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Cannot make a PR with requirement of running make check-before-commit which crashes #2946

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Cannot make a PR with requirement of running make check-before-commit which crashes#2946
@mick-d

Description

@mick-d
mick-d
opened on Jun 21, 2019

Summary

I forked the NiPype repo and followed the requirement of running make check-before-commit before submitting a PR but I got the output below ending with an error.

I am in a conda environment with Python 3.7 but somehow there are some references to python 2.7.

Due to the long output, click the arrow below to see the whole output. 
$> make check-before-commit Checking specs and autogenerating spec tests env PYTHONPATH=".:" python tools/checkspecs.py CompCor has nonautotest TSNR has nonautotest 190621-17:16:06,721 nipype.interface WARNING: VTK was not found 190621-17:16:06,722 nipype.interface WARNING: tvtk wasn't found ErrorMap has nonautotest Overlap has nonautotest Overlap has nonautotest TSNR has nonautotest FSSurfaceCommand has nonautotest BBRegister has nonautotest FILMGLS has nonautotest nipype.algorithms.modelgen:SpecifyModel:Inputs:bids_amplitude_column:exists nipype.algorithms.modelgen:SpecifyModel:Inputs:bids_amplitude_column:mandatory=False nipype.algorithms.modelgen:SpecifyModel:Inputs:bids_condition_column:exists nipype.algorithms.modelgen:SpecifyModel:Inputs:bids_condition_column:mandatory=False nipype.algorithms.modelgen:SpecifySPMModel:Inputs:bids_amplitude_column:exists nipype.algorithms.modelgen:SpecifySPMModel:Inputs:bids_amplitude_column:mandatory=False nipype.algorithms.modelgen:SpecifySPMModel:Inputs:bids_condition_column:exists nipype.algorithms.modelgen:SpecifySPMModel:Inputs:bids_condition_column:mandatory=False nipype.algorithms.modelgen:SpecifySparseModel:Inputs:bids_amplitude_column:exists nipype.algorithms.modelgen:SpecifySparseModel:Inputs:bids_amplitude_column:mandatory=False nipype.algorithms.modelgen:SpecifySparseModel:Inputs:bids_condition_column:exists nipype.algorithms.modelgen:SpecifySparseModel:Inputs:bids_condition_column:mandatory=False find . -name "*[.py|.rst]" -type f | xargs perl -pi -e 's/[ \t]*$//' Reverting test_docparse git checkout nipype/utils/tests/test_docparse.py building docs make -C doc clean htmlonly make[1]: Entering directory '/home/<my_username>/repos/neuro/nipype/doc' rm -rf _build/* *~ api/generated interfaces/generated users/examples documentation.zip sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v2.1.2 ('WARNING: Empty -', 'nipype.caching') ('WARNING: Empty -', 'nipype.interfaces') ('WARNING: Empty -', 'nipype.pipeline') ('WARNING: Empty -', 'nipype.pipeline.engine') ('WARNING: Empty -', 'nipype.refs') ('WARNING: Empty -', 'nipype.sphinxext') 8 files written WARNING: Empty - nipype WARNING: Empty - nipype.algorithms ACompCor CompCor ComputeDVARS FramewiseDisplacement NonSteadyStateDetector TCompCor TSNR ICC 190621-17:17:14,678 nipype.interface WARNING: VTK was not found 190621-17:17:14,679 nipype.interface WARNING: tvtk wasn't found ComputeMeshWarp MeshWarpMaths P2PDistance TVTKBaseInterface WarpPoints Distance ErrorMap FuzzyOverlap Overlap Similarity AddCSVColumn AddCSVRow AddNoise CalculateMedian CalculateNormalizedMoments CreateNifti Distance FuzzyOverlap Gunzip Matlab2CSV MergeCSVFiles MergeROIs ModifyAffine NormalizeProbabilityMapSet Overlap PickAtlas SimpleThreshold SplitROIs TSNR SpecifyModel SpecifySPMModel SpecifySparseModel ArtifactDetect StimulusCorrelation ActivationCount WARNING: Empty - nipype.info WARNING: Empty - nipype.interfaces WARNING: Empty - nipype.interfaces.afni AFNIPythonCommand Deconvolve Remlfit Synthesize AlignEpiAnatPy Allineate AutoTLRC AutoTcorrelate Automask Bandpass BlurInMask BlurToFWHM ClipLevel DegreeCentrality Despike Detrend ECM Fim Fourier Hist LFCD Maskave Means OutlierCount QualityIndex Qwarp QwarpPlusMinus ROIStats Retroicor Seg SkullStrip TCorr1D TCorrMap TCorrelate TNorm TProject TShift Volreg Warp SVMTest SVMTrain ABoverlap AFNItoNIFTI Autobox Axialize BrickStat Bucket Calc Cat CatMatvec CenterMass ConvertDset Copy Dot Edge3 Eval FWHMx GCOR LocalBistat Localstat MaskTool Merge Notes NwarpAdjust NwarpApply NwarpCat OneDToolPy ReHo Refit Resample TCat TCatSubBrick TStat To3D Undump Unifize ZCutUp Zcat Zeropad WARNING: Empty - nipype.interfaces.ants WARNING: Empty - nipype.interfaces.ants.base GenWarpFields antsIntroduction buildtemplateparallel CompositeTransformUtil MeasureImageSimilarity Registration RegistrationSynQuick ApplyTransforms ApplyTransformsToPoints WarpImageMultiTransform WarpTimeSeriesImageMultiTransform AntsJointFusion Atropos BrainExtraction CorticalThickness DenoiseImage JointFusion KellyKapowski LaplacianThickness N4BiasFieldCorrection AffineInitializer AverageAffineTransform AverageImages ComposeMultiTransform CreateJacobianDeterminantImage LabelGeometry MultiplyImages ConvertScalarImageToRGB CreateTiledMosaic WARNING: Empty - nipype.interfaces.base BaseInterface CommandLine Interface LibraryBaseInterface MpiCommandLine SEMLikeCommandLine SimpleInterface StdOutCommandLine Bunch InterfaceResult NipypeInterfaceError Directory File ImageFile InputMultiObject MultiObject OutputMultiObject Str WARNING: Empty - nipype.interfaces.brainsuite BDP Bfc Bse Cerebro Cortex Dewisp Dfs Hemisplit Pialmesh Pvc SVReg Scrubmask Skullfinder Tca ThicknessPVC Bru2 C3d C3dAffineTool WARNING: Empty - nipype.interfaces.camino SFLUTGen SFPICOCalibData Conmat AnalyzeHeader DT2NIfTI Image2Voxel NIfTIDT2Camino ProcStreamlines Shredder TractShredder VtkStreamlines ComputeEigensystem ComputeFractionalAnisotropy ComputeMeanDiffusivity ComputeTensorTrace DTIFit DTLUTGen DTMetric ModelFit PicoPDFs Track TrackBallStick TrackBayesDirac TrackBedpostxDeter TrackBedpostxProba TrackBootstrap TrackDT TrackPICo LinRecon MESD QBallMX SFPeaks ImageStats WARNING: Empty - nipype.interfaces.camino2trackvis Camino2Trackvis Trackvis2Camino WARNING: Empty - nipype.interfaces.cmtk CFFBaseInterface CreateMatrix CreateNodes ROIGen CFFConverter MergeCNetworks NetworkBasedStatistic AverageNetworks NetworkXMetrics Parcellate Dcm2nii Dcm2niix CopyMeta DcmStack GroupAndStack