Release Notes

Bug-fix release in the 1.8.x series.

This release sets a maximum traits version to avoid new, breaking changes.

What's Changed

• MNT: Pin traits < 6.4 (#3501) @effigies
• ENH: Add inputs to mrtrix3.DWIPreprocInputSpec and remove mandatory annotation for pe_dir (#3470) @GalBenZvi

Full Changelog: https://github.com/nipy/nipype/compare/1.8.3...1.8.4

Release Notes

Bug-fix release in the 1.8.x series.

This release includes compatibility fixes for nibabel 4.x and resolves a denial-of-service bug when the etelemetry server is down that resulted in excessive (blocking) network hits that would cause any tools using nipype interfaces to take a very long time.

What's Changed

• FIX: Argument order to numpy.save() (https://github.com/nipy/nipype/pull/3485)
• FIX: Add tolerance parameter to ComputeDVARS (https://github.com/nipy/nipype/pull/3489)
• FIX: Delay access of nibabel.trackvis until actually needed (https://github.com/nipy/nipype/pull/3488)
• FIX: Avoid excessive etelemetry pings (https://github.com/nipy/nipype/pull/3484)
• ENH: Added outputs' generation to DWIBiascorrect interface (https://github.com/nipy/nipype/pull/3476)

New Contributors

• @LostBenjamin made their first contribution in https://github.com/nipy/nipype/pull/3485

Full Changelog: https://github.com/nipy/nipype/compare/1.8.2...1.8.3

1.8.1 (May 16, 2022)

Bug-fix release in the 1.8.x series.

The previous release vendored distutils.version.LooseVersion, and the vendored objects did not preserve compatiblity with the distutils objects. This release switches to the looseversion package that ensures compatiblity.

What's Changed

• RF: Use looseversion package instead of vendoring by @effigies in https://github.com/nipy/nipype/pull/3477

Full Changelog: https://github.com/nipy/nipype/compare/1.8.0...1.8.1

1.8.0 (May 10, 2022)

New feature release in the 1.8.x series.

The primary new features are a batch of PETSurfer interfaces.

This release drops support for Python < 3.7 and Numpy < 1.17, triggering a minor version bump. Additionally, matplotlib < 2.1 will stop working with some interfaces, but more recent versions will start working.

Full changelog: https://github.com/nipy/nipype/milestone/1.8.0?closed=1

• FIX: Change plt.hist() argument from deprecated 'normed' to 'density' (https://github.com/nipy/nipype/pull/3455)
• ENH: Add random seed option to ANTs registration (https://github.com/nipy/nipype/pull/3463)
• ENH: Add PETsurfer interfaces (https://github.com/nipy/nipype/pull/3437)
• ENH: Add Text2Vest and Vest2Text interfaces (https://github.com/nipy/nipype/pull/3447)
• REF: Optimize ICC_rep_anova with a memoized helper function (https://github.com/nipy/nipype/pull/3454)
• REF: Rearranging matmul order and using hermitian flag in ICC_rep_anova (https://github.com/nipy/nipype/pull/3453)
• MNT: Drop distutils (https://github.com/nipy/nipype/pull/3458)
• CI: Cache test data (https://github.com/nipy/nipype/pull/3459)

New Contributors

• @mnoergaard made their first contribution in https://github.com/nipy/nipype/pull/3437
• @kristoferm94 made their first contribution in https://github.com/nipy/nipype/pull/3453
• @sjshim made their first contribution in https://github.com/nipy/nipype/pull/3455
• @ghisvail made their first contribution in https://github.com/nipy/nipype/pull/3463

Full Changelog: https://github.com/nipy/nipype/compare/1.7.1...1.8.0

1.7.1 (April 05, 2022)

Bug-fix release in the 1.7.x series.

