renaming+relocation in the API of extract_wm (#500)
• FIX: Increase fault tolerance of DerivativesDataSink (#497)
• FIX: Match N4-only workflow outputs to brain extraction workflow (#496)
• FIX: Set default volumetric resolution within OutputReferencesAction to native (#494)
• ENH: Upstream NiTransforms module from fMRIPrep (#525)
• ENH: Improve DerivativesDataSink flexibility (#507) (#514) (#516)
• ENH: Add utility function to quickly check for FS license (#505)
• ENH: Add NiBabel-based split and merge interfaces (#489)
• ENH: Show registration reportlets inline within Jupyter notebooks (#493)
• ENH: Ensure subcortical volume in CIFTI is in LAS orientation (#484)
• ENH: Produce carpetplot from CIFTI file (#491)
• ENH: Option to set DerivativesDataSink datatype (#492) (#495)
• MAINT: Revert #496 -- N4-only workflow connections (#498)
• MAINT: Transfer brainmask script from fMRIPrep (#488)

- Python
Published by oesteban almost 6 years ago

niworkflows - 1.2.0rc5

- Python
Published by oesteban almost 6 years ago

niworkflows - 1.2.0rc4

- Python
Published by oesteban almost 6 years ago

niworkflows - 1.1.12

Release Notes

Bug-fix release in the 1.1.x series.

CHANGES

• FIX: Update naming patterns in figures.json (#483)
• FIX: Add CE agent to output figure filename templates (#482)

- Python
Published by effigies almost 6 years ago

niworkflows - 1.1.11

Release Notes

Bug-fix release to improve CIFTI compatibility with workbench tools.

CHANGES

• FIX: Ensure BOLD and label orientations are equal (#477)

- Python
Published by effigies almost 6 years ago

niworkflows - 1.1.10

Release Notes

Bug-fix release in the 1.1.x series.

CHANGES

• ENH: Overwrite attr's string conversion dunders (#475)

- Python
Published by oesteban almost 6 years ago

niworkflows - 1.1.9

Release Notes

Bug-fix release in the 1.1.x series.

This release contains maintenance actions on the CI infrastructure after migration to the NiPreps organization.

CHANGES

• FIX: replace mutable list with tuple in ANTs' workflow (#473)
• MAINT: Pacify security patterns found by Codacy (#474)
• MAINT: Miscellaneous housekeeping (#472)
• MAINT: Fix test_masks (#470)
• MAINT: Use docker-registry for caching on CircleCI (#471)
• MAINT: Revise code coverage collection (#469)
• MAINT: Transfer to nipreps organization (#468)

- Python
Published by oesteban almost 6 years ago

niworkflows - 1.1.8

Release Notes

Bug-fix release in the 1.1.x series.

This release includes some minor improvements to the formatting of reports and derivative metadata.

CHANGES

• FIX: Check fo valid qform before calculating change (#466) @effigies
• ENH: Display errors as summary/details elements (#464) @effigies
• ENH: Add a pure-Python ApplyMask interface, based on NiBabel (#463) @oesteban
• MAINT: Replace os operations with pathlib, indent JSON sidecars (#467) @mgxd

- Python
Published by oesteban almost 6 years ago

niworkflows - 1.1.7

Release Notes

Minor improvements to enable fMRIPrep 20.0.0 release.

CHANGES

• ENH: Revise SpatialReference caching for ease of use, accessibility (#461) @mgxd
• ENH: Downgrade log level for superfluous scans (#460) @mgxd
• ENH: Enable optional BIDS entity filtering to data collection utility (#407) @bpinsard

- Python
Published by mgxd about 6 years ago

niworkflows - 1.1.6

Release Notes

Update NiBabel pinned version.

CHANGES

• MAINT: Update nibabel's pin to >=3.0.1

- Python
Published by oesteban about 6 years ago

niworkflows - 1.1.5

Release Notes

A refactor of recently introduced spaces/references/spatial-references objects, and some methods for upstream pipelines.

CHANGES

• ENH: Revision of spaces module for consistency (#457)
• ENH: Add BIDS output version checker (#456)
• ENH: Standard space querying (#455)
• ENH: Add cache to SpatialReferences (#453)
• ENH: Add helper function for cleaning a directory (#454)
• FIX: Parsing of floats in ResampleImageBySpacing (#452)

- Python
Published by mgxd about 6 years ago

niworkflows - 1.1.4

Release Notes

Minor enhancements to better represent spaces/spatial-references, and increasing the test coverage of the Reports System (with thanks to J. Kent for the contribution):

CHANGES

• ENH: Separate Space and SpatialReferences (#451)
• ENH+TST: Add all valid entities to the default report specification (#447)

- Python
Published by oesteban about 6 years ago

niworkflows - 1.1.3

Release Notes

A fix/enhancement of the report generation system. With thanks to J. Kent for the contribution.

CHANGES

• ENH/FIX: parse orderings to account for missing entities (#443)

- Python
Published by oesteban about 6 years ago

niworkflows - 1.0.3

Release Notes

Hot-fix release in the 1.0.x series. Backported from 1.1.2.

CHANGES

• FIX: IntraModalMerge - Undefined input name used in _run_interface (#442)
• FIX: IntraModalMerge failed for dims (x, y, z, 1) (#441) @oesteban

- Python
Published by oesteban about 6 years ago

niworkflows - 1.1.2

Release Notes

Hotfix of 1.1.1

CHANGES

• FIX: IntraModalMerge - Undefined input name used in _run_interface (#442)

- Python
Published by oesteban about 6 years ago

niworkflows - 1.1.1

Release Notes

A bugfix release to support addressing poldracklab/sdcflows#77. With thanks to Alejandro De La Vega for contributions.

