diff --git a/example-specs/interface/nipype/afni/interfaces/afn_ito_nifti.yaml b/example-specs/interface/nipype/afni/interfaces/afn_ito_nifti.yaml index abee3813..e21fa93d 100644 --- a/example-specs/interface/nipype/afni/interfaces/afn_ito_nifti.yaml +++ b/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=: input file to 3dAFNItoNIFTI callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/example-specs/interface/nipype/afni/interfaces/calc.yaml b/example-specs/interface/nipype/afni/interfaces/calc.yaml index 2f8ef833..71d610a1 100644 --- a/example-specs/interface/nipype/afni/interfaces/calc.yaml +++ b/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=: output image file name callables: diff --git a/example-specs/interface/nipype/afni/interfaces/cat.yaml b/example-specs/interface/nipype/afni/interfaces/cat.yaml index e8b49ae3..cf1cf87d 100644 --- a/example-specs/interface/nipype/afni/interfaces/cat.yaml +++ b/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: diff --git a/example-specs/interface/nipype/afni/interfaces/convert_dset.yaml b/example-specs/interface/nipype/afni/interfaces/convert_dset.yaml index 764d544b..03356166 100644 --- a/example-specs/interface/nipype/afni/interfaces/convert_dset.yaml +++ b/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=: output file for ConvertDset callables: diff --git a/example-specs/interface/nipype/afni/interfaces/deconvolve.yaml b/example-specs/interface/nipype/afni/interfaces/deconvolve.yaml index 7976fc51..4f7c4e72 100644 --- a/example-specs/interface/nipype/afni/interfaces/deconvolve.yaml +++ b/example-specs/interface/nipype/afni/interfaces/deconvolve.yaml @@ -75,7 +75,7 @@ outputs: # type=file|default=: 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=: specify name for saved X matrix callables: diff --git a/example-specs/interface/nipype/afni/interfaces/eval.yaml b/example-specs/interface/nipype/afni/interfaces/eval.yaml index ad97dfcf..31ee91e9 100644 --- a/example-specs/interface/nipype/afni/interfaces/eval.yaml +++ b/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=: input file to 1deval in_file_b: generic/file # type=file|default=: 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=: output image file name callables: diff --git a/example-specs/interface/nipype/afni/interfaces/notes.yaml b/example-specs/interface/nipype/afni/interfaces/notes.yaml index 131e0004..0ad635e3 100644 --- a/example-specs/interface/nipype/afni/interfaces/notes.yaml +++ b/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=: input file to 3dNotes callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/example-specs/interface/nipype/afni/interfaces/one_d_tool_py.yaml b/example-specs/interface/nipype/afni/interfaces/one_d_tool_py.yaml index 50112bec..1d29bcf1 100644 --- a/example-specs/interface/nipype/afni/interfaces/one_d_tool_py.yaml +++ b/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=: input file to OneDTool show_cormat_warnings: generic/file # type=file|default=: Write cormat warnings to a file diff --git a/example-specs/interface/nipype/afni/interfaces/remlfit.yaml b/example-specs/interface/nipype/afni/interfaces/remlfit.yaml index 8132a644..b12c4c92 100644 --- a/example-specs/interface/nipype/afni/interfaces/remlfit.yaml +++ b/example-specs/interface/nipype/afni/interfaces/remlfit.yaml @@ -51,7 +51,7 @@ inputs: # type=file|default=: 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=: 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=: 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). diff --git a/example-specs/interface/nipype/afni/interfaces/retroicor.yaml b/example-specs/interface/nipype/afni/interfaces/retroicor.yaml index b34c7f58..4adb4d1c 100644 --- a/example-specs/interface/nipype/afni/interfaces/retroicor.yaml +++ b/example-specs/interface/nipype/afni/interfaces/retroicor.yaml @@ -58,7 +58,7 @@ inputs: # type=file|default=: Filename for 1D cardiac phase output in_file: medimage/nifti1 # type=file|default=: input file to 3dretroicor - resp: fileformats.medimage_afni.OneD + resp: fileformats.vendor.afni.medimage.OneD # type=file|default=: 1D respiratory waveform data for correction respphase: generic/file # type=file|default=: Filename for 1D resp phase output diff --git a/example-specs/interface/nipype/afni/interfaces/volreg.yaml b/example-specs/interface/nipype/afni/interfaces/volreg.yaml index ed104149..55ddf0a7 100644 --- a/example-specs/interface/nipype/afni/interfaces/volreg.yaml +++ b/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=: 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=: 1D movement parameters output file oned_matrix_save: generic/file diff --git a/example-specs/interface/nipype/afni/package.yaml b/example-specs/interface/nipype/afni/package.yaml index d506fc33..dbdb4571 100644 --- a/example-specs/interface/nipype/afni/package.yaml +++ b/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 diff --git a/example-specs/interface/nipype/freesurfer/interfaces/aparc_2_aseg.yaml b/example-specs/interface/nipype/freesurfer/interfaces/aparc_2_aseg.yaml index 7ce3308d..2e4fb1db 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/aparc_2_aseg.