Sort generated args and list for deterministic generation

example-specs/interface/nipype/afni/interfaces/afn_ito_nifti.yaml

@@ -36,7 +36,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_afni.ThreeD
+    in_file: fileformats.vendor.afni.medimage.ThreeD
     # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`

example-specs/interface/nipype/afni/interfaces/calc.yaml

@@ -72,7 +72,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: fileformats.medimage_afni.All1
+    out_file: fileformats.vendor.afni.medimage.All1
     # type=file: output file
     # type=file|default=<undefined>: output image file name
   callables:

example-specs/interface/nipype/afni/interfaces/cat.yaml

@@ -56,7 +56,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: fileformats.medimage_afni.OneD
+    out_file: fileformats.vendor.afni.medimage.OneD
     # type=file: output file
     # type=file|default='catout.1d': output (concatenated) file name
   callables:

example-specs/interface/nipype/afni/interfaces/convert_dset.yaml

@@ -54,7 +54,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: fileformats.medimage_afni.Dset
+    out_file: fileformats.vendor.afni.medimage.Dset
     # type=file: output file
     # type=file|default=<undefined>: output file for ConvertDset
   callables:

example-specs/interface/nipype/afni/interfaces/deconvolve.yaml

@@ -75,7 +75,7 @@ outputs:
     # type=file|default=<undefined>: output statistics file
     reml_script: generic/file
     # type=file: automatically generated script to run 3dREMLfit
-    x1D: fileformats.medimage_afni.OneD
+    x1D: fileformats.vendor.afni.medimage.OneD
     # type=file: save out X matrix
     # type=file|default=<undefined>: specify name for saved X matrix
   callables:

example-specs/interface/nipype/afni/interfaces/eval.yaml

@@ -39,7 +39,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file_a: fileformats.medimage_afni.OneD
+    in_file_a: fileformats.vendor.afni.medimage.OneD
     # type=file|default=<undefined>: input file to 1deval
     in_file_b: generic/file
     # type=file|default=<undefined>: operand file to 1deval
@@ -63,7 +63,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: fileformats.medimage_afni.OneD
+    out_file: fileformats.vendor.afni.medimage.OneD
     # type=file: output file
     # type=file|default=<undefined>: output image file name
   callables:

example-specs/interface/nipype/afni/interfaces/notes.yaml

@@ -36,7 +36,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_afni.Head
+    in_file: fileformats.vendor.afni.medimage.Head
     # type=file|default=<undefined>: input file to 3dNotes
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`

example-specs/interface/nipype/afni/interfaces/one_d_tool_py.yaml

@@ -31,7 +31,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_afni.OneD
+    in_file: fileformats.vendor.afni.medimage.OneD
     # type=file|default=<undefined>: input file to OneDTool
     show_cormat_warnings: generic/file
     # type=file|default=<undefined>: Write cormat warnings to a file

example-specs/interface/nipype/afni/interfaces/remlfit.yaml

@@ -51,7 +51,7 @@ inputs:
     # type=file|default=<undefined>: filename of 3D mask dataset; only data time series from within the mask will be analyzed; results for voxels outside the mask will be set to zero.
     matim: generic/file
     # type=file|default=<undefined>: read a standard file as the matrix. You can use only Col as a name in GLTs with these nonstandard matrix input methods, since the other names come from the 'matrix' file. These mutually exclusive options are ignored if 'matrix' is used.
-    matrix: fileformats.medimage_afni.OneD
+    matrix: fileformats.vendor.afni.medimage.OneD
     # type=file|default=<undefined>: the design matrix file, which should have been output from Deconvolve via the 'x1D' option
     slibase: generic/file+list-of
     # type=inputmultiobject|default=[]: similar to 'addbase' in concept, BUT each specified file must have an integer multiple of the number of slices in the input dataset(s); then, separate regression matrices are generated for each slice, with the first column of the file appended to the matrix for the first slice of the dataset, the second column of the file appended to the matrix for the first slice of the dataset, and so on. Intended to help model physiological noise in FMRI, or other effects you want to regress out that might change significantly in the inter-slice time intervals. This will slow the program down, and make it use a lot more memory (to hold all the matrix stuff).

example-specs/interface/nipype/afni/interfaces/retroicor.yaml

@@ -58,7 +58,7 @@ inputs:
     # type=file|default=<undefined>: Filename for 1D cardiac phase output
     in_file: medimage/nifti1
     # type=file|default=<undefined>: input file to 3dretroicor
-    resp: fileformats.medimage_afni.OneD
+    resp: fileformats.vendor.afni.medimage.OneD
     # type=file|default=<undefined>: 1D respiratory waveform data for correction
     respphase: generic/file
     # type=file|default=<undefined>: Filename for 1D resp phase output

example-specs/interface/nipype/afni/interfaces/volreg.yaml

@@ -74,7 +74,7 @@ outputs:
     md1d_file: generic/file
     # type=file: max displacement info file
     # type=file|default=<undefined>: max displacement output file
-    oned_file: fileformats.medimage_afni.OneD
+    oned_file: fileformats.vendor.afni.medimage.OneD
     # type=file: movement parameters info file
     # type=file|default=<undefined>: 1D movement parameters output file
     oned_matrix_save: generic/file