LookupMeta MergeNifti NiftiGeneratorBase SplitNifti WARNING: Empty - nipype.interfaces.diffusion_toolkit WARNING: Empty - nipype.interfaces.diffusion_toolkit.base DTIRecon DTITracker HARDIMat ODFRecon ODFTracker SplineFilter TrackMerge WARNING: Empty - nipype.interfaces.dipy APMQball DipyBaseInterface DipyDiffusionInterface Denoise Resample CSD EstimateResponseSH RESTORE WARNING: Empty - nipype.interfaces.dipy.registration SimulateMultiTensor WARNING: Empty - nipype.interfaces.dipy.stats DTI TensorMode StreamlineTractography TrackDensityMap WARNING: Empty - nipype.interfaces.dtitk CommandLineDtitk DTITKRenameMixin AffScalarVol AffSymTensor3DVol Affine AffineTask ComposeXfm ComposeXfmTask Diffeo DiffeoScalarVol DiffeoSymTensor3DVol DiffeoTask Rigid RigidTask affScalarVolTask affSymTensor3DVolTask diffeoScalarVolTask diffeoSymTensor3DVolTask BinThresh BinThreshTask SVAdjustVoxSp SVAdjustVoxSpTask SVResample SVResampleTask TVAdjustOriginTask TVAdjustVoxSp TVAdjustVoxSpTask TVResample TVResampleTask TVtool TVtoolTask SlicerCommandLine WARNING: Empty - nipype.interfaces.elastix WARNING: Empty - nipype.interfaces.elastix.base AnalyzeWarp ApplyWarp PointsWarp Registration EditTransform WARNING: Empty - nipype.interfaces.freesurfer WARNING: Empty - nipype.interfaces.freesurfer.base FuseSegmentations RobustTemplate Binarize Concatenate GLMFit Label2Annot Label2Label Label2Vol MRISPreproc MRISPreprocReconAll MS_LDA OneSampleTTest SegStats SegStatsReconAll SphericalAverage ApplyVolTransform BBRegister BBRegisterInputSpec6 CALabel CANormalize CARegister ConcatenateLTA DICOMConvert EditWMwithAseg FitMSParams MNIBiasCorrection MRIConvert MRIsCALabel Normalize ParseDICOMDir ReconAll Resample RobustRegister SegmentCC SegmentWM Smooth SynthesizeFLASH UnpackSDICOMDir WatershedSkullStrip EMRegister MPRtoMNI305 MRICoreg Paint Register RegisterAVItoTalairach AddXFormToHeader Aparc2Aseg Apas2Aseg ApplyMask CheckTalairachAlignment Contrast Curvature CurvatureStats EulerNumber ExtractMainComponent FixTopology Jacobian LTAConvert MRIFill MRIMarchingCubes MRIPretess MRITessellate MRIsCalc MRIsCombine MRIsConvert MRIsExpand MRIsInflate MakeAverageSubject MakeSurfaces ParcellationStats RelabelHypointensities RemoveIntersection RemoveNeck SampleToSurface SmoothTessellation Sphere Surface2VolTransform SurfaceSmooth SurfaceSnapshots SurfaceTransform TalairachAVI TalairachQC Tkregister2 VolumeMask WARNING: Empty - nipype.interfaces.fsl ICA_AROMA WARNING: Empty - nipype.interfaces.fsl.base BEDPOSTX5 DTIFit DistanceMap FindTheBiggest MakeDyadicVectors ProbTrackX ProbTrackX2 ProjThresh TractSkeleton VecReg XFibres5 ApplyTOPUP EPIDeWarp Eddy EddyCorrect EddyQuad EpiReg PrepareFieldmap SigLoss TOPUP Classifier Cleaner FeatureExtractor Training TrainingSetCreator AR1Image AR1ImageInput ApplyMask ApplyMaskInput BinaryMaths BinaryMathsInput ChangeDataType ChangeDataTypeInput DilateImage DilateInput ErodeImage ErodeInput IsotropicSmooth IsotropicSmoothInput KernelInput MathsCommand MathsInput MathsOutput MaxImage MaxImageInput MaxnImage MaxnImageInput MeanImage MeanImageInput MedianImage MedianImageInput MinImage MinImageInput MultiImageMaths MultiImageMathsInput PercentileImage PercentileImageInput SpatialFilter SpatialFilterInput StdImage StdImageInput TemporalFilter TemporalFilterInput Threshold UnaryMaths UnaryMathsInput Cluster ContrastMgr DualRegression FEAT FEATModel FEATRegister FILMGLS FILMGLSInputSpec505 FILMGLSInputSpec507 FILMGLSOutputSpec507 FLAMEO GLM L2Model Level1Design MELODIC MultipleRegressDesign Randomise SMM SmoothEstimate B0Calc ApplyWarp ApplyXFM BET FAST FIRST FLIRT FNIRT FUGUE MCFLIRT PRELUDE SUSAN SliceTimer AvScale Complex ConvertWarp ConvertXFM CopyGeom ExtractROI FilterRegressor ImageMaths ImageMeants ImageStats InvWarp Merge MotionOutliers Overlay PlotMotionParams PlotTimeSeries PowerSpectrum Reorient2Std RobustFOV SigLoss Slice Slicer Smooth Split SwapDimensions WarpPoints WarpPointsFromStd WarpPointsToStd WarpUtils Reorient Rescale BIDSDataGrabber DataFinder DataGrabber DataSink FreeSurferSource IOBase JSONFileGrabber JSONFileSink MySQLSink ProgressPercentage S3DataGrabber SQLiteSink SSHDataGrabber SelectFiles XNATSink XNATSource MeshFix WARNING: Empty - nipype.interfaces.minc Average BBox Beast BestLinReg BigAverage Blob Blur Calc Convert Copy Dump Extract Gennlxfm Math NlpFit Norm Pik Resample Reshape ToEcat ToRaw VolSymm Volcentre Voliso Volpad XfmAvg XfmConcat XfmInvert WARNING: Empty - nipype.interfaces.mipav JistBrainMgdmSegmentation JistBrainMp2rageDuraEstimation JistBrainMp2rageSkullStripping JistBrainPartialVolumeFilter JistCortexSurfaceMeshInflation JistIntensityMp2rageMasking JistLaminarProfileCalculator JistLaminarProfileGeometry JistLaminarProfileSampling JistLaminarROIAveraging JistLaminarVolumetricLayering MedicAlgorithmImageCalculator MedicAlgorithmLesionToads MedicAlgorithmMipavReorient MedicAlgorithmN3 MedicAlgorithmSPECTRE2010 MedicAlgorithmThresholdToBinaryMask RandomVol WARNING: Empty - nipype.interfaces.mipav.generate_classes WARNING: Empty - nipype.interfaces.mixins ReportCapableInterface WARNING: Empty - nipype.interfaces.mne WatershedBEM WARNING: Empty - nipype.interfaces.mrtrix MRTrix2TrackVis DWI2Tensor Erode GenerateWhiteMatterMask MRConvert MRMultiply MRTransform MRTrixViewer MedianFilter3D Tensor2ApparentDiffusion Tensor2FractionalAnisotropy Tensor2Vector Threshold ConstrainedSphericalDeconvolution DWI2SphericalHarmonicsImage Directions2Amplitude EstimateResponseForSH FindShPeaks GenerateDirections DiffusionTensorStreamlineTrack FilterTracks ProbabilisticSphericallyDeconvolutedStreamlineTrack SphericallyDeconvolutedStreamlineTrack StreamlineTrack Tracks2Prob WARNING: Empty - nipype.interfaces.mrtrix3 MRTrix3Base BuildConnectome LabelConfig LabelConvert DWIBiasCorrect DWIDenoise MRDeGibbs ResponseSD EstimateFOD FitTensor Tractography BrainMask ComputeTDI DWIExtract Generate5tt MRConvert MRMath Mesh2PVE TCK2VTK TensorMetrics WARNING: Empty - nipype.interfaces.niftyfit FitAsl NiftyFitCommand DwiTool FitDwi FitQt1 WARNING: Empty - nipype.interfaces.niftyreg NiftyRegCommand RegAladin RegF3D RegAverage RegJacobian RegMeasure RegResample RegTools RegTransform WARNING: Empty - nipype.interfaces.niftyseg NiftySegCommand EM CalcTopNCC LabelFusion LabelFusionInput LabelFusionOutput FillLesions BinaryMaths BinaryMathsInput BinaryMathsInputInteger BinaryMathsInteger MathsCommand MathsInput MathsOutput Merge MergeInput TupleMaths TupleMathsInput UnaryMaths UnaryMathsInput PatchMatch BinaryStats BinaryStatsInput StatsCommand StatsInput StatsOutput UnaryStats UnaryStatsInput NilearnBaseInterface SignalExtraction WARNING: Empty - nipype.interfaces.nipy NipyBaseInterface EstimateContrast FitGLM ComputeMask SpaceTimeRealigner Trim Similarity WARNING: Empty - nipype.interfaces.nitime CoherenceAnalyzer NitimeBaseInterface PETPVC Quickshear WARNING: Empty - nipype.interfaces.semtools WARNING: Empty - nipype.interfaces.semtools.brains BRAINSPosteriorToContinuousClass BRAINSTalairach BRAINSTalairachMask SimilarityIndex GenerateEdgeMapImage GeneratePurePlugMask HistogramMatchingFilter DWICompare DWISimpleCompare WARNING: Empty - nipype.interfaces.semtools.diffusion DWIConvert dtiaverage dtiestim dtiprocess compareTractInclusion extractNrrdVectorIndex gtractAnisotropyMap gtractAverageBvalues gtractClipAnisotropy gtractCoRegAnatomy gtractConcatDwi gtractCopyImageOrientation gtractCoregBvalues gtractCostFastMarching gtractCreateGuideFiber gtractFastMarchingTracking gtractFiberTracking gtractImageConformity gtractInvertBSplineTransform gtractInvertDisplacementField gtractInvertRigidTransform gtractResampleAnisotropy gtractResampleB0 gtractResampleCodeImage gtractResampleDWIInPlace gtractResampleFibers gtractTensor gtractTransformToDisplacementField maxcurvature WARNING: Empty - nipype.interfaces.semtools.diffusion.tractography fiberstats fiberprocess fibertrack UKFTractography GenerateCsfClippedFromClassifiedImage WARNING: Empty - nipype.interfaces.semtools.filtering UnbiasedNonLocalMeans CannyEdge CannySegmentationLevelSetImageFilter DilateImage DilateMask DistanceMaps DumpBinaryTrainingVectors ErodeImage FlippedDifference GenerateBrainClippedImage GenerateSummedGradientImage GenerateTestImage GradientAnisotropicDiffusionImageFilter HammerAttributeCreator NeighborhoodMean NeighborhoodMedian STAPLEAnalysis TextureFromNoiseImageFilter TextureMeasureFilter WARNING: Empty - nipype.interfaces.semtools.legacy scalartransform WARNING: Empty - nipype.interfaces.semtools.registration BRAINSFit BRAINSResample BRAINSResize BRAINSDemonWarp BRAINSTransformFromFiducials VBRAINSDemonWarp WARNING: Empty - nipype.interfaces.semtools.segmentation BRAINSABC BRAINSConstellationDetector BRAINSCreateLabelMapFromProbabilityMaps BRAINSCut BRAINSMultiSTAPLE BRAINSROIAuto BinaryMaskEditorBasedOnLandmarks ESLR WARNING: Empty - nipype.interfaces.semtools.utilities BRAINSAlignMSP BRAINSClipInferior BRAINSConstellationModeler BRAINSEyeDetector BRAINSInitializedControlPoints BRAINSLandmarkInitializer BRAINSLinearModelerEPCA BRAINSLmkTransform BRAINSMush BRAINSSnapShotWriter BRAINSTransformConvert BRAINSTrimForegroundInDirection CleanUpOverlapLabels FindCenterOfBrain GenerateLabelMapFromProbabilityMap ImageRegionPlotter JointHistogram ShuffleVectorsModule fcsv_to_hdf5 insertMidACPCpoint landmarksConstellationAligner landmarksConstellationWeights WARNING: Empty - nipype.interfaces.slicer SlicerCommandLine DicomToNrrdConverter OrientScalarVolume WARNING: Empty - nipype.interfaces.slicer.diffusion DTIexport DTIimport DWIJointRicianLMMSEFilter DWIRicianLMMSEFilter DWIToDTIEstimation DiffusionTensorScalarMeasurements DiffusionWeightedVolumeMasking ResampleDTIVolume TractographyLabelMapSeeding WARNING: Empty - nipype.interfaces.slicer.filtering AddScalarVolumes CastScalarVolume MaskScalarVolume MultiplyScalarVolumes SubtractScalarVolumes CheckerBoardFilter CurvatureAnisotropicDiffusion GaussianBlurImageFilter GradientAnisotropicDiffusion MedianImageFilter ExtractSkeleton HistogramMatching ImageLabelCombine GrayscaleFillHoleImageFilter GrayscaleGrindPeakImageFilter N4ITKBiasFieldCorrection ResampleScalarVectorDWIVolume ThresholdScalarVolume VotingBinaryHoleFillingImageFilter WARNING: Empty - nipype.interfaces.slicer.legacy BSplineToDeformationField WARNING: Empty - nipype.interfaces.slicer.legacy.diffusion DWIUnbiasedNonLocalMeansFilter OtsuThresholdImageFilter ResampleScalarVolume AffineRegistration BSplineDeformableRegistration ExpertAutomatedRegistration LinearRegistration MultiResolutionAffineRegistration RigidRegistration OtsuThresholdSegmentation WARNING: Empty - nipype.interfaces.slicer.quantification IntensityDifferenceMetric PETStandardUptakeValueComputation WARNING: Empty - nipype.interfaces.slicer.registration BRAINSFit BRAINSResample ACPCTransform BRAINSDemonWarp FiducialRegistration VBRAINSDemonWarp WARNING: Empty - nipype.interfaces.slicer.segmentation SimpleRegionGrowingSegmentation BRAINSROIAuto EMSegmentCommandLine RobustStatisticsSegmenter GrayscaleModelMaker LabelMapSmoothing MergeModels ModelMaker ModelToLabelMap ProbeVolumeWithModel EMSegmentTransformToNewFormat WARNING: Empty - nipype.interfaces.spm EstimateContrast EstimateModel FactorialDesign Level1Design MultipleRegressionDesign OneSampleTTestDesign PairedTTestDesign Threshold ThresholdStatistics TwoSampleTTestDesign ApplyDeformations Coregister CreateWarped DARTEL DARTELNorm2MNI FieldMap NewSegment Normalize Normalize12 Realign RealignUnwarp Segment SliceTiming Smooth VBMSegment Analyze2nii ApplyInverseDeformation ApplyInverseDeformationInput ApplyInverseDeformationOutput ApplyTransform CalcCoregAffine DicomImport Reslice ResliceToReference ResliceToReferenceInput ResliceToReferenceOutput WARNING: Empty - nipype.interfaces.utility AssertEqual IdentityInterface Merge Rename Select Split CSVReader Function WARNING: Empty - nipype.interfaces.vista Vnifti2Image VtoMat WARNING: Empty - nipype.interfaces.workbench WBCommand CiftiSmooth MetricResample WARNING: Empty - nipype.refs WARNING: Empty - nipype.sphinxext GraphError ImageFile WARNING: Empty - nipype.workflows WARNING: Empty - nipype.workflows.dmri WARNING: Empty - nipype.workflows.dmri.camino /home/<my_username>/repos/neuro/nipype/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed warnings.warn('cmp not installed') 190621-17:17:41,251 nipype.interface WARNING: Unable to import ['cfflib']; CFFConverter interface may fail to run 190621-17:17:42,237 nipype.workflow INFO: Generated workflow graph: /tmp/tmpm2cv51lg.png (graph2use=hierarchical, simple_form=True). 