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Recent Releases of nipype

nipype - 1.10.0

Release Notes

New feature release in the 1.10.x series.

This release adds GPUs to multiprocess resource management. In general, no changes to existing code should be required if the GPU-enabled interface has a use_gpu input. The n_gpu_procs can be used to set the number of GPU processes that may be run in parallel, which will override the default of GPUs identified by nvidia-smi, or 1 if no GPUs are detected.

What's Changed

  • FIX: Reimplement gpu_count() (https://github.com/nipy/nipype/pull/3718)
  • FIX: Avoid 0D array in algorithms.misc.merge_rois (https://github.com/nipy/nipype/pull/3713)
  • FIX: Allow nipype.sphinx.ext.apidoc Config to work with Sphinx 8.2.1+ (https://github.com/nipy/nipype/pull/3716)
  • FIX: Resolve crashes when running workflows with updatehash=True (https://github.com/nipy/nipype/pull/3709)
  • ENH: Support for gpu queue (https://github.com/nipy/nipype/pull/3642)
  • ENH: Update to .wci.yml (https://github.com/nipy/nipype/pull/3708)
  • ENH: Add Workflow Community Initiative (WCI) descriptor (https://github.com/nipy/nipype/pull/3608)

New Contributors

  • @u11kumar made their first contribution in https://github.com/nipy/nipype/pull/3608
  • @rafaelfsilva made their first contribution in https://github.com/nipy/nipype/pull/3708
  • @man-shu made their first contribution in https://github.com/nipy/nipype/pull/3713

Full Changelog: https://github.com/nipy/nipype/compare/1.9.2...1.10.0

- Python
Published by effigies 11 months ago

nipype - 1.9.2

Release Notes

Bug fix release in the 1.9.x series.

What's Changed

  • FIX: Missed np.savetxt bstring (https://github.com/nipy/nipype/pull/3704)
  • MAINT: Bump astral-sh/setup-uv from 3 to 4 (https://github.com/nipy/nipype/pull/3702)
  • MAINT: Bump codecov/codecov-action from 4 to 5 (https://github.com/nipy/nipype/pull/3703)

Full Changelog: https://github.com/nipy/nipype/compare/1.9.1...1.9.2

- Python
Published by effigies 11 months ago

nipype - 1.9.1

Release Notes

Bug fix release in the 1.9.x series.

This release adds support for Numpy 2 and Python 3.13.

What's Changed

  • FIX: Restore generateganttchart functionality (https://github.com/nipy/nipype/pull/3290)
  • FIX: Address numpy and traits deprecations (https://github.com/nipy/nipype/pull/3699)
  • FIX: ts_Z_corr → ts_wb_Z (https://github.com/nipy/nipype/pull/3697)
  • ENH: Remove unused and recently unsupported antsRegistration flag (https://github.com/nipy/nipype/pull/3695)
  • MAINT: Bump codecov/codecov-action from 4 to 5 (https://github.com/nipy/nipype/pull/3698)

New Contributors

  • @shnizzedy made their first contribution in https://github.com/nipy/nipype/pull/3697

Full Changelog: https://github.com/nipy/nipype/compare/1.9.0...1.9.1

- Python
Published by effigies 11 months ago

nipype - 1.9.0

Release Notes

New feature release in the 1.9.x series.

What's Changed

  • FIX: Remove exists=True from fsl.MotionOutliers output that might not exist (https://github.com/n
  • FIX: Improve evaluateconnectfunction errors across Python versions (https://github.com/nipy/nip
  • FIX: Changed inheritance of TensorMetricsInputSpec (https://github.com/nipy/nipype/pull/3663)
  • FIX: Add cropped files to dcm2niix output (https://github.com/nipy/nipype/pull/3609)
  • FIX: Deduplicate dcm2niix output (https://github.com/nipy/nipype/pull/3610)
  • FIX: Parse commas in CSV fields (https://github.com/nipy/nipype/pull/3637)
  • FIX: MRTrix3 change inputs position for MRTransform (https://github.com/nipy/nipype/pull/3611)
  • FIX: Use out_prefix instead of "w" in spm.Normalize12 (https://github.com/nipy/nipype/pull/3600)
  • FIX: Fix typo in spm.Normalize12 process (https://github.com/nipy/nipype/pull/3599)
  • FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596)
  • FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596)
  • FIX: Fix bugs with fsl_out=True and lta_out=True (https://github.com/nipy/nipype/pull/358
  • FIX: Test failures (https://github.com/nipy/nipype/pull/3587)
  • FIX: update merge_imgs input type of dcm2niix Node (https://github.com/nipy/nipype/pull/3548)
  • FIX: update samplerandompoints and random_seed type of ProbTrackXBaseInputSpec (https://github.
  • FIX: update self.inputs.optimization in outputs for GTMPVC (https://github.com/nipy/nipype/pull/3
  • ENH: Support HDF5 (mat 7.3) SPM.mat files (https://github.com/nipy/nipype/pull/3650)
  • ENH: FILMGLS gifti output support in surface mode (https://github.com/nipy/nipype/pull/3652)
  • ENH: Added available inputs for MRTrix3's 5ttgen (https://github.com/nipy/nipype/pull/3658)
  • ENH: Add functions to mrtrix3 interface (https://github.com/nipy/nipype/pull/3613)
  • ENH: Update PETsurfer interface (https://github.com/nipy/nipype/pull/3602)
  • ENH: Add 'hsvs' option to 5ttgen + mrtransform fix (https://github.com/nipy/nipype/pull/3630)
  • ENH: add STC PVC to PETPVC interface (https://github.com/nipy/nipype/pull/3634)
  • ENH: Add GenericLabel to ANTS ApplyTransforms. (https://github.com/nipy/nipype/pull/3617)
  • ENH: Issue 3553 add mvecs to dcm2niix (https://github.com/nipy/nipype/pull/3554)
  • ENH: add contrast outputs for EstimatedModel (https://github.com/nipy/nipype/pull/3577)
  • ENH: Issue 3345: Adding FreeSurfer longitudinal interfaces (https://github.com/nipy/nipype/pull/3
  • ENH: Enable SPM voxel-based FDR (https://github.com/nipy/nipype/pull/3558)
  • REF: Replace deprecated pkgutil.findloader with importlib.util.findspec (https://github.com/nip
  • REF: io.open() → open() (https://github.com/nipy/nipype/pull/3575)
  • REF: Stop using deprecated import internally (https://github.com/nipy/nipype/pull/3561)
  • DOC: Patch doc/conf.py to work with latest ReadTheDocs (https://github.com/nipy/nipype/pull/3691)
  • DOC/FIX: Fix wrong name, should be al_ea (https://github.com/nipy/nipype/pull/3629)
  • DOC: Fix typos newly found by codespell (https://github.com/nipy/nipype/pull/3606)
  • STY: Apply ruff/pycodestyle rules (E) (https://github.com/nipy/nipype/pull/3689)
  • STY: Apply ruff rules (RUF) again (https://github.com/nipy/nipype/pull/3688)
  • STY: Apply ruff/Pyflakes rules (F) (https://github.com/nipy/nipype/pull/3681)
  • STY: Apply ruff/Perflint rules (PERF) again (https://github.com/nipy/nipype/pull/3687)
  • STY: Apply ruff/flake8-comprehensions preview rules (C4) (https://github.com/nipy/nipype/pull/368
  • STY: Apply ruff/flake8-simplify rules (SIM) (https://github.com/nipy/nipype/pull/3676)
  • STY: Apply ruff/flake8-bugbear rules (B) (https://github.com/nipy/nipype/pull/3671)
  • STY: Apply ruff/flake8-comprehensions rules (C4) (https://github.com/nipy/nipype/pull/3680)
  • STY: Apply ruff/Perflint rules (PERF) (https://github.com/nipy/nipype/pull/3674)
  • STY: Apply ruff/flake8-implicit-str-concat rules (ISC) (https://github.com/nipy/nipype/pull/3679)
  • STY: Apply ruff/flake8-pie rules (PIE) (https://github.com/nipy/nipype/pull/3678)
  • STY: Apply ruff/flake8-raise rules (RSE) (https://github.com/nipy/nipype/pull/3677)
  • STY: Apply ruff/flynt rules (FLY) (https://github.com/nipy/nipype/pull/3675)
  • STY: Apply ruff rules (RUF) (https://github.com/nipy/nipype/pull/3673)
  • STY: Codespell (https://github.com/nipy/nipype/pull/3672)
  • STY: Apply ruff/refurb rules (https://github.com/nipy/nipype/pull/3648)
  • STY: Apply ruff/pyupgrade rules (https://github.com/nipy/nipype/pull/3647)
  • STY: Adjusted variable names for clarity and codespell false positives (https://github.com/nipy/n
  • STY: Remove duplicated trait in EddyOutputSpec (https://github.com/nipy/nipype/pull/3568)
  • STY: Black edits (https://github.com/nipy/nipype/pull/1)
  • MNT: Replace deprecated imghdr (https://github.com/nipy/nipype/pull/3659)
  • MNT: Use regular ".now" instead of ".utcnow" with UTC zone (https://github.com/nipy/nipype/pull/3
  • MNT: Apply assorted repo-review rules (https://github.com/nipy/nipype/pull/3682)
  • MNT: Drop traits upper bound (https://github.com/nipy/nipype/pull/3685)
  • MNT: Configure dependabot to update GH workflows (https://github.com/nipy/nipype/pull/3597)
  • MNT: Replace deprecated locale.getdefaultlocale (https://github.com/nipy/nipype/pull/3590)
  • MNT: Require Python 3.8+, auto-upgrade syntax (https://github.com/nipy/nipype/pull/3588)
  • CI: Test Python 3.12 support (https://github.com/nipy/nipype/pull/3638)
  • CI: Test on Python 3.11 (https://github.com/nipy/nipype/pull/3589)
  • CI/FIX: configure codespell, add workflow, typos fixed (https://github.com/nipy/nipype/pull/3549)