• FIX: Allow ConvertScalarImageToRGBInputSpec.mask_file to be "none" (https://github.com/nipy/nipype/pull/3364)
• FIX: Use a more robust strategy for detecting ANTs version (https://github.com/nipy/nipype/pull/3444)
• FIX: Retry renaming pkl(z) files on failure (https://github.com/nipy/nipype/pull/3404)
• FIX: Escape metacharacters when parsing dcm2niix outputs (https://github.com/nipy/nipype/pull/3417)
• FIX: Import error for nipype.interfaces.dipy.base (https://github.com/nipy/nipype/pull/3414)
• FIX: ValueError when using ResourceMonitor (https://github.com/nipy/nipype/pull/3419)
• FIX: Improve error handling of CommandLine interfaces (https://github.com/nipy/nipype/pull/3395)
• FIX: Bugs in ApplyVDM interface (https://github.com/nipy/nipype/pull/3396)
• ENH: Add MRTrix3 interfaces (pared-down gh-3426) (https://github.com/nipy/nipype/pull/3445)
• ENH: Enable BidsDataGrabber to load saved layouts (https://github.com/nipy/nipype/pull/3421)
• ENH: ROBEX interface (https://github.com/nipy/nipype/pull/3443)
• ENH: Include several operations to ANTs's ImageMath interface, including ReplicateImage and ReplicateDisplacement (https://github.com/nipy/nipype/pull/3435)
• ENH: Add "GenericLabel" to antsRegistration interpolation option. (https://github.com/nipy/nipype/pull/3424)
• ENH: added Apply VDM functionality to FieldMap SPM interface (https://github.com/nipy/nipype/pull/3394)
• DOC: Side bar and main page fixes (https://github.com/nipy/nipype/pull/3397)
• TEST: Allow SVD columns to flip sign (https://github.com/nipy/nipype/pull/3405)
• MNT: rename dipy move_streamlines to transform_tracking_output (https://github.com/nipy/nipype/pull/3412)
• MNT: Test on Python 3.10 (https://github.com/nipy/nipype/pull/3438)
• MNT: Added ORCID iD (https://github.com/nipy/nipype/pull/3436)

New Contributors

• @fabioboh made their first contribution in https://github.com/nipy/nipype/pull/3394
• @qian587 made their first contribution in https://github.com/nipy/nipype/pull/3417
• @dmartindeblas made their first contribution in https://github.com/nipy/nipype/pull/3435
• @gaunab made their first contribution in https://github.com/nipy/nipype/pull/3421
• @ChristianHinge made their first contribution in https://github.com/nipy/nipype/pull/3364

Full Changelog: https://github.com/nipy/nipype/compare/1.7.0...1.7.1

1.7.0 (October 20, 2021)

New feature release in the 1.7.x series.

(Full changelog

• FIX: Make ants.LaplacianThickness output_image a string, not file (https://github.com/nipy/nipype/pull/3393)
• FIX: coord for mrconvert (https://github.com/nipy/nipype/pull/3369)
• FIX: antsRegistration allows the restrict_deformation to be float (https://github.com/nipy/nipype/pull/3387)
• FIX: Also allow errno.EBUSY during emptydirs on NFS (https://github.com/nipy/nipype/pull/3357)
• FIX: Removed exists=True from MathsOutput (https://github.com/nipy/nipype/pull/3385)
• FIX: Extension not extensions, after pybids v0.9 (https://github.com/nipy/nipype/pull/3380)
• ENH: Add CAT12 SANLM denoising filter (https://github.com/nipy/nipype/pull/3374)
• ENH: Add expected steps for FreeSurfer 7 recon-all (https://github.com/nipy/nipype/pull/3389)
• ENH: Stop printing false positive differences when logging cached nodes (https://github.com/nipy/nipype/pull/3376)
• ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform) (https://github.com/nipy/nipype/pull/3365)
• ENH: verbose input should not be hashed in ants.Registration (https://github.com/nipy/nipype/pull/3377)
• REF: Clean-up the BaseInterface run() function using context (https://github.com/nipy/nipype/pull/3347)
• DOC: Fix typo in README (https://github.com/nipy/nipype/pull/3386)
• STY: Make private member name consistent with the rest of them (https://github.com/nipy/nipype/pull/3346)
• MNT: Simplify interface execution and better error handling of Node (https://github.com/nipy/nipype/pull/3349)
• MNT: Add user name and email to Docker to appease git/annex/datalad (https://github.com/nipy/nipype/pull/3378)
• CI: Update CircleCI machine image (https://github.com/nipy/nipype/pull/3391)

1.5.1 (August 16, 2020)

Bug-fix release in the 1.5.x series.

This release includes small updates to ANTs utilities that lie somewhere between bug fixes and enhancements.

(Full changelog)

• FIX: Warn for min/max_ver traits when tool version can't be parsed (#3241)
• FIX: Serialize all interface arguments when exporting workflows (#3240)
• FIX: Permit identity transforms in list of transforms given to ants.ApplyTransforms (#3237)
• FIX: ANTs' utilities revision - bug fixes and add more operations to ants.ImageMath (#3236)
• DOC: Skip BIDSDataGrabber doctest if pybids is missing (#3224)

1.5.0 (June 03, 2020)

New feature release in the 1.5.x series.

In this release, the example scripts have been split out into their own package: niflow-nipype1-examples.

