added nipype.interfaces. prefix to nipype package generation spec

example-specs/pkg-gen/nipype.yaml

@@ -1,4 +1,4 @@
-afni:
+nipype.interfaces.afni:
   target_version: v25_2_06
   interfaces:
     - nipype.interfaces.afni.model.Deconvolve
@@ -81,7 +81,7 @@ afni:
     - nipype.interfaces.afni.utils.Axialize
     - nipype.interfaces.afni.utils.Zcat
     - nipype.interfaces.afni.utils.Zeropad
-ants:
+nipype.interfaces.ants:
   target_version: v2
   interfaces:
     - nipype.interfaces.ants.legacy.antsIntroduction
@@ -119,7 +119,7 @@ ants:
     - nipype.interfaces.ants.visualization.CreateTiledMosaic
   classes:
     - nipype.interfaces.ants.base.Info
-brainsuite:
+nipype.interfaces.brainsuite:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.brainsuite.brainsuite.Bse
@@ -137,16 +137,16 @@ brainsuite:
     - nipype.interfaces.brainsuite.brainsuite.SVReg
     - nipype.interfaces.brainsuite.brainsuite.BDP
     - nipype.interfaces.brainsuite.brainsuite.ThicknessPVC
-bru2nii:
+nipype.interfaces.bru2nii:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.bru2nii.Bru2
-c3:
+nipype.interfaces.c3:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.c3.C3dAffineTool
     - nipype.interfaces.c3.C3d
-camino:
+nipype.interfaces.camino:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.camino.calib.SFPICOCalibData
@@ -183,19 +183,19 @@ camino:
     - nipype.interfaces.camino.odf.MESD
     - nipype.interfaces.camino.odf.SFPeaks
     - nipype.interfaces.camino.utils.ImageStats
-camino2trackvis:
+nipype.interfaces.camino2trackvis:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.camino2trackvis.convert.Camino2Trackvis
     - nipype.interfaces.camino2trackvis.convert.Trackvis2Camino
-cat12:
+nipype.interfaces.cat12:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.cat12.preprocess.CAT12Segment
     - nipype.interfaces.cat12.preprocess.CAT12SANLMDenoising
     - nipype.interfaces.cat12.surface.ExtractAdditionalSurfaceParameters
     - nipype.interfaces.cat12.surface.ExtractROIBasedSurfaceMeasures
-cmtk:
+nipype.interfaces.cmtk:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.cmtk.cmtk.CreateMatrix
@@ -207,13 +207,13 @@ cmtk:
     - nipype.interfaces.cmtk.nx.NetworkXMetrics
     - nipype.interfaces.cmtk.nx.AverageNetworks
     - nipype.interfaces.cmtk.parcellation.Parcellate
-dcm2nii:
+nipype.interfaces.dcm2nii:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.dcm2nii.Info
     - nipype.interfaces.dcm2nii.Dcm2nii
     - nipype.interfaces.dcm2nii.Dcm2niix
-dcmstack:
+nipype.interfaces.dcmstack:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.dcmstack.NiftiGeneratorBase
@@ -223,7 +223,7 @@ dcmstack:
     - nipype.interfaces.dcmstack.CopyMeta
     - nipype.interfaces.dcmstack.MergeNifti
     - nipype.interfaces.dcmstack.SplitNifti
-diffusion_toolkit:
+nipype.interfaces.diffusion_toolkit:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.diffusion_toolkit.dti.DTIRecon
@@ -233,7 +233,7 @@ diffusion_toolkit:
     - nipype.interfaces.diffusion_toolkit.odf.ODFTracker
     - nipype.interfaces.diffusion_toolkit.postproc.SplineFilter
     - nipype.interfaces.diffusion_toolkit.postproc.TrackMerge
-dipy:
+nipype.interfaces.dipy:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.dipy.anisotropic_power.APMQball
@@ -247,7 +247,7 @@ dipy:
     - nipype.interfaces.dipy.tensors.TensorMode
     - nipype.interfaces.dipy.tracks.TrackDensityMap
     - nipype.interfaces.dipy.tracks.StreamlineTractography
-dtitk:
+nipype.interfaces.dtitk:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.dtitk.registration.Rigid
@@ -279,19 +279,19 @@ dtitk:
     - nipype.interfaces.dtitk.utils.TVAdjustVoxSpTask
     - nipype.interfaces.dtitk.utils.TVResampleTask
     - nipype.interfaces.dtitk.utils.TVtoolTask
-dynamic_slicer:
+nipype.interfaces.dynamic_slicer:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.dynamic_slicer.SlicerCommandLine
-elastix:
+nipype.interfaces.elastix:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.elastix.registration.Registration
     - nipype.interfaces.elastix.registration.ApplyWarp
     - nipype.interfaces.elastix.registration.AnalyzeWarp
     - nipype.interfaces.elastix.registration.PointsWarp
     - nipype.interfaces.elastix.utils.EditTransform
-freesurfer:
+nipype.interfaces.freesurfer:
   target_version: v8
   interfaces:
     - nipype.interfaces.freesurfer.longitudinal.RobustTemplate
@@ -383,7 +383,7 @@ freesurfer:
     - nipype.interfaces.freesurfer.utils.Apas2Aseg
     - nipype.interfaces.freesurfer.utils.MRIsExpand
     - nipype.interfaces.freesurfer.utils.LTAConvert
-fsl:
+nipype.interfaces.fsl:
   target_version: v6_0
   interfaces:
     - nipype.interfaces.fsl.aroma.ICA_AROMA
@@ -492,16 +492,16 @@ fsl:
     - nipype.interfaces.fsl.utils.MotionOutliers
     - nipype.interfaces.fsl.utils.Text2Vest
     - nipype.interfaces.fsl.utils.Vest2Text
-image:
+nipype.interfaces.image:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.image.Rescale
     - nipype.interfaces.image.Reorient
-meshfix:
+nipype.interfaces.meshfix:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.meshfix.MeshFix
-minc:
+nipype.interfaces.minc:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.minc.minc.Extract
@@ -532,7 +532,7 @@ minc:
     - nipype.interfaces.minc.minc.BigAverage
     - nipype.interfaces.minc.minc.Reshape
     - nipype.interfaces.minc.minc.VolSymm
-mipav:
+nipype.interfaces.mipav:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.mipav.developer.JistLaminarVolumetricLayering
@@ -553,14 +553,14 @@ mipav:
     - nipype.interfaces.mipav.developer.JistBrainPartialVolumeFilter
     - nipype.interfaces.mipav.developer.JistIntensityMp2rageMasking
     - nipype.interfaces.mipav.developer.MedicAlgorithmThresholdToBinaryMask
-niftyfit:
+nipype.interfaces.niftyfit:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.niftyfit.asl.FitAsl
     - nipype.interfaces.niftyfit.dwi.FitDwi
     - nipype.interfaces.niftyfit.dwi.DwiTool
     - nipype.interfaces.niftyfit.qt1.FitQt1
-niftyreg:
+nipype.interfaces.niftyreg:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.niftyreg.reg.RegAladin
@@ -571,7 +571,7 @@ niftyreg:
     - nipype.interfaces.niftyreg.regutils.RegAverage
     - nipype.interfaces.niftyreg.regutils.RegTransform
     - nipype.interfaces.niftyreg.regutils.RegMeasure
-niftyseg:
+nipype.interfaces.niftyseg:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.niftyseg.em.EM
@@ -588,28 +588,28 @@ niftyseg:
     - nipype.interfaces.niftyseg.stats.StatsCommand
     - nipype.interfaces.niftyseg.stats.UnaryStats
     - nipype.interfaces.niftyseg.stats.BinaryStats
-nilearn:
+nipype.interfaces.nilearn:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.nilearn.NilearnBaseInterface
     - nipype.interfaces.nilearn.SignalExtraction
-nitime:
+nipype.interfaces.nitime:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.nitime.analysis.CoherenceAnalyzer
-petpvc:
+nipype.interfaces.petpvc:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.petpvc.PETPVC
-quickshear:
+nipype.interfaces.quickshear:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.quickshear.Quickshear
-robex:
+nipype.interfaces.robex:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.robex.preprocess.RobexSegment
-semtools:
+nipype.interfaces.semtools:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.semtools.brains.classify.BRAINSPosteriorToContinuousClass
@@ -714,7 +714,7 @@ semtools:
     - nipype.interfaces.semtools.utilities.brains.ImageRegionPlotter
     - nipype.interfaces.semtools.utilities.brains.fcsv_to_hdf5
     - nipype.interfaces.semtools.utilities.brains.FindCenterOfBrain
-slicer:
+nipype.interfaces.slicer:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.slicer.converters.DicomToNrrdConverter
@@ -777,7 +777,7 @@ slicer:
     - nipype.interfaces.slicer.surface.LabelMapSmoothing
     - nipype.interfaces.slicer.surface.ModelMaker
     - nipype.interfaces.slicer.utilities.EMSegmentTransformToNewFormat
-spm:
+nipype.interfaces.spm:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.spm.model.Level1Design
@@ -814,12 +814,12 @@ spm:
     - nipype.interfaces.spm.utils.ApplyInverseDeformation
     - nipype.interfaces.spm.utils.ResliceToReference
     - nipype.interfaces.spm.utils.DicomImport
-vista:
+nipype.interfaces.vista:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.vista.vista.Vnifti2Image
     - nipype.interfaces.vista.vista.VtoMat
-workbench:
+nipype.interfaces.workbench:
   target_version: v1_0
   interfaces:
     - nipype.interfaces.workbench.cifti.CiftiSmooth

