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mick-d opened this issue Jun 21, 2019 · 7 comments
Open

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

mick-d opened this issue Jun 21, 2019 · 7 comments

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@mick-d
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mick-d commented 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... [100%] version                                                                     
WARNING: toctree references unknown document 'api/generated/nipype.caching.memory.Memory.cache'
WARNING: toctree references unknown document 'api/generated/nipype.caching.memory.Memory.clear_previous_runs'
WARNING: toctree references unknown document 'api/generated/nipype.caching.memory.Memory.clear_previous_runs'
WARNING: toctree references unknown document 'api/generated/nipype.caching.memory.PipeFunc.__call__'
WARNING: autodoc: failed to import module 'conftest' from module 'nipype'; the following exception was raised:
No module named 'pytest'
WARNING: autodoc: failed to import function 'conftest.add_np' from module 'nipype'; the following exception was raised:
No module named 'pytest'
WARNING: autodoc: failed to import function 'conftest.pytest_unconfigure' from module 'nipype'; the following exception was raised:
No module named 'pytest'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.aggregate_outputs'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.help'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.input_spec'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.load_inputs_from_json'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.run'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.save_inputs_to_json'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_matlab_cmd'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_mfile'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_paths'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabCommand.set_default_terminal_output'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.add_class_trait'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.add_trait'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.add_trait_category'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.all_trait_names'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.base_trait'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_default_traits_view'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_editable_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_trait_names'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_trait_view_elements'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.class_visible_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.clone_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.configure_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.copy_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.copyable_trait_names'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.default_traits_view'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.edit_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.editable_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.get'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.get_hashval'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.get_traitsfree'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.has_metadata'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.has_traits_interface'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.items'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.on_trait_change'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.on_trait_event'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.print_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.remove_trait'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.reset_traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.set'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.set_trait_dispatch_handler'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.sync_trait'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_context'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_get'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_items_event'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_monitor'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_names'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_property_changed'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_set'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_setq'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_subclasses'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_view'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_view_elements'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.trait_views'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.traits'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.traits_init'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.traits_inited'
WARNING: toctree references unknown document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.validate_trait'
WARNING: toctree references unknown document '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 'api/generated/nipype.pipeline.engine.nodes.JoinNode.set_input'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.JoinNode.update'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.clone'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.get_output'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.get_subnodes'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.hash_exists'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.help'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.is_cached'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.num_subnodes'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.output_dir'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.run'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.set_input'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.MapNode.update'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.clone'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.get_output'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.hash_exists'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.help'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.is_cached'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.output_dir'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.run'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.set_input'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.nodes.Node.update'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.add_nodes'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.clone'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.connect'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.disconnect'
WARNING: toctree references unknown document 'api/generated/nipype.pipeline.engine.workflows.Workflow.export'
WARNING: toctree references unknown document '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.
WARNING: toctree references unknown document 'api/generated/nipype.sphinxext.plot_workflow.GraphError.with_traceback'
/home/<my_username>/repos/neuro/nipype/doc/changes.rst:9: WARNING: Problems with "include" directive path:
InputError: [Errno 2] No such file or directory: '../CHANGES'.
/home/<my_username>/repos/neuro/nipype/doc/devel/interface_specs.rst:474: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/<my_username>/repos/neuro/nipype/doc/devel/testing_nipype.rst:93: WARNING: Unexpected indentation.
/home/<my_username>/repos/neuro/nipype/doc/devel/testing_nipype.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/<my_username>/repos/neuro/nipype/doc/documentation.rst:7: WARNING: Unknown directive type "htmlonly".