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/aparc_2_aseg.yaml @@ -63,13 +63,13 @@ inputs: # type=file|default=: Implicit input filled file. Only required with FS v5.3. lh_annotation: generic/file # type=file|default=: Input file must be /label/lh.aparc.annot - lh_pial: fileformats.medimage_freesurfer.Pial + lh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/lh.pial lh_ribbon: medimage/mgh-gz # type=file|default=: Input file must be /mri/lh.ribbon.mgz - lh_white: fileformats.medimage_freesurfer.Pial + lh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/lh.white - rh_annotation: fileformats.medimage_freesurfer.Pial + rh_annotation: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /label/rh.aparc.annot rh_pial: generic/file # type=file|default=: Input file must be /surf/rh.pial diff --git a/example-specs/interface/nipype/freesurfer/interfaces/concatenate_lta.yaml b/example-specs/interface/nipype/freesurfer/interfaces/concatenate_lta.yaml index dd1cb089..e676f281 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/concatenate_lta.yaml +++ b/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=: maps some src1 to dst1 subjects_dir: generic/directory # type=directory|default=: 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=: the combined LTA maps: src1 to dst2 = LTA2*LTA1 callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/contrast.yaml b/example-specs/interface/nipype/freesurfer/interfaces/contrast.yaml index 3c13671b..5d935674 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/contrast.yaml +++ b/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=: Input annotation file must be /label/.aparc.annot cortex: generic/file # type=file|default=: Input cortex label must be /label/.cortex.label @@ -49,7 +49,7 @@ inputs: # type=directory|default=: subjects directory thickness: generic/file # type=file|default=: Input file must be /surf/?h.thickness - white: fileformats.medimage_freesurfer.White + white: fileformats.vendor.freesurfer.medimage.White # type=file|default=: Input file must be /surf/.white callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/example-specs/interface/nipype/freesurfer/interfaces/curvature.yaml b/example-specs/interface/nipype/freesurfer/interfaces/curvature.yaml index 748c88b3..a8376c39 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/curvature.yaml +++ b/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=: Input file for Curvature subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/curvature_stats.yaml b/example-specs/interface/nipype/freesurfer/interfaces/curvature_stats.yaml index 2e93873e..e3678bc6 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/curvature_stats.yaml +++ b/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=: Input file for CurvatureStats - curvfile2: fileformats.medimage_freesurfer.Pial + curvfile2: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file for CurvatureStats subjects_dir: generic/directory # type=directory|default=: 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=: Output curvature stats file callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/em_register.yaml b/example-specs/interface/nipype/freesurfer/interfaces/em_register.yaml index 8c3ef93b..525bdf65 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/em_register.yaml +++ b/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=: output transform callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/euler_number.yaml b/example-specs/interface/nipype/freesurfer/interfaces/euler_number.yaml index 963344b7..fe7f45b8 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/euler_number.yaml +++ b/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=: Input file for EulerNumber subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/extract_main_component.yaml b/example-specs/interface/nipype/freesurfer/interfaces/extract_main_component.yaml index 4fc35138..809d67ed 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/extract_main_component.yaml +++ b/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=: input surface file callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/example-specs/interface/nipype/freesurfer/interfaces/fix_topology.yaml b/example-specs/interface/nipype/freesurfer/interfaces/fix_topology.yaml index 3d5addd9..45d8d985 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/fix_topology.