1.8.3 (July 14, 2022)

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.

(Full changelog)

FIX: Argument order to numpy.save() (#3485)

FIX: Add tolerance parameter to ComputeDVARS (#3489)

FIX: Delay access of nibabel.trackvis until actually needed (#3488)

FIX: Avoid excessive etelemetry pings (#3484)

ENH: Added outputs' generation to DWIBiascorrect interface (#3476)

1.8.2 (June 06, 2022)

Bug-fix release in the 1.8.x series.

This release restores compatibility with networkx 2.8.3, which errors when graph nodes might conflict with pydot parsing.

(Full changelog)

ENH: Enable compression with Gunzip interface (#3472)

CI: Schedule weekly tests with cron (#3480)

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.

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)

FIX: Change plt.hist() argument from deprecated 'normed' to 'density' (#3455)

ENH: Add random seed option to ANTs registration (#3463)

ENH: Add PETsurfer interfaces (#3437)

ENH: Add Text2Vest and Vest2Text interfaces (#3447)

REF: Optimize ICC_rep_anova with a memoized helper function (#3454)

REF: Rearranging matmul order and using hermitian flag in ICC_rep_anova (#3453)

MNT: Drop distutils (#3458)

CI: Cache test data (#3459)

1.7.1 (April 05, 2022)

(Full changelog)

FIX: Allow ConvertScalarImageToRGBInputSpec.mask_file to be "none" (#3364)

FIX: Use a more robust strategy for detecting ANTs version (#3444)

FIX: Retry renaming pkl(z) files on failure (#3404)

FIX: Escape metacharacters when parsing dcm2niix outputs (#3417)

FIX: Import error for nipype.interfaces.dipy.base (#3414)

FIX: ValueError when using ResourceMonitor (#3419)

FIX: Improve error handling of CommandLine interfaces (#3395)

FIX: Bugs in ApplyVDM interface (#3396)

ENH: Add MRTrix3 interfaces (pared-down gh-3426) (#3445)

ENH: Enable BidsDataGrabber to load saved layouts (#3421)

ENH: ROBEX interface (#3443)

ENH: Include several operations to ANTs's ImageMath interface, including ReplicateImage and ReplicateDisplacement (#3435)

ENH: Add "GenericLabel" to antsRegistration interpolation option. (#3424)

ENH: added Apply VDM functionality to FieldMap SPM interface (#3394)

DOC: Side bar and main page fixes (#3397)

TEST: Allow SVD columns to flip sign (#3405)

MNT: rename dipy move_streamlines to transform_tracking_output (#3412)

MNT: Test on Python 3.10 (#3438)

MNT: Added ORCID iD (#3436)

1.7.0 (October 20, 2021)

(Full changelog)

FIX: Make ants.LaplacianThickness output_image a string, not file (#3393)

FIX: coord for mrconvert (#3369)

FIX: antsRegistration allows the restrict_deformation to be float (#3387)

FIX: Also allow errno.EBUSY during emptydirs on NFS (#3357)

FIX: Removed exists=True from MathsOutput (#3385)

FIX: Extension not extensions, after pybids v0.9 (#3380)

ENH: Add CAT12 SANLM denoising filter (#3374)

ENH: Add expected steps for FreeSurfer 7 recon-all (#3389)

ENH: Stop printing false positive differences when logging cached nodes (#3376)

ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform) (#3365)

ENH: verbose input should not be hashed in ants.Registration (#3377)

REF: Clean-up the BaseInterface run() function using context (#3347)

DOC: Fix typo in README (#3386)

STY: Make private member name consistent with the rest of them (#3346)

MNT: Simplify interface execution and better error handling of Node (#3349)

MNT: Add user name and email to Docker to appease git/annex/datalad (#3378)

CI: Update CircleCI machine image (#3391)

1.6.1 (June 16, 2021)

Bug-fix release in the 1.6.x series.