.. htmlonly::

   :Release: |version|
   :Date: |today|
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/preprocess.rst:1929: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/preprocess.rst:4: WARNING: Duplicate explicit target name: "3dqwarp documentation.".
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/preprocess.rst:4: WARNING: Duplicate explicit target name: "3dqwarp documentation.".
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/utils.rst:4: WARNING: Duplicate explicit target name: "3dcopy documentation.".
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/utils.rst:1130: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/utils.rst:1132: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/utils.rst:1140: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/utils.rst:1142: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.afni/utils.rst:1142: WARNING: Unknown target name: "references".
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.base/core.rst:40: WARNING: Unexpected indentation.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.base/core.rst:41: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.base/core.rst:88: WARNING: Unexpected indentation.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.camino/calib.rst:31: WARNING: Inline emphasis start-string without end-string.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.camino/calib.rst:31: WARNING: Inline emphasis start-string without end-string.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.dipy/tensors.rst:71: WARNING: Footnote [1] is not referenced.
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.dtitk/utils.rst:132: WARNING: Unexpected section title.

Example
~~~~~~~
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.dtitk/utils.rst:239: WARNING: Unexpected section title.

Example
~~~~~~~
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.dtitk/utils.rst:516: WARNING: Unexpected section title.

Example
~~~~~~~
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.dtitk/utils.rst:645: WARNING: Unexpected section title.

Example
~~~~~~~
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.freesurfer/preprocess.rst:4: WARNING: Duplicate explicit target name: "fs documentation".
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.freesurfer/preprocess.rst:4: WARNING: Duplicate explicit target name: "fs documentation".
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.freesurfer/preprocess.rst:807: WARNING: Title underline too short.

References:
~~~~~~~~~~
/home/<my_username>/repos/neuro/nipype/doc/interfaces/generated/interfaces.freesurfer/preprocess.rst:807: WARNING: Title underline too short.

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Examples
~~~~~~~~
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.. htmlonly::

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   :Date: |today|
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/home/<my_username>/repos/neuro/nipype/doc/documentation.rst:5: WARNING: toctree contains reference to nonexisting document 'api/generated/nipype.interfaces.matlab.MatlabInputSpec.get'
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/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'
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/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'
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/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

Choose one

  • My python environment outside container
@effigies
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Member

Just use make specs. make check-before-commit assumes that you have all dependencies installed, and you don't have prov installed. You could do pip install prov; pip install neurdflib, if you want to do the full check.

@mick-d
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Contributor Author

mick-d commented Jun 24, 2019 •
edited
Loading

Thanks for the feedback Chris. I actually had prov and neurdflib already installed in that environment. Below are all the packages i have installed:

conda list
# packages in environment at /home/<my_username>/python_envs/mri37:
#
# Name                    Version                   Build  Channel
alabaster                 0.7.12                     py_0    conda-forge
asn1crypto                0.24.0                py37_1003    conda-forge
babel                     2.7.0                      py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
blosc                     1.16.3               hf484d3e_0    conda-forge
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
cairo                     1.14.12           h80bd089_1005    conda-forge
certifi                   2019.6.16                py37_0    conda-forge
cffi                      1.12.3           py37h8022711_0    conda-forge
chardet                   3.0.4                 py37_1003    conda-forge
click                     7.0                      pypi_0    pypi
cryptography              2.7              py37h72c5cf5_0    conda-forge
cvxopt                    1.2.3           py37h5740f57_201    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cython                    0.29.6           py37hf484d3e_0    conda-forge
dbus                      1.13.2               h714fa37_1  
decorator                 4.4.0                      py_0    conda-forge
dipy                      0.16.0           py37h3010b51_0    conda-forge
docutils                  0.14                  py37_1001    conda-forge
dsdp                      5.8               h23d7751_1203    conda-forge
expat                     2.2.5             hf484d3e_1002    conda-forge
fastcache                 1.0.2           py37h14c3975_1001    conda-forge
fftw                      3.3.8             h9ac9557_1003    conda-forge
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.10.0               he983fc9_0    conda-forge
funcsigs                  1.0.2                      py_3    conda-forge
future                    0.17.1                py37_1000    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
glpk                      4.65              ha14ba45_1001    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gmpy2                     2.0.8           py37hb20f59a_1002    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
graphviz                  2.38.0            hcf1ce16_1009    conda-forge
gsl                       2.4               h294904e_1005    conda-forge
gst-plugins-base          1.14.0               hbbd80ab_1  
gstreamer                 1.14.0               hb453b48_1  
h5py                      2.9.0           nompi_py37hf008753_1102    conda-forge
harfbuzz                  1.9.0             he243708_1001    conda-forge
hdf5                      1.10.4          nompi_h3c11f04_1106    conda-forge
html5lib                  1.0.1                      py_0    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                   py37_1000    conda-forge
imagesize                 1.1.0                      py_0    conda-forge
ipykernel                 5.1.0           py37h24bf2e0_1002    conda-forge
ipython                   7.4.0            py37h24bf2e0_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
isodate                   0.6.0                      py_1    conda-forge
jedi                      0.13.3                   py37_0    conda-forge
jinja2                    2.10.1                     py_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jupyter_client            5.2.4                      py_3    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
keepalive                 0.5                        py_1    conda-forge
kiwisolver                1.0.1           py37h6bb024c_1002    conda-forge
libblas                   3.8.0                4_openblas    conda-forge
libcblas                  3.8.0                4_openblas    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 8.2.0                hdf63c60_1  
libgfortran-ng            7.3.0                hdf63c60_0  
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0                4_openblas    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libsodium                 1.0.16            h14c3975_1001    conda-forge
libstdcxx-ng              8.2.0                hdf63c60_1  
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libtool                   2.4.6             h14c3975_1002    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
libxslt                   1.1.32            h4785a14_1002    conda-forge
lxml                      4.3.3            py37h7ec2d77_0    conda-forge
lzo                       2.10              h14c3975_1000    conda-forge
markupsafe                1.1.1            py37h14c3975_0    conda-forge
matplotlib                3.0.3                    py37_0    conda-forge
matplotlib-base           3.0.3            py37h167e16e_0    conda-forge
metis                     5.1.0             hf484d3e_1003    conda-forge
mock                      2.0.0                 py37_1001    conda-forge
mpc                       1.1.0             hb20f59a_1006    conda-forge
mpfr                      4.0.1             ha14ba45_1000    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
networkx                  2.3                      pypi_0    pypi
neurdflib                 5.0.0.post1              pypi_0    pypi
nibabel                   2.4.0                      py_0    conda-forge
