replaced auto with specifiable "target_version" for target of interface only packages

Author: tclose

example-specs/interface/nipype/afni/package.yaml

@@ -31,3 +31,4 @@ init_depth: 3
 auto_import_init_depth: 4
 # Packages that should be copied directly into the new package without modification
 copy_packages: null
+target_version: v25_2_06

example-specs/interface/nipype/ants/package.yaml

@@ -31,3 +31,4 @@ init_depth: 3
 auto_import_init_depth: 4
 # Packages that should be copied directly into the new package without modification
 copy_packages: null
+target_version: v2

example-specs/interface/nipype/freesurfer/package.yaml

@@ -31,3 +31,4 @@ init_depth: 3
 auto_import_init_depth: 4
 # Packages that should be copied directly into the new package without modification
 copy_packages: null
+target_version: v8

example-specs/interface/nipype/fsl/package.yaml

@@ -31,3 +31,4 @@ init_depth: 3
 auto_import_init_depth: 4
 # Packages that should be copied directly into the new package without modification
 copy_packages: null
+target_version: v6_0

example-specs/pkg-gen/nipype.yaml

@@ -1,4 +1,5 @@
 afni:
+  target_version: v25_2_06
   interfaces:
     - nipype.interfaces.afni.model.Deconvolve
     - nipype.interfaces.afni.model.Remlfit
@@ -81,6 +82,7 @@ afni:
     - nipype.interfaces.afni.utils.Zcat
     - nipype.interfaces.afni.utils.Zeropad
 ants:
+  target_version: v2
   interfaces:
     - nipype.interfaces.ants.legacy.antsIntroduction
     - nipype.interfaces.ants.legacy.GenWarpFields
@@ -118,6 +120,7 @@ ants:
   classes:
     - nipype.interfaces.ants.base.Info
 brainsuite:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.brainsuite.brainsuite.Bse
     - nipype.interfaces.brainsuite.brainsuite.Bfc
@@ -135,13 +138,16 @@ brainsuite:
     - nipype.interfaces.brainsuite.brainsuite.BDP
     - nipype.interfaces.brainsuite.brainsuite.ThicknessPVC
 bru2nii:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.bru2nii.Bru2
 c3:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.c3.C3dAffineTool
     - nipype.interfaces.c3.C3d
 camino:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.camino.calib.SFPICOCalibData
     - nipype.interfaces.camino.calib.SFLUTGen
@@ -178,16 +184,19 @@ camino:
     - nipype.interfaces.camino.odf.SFPeaks
     - nipype.interfaces.camino.utils.ImageStats
 camino2trackvis:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.camino2trackvis.convert.Camino2Trackvis
     - nipype.interfaces.camino2trackvis.convert.Trackvis2Camino
 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:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.cmtk.cmtk.CreateMatrix
     - nipype.interfaces.cmtk.cmtk.ROIGen
@@ -199,11 +208,13 @@ cmtk:
     - nipype.interfaces.cmtk.nx.AverageNetworks
     - nipype.interfaces.cmtk.parcellation.Parcellate
 dcm2nii:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.dcm2nii.Info
     - nipype.interfaces.dcm2nii.Dcm2nii
     - nipype.interfaces.dcm2nii.Dcm2niix
 dcmstack:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.dcmstack.NiftiGeneratorBase
     - nipype.interfaces.dcmstack.DcmStack
@@ -213,6 +224,7 @@ dcmstack:
     - nipype.interfaces.dcmstack.MergeNifti
     - nipype.interfaces.dcmstack.SplitNifti
 diffusion_toolkit:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.diffusion_toolkit.dti.DTIRecon
     - nipype.interfaces.diffusion_toolkit.dti.DTITracker
@@ -222,6 +234,7 @@ diffusion_toolkit:
     - nipype.interfaces.diffusion_toolkit.postproc.SplineFilter
     - nipype.interfaces.diffusion_toolkit.postproc.TrackMerge
 dipy:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.dipy.anisotropic_power.APMQball
     - nipype.interfaces.dipy.preprocess.Resample
@@ -235,6 +248,7 @@ dipy:
     - nipype.interfaces.dipy.tracks.TrackDensityMap
     - nipype.interfaces.dipy.tracks.StreamlineTractography
 dtitk:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.dtitk.registration.Rigid
     - nipype.interfaces.dtitk.registration.Affine
@@ -266,16 +280,19 @@ dtitk:
     - nipype.interfaces.dtitk.utils.TVResampleTask
     - nipype.interfaces.dtitk.utils.TVtoolTask
 dynamic_slicer:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.dynamic_slicer.SlicerCommandLine
 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:
+  target_version: v8
   interfaces:
     - nipype.interfaces.freesurfer.longitudinal.RobustTemplate
     - nipype.interfaces.freesurfer.longitudinal.FuseSegmentations
@@ -367,6 +384,7 @@ freesurfer:
     - nipype.interfaces.freesurfer.utils.MRIsExpand
     - nipype.interfaces.freesurfer.utils.LTAConvert
 fsl:
+  target_version: v6_0
   interfaces:
     - nipype.interfaces.fsl.aroma.ICA_AROMA
     - nipype.interfaces.fsl.dti.DTIFit
@@ -475,13 +493,16 @@ fsl:
     - nipype.interfaces.fsl.utils.Text2Vest
     - nipype.interfaces.fsl.utils.Vest2Text
 image:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.image.Rescale
     - nipype.interfaces.image.Reorient
 meshfix:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.meshfix.MeshFix
 minc:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.minc.minc.Extract
     - nipype.interfaces.minc.minc.ToRaw
@@ -512,6 +533,7 @@ minc:
     - nipype.interfaces.minc.minc.Reshape
     - nipype.interfaces.minc.minc.VolSymm
 mipav:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.mipav.developer.JistLaminarVolumetricLayering
     - nipype.interfaces.mipav.developer.JistBrainMgdmSegmentation
@@ -532,12 +554,14 @@ mipav:
     - nipype.interfaces.mipav.developer.JistIntensityMp2rageMasking
     - nipype.interfaces.mipav.developer.MedicAlgorithmThresholdToBinaryMask
 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:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.niftyreg.reg.RegAladin
     - nipype.interfaces.niftyreg.reg.RegF3D
@@ -548,6 +572,7 @@ niftyreg:
     - nipype.interfaces.niftyreg.regutils.RegTransform
     - nipype.interfaces.niftyreg.regutils.RegMeasure
 niftyseg:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.niftyseg.em.EM
     - nipype.interfaces.niftyseg.label_fusion.LabelFusion
@@ -564,22 +589,28 @@ niftyseg:
     - nipype.interfaces.niftyseg.stats.UnaryStats
     - nipype.interfaces.niftyseg.stats.BinaryStats
 nilearn:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.nilearn.NilearnBaseInterface
     - nipype.interfaces.nilearn.SignalExtraction
 nitime:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.nitime.analysis.CoherenceAnalyzer
 petpvc:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.petpvc.PETPVC
 quickshear:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.quickshear.Quickshear
 robex:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.robex.preprocess.RobexSegment
 semtools:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.semtools.brains.classify.BRAINSPosteriorToContinuousClass
     - nipype.interfaces.semtools.brains.segmentation.SimilarityIndex
@@ -684,6 +715,7 @@ semtools:
     - nipype.interfaces.semtools.utilities.brains.fcsv_to_hdf5
     - nipype.interfaces.semtools.utilities.brains.FindCenterOfBrain
 slicer:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.slicer.converters.DicomToNrrdConverter
     - nipype.interfaces.slicer.converters.OrientScalarVolume
@@ -746,6 +778,7 @@ slicer:
     - nipype.interfaces.slicer.surface.ModelMaker
     - nipype.interfaces.slicer.utilities.EMSegmentTransformToNewFormat
 spm:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.spm.model.Level1Design
     - nipype.interfaces.spm.model.EstimateModel
@@ -782,10 +815,12 @@ spm:
     - nipype.interfaces.spm.utils.ResliceToReference
     - nipype.interfaces.spm.utils.DicomImport
 vista:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.vista.vista.Vnifti2Image
     - nipype.interfaces.vista.vista.VtoMat
 workbench:
+  target_version: v1_0
   interfaces:
     - nipype.interfaces.workbench.cifti.CiftiSmooth
     - nipype.interfaces.workbench.metric.MetricResample

