1.3.0-rc1

1.3.0-rc1 (October 8, 2019)

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

1.2.3

1.2.3 (September 23, 2019)

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

Full changelog

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

1.2.2

1.2.2 (September 07, 2019)

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 index_mask_file input to ImageStats (#3005)
• RF: Remove versioning from loadpkl (#3019)
• MAINT: Add python_requires to package metadata (#3006)

1.2.1

1.2.1 (August 19, 2019)

Full changelog

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

1.2.0

1.2.0 (May 09, 2019)

Full changelog

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

1.1.9

1.1.9 (February 25, 2019)

Full changelog

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

1.1.8

1.1.8 (January 28, 2019)

Full changelog

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

1.1.7

1.1.7 (December 17, 2018)

Full changelog

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

1.1.6

1.1.6 (November 26, 2018)

Full changelog

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

1.1.5

1.1.5 (November 08, 2018)

Hotfix release.

Full changelog

• ENH: Allow timeouts during SLURM job status checks (#2767)
• RF: Subclass non-daemon variants of all multiprocessing contexts (#2771)