(Full changelog)

• FIX: volterra_expansion_order documentation error (https://github.com/nipy/nipype/pull/3213)
• FIX: BET incorrect output paths (https://github.com/nipy/nipype/pull/3214)
• FIX: Terminal output in report.rst spreads one line per character (https://github.com/nipy/nipype/pull/3220)
• FIX: Allow parsing freesurfer 7 version string (https://github.com/nipy/nipype/pull/3216)
• FIX: Use PackageInfo to get NiftyReg version (https://github.com/nipy/nipype/pull/3194)
• FIX: Partial rollback of N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3188)
• FIX: ANTs' tools maintenance overhaul (https://github.com/nipy/nipype/pull/3180)
• FIX: load_resultfile crashes if open resultsfile from crashed job (https://github.com/nipy/nipype/pull/3182)
• FIX: FSL model.py make multiple F-tests (https://github.com/nipy/nipype/pull/3166)
• ENH: Restore ants.legacy interfaces (https://github.com/nipy/nipype/pull/3222)
• ENH: Add "TruncateImageIntensity" operation to ants.utils.Image.Math (https://github.com/nipy/nipype/pull/3210)
• ENH: SPM NewSegment multi-channel segmentation (https://github.com/nipy/nipype/pull/3162)
• ENH: Add reverse-ordered transform lists to ants.Registration outputs (https://github.com/nipy/nipype/pull/3192)
• ENH: Improve workflow connect performance (https://github.com/nipy/nipype/pull/3184)
• ENH: Add ConstrainedSphericalDeconvolution interface to replace EstimateFOD for MRtrix3's dwi2fod (https://github.com/nipy/nipype/pull/3176)
• ENH: Detect values for EulerNumber interface (https://github.com/nipy/nipype/pull/3173)
• ENH: Remove examples from repository (https://github.com/nipy/nipype/pull/3172)
• TEST: Clean up tests (https://github.com/nipy/nipype/pull/3195)
• TEST: Mock terminal output before testing changing default value (https://github.com/nipy/nipype/pull/3193)
• REF: make invocations of python and pytest consistent with the one used/desired python (https://github.com/nipy/nipype/pull/3208)
• REF: Prefer math.gcd to hand-rolled Euclid's algorithm (https://github.com/nipy/nipype/pull/3177)
• REF: Removed all uses of numpy_mmap (https://github.com/nipy/nipype/pull/3121)
• DOC: Sphinx 3 compatibility (https://github.com/nipy/nipype/pull/3206)
• DOC: Update links, typos in contributing guide (https://github.com/nipy/nipype/pull/3160)
• DOC: Update SelectFiles docstring to match actual behavior (https://github.com/nipy/nipype/pull/3041)
• DOC: Updated .zenodo.json file (https://github.com/nipy/nipype/pull/3167)
• DOC: Update .zenodo.json (https://github.com/nipy/nipype/pull/3165)
• MNT: Permit recent nilearns (https://github.com/nipy/nipype/pull/2841)
• MNT: Test Python 3.8 (https://github.com/nipy/nipype/pull/3154)
• MNT: Restore ReadTheDocs (https://github.com/nipy/nipype/pull/3207)
• MNT: Update Zenodo ordering based on commit count (https://github.com/nipy/nipype/pull/3169)

1.4.2 (February 14, 2020)

Bug-fix release in the 1.4.x series. Contains patches to accommodate API changes in Traits 6.0.

Full changelog

• FIX: Allow fsl.MultipleRegressDesign to create multiple F-tests (https://github.com/nipy/nipype/pull/3166)
• FIX: Reliably parse SGE job IDs in the presence of warnings (https://github.com/nipy/nipype/pull/3168)
• FIX: Move TraitType import, handle API change for NoDefaultSpecified (https://github.com/nipy/nipype/pull/3159)

1.4.1 (January 27, 2020)

Full changelog

• FIX: DataSink to S3 buckets (https://github.com/nipy/nipype/pull/3130)
• FIX: improve version checking for nodes of workflows (https://github.com/nipy/nipype/pull/3152)
• FIX: mapnode to generate result file when crashes in single node mode (https://github.com/nipy/nipype/pull/3143)
• FIX: Can't seem to import workflows from niflows in CircleCI (https://github.com/nipy/nipype/pull/3134)
• FIX: Repair aftermath of docs refactor (https://github.com/nipy/nipype/pull/3133)
• FIX: change ANTS number_of_time_steps from Float to Int (https://github.com/nipy/nipype/pull/3118)
• DOC: Revise generation of examples to work in RTD (https://github.com/nipy/nipype/pull/3132)
• DOC: Bring examples generation back to doc/conf.py (https://github.com/nipy/nipype/pull/3131)
• DOC: Documentation overhaul (https://github.com/nipy/nipype/pull/3124)
• DOC: Deep revision of documentation building (https://github.com/nipy/nipype/pull/3120)
• DOC: Deduplicate code for Sphinx's APIdoc generation (https://github.com/nipy/nipype/pull/3119)
• MNT: Update requirements.txt post-1.4 (https://github.com/nipy/nipype/pull/3153)