(Full changelog)

FIX: Set DistributedPluginBase.refidx type correctly (#3340)

FIX: change fsl interface randomise --f_only to --fonly for #3322 (#3325)

FIX: BET raising "No image files match: ..." with very long file names (#3309)

FIX: Update SmoothEstimateOutputSpec resels description (#3316)

ENH: Adds interfaces for MRtrix utils shconv and sh2amp (#3280)

ENH: Interface for R (#3291)

ENH: Add CAT12 interfaces (#3310)

ENH: AFNI 3dNetCorr as afni.NetCorr (#3263)

ENH: Skip newline before Python call in batch submission to facilitate containerized runs (#3297)

ENH: Add new dwifslpreproc interface for MRtrix3 (#3278)

REF: Cache nodes in workflow to speed up construction, other optimizations (#3331)

DOC: Fixed Developer Setup Link in install.rst (#3330)

MNT: Blacklist Dipy 1.4.1 (#3335)

MNT: Drop support for numpy < 1.15.3 (#3284)

CI: Build docker images with Python 3.8 (#3287)

CI: Drop Circle doc builds (#3338)

CI: Drop Travis (#3332)

CI: Build docker images with Python 3.8 (#3287)

CI: Add specs and style checks (#3321)

CI: Move from Travis to GitHub actions (#3318)

1.6.0 (November 28, 2020)

New feature release in the 1.6.x series.

In addition to the usual bug fixes, significant reductions were made in workflow startup costs.

(Full changelog)

FIX: Canonicalize environment dicts to strings in Windows (#3267)

FIX: Purge deprecated exception content accesses (#3272)

FIX: Handle changes in CLI structure of mrtrix3.DWIBiasCorrect (#3248)

FIX: EpiReg changed to not list certain outputs when 'wmseg' input is specified (#3265)

FIX: CI issues (#3262)

FIX: SPM SliceTiming must accept either Int or float for ref_slice and sli… (#3255)

FIX: Raise version error when using -g with antsAI < 2.3.0 (#3256)

FIX: No longer depending on pydotplus (networkx >=2.0 update) (#3251)

FIX: ANTs' utilities revision - bug fixes and add more operations to ants.ImageMath (#3236)

ENH: Handle unavailable traits due to version differences (#3273)

ENH: Optimize workflow.run performance (#3260)

DOC: Remove myself (@mr-c) from the zenodo metadata (#3271)

1.5.1 (August 16, 2020)

Bug-fix release in the 1.5.x series.

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

(Full changelog)

FIX: Warn for min/max_ver traits when tool version can't be parsed (#3241)

FIX: Serialize all interface arguments when exporting workflows (#3240)

FIX: Permit identity transforms in list of transforms given to ants.ApplyTransforms (#3237)

FIX: ANTs' utilities revision - bug fixes and add more operations to ants.ImageMath (#3236)

DOC: Skip BIDSDataGrabber doctest if pybids is missing (#3224)

1.5.0 (June 03, 2020)

New feature release in the 1.5.x series.

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

(Full changelog)

FIX: volterra_expansion_order documentation error (#3213)

FIX: BET incorrect output paths (#3214)

FIX: Terminal output in report.rst spreads one line per character (#3220)

FIX: Allow parsing freesurfer 7 version string (#3216)

FIX: Use PackageInfo to get NiftyReg version (#3194)

FIX: Partial rollback of N4BiasFieldCorrection (#3188)

FIX: ANTs' tools maintenance overhaul (#3180)

FIX: load_resultfile crashes if open resultsfile from crashed job (#3182)

FIX: FSL model.py make multiple F-tests (#3166)

ENH: Restore ants.legacy interfaces (#3222)

ENH: Add "TruncateImageIntensity" operation to ants.utils.Image.Math (#3210)

ENH: SPM NewSegment multi-channel segmentation (#3162)

ENH: Add reverse-ordered transform lists to ants.Registration outputs (#3192)

ENH: Improve workflow connect performance (#3184)

ENH: Add ConstrainedSphericalDeconvolution interface to replace EstimateFOD for MRtrix3's dwi2fod (#3176)

ENH: Detect values for EulerNumber interface (#3173)

ENH: Remove examples from repository (#3172)

TEST: Clean up tests (#3195)

TEST: Mock terminal output before testing changing default value (#3193)

REF: make invocations of python and pytest consistent with the one used/desired python (#3208)

REF: Prefer math.gcd to hand-rolled Euclid's algorithm (#3177)

REF: Removed all uses of numpy_mmap (#3121)

DOC: Sphinx 3 compatibility (#3206)

DOC: Update links, typos in contributing guide (#3160)

DOC: Update SelectFiles docstring to match actual behavior (#3041)

DOC: Updated .zenodo.json file (#3167)

DOC: Update .zenodo.json (#3165)

MNT: Permit recent nilearns (#2841)

MNT: Test Python 3.8 (#3154)

MNT: Restore ReadTheDocs (#3207)

MNT: Update Zenodo ordering based on commit count (#3169)