New Contributors

  • @asmacdo made their first contribution in https://github.com/nipy/nipype/pull/3561
  • @yibeichan made their first contribution in https://github.com/nipy/nipype/pull/3568
  • @mmbannert made their first contribution in https://github.com/nipy/nipype/pull/3558
  • @l-espana made their first contribution in https://github.com/nipy/nipype/pull/3529
  • @jadecci made their first contribution in https://github.com/nipy/nipype/pull/3583
  • @manuegrx made their first contribution in https://github.com/nipy/nipype/pull/3577
  • @pvelasco made their first contribution in https://github.com/nipy/nipype/pull/3554
  • @stebo85 made their first contribution in https://github.com/nipy/nipype/pull/3629
  • @zachlindsey made their first contribution in https://github.com/nipy/nipype/pull/3637
  • @teanijarv made their first contribution in https://github.com/nipy/nipype/pull/3630
  • @lbutry made their first contribution in https://github.com/nipy/nipype/pull/3613
  • @penguinpee made their first contribution in https://github.com/nipy/nipype/pull/3659
  • @bogpetre made their first contribution in https://github.com/nipy/nipype/pull/3652
  • @scott-huberty made their first contribution in https://github.com/nipy/nipype/pull/3655
  • @adamnarai made their first contribution in https://github.com/nipy/nipype/pull/3650
  • @beausievers made their first contribution in https://github.com/nipy/nipype/pull/1428

Full Changelog: https://github.com/nipy/nipype/compare/1.8.6...1.9.0

- Python
Published by effigies 11 months ago

nipype - 1.8.6

Release Notes

Bug-fix release in the 1.8.x series.

What's Changed

  • FIX: Update dcmstack interface for Py3 / newer pydicom (https://github.com/nipy/nipype/pull/3541)
  • FIX: NiBabel 5, and NetworkX 3 and DIPY 1.6 compatibility (https://github.com/nipy/nipype/pull/3538)
  • FIX: Check for non-mandatory output in DWIBiasCorrect (https://github.com/nipy/nipype/pull/3523)
  • FIX: Removed leftover debug print statement in FEAT class (https://github.com/nipy/nipype/pull/3521)
  • DOC: Fix a few more typos (https://github.com/nipy/nipype/pull/3516)
  • DOC: Fix typos found by codespell (https://github.com/nipy/nipype/pull/3512)
  • CI: Drop nipy tests until a fixed nipy is released (https://github.com/nipy/nipype/pull/3559)
  • CI: Disable nipy tests generally, re-add with max numpy (https://github.com/nipy/nipype/pull/3532)
  • CI: GitHub Workflows security hardening (https://github.com/nipy/nipype/pull/3519)
  • CI: Allow tutorial test cancellation (https://github.com/nipy/nipype/pull/3514)

New Contributors

  • @somso2e made their first contribution in https://github.com/nipy/nipype/pull/3521
  • @MatthieuJoulot made their first contribution in https://github.com/nipy/nipype/pull/3523
  • @sashashura made their first contribution in https://github.com/nipy/nipype/pull/3519

Full Changelog: https://github.com/nipy/nipype/compare/1.8.5...1.8.6

- Python
Published by effigies 11 months ago

nipype - 1.8.5

Release notes

Bug-fix release in the 1.8.x series.

What's Changed

  • FIX: Use interpolation/method in numpy.percentile as available (https://github.com/nipy/nipype/pull/3506)
  • FIX: Deployed Matlab applications must not call addpath() (https://github.com/nipy/nipype/pull/3509)
  • FIX: Provide more runtime information when node execution fails (https://github.com/nipy/nipype/pull/3505)
  • FIX: Fixed bug for work dirs longer than 255 characters, fixes #2061 (https://github.com/nipy/nipype/pull/3495)
  • FIX: Update ApplyVDM to handle 4D inputs (https://github.com/nipy/nipype/pull/3500)
  • ENH: Explicitly specify write_text encoding format (https://github.com/nipy/nipype/pull/3508)
  • DOC: Fix typos found by copdespell (https://github.com/nipy/nipype/pull/3510)
  • MAINT: Add github action to trigger tutorials for release branches (https://github.com/nipy/nipype/pull/3504)
  • CI: Set up build-test-deploy workflow on GHA (https://github.com/nipy/nipype/pull/3513)

New Contributors

  • @prioux made their first contribution in https://github.com/nipy/nipype/pull/3495

Full Changelog: https://github.com/nipy/nipype/compare/1.8.4...1.8.5

- Python
Published by effigies 11 months ago

nipype - 1.8.4

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

- Python
Published by release-drafter[bot] over 3 years ago

nipype - 1.8.3

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

- Python
Published by effigies over 3 years ago

nipype - 1.8.1

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

- Python
Published by effigies almost 4 years ago

nipype - 1.8.0

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 ICCrepanova with a memoized helper function (https://github.com/nipy/nipype/pull/3454)
  • REF: Rearranging matmul order and using hermitian flag in ICCrepanova (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

- Python
Published by effigies almost 4 years ago

nipype - 1.7.1

DOI

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

- Python
Published by effigies almost 4 years ago

nipype - 1.7.0

DOI

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)

- Python
Published by effigies over 4 years ago

nipype - 1.5.1

DOI

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)

- Python
Published by effigies over 5 years ago

nipype - 1.5.0

1.5.0 (June 03, 2020)

DOI

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: volterraexpansionorder 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)

- Python
Published by effigies over 5 years ago

nipype - 1.4.2

1.4.2 (February 14, 2020)

DOI

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)

- Python
Published by effigies about 6 years ago

nipype - 1.4.1

1.4.1 (January 27, 2020)

DOI

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 numberoftime_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)

- Python
Published by effigies about 6 years ago

nipype - 1.4.0

1.4.0 (December 20, 2019)

DOI

Full changelog
  • FIX: Mark strings containing regex escapes as raw (https://github.com/nipy/nipype/pull/3106)
  • ENH: Pacify DeprecationWarnings caused by nibabel 3 pre-release (https://github.com/nipy/nipype/pull/3099)
  • ENH: Allow Nipype configuration directory to be specified with NIPYPECONFIGDIR environment variable (https://github.com/nipy/nipype/pull/3073)
  • ENH: Add options and outputs to fsl.Eddy interface (https://github.com/nipy/nipype/pull/3034)
  • ENH: Add skull_file output to fsl.BET interface (https://github.com/nipy/nipype/pull/3095)
  • RF: Drop various remaining compatibilities for Python < 3.5 (https://github.com/nipy/nipype/pull/2831)
  • DOC: Add Python 2 statement to README, reference maintenance branch in CONTRIBUTING (https://github.com/nipy/nipype/pull/3115)
  • DOC: Miss underline before cmd in example code (https://github.com/nipy/nipype/pull/3107)
  • STY: Black (https://github.com/nipy/nipype/pull/3096)
  • MNT: Set junit_family to suppress pytest warning (https://github.com/nipy/nipype/pull/3111)
  • MNT: Fix Dorota Jarecka ORCID (https://github.com/nipy/nipype/pull/3100)
  • MNT: Drop Python 2 support (https://github.com/nipy/nipype/pull/2654)

- Python
Published by effigies about 6 years ago

nipype - 1.3.1

1.3.1 (November 12, 2019)

  • FIX: Restore checking traits or bunch (https://github.com/nipy/nipype/pull/3094)

- Python
Published by effigies over 6 years ago

nipype - 1.3.0

1.3.0 (November 11, 2019)

DOI

Full changelog
  • FIX: Fixed typo in QwarpInputSpec Trait description (https://github.com/nipy/nipype/pull/3079)
  • FIX: Restore AFNICommand._get_fname, required by some interfaces (https://github.com/nipy/nipype/pull/3071)
  • FIX: Remove asynchronous chdir callback (https://github.com/nipy/nipype/pull/3060)
  • FIX: Minimize scope for directory changes while loading results file (https://github.com/nipy/nipype/pull/3061)
  • ENH: Minimize the number of calls to _load_results when populating inputs (https://github.com/nipy/nipype/pull/3075)
  • ENH: Refactor savepkl/loadpkl - add a window for loadpkl to wait for the file (https://github.com/nipy/nipype/pull/3089)
  • ENH: Add "ExportFile" interface as simple alternative to "DataSink" (https://github.com/nipy/nipype/pull/3054)
  • ENH: Allow nipype.cfg in cwd to be read even if ~/.nipype does not exist (https://github.com/nipy/nipype/pull/3072)
  • ENH: Add precommit information for contributors and pre-commit style (https://github.com/nipy/nipype/pull/3063)
  • ENH: Delay etelemetry for non-interactive sessions, report bad versions (https://github.com/nipy/nipype/pull/3049)
  • ENH: Run memoized check_version at REPL import, Node/Workflow/Interface init (https://github.com/nipy/nipype/pull/30)
  • RF: Provide functions to augment old Path.mkdir, Path.resolve methods (https://github.com/nipy/nipype/pull/3050)
  • RF: Redirect nipype.workflows to niflow.nipype1.workflows (https://github.com/nipy/nipype/pull/3067)
  • TST: Skip dcm2niix test if data fails to download (https://github.com/nipy/nipype/pull/3059)
  • TST: dcm2niix test fix (https://github.com/nipy/nipype/pull/3058)
  • MAINT: Drop Python 3.4 support (https://github.com/nipy/nipype/pull/3062)
  • CI: make specs on Travis (https://github.com/nipy/nipype/pull/3066)

- Python
Published by effigies over 6 years ago

nipype - 1.3.0-rc1

1.3.0-rc1 (October 8, 2019)

DOI

Release candidate for Nipype 1.3.0, released off-schedule to enable testing and allow downstream projects to move off of 1.2.3.