nipy                      0.4.1           py37h3010b51_1001    conda-forge
nipype                    1.2.1.dev0+g7fbc7cbac          pypi_0    pypi
numexpr                   2.6.9           py37h637b7d7_1000    conda-forge
numpy                     1.16.2           py37h8b7e671_1    conda-forge
numpydoc                  0.9.1                      py_0    conda-forge
openblas                  0.3.5             h9ac9557_1001    conda-forge
openssl                   1.1.1b               h14c3975_1    conda-forge
packaging                 19.0                       py_0    conda-forge
pandas                    0.24.2           py37hf484d3e_0    conda-forge
pango                     1.40.14           hf0c64fd_1003    conda-forge
parso                     0.3.4                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pbr                       5.1.3                      py_0    conda-forge
pcre                      8.43                 he6710b0_0  
pexpect                   4.6.0                 py37_1000    conda-forge
pickleshare               0.7.5                 py37_1000    conda-forge
pip                       19.0.3                   py37_0    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
prompt_toolkit            2.0.9                      py_0    conda-forge
prov                      1.5.3                    pypi_0    pypi
psutil                    5.6.1            py37h14c3975_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                 py37_1000    conda-forge
pycparser                 2.19                     py37_1    conda-forge
pydicom                   1.2.2                      py_0    conda-forge
pydot                     1.4.1                 py37_1000    conda-forge
pydotplus                 2.0.2                      py_2    conda-forge
pygments                  2.3.1                      py_0    conda-forge
pyopenssl                 19.0.0                   py37_0    conda-forge
pyparsing                 2.3.1                      py_0    conda-forge
pyqt                      5.6.0           py37h13b7fb3_1008    conda-forge
pysocks                   1.7.0                    py37_0    conda-forge
pytables                  3.5.1            py37h442f067_1    conda-forge
python                    3.7.3                h5b0a415_0    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
pytz                      2018.9                     py_0    conda-forge
pyzmq                     18.0.1           py37h0e1adb2_0    conda-forge
qt                        5.6.3                h8bf5577_3  
rdflib                    4.2.2                 py37_1000    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
requests                  2.22.0                   py37_0    conda-forge
scikit-learn              0.20.3           py37ha8026db_1    conda-forge
scipy                     1.2.1            py37h09a28d5_1    conda-forge
seaborn                   0.9.0                      py_0    conda-forge
setuptools                40.8.0                   py37_0    conda-forge
simplejson                3.16.0          py37h14c3975_1002    conda-forge
sip                       4.18.1          py37hf484d3e_1000    conda-forge
six                       1.12.0                py37_1000    conda-forge
snowballstemmer           1.2.1                      py_1    conda-forge
sparqlwrapper             1.8.2                 py37_1000    conda-forge
sphinx                    2.1.2                      py_0    conda-forge
sphinxcontrib-applehelp   1.0.1                      py_0    conda-forge
sphinxcontrib-devhelp     1.0.1                      py_0    conda-forge
sphinxcontrib-htmlhelp    1.0.2                      py_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.2                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.1                      py_0    conda-forge
sqlite                    3.26.0            h67949de_1001    conda-forge
statsmodels               0.9.0           py37h3010b51_1000    conda-forge
suitesparse               4.5.6             heab0a99_1202    conda-forge
sympy                     1.3                   py37_1000    conda-forge
tbb                       2019.5               hc9558a2_0    conda-forge
tk                        8.6.9             h84994c4_1001    conda-forge
tornado                   6.0.2            py37h516909a_0    conda-forge
traitlets                 4.3.2                 py37_1000    conda-forge
traits                    5.1.1                    pypi_0    pypi
urllib3                   1.24.3                   py37_0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.33.1                   py37_0    conda-forge
xlrd                      1.2.0                      py_0    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h516909a_1004    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxpm               3.5.12            h14c3975_1002    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.1.5             h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xvfbwrapper               0.2.9                 py37_1000    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yapf                      0.27.0                     py_0    conda-forge
zeromq                    4.2.5             hf484d3e_1006    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge

@mick-d
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mick-d commented Jun 24, 2019 •
edited
Loading

I have no errors when importing "manually" prov.model inside that environment:

$ python
Python 3.7.3 | packaged by conda-forge | (default, Mar 27 2019, 23:01:00) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import prov.model as pm
>>> quit()

@effigies
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Ah. It looks like you don't have pytest installed in this environment, so at some point it's calling out to a pytest installed in /usr/lib/python2.7/dist-packages/_pytest.

@mick-d
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mick-d commented Jun 25, 2019

Ah I see, apologies for the oversight.

The remaining errors seem to be due to different nilearn outputs than expected (cf below), creating several AssertionError. Not sure why this is happening, i have the latest nilearn version, 0.5.2 :

$ python
Python 3.7.3 | packaged by conda-forge | (default, Mar 27 2019, 23:01:00) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import nilearn
>>> nilearn.__version__
'0.5.2'
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
190624-16:13:38,851 nipype.interface WARNING:
	 VTK was not found
190624-16:13:38,851 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
^[[Bnipype.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
190624-16:14:45,551 nipype.interface WARNING:
	 VTK was not found
190624-16:14:45,552 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
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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
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Skullfinder
Tca
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Bru2
C3d
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NIfTIDT2Camino
ProcStreamlines
Shredder
TractShredder
VtkStreamlines
ComputeEigensystem
ComputeFractionalAnisotropy
ComputeMeanDiffusivity
ComputeTensorTrace
DTIFit
DTLUTGen
DTMetric
ModelFit
PicoPDFs
Track
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TrackBayesDirac
TrackBedpostxDeter
TrackBedpostxProba
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WARNING: Empty - nipype.interfaces.camino2trackvis
Camino2Trackvis
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CFFBaseInterface
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CreateNodes
ROIGen
CFFConverter
MergeCNetworks
NetworkBasedStatistic
AverageNetworks
NetworkXMetrics
Parcellate
Dcm2nii
Dcm2niix
CopyMeta
DcmStack
GroupAndStack
LookupMeta
MergeNifti
NiftiGeneratorBase
SplitNifti
WARNING: Empty - nipype.interfaces.diffusion_toolkit
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DTIRecon
DTITracker
HARDIMat
ODFRecon
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SplineFilter
TrackMerge
WARNING: Empty - nipype.interfaces.dipy
APMQball
DipyBaseInterface
DipyDiffusionInterface
Denoise
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CSD
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RESTORE
WARNING: Empty - nipype.interfaces.dipy.registration
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WARNING: Empty - nipype.interfaces.dipy.stats
DTI
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WARNING: Empty - nipype.interfaces.dtitk
CommandLineDtitk
DTITKRenameMixin
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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
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PointsWarp
Registration
EditTransform
WARNING: Empty - nipype.interfaces.freesurfer
WARNING: Empty - nipype.interfaces.freesurfer.base
FuseSegmentations
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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
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BEDPOSTX5
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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
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Beast
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BigAverage
Blob
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Copy
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Gennlxfm
Math
NlpFit
Norm
Pik
Resample
Reshape
ToEcat
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XfmConcat
XfmInvert
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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
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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
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TCK2VTK
TensorMetrics
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FitAsl
NiftyFitCommand
DwiTool
FitDwi
FitQt1
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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
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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
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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
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DTIexport
DTIimport
DWIJointRicianLMMSEFilter
DWIRicianLMMSEFilter
DWIToDTIEstimation
DiffusionTensorScalarMeasurements
DiffusionWeightedVolumeMasking
ResampleDTIVolume
TractographyLabelMapSeeding
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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
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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
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AssertEqual
IdentityInterface
Merge
Rename
Select
Split
CSVReader
Function
WARNING: Empty - nipype.interfaces.vista
Vnifti2Image
VtoMat
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WBCommand
CiftiSmooth
MetricResample
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GraphError
ImageFile
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/home/<my_username>/repos/neuro/nipype/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed
  warnings.warn('cmp not installed')
190624-16:15:12,468 nipype.interface WARNING:
	 Unable to import ['cfflib']; CFFConverter interface may fail to run
190624-16:15:13,493 nipype.workflow INFO:
	 Generated workflow graph: /tmp/tmpp1gurgd_.png (graph2use=hierarchical, simple_form=True).
190624-16:15:13,875 nipype.workflow INFO:
	 Generated workflow graph: /tmp/tmp5qpp7iwg.png (graph2use=hierarchical, simple_form=True).
WARNING: Empty - nipype.workflows.dmri.connectivity
190624-16:15:14,352 nipype.workflow INFO:
	 Generated workflow graph: /tmp/tmphkqpu_la.png (graph2use=hierarchical, simple_form=True).
190624-16:15:14,606 nipype.workflow INFO:
	 Generated workflow graph: /tmp/tmpw773wd6e.png (graph2use=hierarchical, simple_form=True).
WARNING: Empty - nipype.workflows.dmri.dipy
190624-16:15:14,888 nipype.workflow INFO:
	 Generated workflow graph: /tmp/tmpry66zt7s.png (graph2use=hierarchical, simple_form=True).
WARNING: Empty - nipype.workflows.dmri.dtitk
190624-16:15:15,177 nipype.workflow INFO:
	 Generated workflow graph: /tmp/tmpz7qkdw5p.png (graph2use=hierarchical, simple_form=True).
190624-16:15:15,466 nipype.workflow INFO:
	 Generated workflow graph: /tmp/tmpe066q1t2.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.')