nipype2pydra/interface/base.py

@@ -1159,7 +1159,7 @@ def process_method(
             pass
         if "runtime" in args:
             args.remove("runtime")
-        args_to_add = list(self.used.method_args.get(method.__name__, [])) + list(
+        args_to_add = sorted(self.used.method_args.get(method.__name__, [])) + sorted(
             additional_args
         )
         if args_to_add:
@@ -1338,7 +1338,7 @@ def unwrap_nested_methods(
                     )
             # Insert additional arguments to the method call (which were previously
             # accessed via member attributes)
-            args_to_be_inserted = list(self.used.method_args[name]) + list(
+            args_to_be_inserted = sorted(self.used.method_args[name]) + sorted(
                 additional_args
             )
             try:
@@ -1405,8 +1405,7 @@ def unwrap_nested_methods(
         "trait_modified",
     ]
 
-    CONFTEST = """
-# For debugging in IDE's don't catch raised exceptions and let the IDE
+    CONFTEST = """# For debugging in IDE's don't catch raised exceptions and let the IDE
 # break at it
 import os
 import pytest
@@ -1423,7 +1422,7 @@ def pytest_internalerror(excinfo):
         raise excinfo.value  # raise internal errors instead of capturing them
 
     def pytest_configure(config):
-        config.option.capture = 'no'  # allow print statements to show up in the console
+        config.option.capture = "no"  # allow print statements to show up in the console
         config.option.log_cli = True  # show log messages in the console
         config.option.log_level = "INFO"  # set the log level to INFO
 

nipype2pydra/interface/shell.py

@@ -190,7 +190,9 @@ def generate_code(self, input_fields, nonstd_types, output_fields) -> str:
 
         spec_str += "@shell.define"
         if xor_sets:
-            spec_str += f"(xor={[list(x) for x in xor_sets]})"
+            spec_str += (
+                f"(xor={[list(x) for x in sorted(tuple(sorted(s)) for s in xor_sets)]})"
+            )
         spec_str += (
             f"\nclass {self.task_name}(shell.Task['{self.task_name}.Outputs']):\n"
         )

nipype2pydra/package.py

@@ -708,7 +708,7 @@ def write_post_release_file(self, fspath: Path):
 src_pkg_version = "{src_pkg_version}"
 nipype2pydra_version = "{nipype2pydra_version}"
 post_release = "{post_release}"
-        """
+"""
             )
 
     @classmethod

nipype2pydra/statements/imports.py

@@ -217,6 +217,9 @@ def __str__(self):
         if self.from_:
             imported_str = ", ".join(str(i) for i in sorted(self.imported.values()))
             module = self.translation if self.translation else self.from_
+            # Drop trailing hidden module (e.g. '_local' from 'pathlib._local')
+            if module.split(".")[-1].startswith("_"):
+                module = ".".join(module.split(".")[:-1])
             stmt_str = f"{self.indent}from {module} import {imported_str}"
         elif self.translation:
             stmt_str = f"{self.indent}import {self.translation}"
@@ -614,7 +617,7 @@ def to_statement(self):
 
 
 def from_list_to_imports(
-    obj: ty.Union[ty.List[ExplicitImport], list]
+    obj: ty.Union[ty.List[ExplicitImport], list],
 ) -> ty.List[ExplicitImport]:
     if obj is None:
         return []

nipype2pydra/workflow.py

@@ -44,7 +44,7 @@
 
 
 def convert_node_prefixes(
-    nodes: ty.Union[ty.Dict[str, str], ty.Sequence[ty.Union[ty.Tuple[str, str], str]]]
+    nodes: ty.Union[ty.Dict[str, str], ty.Sequence[ty.Union[ty.Tuple[str, str], str]]],
 ) -> ty.Dict[str, str]:
     if isinstance(nodes, dict):
         nodes_it = nodes.items()
@@ -1310,8 +1310,7 @@ def default_spec(
                 )
         return yaml_str
 
-    CONFTEST = """
-# For debugging in IDE's don't catch raised exceptions and let the IDE
+    CONFTEST = """# For debugging in IDE's don't catch raised exceptions and let the IDE
 # break at it
 import os
 import pytest
@@ -1328,7 +1327,7 @@ def pytest_internalerror(excinfo):
         raise excinfo.value  # raise internal errors instead of capturing them
 
     def pytest_configure(config):
-        config.option.capture = 'no'  # allow print statements to show up in the console
+        config.option.capture = "no"  # allow print statements to show up in the console
         config.option.log_cli = True  # show log messages in the console
         config.option.log_level = "INFO"  # set the log level to INFO