Final release scheduled for Monday, October 28.

Full changelog
  • FIX: Restore AFNICommand._get_fname, required by some interfaces (https://github.com/nipy/nipype/pull/3071)
  • FIX: Remove asynchronous chdir callback (https://github.com/nipy/nipype/pull/3060)
  • FIX: Minimize scope for directory changes while loading results file (https://github.com/nipy/nipype/pull/3061)
  • ENH: Add precommit information for contributors and pre-commit style (https://github.com/nipy/nipype/pull/3063)
  • ENH: Delay etelemetry for non-interactive sessions, report bad versions (https://github.com/nipy/nipype/pull/3049)
  • ENH: Run memoized check_version at REPL import, Node/Workflow/Interface init (https://github.com/nipy/nipype/pull/30)
  • RF: Provide functions to augment old Path.mkdir, Path.resolve methods (https://github.com/nipy/nipype/pull/3050)
  • RF: Redirect nipype.workflows to niflow.nipype1.workflows (https://github.com/nipy/nipype/pull/3067)
  • TST: Skip dcm2niix test if data fails to download (https://github.com/nipy/nipype/pull/3059)
  • TST: dcm2niix test fix (https://github.com/nipy/nipype/pull/3058)
  • MAINT: Drop Python 3.4 support (https://github.com/nipy/nipype/pull/3062)
  • CI: make specs on Travis (https://github.com/nipy/nipype/pull/3066)

- Python
Published by effigies over 6 years ago

nipype - 1.2.3

1.2.3 (September 23, 2019)

DOI

Python 1.2.3 will be the last version to support Python 3.4.

Full changelog
  • FIX: Patch Path.mkdir for Python 2 (https://github.com/nipy/nipype/pull/3037)
  • FIX: Drop deprecated message argument to FileNotFoundError (https://github.com/nipy/nipype/pull/3035)
  • FIX: Handle NIFTI extensions in afni.Qwarp (https://github.com/nipy/nipype/pull/3028)
  • FIX: Disallow returning None in pipeline.utils.load_resultfile (https://github.com/nipy/nipype/pull/3023)
  • ENH: Allow afni.CatMatvec to accept empty string opkeys (https://github.com/nipy/nipype/pull/2943)
  • ENH: Add mrrtrix3.MRResize interface (https://github.com/nipy/nipype/pull/3031)
  • ENH: Add version check / telemetry to Nipype (https://github.com/nipy/nipype/pull/3027)
  • ENH: Update MCFLIRT outputs for FSL 6+ (https://github.com/nipy/nipype/pull/3029)
  • ENH: Lightweight node cache checking (https://github.com/nipy/nipype/pull/3026)
  • ENH: Avoid loading result from file when writing reports (https://github.com/nipy/nipype/pull/3024)
  • ENH: replace portalocker with filelock (https://github.com/nipy/nipype/pull/3025)
  • MAINT: Set minimum yapf for checkspecs to 0.27 (https://github.com/nipy/nipype/pull/3033)

- Python
Published by effigies over 6 years ago

nipype - 1.2.2

1.2.2 (September 07, 2019)

DOI

Full changelog
  • FIX: Ensure loadpkl returns a not None value (#3020)
  • FIX: loadpkl failed when pklz file contained versioning info (#3017)
  • FIX: Update mne.WatershedBEM command line (#3007)
  • FIX: Specify correct stop criterion flag in PETPVC (#3010)
  • ENH: Add interface for AFNI 3dTsmooth (#2948)
  • ENH: Additional arguments to ANTs N4BiasFieldCorrection (#3012)
  • ENH: Add --rescale-intensities and name_source to N4BiasFieldCorrection (#3011)
  • ENH: Add indexmaskfile input to ImageStats (#3005)
  • RF: Remove versioning from loadpkl (#3019)
  • MAINT: Add python_requires to package metadata (#3006)

- Python
Published by oesteban over 6 years ago

nipype - 1.2.1

1.2.1 (August 19, 2019)

DOI

Full changelog
  • FIX: Resolve/rebase paths from/to results files (https://github.com/nipy/nipype/pull/2971)
  • FIX: Use load_resultfile when loading a results pickle (https://github.com/nipy/nipype/pull/2985)
  • FIX: Incorrect extension identified when checking File traits (https://github.com/nipy/nipype/pull/2987)
  • FIX: Correctly pickle OuputMultiObject traits (https://github.com/nipy/nipype/pull/2983)
  • FIX: Improve output handling in DWIDenoise and DWIBiasCorrect (https://github.com/nipy/nipype/pull/2978)
  • FIX: Docker build (https://github.com/nipy/nipype/pull/2963)
  • FIX: Remove '=' signs from EddyQuad argument specifications (https://github.com/nipy/nipype/pull/2941)
  • FIX: Set input model to bedpostx for camino.TrackBedpostxProba (https://github.com/nipy/nipype/pull/2947)
  • FIX: Allow max_shnot to be set (auto mode) (https://github.com/nipy/nipype/pull/2940)
  • ENH: Update mrtrix reconst.py EstimateFOD max_sh to be able to accept list (https://github.com/nipy/nipype/pull/2990)
  • ENH: Let indirectory handle nipype.utils.filemanip.Path (https://github.com/nipy/nipype/pull/2989)
  • ENH: Add resolve/rebase BasePath traits methods & tests (https://github.com/nipy/nipype/pull/2970)
  • ENH: Modify Directory and File traits to get along with pathlib (https://github.com/nipy/nipype/pull/2962)
  • REF: Update nipype2boutiques script (https://github.com/nipy/nipype/pull/2894)
  • TST: Parametrize JoinNode expansion tests over config needed_outputs (https://github.com/nipy/nipype/pull/2981)
  • MAINT: Pin lxml<4.4.0 for Python 3.4 (https://github.com/nipy/nipype/pull/2980)
  • MAINT: Refactor aggregate_outputs for readability (https://github.com/nipy/nipype/pull/2969)
  • MAINT: Bump neurodocker version (https://github.com/nipy/nipype/pull/2965)
  • MAINT: Various minor improvements to complement previous PR (https://github.com/nipy/nipype/pull/2964)
  • MAINT: Sort dependencies alphabetically (https://github.com/nipy/nipype/pull/2961)

- Python
Published by effigies over 6 years ago

nipype - 1.2.0

1.2.0 (May 09, 2019)

DOI

Full changelog
  • FIX: Parsing of filename in AlignEpiAnatPy when filename does not have + (https://github.com/nipy/nipype/pull/2909)
  • FIX: Import nibabel reorientation bug fix (https://github.com/nipy/nipype/pull/2912)
  • FIX: Update FNIRT outputs for warpedfile logfile to include cwd (https://github.com/nipy/nipype/pull/2900)
  • FIX: Sort conditions in bidsgeninfo to ensure consistent order (https://github.com/nipy/nipype/pull/2867)
  • FIX: Some traits-5.0.0 don't work with Python 2.7 (https://github.com/nipy/nipype/pull/1)
  • ENH: CompCor enhancement (https://github.com/nipy/nipype/pull/2878)
  • ENH: Do not override caught exceptions with FileNotFoundError from unfinished hashfile (https://github.com/nipy/nipype/pull/2919)
  • ENH: More verbose description when a faulty results file is loaded (https://github.com/nipy/nipype/pull/2920)
  • ENH: Add all DIPY workflows dynamically (https://github.com/nipy/nipype/pull/2905)
  • ENH: Add mrdegibbs and dwibiascorrect from mrtrix3 (https://github.com/nipy/nipype/pull/2904)
  • TEST: Fix CI builds (https://github.com/nipy/nipype/pull/2927)
  • MAINT: Reduce deprecation warnings (https://github.com/nipy/nipype/pull/2903)

- Python
Published by effigies almost 7 years ago

nipype - 1.1.9

1.1.9 (February 25, 2019)

DOI

Full changelog
  • FIX: Make positional arguments to LaplacianThickness require previous argument (https://github.com/nipy/nipype/pull/2848)
  • FIX: Import math and csv modules for bidsgeninfo (https://github.com/nipy/nipype/pull/2881)
  • FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (https://github.com/nipy/nipype/pull/2739)
  • ENH: Allow afni.MaskTool to take multiple input files (https://github.com/nipy/nipype/pull/2892)
  • ENH: Add flags dictionary input to spm.Level1Design (https://github.com/nipy/nipype/pull/2861)
  • ENH: Threshold stddev once only in TSNR (https://github.com/nipy/nipype/pull/2883)
  • ENH: Add workbench.CiftiSmooth interface (https://github.com/nipy/nipype/pull/2871)
  • DOC: Replace initialism typo in comment with intended phrase (https://github.com/nipy/nipype/pull/2875)
  • DOC: Fix typos in ANTs Registration input documentation (https://github.com/nipy/nipype/pull/2869)

- Python
Published by effigies about 7 years ago

nipype - 1.1.8

1.1.8 (January 28, 2019)