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

@@ -31,4 +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
+target_version: v25

example-specs/interface/nipype/freesurfer/interfaces/aparc_2_aseg.yaml

@@ -63,13 +63,13 @@ inputs:
     # type=file|default=<undefined>: Implicit input filled file. Only required with FS v5.3.
     lh_annotation: generic/file
     # type=file|default=<undefined>: Input file must be <subject_id>/label/lh.aparc.annot
-    lh_pial: fileformats.medimage_freesurfer.Pial
+    lh_pial: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/lh.pial
     lh_ribbon: medimage/mgh-gz
     # type=file|default=<undefined>: Input file must be <subject_id>/mri/lh.ribbon.mgz
-    lh_white: fileformats.medimage_freesurfer.Pial
+    lh_white: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/lh.white
-    rh_annotation: fileformats.medimage_freesurfer.Pial
+    rh_annotation: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file must be <subject_id>/label/rh.aparc.annot
     rh_pial: generic/file
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/rh.pial

example-specs/interface/nipype/freesurfer/interfaces/concatenate_lta.yaml

@@ -47,7 +47,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_lta1: fileformats.medimage_freesurfer.Lta
+    in_lta1: fileformats.vendor.freesurfer.medimage.Lta
     # type=file|default=<undefined>: maps some src1 to dst1
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory
@@ -71,7 +71,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: fileformats.medimage_freesurfer.Lta
+    out_file: fileformats.vendor.freesurfer.medimage.Lta
     # type=file: the combined LTA maps: src1 to dst2 = LTA2*LTA1
     # type=file|default=<undefined>: the combined LTA maps: src1 to dst2 = LTA2*LTA1
   callables:

example-specs/interface/nipype/freesurfer/interfaces/contrast.yaml

@@ -37,7 +37,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    annotation: fileformats.medimage_freesurfer.Annot
+    annotation: fileformats.vendor.freesurfer.medimage.Annot
     # type=file|default=<undefined>: Input annotation file must be <subject_id>/label/<hemisphere>.aparc.annot
     cortex: generic/file
     # type=file|default=<undefined>: Input cortex label must be <subject_id>/label/<hemisphere>.cortex.label
@@ -49,7 +49,7 @@ inputs:
     # type=directory|default=<undefined>: subjects directory
     thickness: generic/file
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/?h.thickness
-    white: fileformats.medimage_freesurfer.White
+    white: fileformats.vendor.freesurfer.medimage.White
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/<hemisphere>.white
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`

example-specs/interface/nipype/freesurfer/interfaces/curvature.yaml

@@ -33,7 +33,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_freesurfer.Pial
+    in_file: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file for Curvature
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

example-specs/interface/nipype/freesurfer/interfaces/curvature_stats.yaml

@@ -58,7 +58,7 @@ inputs:
   # passed to the field in the automatically generated unittests.
     curvfile1: generic/file
     # type=file|default=<undefined>: Input file for CurvatureStats
-    curvfile2: fileformats.medimage_freesurfer.Pial
+    curvfile2: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file for CurvatureStats
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory
@@ -80,7 +80,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: fileformats.medimage_freesurfer.Stats
+    out_file: fileformats.vendor.freesurfer.medimage.Stats
     # type=file: Output curvature stats file
     # type=file|default=<undefined>: Output curvature stats file
   callables:

example-specs/interface/nipype/freesurfer/interfaces/em_register.yaml

@@ -59,7 +59,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: fileformats.medimage_freesurfer.Lta
+    out_file: fileformats.vendor.freesurfer.medimage.Lta
     # type=file: output transform
     # type=file|default=<undefined>: output transform
   callables:

example-specs/interface/nipype/freesurfer/interfaces/euler_number.yaml

@@ -30,7 +30,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_freesurfer.Pial
+    in_file: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file for EulerNumber
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

example-specs/interface/nipype/freesurfer/interfaces/extract_main_component.yaml

@@ -30,7 +30,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_freesurfer.Pial
+    in_file: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: input surface file
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`

example-specs/interface/nipype/freesurfer/interfaces/fix_topology.yaml

@@ -42,11 +42,11 @@ inputs:
     # type=file|default=<undefined>: Implicit input brain.mgz
     in_inflated: generic/file
     # type=file|default=<undefined>: Undocumented input file <hemisphere>.inflated
-    in_orig: fileformats.medimage_freesurfer.Orig
+    in_orig: fileformats.vendor.freesurfer.medimage.Orig
     # type=file|default=<undefined>: Undocumented input file <hemisphere>.orig
     in_wm: generic/file
     # type=file|default=<undefined>: Implicit input wm.mgz
-    sphere: fileformats.medimage_freesurfer.Nofix
+    sphere: fileformats.vendor.freesurfer.medimage.Nofix
     # type=file|default=<undefined>: Sphere input file
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