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/fix_topology.yaml @@ -42,11 +42,11 @@ inputs: # type=file|default=: Implicit input brain.mgz in_inflated: generic/file # type=file|default=: Undocumented input file .inflated - in_orig: fileformats.medimage_freesurfer.Orig + in_orig: fileformats.vendor.freesurfer.medimage.Orig # type=file|default=: Undocumented input file .orig in_wm: generic/file # type=file|default=: Implicit input wm.mgz - sphere: fileformats.medimage_freesurfer.Nofix + sphere: fileformats.vendor.freesurfer.medimage.Nofix # type=file|default=: Sphere input file subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/gtmpvc.yaml b/example-specs/interface/nipype/freesurfer/interfaces/gtmpvc.yaml index 90b84fbc..7254f9d5 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/gtmpvc.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/gtmpvc.yaml @@ -55,7 +55,7 @@ inputs: # type=file|default=: input volume - source data to pvc mask_file: generic/file # type=file|default=: 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=: LTA registration file that maps PET to anatomical segmentation: generic/file # type=file|default=: segfile : anatomical segmentation to define regions for GTM diff --git a/example-specs/interface/nipype/freesurfer/interfaces/jacobian.yaml b/example-specs/interface/nipype/freesurfer/interfaces/jacobian.yaml index 14fc8deb..37a393c3 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/jacobian.yaml +++ b/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=: Mapped surface - in_origsurf: fileformats.medimage_freesurfer.Pial + in_origsurf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Original surface subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/label_2_label.yaml b/example-specs/interface/nipype/freesurfer/interfaces/label_2_label.yaml index 934f9f55..b4376b4a 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/label_2_label.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/label_2_label.yaml @@ -49,9 +49,9 @@ inputs: # type=file|default=: Source label source_sphere_reg: generic/file # type=file|default=: Implicit input .sphere.reg - source_white: fileformats.medimage_freesurfer.Pial + source_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input .white - sphere_reg: fileformats.medimage_freesurfer.Pial + sphere_reg: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input .sphere.reg subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/label_2_vol.yaml b/example-specs/interface/nipype/freesurfer/interfaces/label_2_vol.yaml index eecb7bd4..b6e681b8 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/label_2_vol.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/label_2_vol.yaml @@ -36,7 +36,7 @@ inputs: # type=file|default=: file with each frame is nhits for a label map_label_stat: generic/file # type=file|default=: map the label stats field into the vol - reg_file: fileformats.medimage_freesurfer.Dat + reg_file: fileformats.vendor.freesurfer.medimage.Dat # type=file|default=: tkregister style matrix VolXYZ = R*LabelXYZ reg_header: generic/file # type=file|default=: label template volume diff --git a/example-specs/interface/nipype/freesurfer/interfaces/make_surfaces.yaml b/example-specs/interface/nipype/freesurfer/interfaces/make_surfaces.yaml index b61d5b40..cefef373 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/make_surfaces.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/make_surfaces.yaml @@ -49,7 +49,7 @@ inputs: # type=file|default=: Implicit input file filled.mgz in_label: generic/file # type=file|default=: Implicit input label/.aparc.annot - in_orig: fileformats.medimage_freesurfer.Pial + in_orig: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input file .orig in_white: generic/file # type=file|default=: Implicit input that is sometimes used diff --git a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_ca_label.yaml b/example-specs/interface/nipype/freesurfer/interfaces/mr_is_ca_label.yaml index 1f61ee3f..585cf810 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_ca_label.