DOI

Full changelog
  • FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
  • FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
  • ENH: Add interfaces wrapping DIPY worflows (https://github.com/nipy/nipype/pull/2830)
  • ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)
  • ENH: Add FSL eddy_quad interface (https://github.com/nipy/nipype/pull/2825)
  • ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)
  • ENH: Support for BIDS event files (https://github.com/nipy/nipype/pull/2845)
  • ENH: CompositeTransformUtil, new ANTs interface (https://github.com/nipy/nipype/pull/2785)
  • RF: Move pytest and pytest-xdist from general requirement into tests_required (https://github.com/nipy/nipype/pull/2850)
  • DOC: Add S3DataGrabber example (https://github.com/nipy/nipype/pull/2849)
  • DOC: Skip conftest module in API generation (https://github.com/nipy/nipype/pull/2852)
  • DOC: Hyperlink DOIs to preferred resolver (https://github.com/nipy/nipype/pull/2833)
  • MAINT: Install numpy!=1.16.0 from conda in Docker (https://github.com/nipy/nipype/pull/2862)
  • MAINT: Drop pytest-xdist requirement, minimum pytest version (https://github.com/nipy/nipype/pull/2856)
  • MAINT: Disable numpy 1.16.0 for Py2.7 (https://github.com/nipy/nipype/pull/2855)

- Python
Published by effigies about 7 years ago

nipype - 1.1.7

1.1.7 (December 17, 2018)

DOI

Full changelog
  • FIX: Copy node list before generating a flat graph (https://github.com/nipy/nipype/pull/2828)
  • FIX: Update pytest req'd version to 3.6 (https://github.com/nipy/nipype/pull/2827)
  • FIX: Set ResourceMonitor.fname to an absolute path (https://github.com/nipy/nipype/pull/2824)
  • FIX: Order of SPM.NewSegment channel_info boolean tuple is (Field, Corrected) (https://github.com/nipy/nipype/pull/2817)
  • FIX: Indices were swapped for memory and cpu profile data (https://github.com/nipy/nipype/pull/2816)
  • FIX: status_callback not called with stop_on_first_crash (https://github.com/nipy/nipype/pull/2810)
  • FIX: Change undefined ScriptError on LFS plugin to IOError (https://github.com/nipy/nipype/pull/2803)
  • ENH: Add NaN failure mode to CompCor interfaces (https://github.com/nipy/nipype/pull/2819)
  • ENH: Enable cnr_maps and residuals outputs for FSL eddy (https://github.com/nipy/nipype/pull/2750)
  • ENH: Improve str2bool + doctests (https://github.com/nipy/nipype/pull/2807)
  • TST: Improve py.test configuration of doctests (https://github.com/nipy/nipype/pull/2802)
  • DOC: Update DOI badge to point to all versions (https://github.com/nipy/nipype/pull/2804)
  • MAINT: Offload interfaces with help formatting (https://github.com/nipy/nipype/pull/2797)
  • MAINT: Reduce minimal code redundancy in filemanip.get_dependencies (https://github.com/nipy/nipype/pull/2782)
  • MAINT: Delayed imports to reduce import time (https://github.com/nipy/nipype/pull/2809)

- Python
Published by effigies about 7 years ago

nipype - 1.1.6

1.1.6 (November 26, 2018)

DOI

Full changelog
  • [FIX] MapNodes fail when MultiProcPlugin passed by instance (https://github.com/nipy/nipype/pull/2786)
  • [FIX] --fineTune arguments order for MeshFix command (https://github.com/nipy/nipype/pull/2780)
  • [ENH] Add mp_context plugin arg for MultiProc (https://github.com/nipy/nipype/pull/2778)
  • [ENH] Create a crashfile even if 'stoponfirst_crash' is set (https://github.com/nipy/nipype/pull/2774)
  • [ENH] Add ExtractedBrainN4 output to ANTs CorticalThickness interface (https://github.com/nipy/nipype/pull/2784)
  • [STY] Combine split import (https://github.com/nipy/nipype/pull/2801)
  • [DOC] use https in css stylesheet url (https://github.com/nipy/nipype/pull/2779)
  • [MAINT] Outsource get_filecopy_info() from interfaces (https://github.com/nipy/nipype/pull/2798)
  • [MAINT] Import only Sequence to avoid DeprecationWarning (https://github.com/nipy/nipype/pull/2793)
  • [MAINT] One less DeprecationWarning (configparser) (https://github.com/nipy/nipype/pull/2794)
  • [MAINT] DeprecationWarning: use HasTraits.trait_set instead (https://github.com/nipy/nipype/pull/2792)
  • [MAINT] Stop using deprecated logger.warn() (https://github.com/nipy/nipype/pull/2788)
  • [MAINT] Move interfaces.base.run_command to nipype.utils.subprocess (https://github.com/nipy/nipype/pull/2777)
  • [MAINT] Force numpy>=1.15.4 when Python>=3.7 (https://github.com/nipy/nipype/pull/2775)

- Python
Published by effigies over 7 years ago

nipype - 1.1.5

1.1.5 (November 08, 2018)

DOI

Hotfix release.

Full changelog
  • ENH: Allow timeouts during SLURM job status checks (https://github.com/nipy/nipype/pull/2767)
  • RF: Subclass non-daemon variants of all multiprocessing contexts (https://github.com/nipy/nipype/pull/2771)

- Python
Published by effigies over 7 years ago

nipype - 1.1.4

1.1.4 (October 31, 2018)

DOI

Full changelog
  • FIX: Python 2.7-3.7.1 compatible NonDaemonPool (https://github.com/nipy/nipype/pull/2754)
  • FIX: VRML typo (VMRL) in MeshFix (https://github.com/nipy/nipype/pull/2757)
  • FIX: Refine FSL.split output identification (https://github.com/nipy/nipype/pull/2746)
  • FIX: Reuse genfilename logic in ants.LaplacianThickness (https://github.com/nipy/nipype/pull/2734)
  • FIX: Remove 'reg_term' default from dwi2tensor interface (https://github.com/nipy/nipype/pull/2731)
  • FIX: Keep profile files when remove_unnecessary_outputs = true (https://github.com/nipy/nipype/pull/2718)
  • ENH: Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs (https://github.com/nipy/nipype/pull/2740)
  • ENH: Add compression option for bru2nii (https://github.com/nipy/nipype/pull/2762)
  • ENH: Add sliceencodingdirection input to TShift (https://github.com/nipy/nipype/pull/2753)
  • ENH: Add 'sse' output to FSL DTIFit interface (https://github.com/nipy/nipype/pull/2749)
  • ENH: Update ants.LaplacianThickness to use name_source (https://github.com/nipy/nipype/pull/2747)
  • ENH: Add tab completion for node and interface inputs properties (https://github.com/nipy/nipype/pull/2735)
  • ENH: enable/disable resource monitor in the fixture per test (https://github.com/nipy/nipype/pull/2725)
  • TEST: Update expected dotfile text for networkx 1.x (https://github.com/nipy/nipype/pull/2730)
  • DOC: Move user docs from nipype to nipype_tutorial (https://github.com/nipy/nipype/pull/2726)
  • DOC: Use consistent name in reconall workflow docstring (https://github.com/nipy/nipype/pull/2758)
  • MAINT: Use neurodocker 0.4.1 + apt install afni (https://github.com/nipy/nipype/pull/2707)
  • MAINT: Fix prov and rdflib in nipype (https://github.com/nipy/nipype/pull/2701)
  • MAINT: Correct readthedocs build error (https://github.com/nipy/nipype/pull/2723)
  • MAINT: Pin codecov to <5.0 so Travis is fixed (https://github.com/nipy/nipype/pull/2728)
  • CI: Lock travis pybids 0.6.5 (https://github.com/nipy/nipype/pull/2720)

- Python
Published by effigies over 7 years ago

nipype - 1.1.3

1.1.3 (September 24, 2018)

DOI

Full changelog
  • FIX: Return afni.Qwarp outputs as absolute paths (https://github.com/nipy/nipype/pull/2705)
  • FIX: Add informative error for interfaces that fail to return valid runtime object (https://github.com/nipy/nipype/pull/2692)
  • FIX: Construct MCFLIRT output paths relative to out_file (https://github.com/nipy/nipype/pull/2703)
  • FIX: SLURM plugin polling (https://github.com/nipy/nipype/pull/2693)
  • FIX: Handle missing substring in SPM docs (https://github.com/nipy/nipype/pull/2691)
  • ENH: Add colorFA output to DIPY DTI interface (https://github.com/nipy/nipype/pull/2695)
  • RF: Use runtime.cwd in Rename (https://github.com/nipy/nipype/pull/2688)
  • DOC: Fix naming of motion parameters (roll/yaw swapped) (https://github.com/nipy/nipype/pull/2696)
  • DOC: Update links to user and developer help forums (https://github.com/nipy/nipype/pull/2686)
    • CI: Test 3.7, resume testing nipy extras (https://github.com/nipy/nipype/pull/2682)

- Python
Published by effigies over 7 years ago

nipype - 1.1.2

1.1.2 (August 11, 2018)

DOI

Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.