nipype2pydra/cli/convert.py

@@ -66,7 +66,7 @@ def convert(
     # Clean previous version of output dir
     package_dir = converter.package_dir(package_root)
     if converter.interface_only:
-        auto_dir = package_dir / "auto"
+        auto_dir = package_dir / converter.target_version
         if auto_dir.exists():
             shutil.rmtree(auto_dir)
     else:

nipype2pydra/cli/pkg_gen.py

@@ -113,7 +113,11 @@ def pkg_gen(
         with_fileformats = spec.get("with_fileformats")
         interface_only_pkg = "workflows" not in spec
         pkg_dir = initialise_task_repo(
-            output_dir, task_template, pkg, interface_only=interface_only_pkg
+            output_dir,
+            task_template,
+            pkg,
+            spec["target_version"],
+            interface_only=interface_only_pkg,
         )
         pkg_formats = set()
 

nipype2pydra/interface/base.py

@@ -372,9 +372,7 @@ def __attrs_post_init__(self):
         if self.output_module is None:
             if self.nipype_module.__name__.startswith("nipype.interfaces."):
                 pkg_name = self.nipype_module.__name__.split(".")[2]
-                self.output_module = (
-                    f"pydra.tasks.{pkg_name}.auto.{to_snake_case(self.task_name)}"
-                )
+                self.output_module = f"pydra.tasks.{pkg_name}.{self.package.target_version}.{to_snake_case(self.task_name)}"
             else:
                 raise RuntimeError(
                     "Output-module needs to be explicitly provided to task converter "

nipype2pydra/package.py

@@ -274,6 +274,11 @@ class PackageConverter:
         },
     )
 
