1.7.0 (October 20, 2021)¶
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 therestrict_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 inants.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)
1.6.1 (June 16, 2021)¶
Bug-fix release in the 1.6.x series.
FIX: Set DistributedPluginBase.refidx type correctly (https://github.com/nipy/nipype/pull/3340)
FIX: change fsl interface randomise –f_only to –fonly for #3322 (https://github.com/nipy/nipype/pull/3325)
FIX: BET raising “No image files match: …” with very long file names (https://github.com/nipy/nipype/pull/3309)
FIX: Update SmoothEstimateOutputSpec resels description (https://github.com/nipy/nipype/pull/3316)
ENH: Adds interfaces for MRtrix utils shconv and sh2amp (https://github.com/nipy/nipype/pull/3280)
ENH: Interface for R (https://github.com/nipy/nipype/pull/3291)
ENH: Add CAT12 interfaces (https://github.com/nipy/nipype/pull/3310)
ENH: AFNI 3dNetCorr as afni.NetCorr (https://github.com/nipy/nipype/pull/3263)
ENH: Skip newline before Python call in batch submission to facilitate containerized runs (https://github.com/nipy/nipype/pull/3297)
ENH: Add new dwifslpreproc interface for MRtrix3 (https://github.com/nipy/nipype/pull/3278)
REF: Cache nodes in workflow to speed up construction, other optimizations (https://github.com/nipy/nipype/pull/3331)
DOC: Fixed Developer Setup Link in install.rst (https://github.com/nipy/nipype/pull/3330)
MNT: Blacklist Dipy 1.4.1 (https://github.com/nipy/nipype/pull/3335)
MNT: Drop support for numpy < 1.15.3 (https://github.com/nipy/nipype/pull/3284)
CI: Build docker images with Python 3.8 (https://github.com/nipy/nipype/pull/3287)
CI: Drop Circle doc builds (https://github.com/nipy/nipype/pull/3338)
CI: Drop Travis (https://github.com/nipy/nipype/pull/3332)
CI: Build docker images with Python 3.8 (https://github.com/nipy/nipype/pull/3287)
CI: Add specs and style checks (https://github.com/nipy/nipype/pull/3321)
CI: Move from Travis to GitHub actions (https://github.com/nipy/nipype/pull/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.
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
-g
withantsAI
< 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.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 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
ConstrainedSphericalDeconvolution
interface to replaceEstimateFOD
for 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.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)
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.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)
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_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)
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
None
inpipeline.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)
1.2.2 (September 07, 2019)¶
FIX: Ensure
loadpkl
returns a not None value (https://github.com/nipy/nipype/pull/3020)FIX:
loadpkl
failed 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-intensities
and 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_requires
to 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_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_sh
to 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
indirectory
handlenipype.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
andFile
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)
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_callback
not 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
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 ‘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_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
tonipype.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.LaplacianThickness
to 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.get
withtrait_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 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)