Full changelog
  • FIX: Read BIDS config.json under grabbids or layout (https://github.com/nipy/nipype/pull/2679)
  • FIX: Node __repr__ and detailed graph expansion (https://github.com/nipy/nipype/pull/2669)
  • FIX: Prevent double-collapsing of nested lists by OutputMultiObject (https://github.com/nipy/nipype/pull/2673)
  • ENH: Add interface to SPM realign_unwarp (https://github.com/nipy/nipype/pull/2635)
  • MAINT: Fix wheel build to ensure futures is only required in Python 2 (https://github.com/nipy/nipype/pull/2678)
  • MAINT: ensure interface _cmd only includes executable (https://github.com/nipy/nipype/pull/2674)
  • MAINT: Issue template: Pretty print platform details (https://github.com/nipy/nipype/pull/2671)
    • CI: removing travis_retry for pip install pytest xdist 1.22.5 (https://github.com/nipy/nipype/pull/2664)

- Python
Published by effigies over 7 years ago

nipype - 1.1.1

1.1.1 (July 30, 2018)

DOI

Full changelog
  • FIX: Un-set incorrect default options in TOPUP (https://github.com/nipy/nipype/pull/2637)
  • FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656)
  • FIX: Various BIDSDataGrabber fixes (https://github.com/nipy/nipype/pull/2651)
  • FIX: changing Node.outputdir to realpath (https://github.com/nipy/nipype/pull/2639)
  • FIX: Typo in DWIExtract of Mrtrix3interface (https://github.com/nipy/nipype/pull/2634)
  • FIX: Typo in FSLXCommandInputSpec (https://github.com/nipy/nipype/pull/2628)
  • ENH: Allow transform to be saved from AFNI 3dWarp (https://github.com/nipy/nipype/pull/2642)
  • ENH: Allow BIDS-style slice timings to be passed directly to TShift (https://github.com/nipy/nipype/pull/2608)
  • ENH: S3 access using instance role (https://github.com/nipy/nipype/pull/2621)
  • ENH Minor improvements to PR template (https://github.com/nipy/nipype/pull/2636)
  • TEST: make specs (https://github.com/nipy/nipype/pull/2653)
  • DOC: update neurodocker tutorial for neurodocker version 0.4.0 (https://github.com/nipy/nipype/pull/2647)
  • MAINT: Remove vestiges of nose testing library (https://github.com/nipy/nipype/pull/2662)
  • MAINT: Make pytest-xdist a dependency (https://github.com/nipy/nipype/pull/2649)
  • CI: Install pytest>=3.4 in Travis (https://github.com/nipy/nipype/pull/2659)

- Python
Published by effigies over 7 years ago

nipype - 1.1.0

1.1.0 (July 04, 2018)

DOI

Full changelog
  • RF: Futures-based MultiProc (https://github.com/nipy/nipype/pull/2598)
  • FIX: Avoid closing file descriptors on Windows (https://github.com/nipy/nipype/pull/2617)
  • MAINT: Play nice with external logging (https://github.com/nipy/nipype/pull/2611)
  • MAINT: Remove ignoreexception and terminaloutput traits from input specs (https://github.com/nipy/nipype/pull/2618)
  • MAINT: Converge autotest names (https://github.com/nipy/nipype/pull/2610)
  • ENH: Add versioning metadata to crash files (https://github.com/nipy/nipype/pull/2626)
  • ENH add -dsort option to TProject (https://github.com/nipy/nipype/pull/2623)
  • ENH: Add Rescale interface (https://github.com/nipy/nipype/pull/2599)
  • DOC: Improve documentation for ANTs/FSL interfaces (https://github.com/nipy/nipype/pull/2593)
  • CI: Stop using Miniconda on Travis (https://github.com/nipy/nipype/pull/2600)
  • CI: Add PyPI validation on rel/* branches (https://github.com/nipy/nipype/pull/2603)

- Python
Published by mgxd over 7 years ago

nipype - 1.0.4

1.0.4 (May 29, 2018)

DOI

Full changelog
  • FIX: Update logging levels in enabledebugmode (https://github.com/nipy/nipype/pull/2595)
  • FIX: Set default result in DistributedPluginBase.cleanqueue (https://github.com/nipy/nipype/pull/2596)
  • FIX: Correctly connect JoinNodes in nested iterables (https://github.com/nipy/nipype/pull/2597)
  • FIX: DTITK nonlinear workflow origin reslicing (https://github.com/nipy/nipype/pull/2561)
  • FIX: ResponseSD support for multiple b-vals (https://github.com/nipy/nipype/pull/2582)
  • FIX: Workaround to ICA-AROMA change of directory (https://github.com/nipy/nipype/pull/2566)
  • FIX/TEST: Gunzip cleanup and test (https://github.com/nipy/nipype/pull/2564)
  • FIX: Print UID in crashfile if login name is unavailable (https://github.com/nipy/nipype/pull/2563)
  • ENH: initial connectome workbench support (https://github.com/nipy/nipype/pull/2594)
  • ENH: AFNI (3d)LocalBistat interface (https://github.com/nipy/nipype/pull/2590)
  • ENH: Reorient interface (https://github.com/nipy/nipype/pull/2572)
  • ENH: FSL slice interface (https://github.com/nipy/nipype/pull/2585)
  • ENH: LabelGeometryMeasures interface (https://github.com/nipy/nipype/pull/2586)
  • ENH: MRTrix3 dwidenoise interface (https://github.com/nipy/nipype/pull/2568)
  • ENH: ReportCapableInterface mix-in/base interface (https://github.com/nipy/nipype/pull/2560)
  • CI: Move PyPI deployment to Circle (https://github.com/nipy/nipype/pull/2587)
  • CI: Submit Travis results to codecov (https://github.com/nipy/nipype/pull/2574)

- Python
Published by effigies almost 8 years ago

nipype - Nipype 1.0.3

1.0.3 (April 30, 2018)

Full changelog
  • FIX: Propagate explicit Workflow config to Nodes (https://github.com/nipy/nipype/pull/2559)
  • FIX: Return non-enhanced volumes from dwi_flirt (https://github.com/nipy/nipype/pull/2547)
  • FIX: Skip filename generation when required fields are missing (https://github.com/nipy/nipype/pull/2549)
  • FIX: Fix Afni's Allineate hashing and out_file (https://github.com/nipy/nipype/pull/2502)
  • FIX: Replace deprecated HasTraits.get with trait_get (https://github.com/nipy/nipype/pull/2534)
  • FIX: Typo in "antsRegistrationSyNQuick.sh" (https://github.com/nipy/nipype/pull/2544)
  • FIX: DTITK Interface (https://github.com/nipy/nipype/pull/2514)
  • FIX: Add -mas argument to fsl.utils.ImageMaths (https://github.com/nipy/nipype/pull/2529)
  • FIX: Build cmdline from working directory (https://github.com/nipy/nipype/pull/2521)
  • FIX: FSL orthogonalization bug (https://github.com/nipy/nipype/pull/2523)
  • FIX: Re-enable dcm2niix source_names (https://github.com/nipy/nipype/pull/2550)
  • ENH: Add an activation count map interface (https://github.com/nipy/nipype/pull/2522)
  • ENH: Revise the implementation of FuzzyOverlap (https://github.com/nipy/nipype/pull/2530)
  • ENH: Add MultiObject, ensure/simplify_list; alias old names for 1.x compatibility (https://github.com/nipy/nipype/pull/2517)
  • ENH: Add LibraryBaseInterface (https://github.com/nipy/nipype/pull/2538)
  • ENH: Define default output file template for afni.CatMatvec (https://github.com/nipy/nipype/pull/2527)
  • MAINT: Deprecate terminaloutput and ignoreexception from CommandLine (https://github.com/nipy/nipype/pull/2552)
  • MAINT: Set traits default values properly (https://github.com/nipy/nipype/pull/2533)
  • MAINT: use RawConfigParser (https://github.com/nipy/nipype/pull/2542)
  • MAINT: Minor autotest cleanups (https://github.com/nipy/nipype/pull/2519)
  • CI: Add retry script for Docker commands (https://github.com/nipy/nipype/pull/2516)

- Python
Published by mgxd almost 8 years ago

nipype - 1.0.2

1.0.2 (March 27, 2018)

Full changelog
  • FIX: dcm2niix interface (https://github.com/nipy/nipype/pull/2498)
  • FIX: mark .niml.dset as special extension in utils.filemanip (https://github.com/nipy/nipype/pull/2495)
  • FIX: handle automatic module creation, name extraction, default value (https://github.com/nipy/nipype/pull/2490)
  • FIX: Check and report mount table parsing failures (https://github.com/nipy/nipype/pull/2476)
  • FIX: Check against full node name when reconnecting JoinNodes (https://github.com/nipy/nipype/pull/2479)
  • DOC: Add tutorials, porcupine to users TOC (https://github.com/nipy/nipype/pull/2503)
  • DOC: Contributing and testing (https://github.com/nipy/nipype/pull/2482)
  • DOC: Describe 'orphaned' tag in CONTRIBUTING (https://github.com/nipy/nipype/pull/2481)
  • DOC: Add details for dcm2niix output filename pattern (https://github.com/nipy/nipype/pull/2512)
  • ENH: Add interface for AFNI 3dNwarpAdjust (https://github.com/nipy/nipype/pull/2450)
  • ENH: Update SSHDataGrabber to fetch related files (https://github.com/nipy/nipype/pull/2104)
  • ENH: Add interpolation order parameter to NiftyReg's RegTools (https://github.com/nipy/nipype/pull/2471)
  • MAINT: Stray warnings and exceptions (https://github.com/nipy/nipype/pull/2478)
  • MAINT: Add dev install option, update CONTRIBUTING (https://github.com/nipy/nipype/pull/2477)
  • MAINT: Sync requirements with info.py (https://github.com/nipy/nipype/pull/2472)
  • CI: Update Travis builds, Docker to use latest miniconda (https://github.com/nipy/nipype/pull/2455)
  • TEST: Parallelize pytest (https://github.com/nipy/nipype/pull/2469)

- Python
Published by mgxd almost 8 years ago

nipype - 1.0.1

1.0.1 (February 27, 2018)