190621-17:17:42,590 nipype.workflow INFO: Generated workflow graph: /tmp/tmp74e09pck.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.dmri.connectivity 190621-17:17:43,29 nipype.workflow INFO: Generated workflow graph: /tmp/tmpoo7v3xmd.png (graph2use=hierarchical, simple_form=True). 190621-17:17:43,294 nipype.workflow INFO: Generated workflow graph: /tmp/tmpekr_462f.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.dmri.dipy 190621-17:17:43,556 nipype.workflow INFO: Generated workflow graph: /tmp/tmpn_8kbord.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.dmri.dtitk 190621-17:17:43,844 nipype.workflow INFO: Generated workflow graph: /tmp/tmpuliogik6.png (graph2use=hierarchical, simple_form=True). 190621-17:17:44,129 nipype.workflow INFO: Generated workflow graph: /tmp/tmpi2h0awe5.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.dmri.fsl /home/<my_username>/repos/neuro/nipype/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /home/<my_username>/repos/neuro/nipype/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') 190621-17:17:45,806 nipype.workflow INFO: Generated workflow graph: /tmp/tmpeoehqszb.png (graph2use=hierarchical, simple_form=True). 190621-17:17:46,166 nipype.workflow INFO: Generated workflow graph: /tmp/tmpswfuvvcq.png (graph2use=hierarchical, simple_form=True). 190621-17:17:46,889 nipype.workflow INFO: Generated workflow graph: /tmp/tmp72huefwl.png (graph2use=hierarchical, simple_form=True). 190621-17:17:47,189 nipype.workflow INFO: Generated workflow graph: /tmp/tmp8w2z1saj.png (graph2use=hierarchical, simple_form=True). 190621-17:17:47,481 nipype.workflow INFO: Generated workflow graph: /tmp/tmpzuwnc3gt.png (graph2use=hierarchical, simple_form=True). 190621-17:17:47,749 nipype.workflow INFO: Generated workflow graph: /tmp/tmprjxuu1aj.png (graph2use=hierarchical, simple_form=True). 190621-17:17:48,229 nipype.workflow INFO: Generated workflow graph: /tmp/tmp3yqrz_t3.png (graph2use=hierarchical, simple_form=True). 190621-17:17:48,489 nipype.workflow INFO: Generated workflow graph: /tmp/tmps679s1v3.png (graph2use=hierarchical, simple_form=True). 190621-17:17:48,869 nipype.workflow INFO: Generated workflow graph: /tmp/tmpk7ek7tnp.png (graph2use=hierarchical, simple_form=True). 190621-17:17:49,133 nipype.workflow INFO: Generated workflow graph: /tmp/tmped7yyqda.png (graph2use=hierarchical, simple_form=True). 190621-17:17:49,351 nipype.workflow INFO: Generated workflow graph: /tmp/tmpg7z0zo2e.png (graph2use=hierarchical, simple_form=True). 190621-17:17:49,564 nipype.workflow INFO: Generated workflow graph: /tmp/tmps7n67984.png (graph2use=hierarchical, simple_form=True). /home/<my_username>/repos/neuro/nipype/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /home/<my_username>/repos/neuro/nipype/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') 190621-17:17:50,202 nipype.workflow INFO: Generated workflow graph: /tmp/tmp0w3ncbiz.png (graph2use=hierarchical, simple_form=True). 190621-17:17:50,480 nipype.workflow INFO: Generated workflow graph: /tmp/tmpval80ig6.png (graph2use=hierarchical, simple_form=True). 190621-17:17:50,814 nipype.workflow INFO: Generated workflow graph: /tmp/tmppoq4x87h.png (graph2use=hierarchical, simple_form=True). 190621-17:17:51,60 nipype.workflow INFO: Generated workflow graph: /tmp/tmpcb1gk781.png (graph2use=hierarchical, simple_form=True). 190621-17:17:51,337 nipype.workflow INFO: Generated workflow graph: /tmp/tmpliacfmfm.png (graph2use=hierarchical, simple_form=True). 190621-17:17:51,581 nipype.workflow INFO: Generated workflow graph: /tmp/tmpxbubx96c.png (graph2use=hierarchical, simple_form=True). 190621-17:17:51,905 nipype.workflow INFO: Generated workflow graph: /tmp/tmpox3a2hfp.png (graph2use=hierarchical, simple_form=True). 190621-17:17:52,150 nipype.workflow INFO: Generated workflow graph: /tmp/tmpw5o7m1mf.png (graph2use=hierarchical, simple_form=True). 190621-17:17:52,399 nipype.workflow INFO: Generated workflow graph: /tmp/tmpxffvvq14.png (graph2use=hierarchical, simple_form=True). 190621-17:17:52,629 nipype.workflow INFO: Generated workflow graph: /tmp/tmpeb6wllig.png (graph2use=hierarchical, simple_form=True). 190621-17:17:52,963 nipype.workflow INFO: Generated workflow graph: /tmp/tmpq3ixifqw.png (graph2use=hierarchical, simple_form=True). 190621-17:17:53,230 nipype.workflow INFO: Generated workflow graph: /tmp/tmpfa0qqc0x.png (graph2use=hierarchical, simple_form=True). 190621-17:17:53,609 nipype.workflow INFO: Generated workflow graph: /tmp/tmp57bbnrdt.png (graph2use=hierarchical, simple_form=True). 190621-17:17:53,890 nipype.workflow INFO: Generated workflow graph: /tmp/tmp2ekd5hx4.png (graph2use=hierarchical, simple_form=True). 190621-17:17:54,196 nipype.workflow INFO: Generated workflow graph: /tmp/tmp3gal_01p.png (graph2use=hierarchical, simple_form=True). 190621-17:17:54,429 nipype.workflow INFO: Generated workflow graph: /tmp/tmpcll5p4hn.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.dmri.mrtrix 190621-17:17:54,918 nipype.interface WARNING: Unable to import ['cmp']; Parcellate interface may fail to run 190621-17:17:54,919 nipype.interface WARNING: Unable to import ['cfflib']; CFFConverter interface may fail to run 190621-17:17:54,928 nipype.interface WARNING: Unable to import ['cfflib']; CFFConverter interface may fail to run 190621-17:17:56,599 nipype.workflow INFO: Generated workflow graph: /tmp/tmp7keogurn.png (graph2use=hierarchical, simple_form=True). 190621-17:17:57,58 nipype.workflow INFO: Generated workflow graph: /tmp/tmpf_d4xhse.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.fmri WARNING: Empty - nipype.workflows.fmri.fsl 190621-17:17:57,398 nipype.workflow INFO: Generated workflow graph: /tmp/tmp31i39xgl.png (graph2use=hierarchical, simple_form=True). 190621-17:17:57,680 nipype.workflow INFO: Generated workflow graph: /tmp/tmpx0hszdfq.png (graph2use=hierarchical, simple_form=True). 190621-17:17:57,906 nipype.workflow INFO: Generated workflow graph: /tmp/tmpzhmh68r2.png (graph2use=hierarchical, simple_form=True). 