Remove internal version of LiterateWorkflow (#8)

* Replace internal Workflow with niworkflows.

* Run isort.

qsirecon/workflows/anatomical/surface.py

@@ -14,10 +14,10 @@
 from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.freesurfer import RobustRegister
 from niworkflows.interfaces.reportlets.segmentation import ReconAllRPT
 
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink as FDerivativesDataSink
 from ...interfaces import (
     FSDetectInputs,

qsirecon/workflows/anatomical/volume.py

@@ -36,12 +36,12 @@
 from nipype.interfaces.ants import BrainExtraction, N4BiasFieldCorrection
 from nipype.interfaces.base import traits
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.images import TemplateDimensions
 from niworkflows.interfaces.reportlets.masks import ROIsPlot
 from pkg_resources import resource_filename as pkgr
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import Conform
 from ...interfaces import DerivativesDataSink as FDerivativesDataSink
 from ...interfaces.anatomical import DesaturateSkull, GetTemplate, VoxelSizeChooser

qsirecon/workflows/base.py

@@ -22,11 +22,11 @@
 from nilearn import __version__ as nilearn_ver
 from nipype import __version__ as nipype_ver
 from nipype.utils.filemanip import split_filename
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from packaging.version import Version
 from pkg_resources import resource_filename as pkgrf
 
 from .. import config
-from ..engine import Workflow
 
 
 def init_qsirecon_wf():

qsirecon/workflows/dwi/base.py

@@ -11,9 +11,9 @@
 from nipype.interfaces import utility as niu
 from nipype.interfaces.base import isdefined
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink, DerivativesMaybeDataSink
 from ...interfaces.confounds import DMRISummary
 from ...interfaces.reports import DiffusionSummary

qsirecon/workflows/dwi/confounds.py

@@ -11,8 +11,8 @@
 from nipype.algorithms import confounds as nac
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
-from ...engine import Workflow
 from ...interfaces import AddTSVHeader, GatherConfounds
 
 DEFAULT_MEMORY_MIN_GB = 0.01

qsirecon/workflows/dwi/derivatives.py

@@ -9,9 +9,9 @@
 from nipype import logging
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink
 
 DEFAULT_MEMORY_MIN_GB = 0.01

qsirecon/workflows/dwi/distortion_group_merge.py

@@ -11,9 +11,9 @@
 
 import nipype.pipeline.engine as pe
 from nipype.interfaces import utility as niu
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink
 from ...interfaces.dsi_studio import DSIStudioBTable
 from ...interfaces.dwi_merge import AveragePEPairs, MergeDWIs

qsirecon/workflows/dwi/finalize.py

@@ -11,10 +11,10 @@
 from nipype.interfaces import utility as niu
 from nipype.interfaces.base import isdefined
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.reportlets.registration import SimpleBeforeAfterRPT
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink
 from ...interfaces.dsi_studio import DSIStudioBTable
 from ...interfaces.dwi_merge import MergeFinalConfounds, SplitResampledDWIs

qsirecon/workflows/dwi/fsl.py

@@ -12,10 +12,10 @@
 from nipype.interfaces import fsl
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from pkg_resources import resource_filename as pkgr_fn
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink
 from ...interfaces.eddy import (
     Eddy2SPMMotion,

qsirecon/workflows/dwi/hmc.py

@@ -10,10 +10,10 @@
 import nipype.pipeline.engine as pe
 from nipype.interfaces import afni, ants
 from nipype.interfaces import utility as niu
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from pkg_resources import resource_filename as pkgrf
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink
 from ...interfaces.gradients import CombineMotions, GradientRotation, MatchTransforms
 from ...interfaces.shoreline import (

qsirecon/workflows/dwi/hmc_sdc.py

@@ -10,9 +10,9 @@
 from nipype.interfaces import ants
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.gradients import CombineMotions, GradientRotation, SliceQC
 from ...interfaces.images import SplitDWIsBvals, TSplit
 from ..fieldmap.base import init_sdc_wf

qsirecon/workflows/dwi/intramodal_template.py

@@ -10,10 +10,10 @@
 import nipype.pipeline.engine as pe
 from nipype.interfaces import ants
 from nipype.interfaces import utility as niu
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from pkg_resources import resource_filename as pkgrf
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink
 from ...interfaces.ants import MultivariateTemplateConstruction2
 from .hmc import init_b0_hmc_wf

qsirecon/workflows/dwi/merge.py

@@ -14,9 +14,9 @@
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from nipype.utils.filemanip import split_filename
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import ConformDwi, DerivativesDataSink
 from ...interfaces.dipy import Patch2Self
 from ...interfaces.dwi_merge import MergeDWIs, PhaseToRad, StackConfounds

qsirecon/workflows/dwi/pre_hmc.py

@@ -8,9 +8,9 @@
 
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.dwi_merge import MergeDWIs
 from ...interfaces.nilearn import Merge
 