Full changelog
  • FIX: Small bug in freesurfer label2annot fill_thresh specs #2377
  • FIX: Error creating gradients in DTIRecon #2460
  • FIX: improve matlab_cmd #2452
  • FIX: Extract unit information from image header in CompCor #2458
  • FIX: Update pybids data directory, unbundle out-of-date numpydoc #2437
  • FIX: Out_file bugs in Afni.Zcat and Afni.Merge interfaces #2424
  • FIX: Re-enable spm.Realign to take lists of lists of files #2409
  • FIX: Remove deprecated output from ICC interface #2422
  • FIX: Argstr for mask in Afni.BlurToFWHM #2418
  • FIX: Default value for sbatch_args (SLURMGraph) #2417
  • FIX: Ortvec argstr for Afni.Deconvolve #2415
  • FIX: Bug fixes for afni.model #2398
  • DOC: Add brief neurodocker tutorial #2464
  • DOC: Fix tutorials #2459
  • ENH: antsRegistrationSyNQuick interface #2453
  • ENH: Automate updates of CHANGES #2440
  • ENH: Add SPM Fieldmap Tool wrapper #1905
  • ENH: Additional option for DataGrabber #1915
  • ENH: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve #2426
  • ENH: c3d/c4d interface #2430
  • ENH: Allow input weight for AFNI's volreg. #2396
  • ENH: Delay crashing if exception is raised in local hash check #2410
  • CI: Add doctests to pytest script #2449
  • CI: Ignore tests in calculating coverage #2443
  • CI: Saturate Circle workflow #2386
  • REF: Update and factor mount table parsing #2444
  • REF: Make ignore_exception a class attribute #2414

- Python
Published by mgxd about 8 years ago

nipype - Nipype - v1.0.0

1.0.0 (January 25, 2018)

Full changelog
  • FIX: PBS plugin submissions (https://github.com/nipy/nipype/pull/2344)
  • FIX: Graph plugins submissions (https://github.com/nipy/nipype/pull/2359)
  • FIX: Logging error if % in interface command (https://github.com/nipy/nipype/pull/2364)
  • FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373)
  • FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369)
  • FIX: Errors parsing $DISPLAY (https://github.com/nipy/nipype/pull/2363)
  • FIX: MultiProc starting workers at dubious wd (https://github.com/nipy/nipype/pull/2368)
  • FIX: Explicitly collect MultiProc job IDs (https://github.com/nipy/nipype/pull/2378)
  • FIX: Correct Windows environment canonicalization (https://github.com/nipy/nipype/pull/2328)
  • FIX: Linked libraries (https://github.com/nipy/nipype/pull/2322)
  • REF+FIX: Move BIDSDataGrabber to interfaces.io + fix correct default behavior (https://github.com/nipy/nipype/pull/2336)
  • REF+MAINT: Simplify hashing (https://github.com/nipy/nipype/pull/2383)
  • MAINT: Cleanup Interfaces base (https://github.com/nipy/nipype/pull/2387)
  • MAINT: Cleanup EngineBase (https://github.com/nipy/nipype/pull/2376)
  • MAINT: Cleaning / simplify Node (https://github.com/nipy/nipype/pull/2325)
  • MAINT+ENH: Update and extend MRtrix3 interfaces (https://github.com/nipy/nipype/pull/2338)
  • ENH: Add AFNI interface for 3dConvertDset (https://github.com/nipy/nipype/pull/2337)
  • ENH: Allow specific interface command prefixes (https://github.com/nipy/nipype/pull/2379)
  • STY: Cleanup of PEP8 violations (https://github.com/nipy/nipype/pull/2358)
  • STY: Cleanup of trailing spaces and adding of missing newlines at end of files (https://github.com/nipy/nipype/pull/2355)
  • STY: Apply yapf to codebase (https://github.com/nipy/nipype/pull/2371)
  • DOC: Updated guide for contributing (https://github.com/nipy/nipype/pull/2393)

- Python
Published by mgxd about 8 years ago

nipype - 0.14.0

0.14.0 (November 29, 2017)

Full changelog
  • FIX+MAINT: Revision of the resource monitor (https://github.com/nipy/nipype/pull/2285)
  • FIX: MultiProc mishandling crashes (https://github.com/nipy/nipype/pull/2301)
  • MAINT: Revise use of subprocess.Popen (https://github.com/nipy/nipype/pull/2289)
  • ENH: Memorize version checks (https://github.com/nipy/nipype/pull/2274, https://github.com/nipy/nipype/pull/2295)

- Python
Published by oesteban about 8 years ago

nipype - 0.14.0-rc1

0.14.0rc1 (November 21, 2017)

  • ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)
  • ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)
  • ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)
  • FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252)
  • ENH: Add elapsedtime and final metricvalue to ants.Registration (https://github.com/nipy/nipype/pull/1985)
  • ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
  • ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
  • ENH: Centralize virtual/physical $DISPLAYs (https://github.com/nipy/nipype/pull/2203, https://github.com/nipy/nipype/pull/2211)
  • ENH: New ResourceMonitor - replaces resource profiler (https://github.com/nipy/nipype/pull/2200)
  • ENH: Quickshear interface (https://github.com/nipy/nipype/pull/2047)
  • MAINT: updated deprecated HasTraits method (https://github.com/nipy/nipype/pull/2048)
  • ENH: CLI versioning (https://github.com/nipy/nipype/pull/2054)
  • ENH: Dual Regression interface (https://github.com/nipy/nipype/pull/2057)
  • ENH: Additional args to ANTs registration (https://github.com/nipy/nipype/pull/2062, https://github.com/nipy/nipype/pull/2078)
  • FIX: Mp2rage interfaces updated for new parameter names in cbstools 3 (https://github.com/nipy/nipype/pull/2065)
  • MAINT: Removed automatic nipype folder creation in HOME (https://github.com/nipy/nipype/pull/2076)
  • MAINT: Additional Windows support (https://github.com/nipy/nipype/pull/2085)
  • ENH: Output realignment matrices from TOPUP (https://github.com/nipy/nipype/pull/2084)
  • ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize, 3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, https://github.com/nipy/nipype/pull/2095, https://github.com/nipy/nipype/pull/2099, https://github.com/nipy/nipype/pull/2103, https://github.com/nipy/nipype/pull/2114, https://github.com/nipy/nipype/pull/2135, https://github.com/nipy/nipype/pull/2186, https://github.com/nipy/nipype/pull/2201, https://github.com/nipy/nipype/pull/2210)
  • MAINT: cleanup and update AFNI's Allineate (https://github.com/nipy/nipype/pull/2098)
  • ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)
  • FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)
  • FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)
  • ENH: ANTs MeasureImageSimilarity Inteface (https://github.com/nipy/nipype/pull/2128)
  • FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)
  • ENH: FreeSurfer ltaconvert and mricoreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)
  • ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)
  • FIX: Allow S3DataGrabber to grab single file (https://github.com/nipy/nipype/pull/2147)
  • FIX: Allow 4D images as inputs to buildtemplateparallel.sh and N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/2151)
  • MAINT: Detect and warn unconnected duplicate nodes (https://github.com/nipy/nipype/pull/2163)
  • ENH: Calcmedian Interface (https://github.com/nipy/nipype/pull/2167)
  • FIX: probtrackx2 outputs (https://github.com/nipy/nipype/pull/2169)
  • ENH: Improve FreeSurfer registration (https://github.com/nipy/nipype/pull/2172)
  • ENH: BIDSDataGrabber interface (https://github.com/nipy/nipype/pull/2174)
  • MAINT: Set minimum numpy version to 1.9.0 (https://github.com/nipy/nipype/pull/2182)
  • ENH: Support for multiple intial-moving-transforms (https://github.com/nipy/nipype/pull/2187)
  • MAINT: Fixes for networkx and afni (https://github.com/nipy/nipype/pull/2196, https://github.com/nipy/nipype/pull/2171)
  • TST: Update C3D version in Docker build (https://github.com/nipy/nipype/pull/2199)
  • ENH: SimpleInterface interface (https://github.com/nipy/nipype/pull/2220)
  • ENH: Add LTA to Tkregister2 (https://github.com/nipy/nipype/pull/2217)

- Python
Published by oesteban about 8 years ago

nipype - Release 0.13.1

0.13.1 (May 20, 2017)

  • FIX: Make release compatible with conda-forge build process (https://github.com/nipy/nipype/pull/2017)
  • ENH: Update some minimum versions in compliance with Debian Jessie (https://github.com/nipy/nipype/pull/2017)
  • ENH: Circle builds use cached docker layers (https://github.com/nipy/nipype/pull/2017)
  • ENH: Base docker to use FS6 and ANTS 2.2.0 (https://github.com/nipy/nipype/pull/2024)
  • FIX: Mailmap and contributor acknowledgment (https://github.com/nipy/nipype/pull/2017)
  • FIX: Preserve node properties in sub nodes of MapNode (https://github.com/nipy/nipype/pull/2019)
  • FIX: Fix interfaces 3DUnifize, ICA_AROMA, BinaryMaths, RegAverage, BBRegister, AffineInitializer (https://github.com/nipy/nipype/pull/2025, https://github.com/nipy/nipype/pull/2027, https://github.com/nipy/nipype/pull/2036, https://github.com/nipy/nipype/pull/2037, https://github.com/nipy/nipype/pull/2031, https://github.com/nipy/nipype/pull/2010)
  • ENH: Add Anisotropic Power interface (https://github.com/nipy/nipype/pull/2039)
  • FIX: Bayesian estimation in SPM (https://github.com/nipy/nipype/pull/2030)

0.13.0 (May 11, 2017)