(...)

=============================================================================================== FAILURES ===============================================================================================
__________________________________________________________________________ TestSignalExtraction.test_signal_extract_no_shared __________________________________________________________________________

self = <nipype.interfaces.tests.test_nilearn.TestSignalExtraction object at 0x7f3abd6f0940>

    def test_signal_extract_no_shared(self):
        # run
        iface.SignalExtraction(
            in_file=self.filenames['in_file'],
            label_files=self.filenames['label_files'],
            class_labels=self.labels,
            incl_shared_variance=False).run()
        # assert
>       self.assert_expected_output(self.labels, self.base_wanted)

/home/<my_username>/repos/neuro/nipype/nipype/interfaces/tests/test_nilearn.py:50: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nipype.interfaces.tests.test_nilearn.TestSignalExtraction object at 0x7f3abd6f0940>, labels = ['CSF', 'GrayMatter', 'WhiteMatter']
wanted = [[-2.33333, 2, 0.5], [0, -2, 0.5], [-0.3333333, -1, 2.5], [0, -2, 0.5], [-1.3333333, -5, 1]]

    def assert_expected_output(self, labels, wanted):
        with open(self.filenames['out_file'], 'r') as output:
            got = [line.split() for line in output]
            labels_got = got.pop(0)  # remove header
            assert labels_got == labels
            assert len(got) == self.fake_fmri_data.shape[
                3], 'num rows and num volumes'
            # convert from string to float
            got = [[float(num) for num in row] for row in got]
            for i, time in enumerate(got):
                assert len(labels) == len(time)
                for j, segment in enumerate(time):
>                   npt.assert_almost_equal(segment, wanted[i][j], decimal=1)
E                   AssertionError: 
E                   Arrays are not almost equal to 1 decimals
E                    ACTUAL: -2.0
E                    DESIRED: -2.33333

/home/<my_username>/repos/neuro/nipype/nipype/interfaces/tests/test_nilearn.py:169: AssertionError
________________________________________________________________________ TestSignalExtraction.test_signal_extr_global_no_shared ________________________________________________________________________

self = <nipype.interfaces.tests.test_nilearn.TestSignalExtraction object at 0x7f3abd6a9208>

    def test_signal_extr_global_no_shared(self):
        # set up
        wanted_global = [[-4. / 6], [-1. / 6], [3. / 6], [-1. / 6], [-7. / 6]]
        for i, vals in enumerate(self.base_wanted):
            wanted_global[i].extend(vals)
    
        # run
        iface.SignalExtraction(
            in_file=self.filenames['in_file'],
            label_files=self.filenames['label_files'],
            class_labels=self.labels,
            include_global=True,
            incl_shared_variance=False).run()
    
        # assert
>       self.assert_expected_output(self.global_labels, wanted_global)

/home/<my_username>/repos/neuro/nipype/nipype/interfaces/tests/test_nilearn.py:89: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nipype.interfaces.tests.test_nilearn.TestSignalExtraction object at 0x7f3abd6a9208>, labels = ['GlobalSignal', 'CSF', 'GrayMatter', 'WhiteMatter']
wanted = [[-0.6666666666666666, -2.33333, 2, 0.5], [-0.16666666666666666, 0, -2, 0.5], [0.5, -0.3333333, -1, 2.5], [-0.16666666666666666, 0, -2, 0.5], [-1.1666666666666667, -1.3333333, -5, 1]]

    def assert_expected_output(self, labels, wanted):
        with open(self.filenames['out_file'], 'r') as output:
            got = [line.split() for line in output]
            labels_got = got.pop(0)  # remove header
            assert labels_got == labels
            assert len(got) == self.fake_fmri_data.shape[
                3], 'num rows and num volumes'
            # convert from string to float
            got = [[float(num) for num in row] for row in got]
            for i, time in enumerate(got):
                assert len(labels) == len(time)
                for j, segment in enumerate(time):
>                   npt.assert_almost_equal(segment, wanted[i][j], decimal=1)
E                   AssertionError: 
E                   Arrays are not almost equal to 1 decimals
E                    ACTUAL: 0.0
E                    DESIRED: -0.6666666666666666