190621-17:17:58,435 nipype.workflow INFO: Generated workflow graph: /tmp/tmpv7vhhugj.png (graph2use=hierarchical, simple_form=True). 190621-17:17:58,817 nipype.workflow INFO: Generated workflow graph: /tmp/tmph1e1iohc.png (graph2use=hierarchical, simple_form=True). 190621-17:17:59,242 nipype.workflow INFO: Generated workflow graph: /tmp/tmpb6odhtyn.png (graph2use=hierarchical, simple_form=True). 190621-17:17:59,515 nipype.workflow INFO: Generated workflow graph: /tmp/tmpp9rbt_hh.png (graph2use=hierarchical, simple_form=True). 190621-17:17:59,760 nipype.workflow INFO: Generated workflow graph: /tmp/tmpn0_qm_ay.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.fmri.spm WARNING: Empty - nipype.workflows.fmri.spm.estimate 190621-17:18:52,448 nipype.workflow INFO: Generated workflow graph: /tmp/tmpb4pkogo_.png (graph2use=hierarchical, simple_form=True). 190621-17:18:52,739 nipype.workflow INFO: Generated workflow graph: /tmp/tmp5ii1h141.png (graph2use=hierarchical, simple_form=True). 190621-17:18:52,982 nipype.workflow INFO: Generated workflow graph: /tmp/tmp36v0j9ba.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.graph WARNING: Empty - nipype.workflows.misc WARNING: Empty - nipype.workflows.rsfmri WARNING: Empty - nipype.workflows.rsfmri.fsl 190621-17:18:53,403 nipype.workflow INFO: Generated workflow graph: /tmp/tmphrnda98q.png (graph2use=hierarchical, simple_form=True). 190621-17:18:53,736 nipype.workflow INFO: Generated workflow graph: /tmp/tmp4wjm3imp.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.smri WARNING: Empty - nipype.workflows.smri.ants 190621-17:18:54,162 nipype.workflow INFO: Generated workflow graph: /tmp/tmpvv_gfe7z.png (graph2use=hierarchical, simple_form=True). 190621-17:18:54,609 nipype.workflow INFO: Generated workflow graph: /tmp/tmp1z9smofo.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.smri.freesurfer WARNING: Empty - nipype.workflows.smri.freesurfer.autorecon3 WARNING: Empty - nipype.workflows.smri.freesurfer.ba_maps 190621-17:18:56,450 nipype.workflow INFO: Generated workflow graph: /tmp/tmpqu2pyiwy.png (graph2use=hierarchical, simple_form=True). 190621-17:18:56,452 nipype.workflow INFO: FreeSurfer Version: v6.0 190621-17:19:08,735 nipype.workflow INFO: Generated workflow graph: /tmp/tmplhdnq57d.png (graph2use=hierarchical, simple_form=True). 190621-17:19:08,997 nipype.workflow INFO: Generated workflow graph: /tmp/tmp6abe0wh6.png (graph2use=hierarchical, simple_form=True). FREESURFER_HOME: /usr/local/neuro/freesurfer FREESURFER_HOME: /usr/local/neuro/freesurfer 190621-17:19:09,268 nipype.workflow INFO: Generated workflow graph: /tmp/tmpuyyqsj51.png (graph2use=hierarchical, simple_form=True). 190621-17:19:09,547 nipype.workflow INFO: Generated workflow graph: /tmp/tmpin74oi5x.png (graph2use=hierarchical, simple_form=True). 190621-17:19:09,857 nipype.workflow INFO: Generated workflow graph: /tmp/tmp_4s2jwg0.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.smri.niftyreg 190621-17:19:09,945 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,950 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,959 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,961 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,969 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,971 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,977 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,978 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,984 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,986 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,992 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,993 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:09,999 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,1 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,13 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,15 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,26 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,28 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,39 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,41 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,53 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,55 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,68 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,69 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,71 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,73 nipype.interface WARNING: version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0 190621-17:19:10,556 nipype.workflow INFO: Generated workflow graph: /tmp/tmpv03ymtj6.png (graph2use=hierarchical, simple_form=True). 190621-17:19:10,824 nipype.workflow INFO: Generated workflow graph: /tmp/tmppu4p7pg7.png (graph2use=hierarchical, simple_form=True). 190621-17:19:11,94 nipype.workflow INFO: Generated workflow graph: /tmp/tmpbli_s9n0.png (graph2use=hierarchical, simple_form=True). WARNING: Empty - nipype.workflows.warp 204 files written /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/sphinx/util/docutils.py:311: RemovedInSphinx30Warning: function based directive support is now deprecated. Use class based directive instead. RemovedInSphinx30Warning) making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 317 source files that are out of date updating environment: 317 added, 0 changed, 0 removed /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.base_trait at 0x7f2b81c83e18> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <bound method HasTraits.class_trait_names of <class 'nipype.interfaces.matlab.MatlabInputSpec'>> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <bound method HasTraits.class_traits of <class 'nipype.interfaces.matlab.MatlabInputSpec'>> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.clone_traits at 0x7f2b81c7dea0> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.configure_traits at 0x7f2b81c83598> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.has_traits_interface at 0x7f2b81c7d620> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.on_trait_change at 0x7f2b81c83950> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.on_trait_change at 0x7f2b81c83950> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.reset_traits at 0x7f2b81c7dbf8> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.set at 0x7f2b81c7db70> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/util/deprecated.