  • ENH: Multi-stage recon-all directives (https://github.com/nipy/nipype/pull/1991)
  • FIX: FEAT "folder does not exist" error (https://github.com/nipy/nipype/pull/2000)
  • ENH: Niftyfit interfaces (https://github.com/nipy/nipype/pull/1910)
  • FIX: Define ANTSPATH for BrainExtraction automatically (https://github.com/nipy/nipype/pull/1986)
  • ENH: New trait for imaging files (https://github.com/nipy/nipype/pull/1949)
  • ENH: Niftyseg interfaces (https://github.com/nipy/nipype/pull/1911)
  • ENH: Niftyreg interfaces (https://github.com/nipy/nipype/pull/1913)
  • MRG: Allow more support for CLI (https://github.com/nipy/nipype/pull/1908)
  • ENH: 3dQwarpPlusMinus interface (https://github.com/nipy/nipype/pull/1974)
  • FIX: PY3.6 support (https://github.com/nipy/nipype/pull/1977)
  • FIX: PY3 and stream fixes for MRTrix2TrackVis (https://github.com/nipy/nipype/pull/1804)
  • ENH: More mask options for CompCor interfaces (https://github.com/nipy/nipype/pull/1968 + https://github.com/nipy/nipype/pull/1992)
  • ENH: Additional TOPUP outputs (https://github.com/nipy/nipype/pull/1976)
  • ENH: Additional Eddy flags (https://github.com/nipy/nipype/pull/1967)
  • ENH: ReconAll handlers for less common cases (https://github.com/nipy/nipype/pull/1966)
  • ENH: FreeSurferSource now finds graymid/midthickness surfs (https://github.com/nipy/nipype/pull/1972)
  • ENH: Additional fslmaths dimensional reduction operations (https://github.com/nipy/nipype/pull/1956)
  • ENH: More options for RobustFOV interface (https://github.com/nipy/nipype/pull/1923)
  • ENH: Add MRIsCombine to FreeSurfer utils (https://github.com/nipy/nipype/pull/1948)
  • FIX: Level1Design EV parameter substitution (https://github.com/nipy/nipype/pull/1953)
  • FIX: Dcm2niix outputs can be uncompressed (https://github.com/nipy/nipype/pull/1951)
  • FIX: Ensure build fails in Circle when tests fail (https://github.com/nipy/nipype/pull/1981)
  • ENH: Add interface to antsAffineInitializer (https://github.com/nipy/nipype/pull/1980)
  • ENH: AFNI motion parameter support for FrameWiseDisplacement (https://github.com/nipy/nipype/pull/1840)
  • ENH: Add ANTs KellyKapowski interface (https://github.com/nipy/nipype/pull/1845)
  • FIX: AFNI interface bug setting OMPNUMTHREADS to 1 (https://github.com/nipy/nipype/pull/1728)
  • FIX: Select Eddy run command at runtime (https://github.com/nipy/nipype/pull/1871)
  • FIX: Increase FLIRT's flexibility with apply_xfm (https://github.com/nipy/nipype/pull/1875)
  • DOC: Update FSL preprocess docstrings (https://github.com/nipy/nipype/pull/1881)
  • ENH: Support GIFTI outputs in SampleToSurface (https://github.com/nipy/nipype/pull/1886)
  • FIX: Configparser differences between PY2 and PY3 (https://github.com/nipy/nipype/pull/1890)
  • ENH: Add mris_expand interface (https://github.com/nipy/nipype/pull/1893)
  • FIX: Split over-eager globs in FreeSurferSource (https://github.com/nipy/nipype/pull/1894)
  • FIX: Store undefined by default so that xor checks don't trip (https://github.com/nipy/nipype/pull/1903)
  • FIX: Gantt chart generator PY3 compatibility (https://github.com/nipy/nipype/pull/1907)
  • FIX: Add DOF and --fsl-dof options to BBRegister (https://github.com/nipy/nipype/pull/1917)
  • ENH: Auto-derive input_names in Function (https://github.com/nipy/nipype/pull/1918)
  • FIX: Minor fixes for NonSteadyStateDetector (https://github.com/nipy/nipype/pull/1926)
  • DOC: Add duecredit references for AFNI and FSL (https://github.com/nipy/nipype/pull/1930)
  • ENH: Added zenodo (https://zenodo.org/) file (https://github.com/nipy/nipype/pull/1924)
  • ENH: Disable symlinks on CIFS filesystems (https://github.com/nipy/nipype/pull/1941)
  • ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896)
  • ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839)
  • ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)
  • REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828)
  • FIX: Makespec now runs with nipype in current directory (https://github.com/nipy/nipype/pull/1813)
  • FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (https://github.com/nipy/nipype/pull/1796 + https://github.com/nipy/nipype/pull/1831)
  • ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827)
  • FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827)
  • ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828)
  • FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833)
  • FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825)
  • ENH: Revised all Dockerfiles and automated deployment to Docker Hub from CircleCI (https://github.com/nipy/nipype/pull/1815)
  • ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
  • FIX: Cast DVARS float outputs to avoid memmap error (https://github.com/nipy/nipype/pull/1777)
  • FIX: FSL FNIRT intensity mapping files (https://github.com/nipy/nipype/pull/1799)
  • ENH: Additional outputs generated by FSL EDDY (https://github.com/nipy/nipype/pull/1793)
  • TST: Parallelize CircleCI build across 4 containers (https://github.com/nipy/nipype/pull/1769)

0.13.0-rc1 (January 4, 2017)

  • FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770)
  • FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756)
  • TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751)
  • FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689)
  • REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680)
  • ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
  • FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
  • FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671)
  • ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
  • ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627)
  • FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
  • TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
  • ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647)
  • ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
  • ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)
  • ENH: Add CompCor (https://github.com/nipy/nipype/pull/1599)
  • ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466)
  • FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572)
  • REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597)
  • REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593)
  • TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609)
  • ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554)
  • ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
  • ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604)
  • FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)
  • TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564)
  • ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
  • FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586)
  • ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
  • ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant (https://github.com/nipy/nipype/pull/1654)

- Python
Published by satra almost 9 years ago

nipype - Release 0.13.0

Release 0.13.0 (May 11, 2017)

  • ENH: Multi-stage recon-all directives (https://github.com/nipy/nipype/pull/1991)
  • FIX: FEAT "folder does not exist" error (https://github.com/nipy/nipype/pull/2000)
  • ENH: Niftyfit interfaces (https://github.com/nipy/nipype/pull/1910)
  • FIX: Define ANTSPATH for BrainExtraction automatically (https://github.com/nipy/nipype/pull/1986)
  • ENH: New trait for imaging files (https://github.com/nipy/nipype/pull/1949)
  • ENH: Niftyseg interfaces (https://github.com/nipy/nipype/pull/1911)
  • ENH: Niftyreg interfaces (https://github.com/nipy/nipype/pull/1913)
  • MRG: Allow more support for CLI (https://github.com/nipy/nipype/pull/1908)
  • ENH: 3dQwarpPlusMinus interface (https://github.com/nipy/nipype/pull/1974)
  • FIX: PY3.6 support (https://github.com/nipy/nipype/pull/1977)
  • FIX: PY3 and stream fixes for MRTrix2TrackVis (https://github.com/nipy/nipype/pull/1804)
  • ENH: More mask options for CompCor interfaces (https://github.com/nipy/nipype/pull/1968 + https://github.com/nipy/nipype/pull/1992)
  • ENH: Additional TOPUP outputs (https://github.com/nipy/nipype/pull/1976)
  • ENH: Additional Eddy flags (https://github.com/nipy/nipype/pull/1967)
  • ENH: ReconAll handlers for less common cases (https://github.com/nipy/nipype/pull/1966)
  • ENH: FreeSurferSource now finds graymid/midthickness surfs (https://github.com/nipy/nipype/pull/1972)
  • ENH: Additional fslmaths dimensional reduction operations (https://github.com/nipy/nipype/pull/1956)
  • ENH: More options for RobustFOV interface (https://github.com/nipy/nipype/pull/1923)
  • ENH: Add MRIsCombine to FreeSurfer utils (https://github.com/nipy/nipype/pull/1948)
  • FIX: Level1Design EV parameter substitution (https://github.com/nipy/nipype/pull/1953)
  • FIX: Dcm2niix outputs can be uncompressed (https://github.com/nipy/nipype/pull/1951)
  • FIX: Ensure build fails in Circle when tests fail (https://github.com/nipy/nipype/pull/1981)
  • ENH: Add interface to antsAffineInitializer (https://github.com/nipy/nipype/pull/1980)
  • ENH: AFNI motion parameter support for FrameWiseDisplacement (https://github.com/nipy/nipype/pull/1840)
  • ENH: Add ANTs KellyKapowski interface (https://github.com/nipy/nipype/pull/1845)
  • FIX: AFNI interface bug setting OMPNUMTHREADS to 1 (https://github.com/nipy/nipype/pull/1728)
  • FIX: Select Eddy run command at runtime (https://github.com/nipy/nipype/pull/1871)
  • FIX: Increase FLIRT's flexibility with apply_xfm (https://github.com/nipy/nipype/pull/1875)
  • DOC: Update FSL preprocess docstrings (https://github.com/nipy/nipype/pull/1881)
  • ENH: Support GIFTI outputs in SampleToSurface (https://github.com/nipy/nipype/pull/1886)
  • FIX: Configparser differences between PY2 and PY3 (https://github.com/nipy/nipype/pull/1890)
  • ENH: Add mris_expand interface (https://github.com/nipy/nipype/pull/1893)
  • FIX: Split over-eager globs in FreeSurferSource (https://github.com/nipy/nipype/pull/1894)
  • FIX: Store undefined by default so that xor checks don't trip (https://github.com/nipy/nipype/pull/1903)
  • FIX: Gantt chart generator PY3 compatibility (https://github.com/nipy/nipype/pull/1907)
  • FIX: Add DOF and --fsl-dof options to BBRegister (https://github.com/nipy/nipype/pull/1917)
  • ENH: Auto-derive input_names in Function (https://github.com/nipy/nipype/pull/1918)
  • FIX: Minor fixes for NonSteadyStateDetector (https://github.com/nipy/nipype/pull/1926)
  • DOC: Add duecredit references for AFNI and FSL (https://github.com/nipy/nipype/pull/1930)
  • ENH: Added zenodo (https://zenodo.org/) file (https://github.com/nipy/nipype/pull/1924)
  • ENH: Disable symlinks on CIFS filesystems (https://github.com/nipy/nipype/pull/1941)
  • ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896)
  • ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839)
  • ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)
  • REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828)
  • FIX: Makespec now runs with nipype in current directory (https://github.com/nipy/nipype/pull/1813)
  • FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (https://github.com/nipy/nipype/pull/1796 + https://github.com/nipy/nipype/pull/1831)
  • ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827)
  • FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827)
  • ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828)
  • FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833)
  • FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825)
  • ENH: Revised all Dockerfiles and automated deployment to Docker Hub from CircleCI (https://github.com/nipy/nipype/pull/1815)
  • ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
  • FIX: Cast DVARS float outputs to avoid memmap error (https://github.com/nipy/nipype/pull/1777)
  • FIX: FSL FNIRT intensity mapping files (https://github.com/nipy/nipype/pull/1799)
  • ENH: Additional outputs generated by FSL EDDY (https://github.com/nipy/nipype/pull/1793)
  • TST: Parallelize CircleCI build across 4 containers (https://github.com/nipy/nipype/pull/1769)
  • FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770)
  • FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756)
  • TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751)
  • FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689)
  • REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680)
  • ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
  • FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
  • FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671)
  • ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
  • ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627)
  • FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
  • TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
  • ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647)
  • ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
  • ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)
  • ENH: Add CompCor (https://github.com/nipy/nipype/pull/1599)
  • ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466)
  • FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572)
  • REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597)
  • REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593)
  • TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609)
  • ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554)
  • ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
  • ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604)
  • FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)
  • TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564)
  • ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
  • FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586)
  • ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
  • ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant (https://github.com/nipy/nipype/pull/1654)

