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.
- FIX: Canonicalize environment dicts to strings in Windows (https://github.com/nipy/nipype/pull/3267)
- FIX: Purge deprecated exception content accesses (https://github.com/nipy/nipype/pull/3272)
- FIX: Handle changes in CLI structure of mrtrix3.DWIBiasCorrect (https://github.com/nipy/nipype/pull/3248)
- FIX: EpiReg changed to not list certain outputs when ‘wmseg’ input is specified (https://github.com/nipy/nipype/pull/3265)
- FIX: CI issues (https://github.com/nipy/nipype/pull/3262)
- FIX: SPM SliceTiming must accept either Int or float for ref_slice and sli… (https://github.com/nipy/nipype/pull/3255)
- FIX: Raise version error when using
-gwithantsAI< 2.3.0 (https://github.com/nipy/nipype/pull/3256)- FIX: No longer depending on pydotplus (networkx >=2.0 update) (https://github.com/nipy/nipype/pull/3251)
- FIX: ANTs’ utilities revision - bug fixes and add more operations to
ants.ImageMath(https://github.com/nipy/nipype/pull/3236)- ENH: Handle unavailable traits due to version differences (https://github.com/nipy/nipype/pull/3273)
- ENH: Optimize workflow.run performance (https://github.com/nipy/nipype/pull/3260)
- DOC: Remove myself (@mr-c) from the zenodo metadata (https://github.com/nipy/nipype/pull/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.
- FIX: Warn for min/max_ver traits when tool version can’t be parsed (https://github.com/nipy/nipype/pull/3241)
- FIX: Serialize all interface arguments when exporting workflows (https://github.com/nipy/nipype/pull/3240)
- FIX: Permit identity transforms in list of transforms given to ants.ApplyTransforms (https://github.com/nipy/nipype/pull/3237)
- FIX: ANTs’ utilities revision - bug fixes and add more operations to
ants.ImageMath(https://github.com/nipy/nipype/pull/3236)- DOC: Skip BIDSDataGrabber doctest if pybids is missing (https://github.com/nipy/nipype/pull/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.
- FIX: volterra_expansion_order documentation error (https://github.com/nipy/nipype/pull/3213)
- FIX: BET incorrect output paths (https://github.com/nipy/nipype/pull/3214)
- FIX: Terminal output in
report.rstspreads 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 toants.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
ConstrainedSphericalDeconvolutioninterface to replaceEstimateFODfor MRtrix3’sdwi2fod(https://github.com/nipy/nipype/pull/3176)- ENH: Detect values for EulerNumber interface (https://github.com/nipy/nipype/pull/3173)
- ENH: Remove examples from repository (https://github.com/nipy/nipype/pull/3172)
- TEST: Clean up tests (https://github.com/nipy/nipype/pull/3195)
- TEST: Mock terminal output before testing changing default value (https://github.com/nipy/nipype/pull/3193)
- REF: make invocations of python and pytest consistent with the one used/desired python (https://github.com/nipy/nipype/pull/3208)
- REF: Prefer math.gcd to hand-rolled Euclid’s algorithm (https://github.com/nipy/nipype/pull/3177)
- REF: Removed all uses of numpy_mmap (https://github.com/nipy/nipype/pull/3121)
- DOC: Sphinx 3 compatibility (https://github.com/nipy/nipype/pull/3206)
- DOC: Update links, typos in contributing guide (https://github.com/nipy/nipype/pull/3160)
- DOC: Update SelectFiles docstring to match actual behavior (https://github.com/nipy/nipype/pull/3041)
- DOC: Updated .zenodo.json file (https://github.com/nipy/nipype/pull/3167)
- DOC: Update .zenodo.json (https://github.com/nipy/nipype/pull/3165)
- MNT: Permit recent nilearns (https://github.com/nipy/nipype/pull/2841)
- MNT: Test Python 3.8 (https://github.com/nipy/nipype/pull/3154)
- MNT: Restore ReadTheDocs (https://github.com/nipy/nipype/pull/3207)
- MNT: Update Zenodo ordering based on commit count (https://github.com/nipy/nipype/pull/3169)
1.4.2 (February 14, 2020)¶
- FIX: Allow
fsl.MultipleRegressDesignto create multiple F-tests (https://github.com/nipy/nipype/pull/3166)- FIX: Reliably parse SGE job IDs in the presence of warnings (https://github.com/nipy/nipype/pull/3168)
- FIX: Move TraitType import, handle API change for NoDefaultSpecified (https://github.com/nipy/nipype/pull/3159)
1.4.1 (January 27, 2020)¶
- FIX: DataSink to S3 buckets (https://github.com/nipy/nipype/pull/3130)
- FIX: improve version checking for nodes of workflows (https://github.com/nipy/nipype/pull/3152)
- FIX: mapnode to generate result file when crashes in single node mode (https://github.com/nipy/nipype/pull/3143)