CHANGES

• FIX: IntraModalMerge failed for dims (x, y, z, 1) (#441) @oesteban
• ENH: Add n4_only workflow -- to skip brain extraction (#435) @adelavega
• MAINT: Update nibabel to 3.0.0rc1 (#439) @mgxd

- Python
Published by oesteban about 6 years ago

niworkflows - 1.0.2

Release Notes

Bug-fix release in the 1.0.x series.

CHANGES

• FIX: Permit dummy scans to be 0 (#438) @jdkent
• MNT: Specify junit_family to suppress pytest DeprecationWarning (#432) @effigies

- Python
Published by effigies about 6 years ago

niworkflows - 1.1.0

Release Notes

The first minor release of the niworkflows 1.x series. Numerous interfaces (GenerateCifti, CiftiNameSource, GiftiNameSource) have been changed to be compatible with HCP grayordinates.

CHANGES

• ENH: CIFTI / fsLR density (#436) @mgxd
• ENH: expand GenerateCifti & MedialNaNs interfaces to support HCP grayordinates / fsLR surfaces (#417) @mgxd

- Python
Published by release-drafter[bot] about 6 years ago

niworkflows - 1.0.1

Release Notes

Bug-fix release in the 1.0.x series.

CHANGES

• FIX: Ensure data type of masked image matches T1.mgz (#430) @effigies

- Python
Published by effigies over 6 years ago

niworkflows - 1.0.0

Release Notes

The first stable release of NIWorkflows.

CHANGES

• CI: Drop setup.py install/develop installs (#428) @effigies
• DOC: Maintenance of the documentation building (#429) @oesteban
• DOC: Generate versioned documentation of the API (#416) @rwblair
• ENH: Add copy_header inputs to some ANTs interfaces (#401) @oesteban
• ENH: Remove the data getters/utils modules (#427) @oesteban
• ENH: Move nilearn interfaces over from fMRIPrep (#414) @oesteban
• ENH: Reports use the default template from niworkflows, allowing overwrite (#419) @oesteban
• FIX: Update all SpatialImage.get_data -> get_fdata (#426) @oesteban
• MAINT: Update .gitignore and .dockerignore (#420) @oesteban
• MAINT: use scikit-image LTS for earlier python versions (#418) @mgxd
• MAINT: Pin nipype>=1.3.1, remove link dependencies from setup.cfg @oesteban

- Python
Published by oesteban over 6 years ago

niworkflows - 1.0.0rc2

- Python
Published by oesteban over 6 years ago

niworkflows - 1.0.0rc1

- Python
Published by oesteban over 6 years ago

niworkflows - 0.10.4

Release Notes

Patch release with a few small bug fixes and improvements.

CHANGES

• FIX: Remove unused, undocumented output from the bold_reference workflow (#409) @oesteban
• FIX: Do not validate built paths (#405) @effigies
• FIX: Ensure that length of indices matches length of values (#397) @rciric
• ENH: Add a new Binarize interface using nibabel (#402) @oesteban
• ENH: Enable BIDSFreeSurferDir to take an absolute path as a subjects directory (#398) @effigies
• TEST: Separate LTA length fixing and add doctest (#403) @davhunt

- Python
Published by oesteban over 6 years ago

niworkflows - 0.10.3

Release Notes

Patch release with several bugfixes and two improvements on how NIfTI files were handled. With thanks to David Hunt and Ursula Tooley for contributions.

CHANGES

• ENH: Memory optimized header rewriting (#386) @effigies
• ENH: Warn about copying sform to qform only if qform changes (#365) @utooley
• FIX: Nonpositive values entered to N4 when calculating BOLDrefs (#389) @oesteban
• FIX: Retain newlines in corrected LTA files (#391) @davhunt
• FIX: Handle singleton decompositions (#383) @rciric
• FIX: Revision of previous PR #337 / MELODIC did not converge (#381) @oesteban
• MAINT:Confound metadata maintenance (#382) @rciric
• TEST: Skip tests with non-Python dependencies when missing (#387) @effigies

- Python
Published by oesteban over 6 years ago

niworkflows - 0.10.3rc1

- Python
Published by oesteban over 6 years ago

niworkflows - 0.10.2

Release Notes

Patch release culminating the migration of workflows from fMRIPrep.

CHANGES

• TST: Bring EPI brain extraction tests from fMRIPrep (#380) @oesteban

- Python
Published by oesteban over 6 years ago

niworkflows - 0.10.1

Release Notes

Patch release with bug fixes and pinning the latest stable release of the TemplateFlow client.

CHANGES

• PIN: latest templateflow client (0.4.1) @oesteban
• FIX: Load file with mmap=False when modifying on-disk dtype (#378) @effigies
• FIX: Require scikit-learn because nilearn does not (#376) @effigies

- Python
Published by oesteban over 6 years ago

niworkflows - 0.10.0

Release Notes

Minor release to allow dependent tools to upgrade to PyBIDS 0.9 series (minimum 0.9.2). We've also moved to a setup.cfg-based setup to standardize configuration.

CHANGES

• MAINT: Use PyBIDS 0.9.2+ (#369) @effigies
• MAINT: Switch to a setup.cfg-based setup (#375) @effigies

- Python
Published by effigies over 6 years ago

niworkflows - 0.9.6

Release Notes

Minor improvements to support some of the requirements generated during the development of fMRIPrep-1.4.1.

CHANGES

• ENH: Improvements to RobustMNINormalization (#368) @oesteban
• RF: Miscellaneous improvements to allow a multiplicity of templates and specs (#366) @oesteban

- Python
Published by oesteban over 6 years ago

niworkflows - 0.9.6rc3

- Python
Published by oesteban over 6 years ago

niworkflows - 0.9.6rc2

- Python
Published by oesteban over 6 years ago