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/mr_is_ca_label.yaml @@ -46,7 +46,7 @@ inputs: # passed to the field in the automatically generated unittests. aseg: generic/file # type=file|default=: 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=: Input canonical surface file classifier: generic/file # type=file|default=: Classifier array input file @@ -54,11 +54,11 @@ inputs: # type=file|default=: implicit input {hemisphere}.curv label: generic/file # type=file|default=: 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=: implicit input {hemisphere}.smoothwm subjects_dir: generic/directory # type=directory|default=: subjects directory - sulc: fileformats.medimage_freesurfer.Pial + sulc: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: implicit input {hemisphere}.sulc callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_calc.yaml b/example-specs/interface/nipype/freesurfer/interfaces/mr_is_calc.yaml index ede76b0f..287e8896 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_calc.yaml +++ b/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=: Input file 1 in_file2: generic/file # type=file|default=: Input file 2 diff --git a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_expand.yaml b/example-specs/interface/nipype/freesurfer/interfaces/mr_is_expand.yaml index b86212dd..297367ae 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_expand.yaml +++ b/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=: Surface to expand subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_inflate.yaml b/example-specs/interface/nipype/freesurfer/interfaces/mr_is_inflate.yaml index 4afb1810..4b0bc460 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/mr_is_inflate.yaml +++ b/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=: Input file for MRIsInflate subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/paint.yaml b/example-specs/interface/nipype/freesurfer/interfaces/paint.yaml index 7859f0e6..780ecfeb 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/paint.yaml +++ b/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=: Surface file with grid (vertices) onto which the template data is to be sampled or 'painted' subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/parcellation_stats.yaml b/example-specs/interface/nipype/freesurfer/interfaces/parcellation_stats.yaml index 3867cf60..525ea356 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/parcellation_stats.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/parcellation_stats.yaml @@ -61,9 +61,9 @@ inputs: # type=file|default=: Input file must be /surf/lh.pial lh_white: generic/file # type=file|default=: Input file must be /surf/lh.white - rh_pial: fileformats.medimage_freesurfer.Pial + rh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/rh.pial - rh_white: fileformats.medimage_freesurfer.White + rh_white: fileformats.vendor.freesurfer.medimage.White # type=file|default=: Input file must be /surf/rh.white ribbon: medimage/mgh-gz # type=file|default=: Input file must be /mri/ribbon.mgz @@ -91,7 +91,7 @@ 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_color: fileformats.medimage_freesurfer.Ctab + out_color: fileformats.vendor.freesurfer.medimage.Ctab # type=file: Output annotation files's colortable to text file # type=file|default=: Output annotation files's colortable to text file out_table: generic/file diff --git a/example-specs/interface/nipype/freesurfer/interfaces/register.yaml b/example-specs/interface/nipype/freesurfer/interfaces/register.yaml index b4caabf5..8f2981f5 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/register.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/register.yaml @@ -36,9 +36,9 @@ inputs: # passed to the field in the automatically generated unittests. in_smoothwm: generic/file # type=file|default=: Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm - in_sulc: fileformats.medimage_freesurfer.Pial + in_sulc: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Undocumented mandatory input file ${SUBJECTS_DIR}/surf/{hemisphere}.sulc - in_surf: fileformats.medimage_freesurfer.Pial + in_surf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Surface to register, often {hemi}.sphere subjects_dir: generic/directory # type=directory|default=: subjects directory @@ -60,7 +60,7 @@ 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.Reg + out_file: fileformats.vendor.freesurfer.medimage.Reg # type=file: Output surface file to capture registration # type=file|default=: Output surface file to capture registration callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/relabel_hypointensities.yaml b/example-specs/interface/nipype/freesurfer/interfaces/relabel_hypointensities.yaml index 8be14235..4ba87aaa 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/relabel_hypointensities.