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.sync_trait at 0x7f2b81c839d8> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait at 0x7f2b81c83d90> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <bound method HasTraits.trait_monitor of <class 'nipype.interfaces.matlab.MatlabInputSpec'>> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_names at 0x7f2b81ca00d0> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_set at 0x7f2b81c7d8c8> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_setq at 0x7f2b81c7da60> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_view at 0x7f2b81c83158> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_views at 0x7f2b81c83400> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.traits at 0x7f2b81c83f28> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.base_trait at 0x7f2b81c83e18> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <bound method HasTraits.class_trait_names of <class 'nipype.interfaces.matlab.MatlabInputSpec'>> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <bound method HasTraits.class_traits of <class 'nipype.interfaces.matlab.MatlabInputSpec'>> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.clone_traits at 0x7f2b81c7dea0> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.configure_traits at 0x7f2b81c83598> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.has_traits_interface at 0x7f2b81c7d620> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.on_trait_change at 0x7f2b81c83950> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.on_trait_change at 0x7f2b81c83950> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.reset_traits at 0x7f2b81c7dbf8> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.set at 0x7f2b81c7db70> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/util/deprecated.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.sync_trait at 0x7f2b81c839d8> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait at 0x7f2b81c83d90> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <bound method HasTraits.trait_monitor of <class 'nipype.interfaces.matlab.MatlabInputSpec'>> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_names at 0x7f2b81ca00d0> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_set at 0x7f2b81c7d8c8> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_setq at 0x7f2b81c7da60> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_view at 0x7f2b81c83158> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.trait_views at 0x7f2b81c83400> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Description in the docstring of <function HasTraits.traits at 0x7f2b81c83f28> in /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/traits/has_traits.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Parameter in the docstring of <function load_resultfile at 0x7f2b81bb3d90> in /home/<my_username>/repos/neuro/nipype/nipype/pipeline/engine/utils.py. warn(msg) /home/<my_username>/repos/neuro/nipype/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed warnings.warn('cmp not installed') 190621-17:19:17,0 nipype.interface WARNING: Unable to import ['cfflib']; CFFConverter interface may fail to run 190621-17:19:20,520 nipype.workflow INFO: Generated workflow graph: /home/<my_username>/repos/neuro/nipype/doc/_build/wf_directive/api/generated/connectivity/nipype-sphinxext-plot_workflow-1_detailed.png (graph2use=flat, simple_form=False). 190621-17:19:21,297 nipype.workflow INFO: Generated workflow graph: /home/<my_username>/repos/neuro/nipype/doc/_build/wf_directive/api/generated/connectivity/nipype-sphinxext-plot_workflow-1_detailed.svg (graph2use=flat, simple_form=False). 190621-17:19:22,153 nipype.workflow INFO: Generated workflow graph: /home/<my_username>/repos/neuro/nipype/doc/_build/wf_directive/api/generated/connectivity/nipype-sphinxext-plot_workflow-1_detailed.pdf (graph2use=flat, simple_form=False). /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section :mod:`nipype.sphinxext.plot_workflow` -- Workflow Plotting Extension in the docstring of <function wf_directive at 0x7f2b7a07a7b8> in /home/<my_username>/repos/neuro/nipype/nipype/sphinxext/plot_workflow.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Options in the docstring of <function wf_directive at 0x7f2b7a07a7b8> in /home/<my_username>/repos/neuro/nipype/nipype/sphinxext/plot_workflow.py. warn(msg) /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/numpydoc/docscrape.py:424: UserWarning: Unknown section Configuration Options in the docstring of <function wf_directive at 0x7f2b7a07a7b8> in /home/<my_username>/repos/neuro/nipype/nipype/sphinxext/plot_workflow.py. warn(msg) reading sources... [ 51%] interfaces/generated/interfaces.semtools/diffusion.tractography.commandlineoreading sources... [ 52%] interfaces/generated/interfaces.semtools/diffusion.tractography.ukftractograreading sources... [ 59%] interfaces/generated/interfaces.slicer/filtering.resamplescalarvectordwivolureading sources... [ 59%] interfaces/generated/interfaces.slicer/filtering.votingbinaryholefillingimagreading sources... [ 62%] interfaces/generated/interfaces.slicer/quantification.petstandarduptakevaluereading sources... [ 63%] interfaces/generated/interfaces.slicer/segmentation.simpleregiongrowingsegme190621-17:19:29,863 nipype.interface WARNING:d/nipype.sphinxext.plot_workflow Unable to import ['cfflib']; CFFConverter interface may fail to run 190621-17:19:33,551 nipype.workflow INFO: Generated workflow graph: /home/<my_username>/repos/neuro/nipype/doc/_build/wf_directive/interfaces/generated/connectivity/nipype-sphinxext-plot_workflow-1_detailed.png (graph2use=flat, simple_form=False). 190621-17:19:34,375 nipype.workflow INFO: Generated workflow graph: /home/<my_username>/repos/neuro/nipype/doc/_build/wf_directive/interfaces/generated/connectivity/nipype-sphinxext-plot_workflow-1_detailed.svg (graph2use=flat, simple_form=False). 