- FIX: Can’t seem to import workflows from niflows in CircleCI (https://github.com/nipy/nipype/pull/3134)
- FIX: Repair aftermath of docs refactor (https://github.com/nipy/nipype/pull/3133)
- FIX: change ANTS number_of_time_steps from Float to Int (https://github.com/nipy/nipype/pull/3118)
- DOC: Revise generation of examples to work in RTD (https://github.com/nipy/nipype/pull/3132)
- DOC: Bring examples generation back to
doc/conf.py(https://github.com/nipy/nipype/pull/3131)- DOC: Documentation overhaul (https://github.com/nipy/nipype/pull/3124)
- DOC: Deep revision of documentation building (https://github.com/nipy/nipype/pull/3120)
- DOC: Deduplicate code for Sphinx’s APIdoc generation (https://github.com/nipy/nipype/pull/3119)
- MNT: Update requirements.txt post-1.4 (https://github.com/nipy/nipype/pull/3153)
1.4.0 (December 20, 2019)¶
- 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 NIPYPE_CONFIG_DIR environment variable (https://github.com/nipy/nipype/pull/3073)
- ENH: Add options and outputs to
fsl.Eddyinterface (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)
1.3.1 (November 12, 2019)¶
- FIX: Restore checking traits or bunch (https://github.com/nipy/nipype/pull/3094)
1.3.0 (November 11, 2019)¶
- 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_resultswhen 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 specson Travis (https://github.com/nipy/nipype/pull/3066)
1.2.3 (September 23, 2019)¶
Python 1.2.3 will be the last version to support Python 3.4.
- 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
Noneinpipeline.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.MRResizeinterface (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)
1.2.2 (September 07, 2019)¶
- FIX: Ensure
loadpklreturns a not None value (https://github.com/nipy/nipype/pull/3020)- FIX:
loadpklfailed when pklz file contained versioning info (https://github.com/nipy/nipype/pull/3017)- FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007)
- FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010)
- ENH: Add interface for AFNI
3dTsmooth(https://github.com/nipy/nipype/pull/2948)- ENH: Additional arguments to ANTs N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3012)
- ENH: Add
--rescale-intensitiesand name_source to N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3011)- ENH: Add index_mask_file input to ImageStats (https://github.com/nipy/nipype/pull/3005)
- RF: Remove versioning from
loadpkl(https://github.com/nipy/nipype/pull/3019)- MAINT: Add
python_requiresto package metadata (https://github.com/nipy/nipype/pull/3006)
1.2.1 (August 19, 2019)¶
- FIX: Resolve/rebase paths from/to results files (https://github.com/nipy/nipype/pull/2971)
- FIX: Use
load_resultfilewhen loading a results pickle (https://github.com/nipy/nipype/pull/2985)- FIX: Incorrect extension identified when checking
Filetraits (https://github.com/nipy/nipype/pull/2987)- FIX: Correctly pickle
OuputMultiObjecttraits (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_shto not 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
indirectoryhandlenipype.utils.filemanip.Path(https://github.com/nipy/nipype/pull/2989)- ENH: Add resolve/rebase
BasePathtraits methods & tests (https://github.com/nipy/nipype/pull/2970)- ENH: Modify
DirectoryandFiletraits 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_outputsfor 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)
1.2.0 (May 09, 2019)¶
- 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 warped_file log_file to include cwd (https://github.com/nipy/nipype/pull/2900)
- FIX: Sort conditions in bids_gen_info 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)
1.1.9 (February 25, 2019)¶
- FIX: Make positional arguments to LaplacianThickness require previous argument (https://github.com/nipy/nipype/pull/2848)
- FIX: Import math and csv modules for bids_gen_info (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)
1.1.8 (January 28, 2019)¶
- 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)
1.1.7 (December 17, 2018)¶
- 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_callbacknot called withstop_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)
1.1.6 (November 26, 2018)¶
- FIX: MapNodes fail when
MultiProcPluginpassed 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 ‘stop_on_first_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_setinstead (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_commandtonipype.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)
1.1.5 (November 08, 2018)¶
Hotfix release.