qsirecon/workflows/dwi/qc.py

@@ -9,9 +9,9 @@
 from nipype.interfaces import afni
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.anatomical import DiceOverlap
 from ...interfaces.dipy import TensorReconstruction
 from ...interfaces.dsi_studio import (

qsirecon/workflows/dwi/registration.py

@@ -5,10 +5,10 @@
 from nipype.interfaces import ants
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from pkg_resources import resource_filename as pkgrf
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.itk import ACPCReport, AffineToRigid
 from ...interfaces.niworkflows import ANTSRegistrationRPT
 

qsirecon/workflows/dwi/resampling.py

@@ -11,9 +11,9 @@
 from nipype.interfaces import ants
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.ants import GetImageType
 from ...interfaces.fmap import ApplyScalingImages
 from ...interfaces.gradients import (  # LocalGradientRotation,

qsirecon/workflows/dwi/util.py

@@ -15,9 +15,9 @@
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from nipype.utils.filemanip import split_filename
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.reportlets.registration import SimpleBeforeAfterRPT
 
-from ...engine import Workflow
 from ...interfaces import DerivativesDataSink
 from ..anatomical import init_synthstrip_wf
 

qsirecon/workflows/fieldmap/base.py

@@ -38,9 +38,9 @@
 
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 
 # Fieldmap workflows
 from .pepolar import init_pepolar_unwarp_wf

qsirecon/workflows/fieldmap/drbuddi.py

@@ -22,9 +22,9 @@
 
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.tortoise import (
     DRBUDDI,
     DRBUDDIAggregateOutputs,

qsirecon/workflows/fieldmap/pepolar.py

@@ -14,11 +14,11 @@
 from nipype.interfaces import afni, ants
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.header import CopyHeader
 from niworkflows.interfaces.reportlets.registration import ANTSApplyTransformsRPT
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces import StructuralReference
 from ...interfaces.fmap import B0RPEFieldmap, PEPOLARReport
 from ...interfaces.images import ExtractWM

qsirecon/workflows/fieldmap/syn.py

@@ -37,9 +37,9 @@
 from nipype.interfaces.image import Rescale
 from nipype.pipeline import engine as pe
 from nipype.utils.filemanip import fname_presuffix
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 
 DEFAULT_MEMORY_MIN_GB = 0.01
 

qsirecon/workflows/recon/amico.py

@@ -8,9 +8,9 @@
 
 import nipype.pipeline.engine as pe
 from nipype.interfaces import utility as niu
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.amico import NODDI
 from ...interfaces.converters import NODDItoFIBGZ
 from ...interfaces.interchange import recon_workflow_input_fields

qsirecon/workflows/recon/anatomical.py

@@ -17,11 +17,11 @@
 from nipype.interfaces import afni, ants, mrtrix3
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.reportlets.registration import SpatialNormalizationRPT
 from pkg_resources import resource_filename as pkgrf
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.anatomical import QSIReconAnatomicalIngress, UKBAnatomicalIngress
 from ...interfaces.ants import ConvertTransformFile
 from ...interfaces.bids import ReconDerivativesDataSink

qsirecon/workflows/recon/build_workflow.py

@@ -1,8 +1,8 @@
 import nipype.pipeline.engine as pe
 from nipype.interfaces import utility as niu
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.interchange import default_input_set, recon_workflow_input_fields
 from .amico import init_amico_noddi_fit_wf
 from .converters import init_mif_to_fibgz_wf, init_qsirecon_to_fsl_wf

qsirecon/workflows/recon/converters.py

@@ -11,8 +11,8 @@
 
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
-from ...engine import Workflow
 from ...interfaces.bids import ReconDerivativesDataSink
 from ...interfaces.converters import FODtoFIBGZ
 from ...interfaces.images import ConformDwi

qsirecon/workflows/recon/dipy.py

@@ -10,9 +10,9 @@
 
 import nipype.pipeline.engine as pe
 from nipype.interfaces import utility as niu
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.dipy import (
     BrainSuiteShoreReconstruction,
     KurtosisReconstruction,

qsirecon/workflows/recon/dsi_studio.py

@@ -12,9 +12,9 @@
 
 import nipype.pipeline.engine as pe
 from nipype.interfaces import utility as niu
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.bids import ReconDerivativesDataSink
 from ...interfaces.converters import DSIStudioTrkToTck
 from ...interfaces.interchange import recon_workflow_input_fields

qsirecon/workflows/recon/mrtrix.py

@@ -17,9 +17,9 @@
 
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ... import config
-from ...engine import Workflow
 from ...interfaces.bids import ReconDerivativesDataSink
 from ...interfaces.interchange import recon_workflow_input_fields
 from ...interfaces.reports import CLIReconPeaksReport, ConnectivityReport

qsirecon/workflows/recon/scalar_mapping.py

@@ -10,8 +10,8 @@
 
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
-from ...engine import Workflow
 from ...interfaces.bids import ReconDerivativesDataSink
 from ...interfaces.interchange import recon_workflow_input_fields
 from ...interfaces.recon_scalars import (