- Python
Published by satra almost 9 years ago

nipype - 0.13.0 Release candidate 1

- Python
Published by satra about 9 years ago

nipype - Patch to disable psutils by default

Release 0.12.1 (August 3, 2016)

  • FIX: runtime profiling is optional and off by default (https://github.com/nipy/nipype/pull/1561)
  • TST: circle CI tests run with docker (https://github.com/nipy/nipype/pull/1541)
  • FIX: workflow export functions without import error (https://github.com/nipy/nipype/pull/1552)

- Python
Published by satra over 9 years ago

nipype - 0.12.0

Release 0.12.0 (July 12, 2016)

  • ENH: New interface for Bruker to Nifti converter (https://github.com/nipy/nipype/pull/1523)
  • FIX: output file naming for FIRST outputs (https://github.com/nipy/nipype/pull/1524)
  • ENH: Adds fslmaths -Tstd to maths interfaces (https://github.com/nipy/nipype/pull/1518)
  • FIX: Selecting "gamma" in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)
  • ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
  • ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
  • ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
  • ENH: Add nipypecrashsearch command (https://github.com/nipy/nipype/pull/1422)
  • ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
  • FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
  • FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
  • FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
  • ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography (https://github.com/nipy/nipype/pull/1090)
  • ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360, https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
  • ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
  • ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
  • ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
  • TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
  • ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
  • ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
  • FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
  • FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
  • ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
  • FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
  • ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
  • ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
  • API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
  • ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
  • ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
  • FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
  • FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
  • ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
  • FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
  • ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
  • ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg (https://github.com/nipy/nipype/pull/1460)

- Python
Published by satra over 9 years ago

nipype - 0.12.0 - Release Candidate 2

Release 0.12.0-rc2 (June 19, 2016)

  • ENH: Adds fslmaths -Tstd to maths interfaces (https://github.com/nipy/nipype/pull/1518)
  • FIX: Selecting "gamma" in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)
  • ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
  • ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
  • ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
  • ENH: Add nipypecrashsearch command (https://github.com/nipy/nipype/pull/1422)
  • ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
  • FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
  • FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
  • FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
  • ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography (https://github.com/nipy/nipype/pull/1090)
  • ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360, https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
  • ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
  • ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
  • ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
  • TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
  • ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
  • ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
  • FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
  • FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
  • ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
  • FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
  • ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
  • ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
  • API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
  • ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
  • ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
  • FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
  • FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
  • ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
  • FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
  • ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
  • ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg (https://github.com/nipy/nipype/pull/1460)

- Python
Published by satra over 9 years ago

nipype - Release candidate 1 for version 0.12.0

Release 0.12.0-rc1 (April 20, 2016)

  • ENH: Add nipypecrashsearch command (https://github.com/nipy/nipype/pull/1422)
  • ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
  • FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
  • FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
  • FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
  • ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography (https://github.com/nipy/nipype/pull/1090)
  • ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360, https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
  • ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
  • ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
  • ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
  • TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
  • ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
  • ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
  • FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
  • FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
  • ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
  • FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
  • ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
  • ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
  • API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
  • ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
  • ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
  • FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
  • FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
  • ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
  • FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
  • ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)

- Python
Published by satra almost 10 years ago

nipype - Release 0.11.0

  • API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
  • ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets (https://github.com/nipy/nipype/pull/889).
  • ENH: New interfaces for MRTrix3 (https://github.com/nipy/nipype/pull/1126)
  • ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (https://github.com/nipy/nipype/pull/1079)
  • FIX: ants.Registration composite transform outputs are no longer returned as lists (https://github.com/nipy/nipype/pull/1183)
  • BUG: ANTs Registration interface failed with multi-modal inputs (https://github.com/nipy/nipype/pull/1176) (https://github.com/nipy/nipype/issues/1175)
  • ENH: dipy.TrackDensityMap interface now accepts a reference image (https://github.com/nipy/nipype/pull/1091)
  • FIX: Bug in XFibres5 (https://github.com/nipy/nipype/pull/1168)
  • ENH: Attempt to use hard links for data sink. (https://github.com/nipy/nipype/pull/1161)
  • FIX: Updates to SGE Plugins (https://github.com/nipy/nipype/pull/1129)
  • ENH: Add ants JointFusion() node with testing (https://github.com/nipy/nipype/pull/1160)
  • ENH: Add --float option for antsRegistration calls (https://github.com/nipy/nipype/pull/1159)
  • ENH: Added interface to simulate DWIs using the multi-tensor model (https://github.com/nipy/nipype/pull/1085)
  • ENH: New interface for FSL fslcpgeom utility (https://github.com/nipy/nipype/pull/1152)
  • ENH: Added SLURMGraph plugin for submitting jobs to SLURM with dependencies (https://github.com/nipy/nipype/pull/1136)
  • FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089, replaced by https://github.com/nipy/nipype/pull/1093)
  • ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings (https://github.com/nipy/nipype/pull/1016)
  • FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests, fix bug in area weighted distance, and added optimizations (https://github.com/nipy/nipype/pull/1016)
  • ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
  • FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
  • ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs. (https://github.com/nipy/nipype/pull/1019)
  • FIX: In the FSLXcommand listoutputs function fixed for loop range (https://github.com/nipy/nipype/pull/1071)
  • ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
  • FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
  • ENH: Added "nipype_cmd" tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
  • FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)
  • ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)
  • ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)
  • ENH: Improve JSON interfaces: default settings when reading and consistent output creation when writing (https://github.com/nipy/nipype/pull/1047)
  • FIX: AddCSVRow problems when using infields (https://github.com/nipy/nipype/pull/1028)
  • FIX: Removed unused ANTS registration flag (https://github.com/nipy/nipype/pull/999)
  • FIX: Amend createtbssnonfa() workflow to match FSL's tbssnon_fa command. (https://github.com/nipy/nipype/pull/1033)
  • FIX: remove unused mandatory flag from spm normalize (https://github.com/nipy/nipype/pull/1048)
  • ENH: Update ANTSCorticalThickness interface (https://github.com/nipy/nipype/pull/1013)
  • FIX: Edge case with sparsemodels and PEP8 cleanup (https://github.com/nipy/nipype/pull/1046)
  • ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
  • ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
  • BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
  • FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
  • ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
  • ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output. New options also include choice of tracker, interpolator, stepsize and curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
  • FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
  • FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
  • ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
  • ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made argument formatting consistent. Cleaned ants.segmentation according to PEP8. (https://github.com/nipy/nipype/pull/990/files)
  • ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)
  • FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
  • FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)
  • ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/992)
  • FIX: Corrected Freesurfer SegStats listoutputs to avoid error if summary_file is undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
  • FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
  • FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
  • ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
  • ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
  • ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
  • FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
  • FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
  • FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
  • FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
  • ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
  • FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)
  • ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (https://github.com/nipy/nipype/pull/1132)
  • ENH: Use a while loop to wait for Xvfb (up to a max wait time "xvfbmaxwait" in config file, default 10) (https://github.com/nipy/nipype/pull/1142)

- Python
Published by satra over 10 years ago