example-specs/interface/nipype/freesurfer/interfaces/gtmpvc.yaml

@@ -55,7 +55,7 @@ inputs:
     # type=file|default=<undefined>: input volume - source data to pvc
     mask_file: generic/file
     # type=file|default=<undefined>: ignore areas outside of the mask (in input vol space)
-    reg_file: fileformats.medimage_freesurfer.Lta
+    reg_file: fileformats.vendor.freesurfer.medimage.Lta
     # type=file|default=<undefined>: LTA registration file that maps PET to anatomical
     segmentation: generic/file
     # type=file|default=<undefined>: segfile : anatomical segmentation to define regions for GTM

example-specs/interface/nipype/freesurfer/interfaces/jacobian.yaml

@@ -33,7 +33,7 @@ inputs:
   # passed to the field in the automatically generated unittests.
     in_mappedsurf: generic/file
     # type=file|default=<undefined>: Mapped surface
-    in_origsurf: fileformats.medimage_freesurfer.Pial
+    in_origsurf: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Original surface
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

example-specs/interface/nipype/freesurfer/interfaces/label_2_label.yaml

@@ -49,9 +49,9 @@ inputs:
     # type=file|default=<undefined>: Source label
     source_sphere_reg: generic/file
     # type=file|default=<undefined>: Implicit input <hemisphere>.sphere.reg
-    source_white: fileformats.medimage_freesurfer.Pial
+    source_white: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Implicit input <hemisphere>.white
-    sphere_reg: fileformats.medimage_freesurfer.Pial
+    sphere_reg: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Implicit input <hemisphere>.sphere.reg
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

example-specs/interface/nipype/freesurfer/interfaces/label_2_vol.yaml

@@ -36,7 +36,7 @@ inputs:
     # type=file|default=<undefined>: file with each frame is nhits for a label
     map_label_stat: generic/file
     # type=file|default=<undefined>: map the label stats field into the vol
-    reg_file: fileformats.medimage_freesurfer.Dat
+    reg_file: fileformats.vendor.freesurfer.medimage.Dat
     # type=file|default=<undefined>: tkregister style matrix VolXYZ = R*LabelXYZ
     reg_header: generic/file
     # type=file|default=<undefined>: label template volume

example-specs/interface/nipype/freesurfer/interfaces/make_surfaces.yaml

@@ -49,7 +49,7 @@ inputs:
     # type=file|default=<undefined>: Implicit input file filled.mgz
     in_label: generic/file
     # type=file|default=<undefined>: Implicit input label/<hemisphere>.aparc.annot
-    in_orig: fileformats.medimage_freesurfer.Pial
+    in_orig: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Implicit input file <hemisphere>.orig
     in_white: generic/file
     # type=file|default=<undefined>: Implicit input that is sometimes used

example-specs/interface/nipype/freesurfer/interfaces/mr_is_ca_label.yaml

@@ -46,19 +46,19 @@ inputs:
   # passed to the field in the automatically generated unittests.
     aseg: generic/file
     # type=file|default=<undefined>: Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file
-    canonsurf: fileformats.medimage_freesurfer.Pial
+    canonsurf: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input canonical surface file
     classifier: generic/file
     # type=file|default=<undefined>: Classifier array input file
     curv: generic/file
     # type=file|default=<undefined>: implicit input {hemisphere}.curv
     label: generic/file
     # type=file|default=<undefined>: Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file
-    smoothwm: fileformats.medimage_freesurfer.Pial
+    smoothwm: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: implicit input {hemisphere}.smoothwm
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory
-    sulc: fileformats.medimage_freesurfer.Pial
+    sulc: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: implicit input {hemisphere}.sulc
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`

example-specs/interface/nipype/freesurfer/interfaces/mr_is_calc.yaml

@@ -42,7 +42,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file1: fileformats.medimage_freesurfer.Area
+    in_file1: fileformats.vendor.freesurfer.medimage.Area
     # type=file|default=<undefined>: Input file 1
     in_file2: generic/file
     # type=file|default=<undefined>: Input file 2

example-specs/interface/nipype/freesurfer/interfaces/mr_is_expand.yaml

@@ -34,7 +34,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_freesurfer.White
+    in_file: fileformats.vendor.freesurfer.medimage.White
     # type=file|default=<undefined>: Surface to expand
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

example-specs/interface/nipype/freesurfer/interfaces/mr_is_inflate.yaml

@@ -31,7 +31,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: fileformats.medimage_freesurfer.Pial
+    in_file: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file for MRIsInflate
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

example-specs/interface/nipype/freesurfer/interfaces/paint.yaml

@@ -37,7 +37,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_surf: fileformats.medimage_freesurfer.Pial
+    in_surf: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Surface file with grid (vertices) onto which the template data is to be sampled or 'painted'
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory