1.1.3

1.1.3 (September 24, 2018)

Full changelog

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

1.1.2

1.1.2 (August 11, 2018)

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

Full changelog

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

1.1.1

1.1.1 (July 30, 2018)

Full changelog

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

1.1.0

1.1.0 (July 04, 2018)

Full changelog

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

1.0.4

1.0.4 (May 29, 2018)

Full changelog

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

Nipype 1.0.3

1.0.3 (April 30, 2018)

Full changelog

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

1.0.2

1.0.2 (March 27, 2018)

Full changelog

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

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

Nipype - v1.0.0

1.0.0 (January 25, 2018)

Full changelog

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

0.14.0

0.14.0 (November 29, 2017)

Full changelog

• FIX+MAINT: Revision of the resource monitor (#2285)
• FIX: MultiProc mishandling crashes (#2301)
• MAINT: Revise use of subprocess.Popen (#2289)
• ENH: Memorize version checks (#2274, #2295)