- 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)
1.1.4 (October 31, 2018)¶
- 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 _gen_filename 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 slice_encoding_direction 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.LaplacianThicknessto usename_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)
1.1.3 (September 24, 2018)¶
- 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)
1.1.2 (August 11, 2018)¶
Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.
- 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)
1.1.1 (July 30, 2018)¶
- 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._output_dir 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)
1.1.0 (July 04, 2018)¶
- 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 ignore_exception and terminal_output 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)
1.0.4 (May 29, 2018)¶
- FIX: Update logging levels in enable_debug_mode (https://github.com/nipy/nipype/pull/2595)
- FIX: Set default result in DistributedPluginBase._clean_queue (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)
1.0.3 (April 30, 2018)¶
- 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.getwithtrait_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
-masargument 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 terminal_output and ignore_exception 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)
1.0.2 (March 27, 2018)¶
- 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)
1.0.1 (February 27, 2018)¶
- FIX: Small bug in freesurfer label2annot fill_thresh specs [#2377](https://github.com/nipy/nipype/pull/2377)
- FIX: Error creating gradients in DTIRecon [#2460](https://github.com/nipy/nipype/pull/2460)
- FIX: improve matlab_cmd [#2452](https://github.com/nipy/nipype/pull/2452)
- FIX: Extract unit information from image header in CompCor [#2458](https://github.com/nipy/nipype/pull/2458)
- FIX: Update pybids data directory, unbundle out-of-date numpydoc [#2437](https://github.com/nipy/nipype/pull/2437)
- FIX: Out_file bugs in Afni.Zcat and Afni.Merge interfaces [#2424](https://github.com/nipy/nipype/pull/2424)
- FIX: Re-enable spm.Realign to take lists of lists of files [#2409](https://github.com/nipy/nipype/pull/2409)
- FIX: Remove deprecated output from ICC interface [#2422](https://github.com/nipy/nipype/pull/2422)
- FIX: Argstr for mask in Afni.BlurToFWHM [#2418](https://github.com/nipy/nipype/pull/2418)
- FIX: Default value for sbatch_args (SLURMGraph) [#2417](https://github.com/nipy/nipype/pull/2417)
- FIX: Ortvec argstr for Afni.Deconvolve [#2415](https://github.com/nipy/nipype/pull/2415)
- FIX: Bug fixes for afni.model [#2398](https://github.com/nipy/nipype/pull/2398)
- DOC: Add brief neurodocker tutorial [#2464](https://github.com/nipy/nipype/pull/2464)
- DOC: Fix tutorials [#2459](https://github.com/nipy/nipype/pull/2459)
- ENH: antsRegistrationSyNQuick interface [#2453](https://github.com/nipy/nipype/pull/2453)
- ENH: Automate updates of CHANGES [#2440](https://github.com/nipy/nipype/pull/2440)
- ENH: Add SPM Fieldmap Tool wrapper [#1905](https://github.com/nipy/nipype/pull/1905)
- ENH: Additional option for DataGrabber [#1915](https://github.com/nipy/nipype/pull/1915)
- ENH: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve [#2426](https://github.com/nipy/nipype/pull/2426)
- ENH: c3d/c4d interface [#2430](https://github.com/nipy/nipype/pull/2430)
- ENH: Allow input weight for AFNI’s volreg. [#2396](https://github.com/nipy/nipype/pull/2396)
- ENH: Delay crashing if exception is raised in local hash check [#2410](https://github.com/nipy/nipype/pull/2410)
- CI: Add doctests to pytest script [#2449](https://github.com/nipy/nipype/pull/2449)
- CI: Ignore tests in calculating coverage [#2443](https://github.com/nipy/nipype/pull/2443)
- CI: Saturate Circle workflow [#2386](https://github.com/nipy/nipype/pull/2386)
- REF: Update and factor mount table parsing [#2444](https://github.com/nipy/nipype/pull/2444)
- REF: Make ignore_exception a class attribute [#2414](https://github.com/nipy/nipype/pull/2414)
1.0.0 (January 24, 2018)¶
- FIX: Change to interface workdir within
Interface.run()instead Node (https://github.com/nipy/nipype/pull/2384) - 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)