+    target_version: str = attrs.field(
+        default="v1_0",
+        metadata={"help": "The target version of the package to generate"},
+    )
+
     def __attrs_post_init__(self):
         # Adds in some default omissions
         self.omit_constants.append("nipype.logging")
@@ -298,13 +303,19 @@ def nipype_module(self):
     def all_import_translations(self) -> ty.List[ty.Tuple[str, str]]:
         all_translations = self.import_translations + [
             (r"nipype\.interfaces\.mrtrix3.\w+\b", r"pydra.tasks.mrtrix3.v3_0"),
-            (r"nipype\.interfaces\.(?!base)(\w+)\b", r"pydra.tasks.\1.auto"),
+            (
+                r"nipype\.interfaces\.(?!base)(\w+)\b",
+                r"pydra.tasks.\1." + self.target_version,
+            ),
         ]
         if self.interface_only:
             all_translations.extend(
                 [
-                    (r"nipype\.(.*)", self.name + r".auto.nipype_ports.\1"),
-                    (self.nipype_name, self.name + ".auto"),
+                    (
+                        r"nipype\.(.*)",
+                        self.name + "." + self.target_version + r".nipype_ports.\1",
+                    ),
+                    (self.nipype_name, self.name + "." + self.target_version),
                 ]
             )
         else:
@@ -471,7 +482,7 @@ def collect_intra_pkg_objects(used: UsedSymbols, port_nipype: bool = True):
 
         post_release_dir = mod_dir
         if self.interface_only:
-            post_release_dir /= "auto"
+            post_release_dir /= self.target_version
         self.write_post_release_file(post_release_dir / "_post_release.py")
 
         if self.copy_packages:
@@ -507,8 +518,8 @@ def translate_submodule(
     def untranslate_submodule(self, pydra_module_name: str) -> str:
         """Translates a module name from the Nipype package to the Pydra package"""
         relpath = ImportStatement.get_relative_package(pydra_module_name, self.name)
-        if relpath.startswith(".auto"):
-            relpath = relpath[5:]
+        if relpath.startswith("." + self.target_version):
+            relpath = relpath[(len(self.target_version) + 1) :]
         if relpath.startswith(".nipype_ports"):
             return "nipype" + relpath[13:]
         if relpath == self.nipype_name:
@@ -611,7 +622,7 @@ def nipype2pydra_module_name(self, nipype_name: str) -> str:
             the Pydra module path
         """
         if self.interface_only:
-            base_pkg = self.name + ".auto"
+            base_pkg = self.name + "." + self.target_version
         else:
             base_pkg = self.name
         if re.match(self.nipype_module.__name__ + r"\b", nipype_name):
@@ -719,15 +730,15 @@ def nipype_port_converters(self) -> ty.Dict[str, interface.BaseInterfaceConverte
                 spec = yaml.safe_load(f)
             callables_file = spec_file.parent / (spec_file.stem + "_callables.py")
             if self.interface_only:
-                mod_base = [self.name, "auto", "nipype_ports"]
+                mod_base = [self.name, self.target_version, "nipype_ports"]
             else:
                 mod_base = [self.name, "nipype_ports"]
             module_name = ".".join(mod_base + spec["nipype_module"].split(".")[1:])
             task_name = spec["task_name"]
             output_module = (
                 self.translate_submodule(
                     module_name,
-                    sub_pkg="auto" if self.interface_only else None,
+                    sub_pkg=self.target_version if self.interface_only else None,
                 )
                 + "."
                 + to_snake_case(task_name)
@@ -748,7 +759,8 @@ def add_interface_from_spec(
         # callables_file: Path
     ) -> interface.BaseInterfaceConverter:
         output_module = self.translate_submodule(
-            spec["nipype_module"], sub_pkg="auto" if self.interface_only else None
+            spec["nipype_module"],
+            sub_pkg=self.target_version if self.interface_only else None,
         )
         output_module += "." + to_snake_case(spec["task_name"])
         converter = self.interfaces[f"{spec['nipype_module']}.{spec['task_name']}"] = (
@@ -1160,7 +1172,7 @@ def write_pkg_inits(
         warn(
             "Nipype interfaces haven't been automatically converted from their specs in "
             f"`nipype-auto-conv`. Please run `{str(pkg_path / 'nipype-auto-conv' / 'generate')}` "
-            "to generated the converted Nipype interfaces in pydra.tasks.{pkg}.auto"
+            "to generated the converted Nipype interfaces in pydra.tasks.{pkg}.{target_version}"
         )
     else:
         n_ver = src_pkg_version.replace(".", "_")