/home/<my_username>/repos/neuro/nipype/nipype/interfaces/tests/test_nilearn.py:169: AssertionError
______________________________________________________________________ TestSignalExtraction.test_signal_extr_4d_global_no_shared _______________________________________________________________________

self = <nipype.interfaces.tests.test_nilearn.TestSignalExtraction object at 0x7f3abd6fb278>

    def test_signal_extr_4d_global_no_shared(self):
        # set up
        wanted_global = [[3. / 8], [-3. / 8], [1. / 8], [-7. / 8], [-9. / 8]]
        for i, vals in enumerate(self.fourd_wanted):
            wanted_global[i].extend(vals)
    
        # run & assert
        self._test_4d_label(
            wanted_global,
            self.fake_4d_label_data,
            include_global=True,
>           incl_shared_variance=False)

/home/<my_username>/repos/neuro/nipype/nipype/interfaces/tests/test_nilearn.py:102: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/home/<my_username>/repos/neuro/nipype/nipype/interfaces/tests/test_nilearn.py:155: in _test_4d_label
    self.assert_expected_output(wanted_labels, wanted)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nipype.interfaces.tests.test_nilearn.TestSignalExtraction object at 0x7f3abd6fb278>, labels = ['GlobalSignal', 'CSF', 'GrayMatter', 'WhiteMatter']
wanted = [[0.375, -5.0652173913, -5.44565217391, 5.50543478261], [-0.375, -7.02173913043, 11.1847826087, -4.33152173913], [0.12...17, 21.2391304348, -4.57608695652], [-0.875, 5.19565217391, -3.66304347826, -1.51630434783], [-1.125, -12.0, 3.0, 0.5]]

    def assert_expected_output(self, labels, wanted):
        with open(self.filenames['out_file'], 'r') as output:
            got = [line.split() for line in output]
            labels_got = got.pop(0)  # remove header
            assert labels_got == labels
            assert len(got) == self.fake_fmri_data.shape[
                3], 'num rows and num volumes'
            # convert from string to float
            got = [[float(num) for num in row] for row in got]
            for i, time in enumerate(got):
                assert len(labels) == len(time)
                for j, segment in enumerate(time):
>                   npt.assert_almost_equal(segment, wanted[i][j], decimal=1)
E                   AssertionError: 
E                   Arrays are not almost equal to 1 decimals
E                    ACTUAL: 0.0
E                    DESIRED: 0.375

/home/<my_username>/repos/neuro/nipype/nipype/interfaces/tests/test_nilearn.py:169: AssertionError

(...)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
============================================================= 3 failed, 2953 passed, 58 skipped, 7 xfailed, 415 warnings in 345.12 seconds =============================================================
Makefile:59: recipe for target 'test-code' failed
make: *** [test-code] Error 1

@effigies
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Yeah, there's an open issue (#2791) for supporting nilearn > 0.5. They made some changes that nobody has had time to look into deeply, and so using the SignalExtraction interface with recent versions of nilearn will round results to integers.

There is related discussion in: nilearn/nilearn#1891, nilearn/nilearn#1892

@mick-d
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mick-d commented Jun 26, 2019

I see, then definitely no check-before-commit until some time. Thanks a lot for helping with all that.

Should i leave the issue open until check-before-commit can work again (i.e. when the new versions of nilearn won't break the testing anymore)?

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