190621-17:19:35,233 nipype.workflow INFO: Generated workflow graph: /home/<my_username>/repos/neuro/nipype/doc/_build/wf_directive/interfaces/generated/connectivity/nipype-sphinxext-plot_workflow-1_detailed.pdf (graph2use=flat, simple_form=False). reading sources... 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'api/generated/nipype.interfaces.matlab.MatlabInputSpec.visible_traits' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.base.EngineBase.clone' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.clone' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.get_output' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.hash_exists' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.help' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.is_cached' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.output_dir' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.run' WARNING: toctree references unknown document 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'api/generated/nipype.pipeline.engine.workflows.Workflow.get_node' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.list_node_names' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.remove_nodes' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.run' WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.write_graph' /home/<my_username>/repos/neuro/nipype/nipype/sphinxext/plot_workflow.py:docstring of nipype.sphinxext.plot_workflow:80: WARNING: Definition list ends without a blank line; unexpected unindent. 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nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabCommand.save_inputs_to_json' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_matlab_cmd' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_mfile' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_paths' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_terminal_output' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.add_class_trait' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.add_trait' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.add_trait_category' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.all_trait_names' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.base_trait' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_default_traits_view' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_editable_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_trait_names' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_trait_view_elements' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_visible_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.clone_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.configure_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.copy_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.copyable_trait_names' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.default_traits_view' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.edit_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.editable_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.get' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.get_hashval' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.get_traitsfree' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.has_metadata' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.has_traits_interface' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.items' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.on_trait_change' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.on_trait_event' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.print_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.remove_trait' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.reset_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.set' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.set_trait_dispatch_handler' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.sync_trait' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_context' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_get' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_items_event' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_monitor' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_names' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_property_changed' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_set' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_setq' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_subclasses' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_view' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_view_elements' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_views' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.traits_init' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.traits_inited' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.validate_trait' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.visible_traits' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.base.EngineBase.clone' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.clone' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.get_output' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.hash_exists' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.help' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.is_cached' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.output_dir' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.run' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.set_input' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.update' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.clone' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.get_output' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.get_subnodes' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.hash_exists' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.help' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.is_cached' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.num_subnodes' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.output_dir' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.run' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.set_input' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