1.4.2 (February 14, 2020)

(Full changelog)

FIX: Allow fsl.MultipleRegressDesign to create multiple F-tests (#3166)

FIX: Reliably parse SGE job IDs in the presence of warnings (#3168)

FIX: Move TraitType import, handle API change for NoDefaultSpecified (#3159)

1.4.1 (January 27, 2020)

(Full changelog)

FIX: DataSink to S3 buckets (#3130)

FIX: improve version checking for nodes of workflows (#3152)

FIX: mapnode to generate result file when crashes in single node mode (#3143)

FIX: Can't seem to import workflows from niflows in CircleCI (#3134)

FIX: Repair aftermath of docs refactor (#3133)

FIX: change ANTS number_of_time_steps from Float to Int (#3118)

DOC: Revise generation of examples to work in RTD (#3132)

DOC: Bring examples generation back to doc/conf.py (#3131)

DOC: Documentation overhaul (#3124)

DOC: Deep revision of documentation building (#3120)

DOC: Deduplicate code for Sphinx's APIdoc generation (#3119)

MNT: Update requirements.txt post-1.4 (#3153)

1.4.0 (December 20, 2019)

(Full changelog)

FIX: Mark strings containing regex escapes as raw (#3106)

ENH: Pacify DeprecationWarnings caused by nibabel 3 pre-release (#3099)

ENH: Allow Nipype configuration directory to be specified with NIPYPE_CONFIG_DIR environment variable (#3073)

ENH: Add options and outputs to fsl.Eddy interface (#3034)

ENH: Add skull_file output to fsl.BET interface (#3095)

RF: Drop various remaining compatibilities for Python < 3.5 (#2831)

DOC: Add Python 2 statement to README, reference maintenance branch in CONTRIBUTING (#3115)

DOC: Miss underline before cmd in example code (#3107)

STY: Black (#3096)

MNT: Set junit_family to suppress pytest warning (#3111)

MNT: Fix Dorota Jarecka ORCID (#3100)

MNT: Drop Python 2 support (#2654)

1.3.1 (November 12, 2019)

FIX: Restore checking traits or bunch (#3094)

1.3.0 (November 11, 2019)

(Full changelog)

FIX: Fixed typo in QwarpInputSpec Trait description (#3079)

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: Minimize the number of calls to _load_results when populating inputs (#3075)

ENH: Refactor savepkl/loadpkl - add a window for loadpkl to wait for the file (#3089)

ENH: Add "ExportFile" interface as simple alternative to "DataSink" (#3054)

ENH: Allow nipype.cfg in cwd to be read even if ~/.nipype does not exist (#3072)

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 (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 (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 (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_sh to not 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 (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 (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 (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 (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 (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 (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)

1.1.4 (October 31, 2018)

(Full changelog)

FIX: Python 2.7-3.7.1 compatible NonDaemonPool (#2754)

FIX: VRML typo (VMRL) in MeshFix (#2757)

FIX: Refine FSL.split output identification (#2746)

FIX: Reuse _gen_filename logic in ants.LaplacianThickness (#2734)

FIX: Remove 'reg_term' default from dwi2tensor interface (#2731)

FIX: Keep profile files when remove_unnecessary_outputs = true (#2718)

ENH: Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs (#2740)

ENH: Add compression option for bru2nii (#2762)

ENH: Add slice_encoding_direction input to TShift (#2753)

ENH: Add 'sse' output to FSL DTIFit interface (#2749)

ENH: Update ants.LaplacianThickness to use name_source (#2747)

ENH: Add tab completion for node and interface inputs properties (#2735)

ENH: enable/disable resource monitor in the fixture per test (#2725)

TEST: Update expected dotfile text for networkx 1.x (#2730)

DOC: Move user docs from nipype to nipype_tutorial (#2726)

DOC: Use consistent name in reconall workflow docstring (#2758)

MAINT: Use neurodocker 0.4.1 + apt install afni (#2707)

MAINT: Fix prov and rdflib in nipype (#2701)

MAINT: Correct readthedocs build error (#2723)

MAINT: Pin codecov to <5.0 so Travis is fixed (#2728)

CI: Lock travis pybids 0.6.5 (#2720)

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 (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 (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 (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 (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)

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 (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 (February 27, 2018)

(Full changelog)

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

1.0.0 (January 24, 2018)

(Full changelog)

FIX: Change to interface workdir within Interface.run() instead Node (#2384)
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)

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