.MapNode.update' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.clone' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.get_output' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.hash_exists' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.help' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.is_cached' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.output_dir' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.run' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.set_input' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.nodes.Node.update' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.add_nodes' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.clone' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.connect' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.disconnect' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.export' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.get_node' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.list_node_names' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.remove_nodes' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.run' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.pipeline.engine.workflows.Workflow.write_graph' /home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.sphinxext.plot_workflow.GraphError.with_traceback' /home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/workflows.dmri/camino.diffusion.rst:19: WARNING: unknown document: ../../users/examples/dmri_camino_dti /home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/workflows.dmri/mrtrix.diffusion.rst:19: WARNING: unknown document: ../../users/examples/dmri_mrtrix_dti /home/<my_username>/repos/neuro/nipype/doc/users/install.rst:111: WARNING: unknown document: neurodocker generating indices... genindex py-modindex writing additional pages... search copying images... [ 14%] api/generated/../../_build/wf_directive/api/generated/nipype-sphinxext-plot_wcopying images... [100%] interfaces/generated/../../_build/wf_directive/interfaces/generated/nipype-sphinxext-plot_workflow-1.png copying downloadable files... [100%] examples/workshop_dartmouth_2010.py copying static files... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 759 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[1]: Leaving directory '/home/<my_username>/repos/neuro/nipype/doc' rm -rf build find . -name "*.pyc" | xargs rm -f find . -name "__pycache__" -type d | xargs rm -rf find . -name "*.so" | xargs rm -f find . -name "*.pyd" | xargs rm -f rm -f tags rm -rf doc/_build rm -f .coverage python setup.py build_ext -i /home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/setuptools/dist.py:475: UserWarning: Normalizing '1.2.1-dev+g7fbc7cbac' to '1.2.1.dev0+g7fbc7cbac' normalized_version, running build_ext py.test --doctest-module nipype Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 365, in _importconftest mod = conftestpath.pyimport() File "/usr/lib/python2.7/dist-packages/py/_path/local.py", line 668, in pyimport __import__(modname) File "/home/<my_username>/repos/neuro/nipype/nipype/__init__.py", line 56, in <module> from .pipeline import Node, MapNode, JoinNode, Workflow File "/home/<my_username>/repos/neuro/nipype/nipype/pipeline/__init__.py", line 11, in <module> from .engine import Node, MapNode, JoinNode, Workflow File "/home/<my_username>/repos/neuro/nipype/nipype/pipeline/engine/__init__.py", line 12, in <module> from .workflows import Workflow File "/home/<my_username>/repos/neuro/nipype/nipype/pipeline/engine/workflows.py", line 27, in <module> from ...interfaces.base import (traits, TraitedSpec, TraitDictObject, File "/home/<my_username>/repos/neuro/nipype/nipype/interfaces/__init__.py", line 13, in <module> from .io import DataGrabber, DataSink, SelectFiles, BIDSDataGrabber File "/home/<my_username>/repos/neuro/nipype/nipype/interfaces/io.py", line 37, in <module> from .base import ( File "/home/<my_username>/repos/neuro/nipype/nipype/interfaces/base/__init__.py", line 11, in <module> from .core import (Interface, BaseInterface, SimpleInterface, CommandLine, File "/home/<my_username>/repos/neuro/nipype/nipype/interfaces/base/core.py", line 32, in <module> from ...utils.provenance import write_provenance File "/home/<my_username>/repos/neuro/nipype/nipype/utils/provenance.py", line 20, in <module> import prov.model as pm ImportError: No module named prov.model ERROR: could not load /home/<my_username>/repos/neuro/nipype/nipype/conftest.py Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/usr/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/home/<my_username>/repos/neuro/nipype/nipype/utils/config.py", line 367, in free_display from .. import config SystemError: Parent module 'nipype' not loaded, cannot perform relative import Error in sys.exitfunc: Traceback (most recent call last): File "/usr/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/home/<my_username>/repos/neuro/nipype/nipype/utils/config.py", line 367, in free_display from .. import config SystemError: Parent module 'nipype' not loaded, cannot perform relative import Makefile:59: recipe for target 'test-code' failed make: *** [test-code] Error 4

Actual behavior

Error when running make check-before-commit

Expected behavior

No errors

How to replicate the behavior

Try to run make check-before-commit on fresh install of nipype

Script/Workflow details

make check-before-commit

Platform details:

{'commit_hash': '7fbc7cbac', 'commit_source': 'installation', 'networkx_version': '2.2', 'nibabel_version': '2.4.0', 'nipype_version': '1.2.1-dev', 'numpy_version': '1.16.2', 'pkg_path': '/home/<my_username>/python_envs/mri37/lib/python3.7/site-packages/nipype-1.2.1.dev0+g7fbc7cbac-py3.7.egg/nipype', 'scipy_version': '1.2.1', 'sys_executable': '/home/<my_username>/python_envs/mri37/bin/python', 'sys_platform': 'linux', 'sys_version': '3.7.3 | packaged by conda-forge | (default, Mar 27 2019, ' '23:01:00) \n' '[GCC 7.3.0]', 'traits_version': '5.1.1'}

Execution environment

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  • My python environment outside container

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