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/relabel_hypointensities.yaml @@ -35,7 +35,7 @@ inputs: # passed to the field in the automatically generated unittests. aseg: generic/file # type=file|default=: Input aseg file - lh_white: fileformats.medimage_freesurfer.Pial + lh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input file must be lh.white rh_white: generic/file # type=file|default=: Implicit input file must be rh.white diff --git a/example-specs/interface/nipype/freesurfer/interfaces/remove_intersection.yaml b/example-specs/interface/nipype/freesurfer/interfaces/remove_intersection.yaml index 18bbe3e4..668211c5 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/remove_intersection.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/remove_intersection.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=: Input file for RemoveIntersection subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/seg_stats.yaml b/example-specs/interface/nipype/freesurfer/interfaces/seg_stats.yaml index d63a5b2f..9708cc10 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/seg_stats.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/seg_stats.yaml @@ -77,7 +77,7 @@ outputs: sf_avg_file: generic/file # type=file: Text file with func statistics averaged over segs and framss # type=traitcompound|default=None: Save mean across space and time - summary_file: fileformats.medimage_freesurfer.Stats + summary_file: fileformats.vendor.freesurfer.medimage.Stats # type=file: Segmentation summary statistics table # type=file|default=: Segmentation stats summary table file callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/seg_stats_recon_all.yaml b/example-specs/interface/nipype/freesurfer/interfaces/seg_stats_recon_all.yaml index 71b4fc10..0a1e4456 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/seg_stats_recon_all.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/seg_stats_recon_all.yaml @@ -80,11 +80,11 @@ inputs: # type=file|default=: Compensate for partial voluming presurf_seg: medimage/mgh-gz # type=file|default=: Input segmentation volume - rh_orig_nofix: fileformats.medimage_freesurfer.Pial + rh_orig_nofix: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input rh.orig.nofix - rh_pial: fileformats.medimage_freesurfer.Pial + rh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/rh.pial - rh_white: fileformats.medimage_freesurfer.Pial + rh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/rh.white ribbon: medimage/mgh-gz # type=file|default=: Input file mri/ribbon.mgz @@ -119,7 +119,7 @@ outputs: sf_avg_file: generic/file # type=file: Text file with func statistics averaged over segs and framss # type=traitcompound|default=None: Save mean across space and time - summary_file: fileformats.medimage_freesurfer.Stats + summary_file: fileformats.vendor.freesurfer.medimage.Stats # type=file: Segmentation summary statistics table # type=file|default=: Segmentation stats summary table file callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/segment_cc.yaml b/example-specs/interface/nipype/freesurfer/interfaces/segment_cc.yaml index f7cf1279..706dd018 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/segment_cc.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/segment_cc.yaml @@ -65,7 +65,7 @@ outputs: out_file: generic/file # type=file: Output segmentation including corpus collosum # type=file|default=: Filename to write aseg including CC - out_rotation: fileformats.medimage_freesurfer.Lta + out_rotation: fileformats.vendor.freesurfer.medimage.Lta # type=file: Output lta rotation file # type=file|default=: Global filepath for writing rotation lta callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/smooth.yaml b/example-specs/interface/nipype/freesurfer/interfaces/smooth.yaml index 7e2d2cdf..7ce3f470 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/smooth.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/smooth.yaml @@ -41,7 +41,7 @@ inputs: # passed to the field in the automatically generated unittests. in_file: medimage/nifti1 # type=file|default=: source volume - reg_file: fileformats.medimage_freesurfer.Dat + reg_file: fileformats.vendor.freesurfer.medimage.Dat # type=file|default=: registers volume to surface anatomical subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/example-specs/interface/nipype/freesurfer/interfaces/sphere.yaml b/example-specs/interface/nipype/freesurfer/interfaces/sphere.yaml index 4fd47875..d456865d 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/sphere.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/sphere.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=: Input file for Sphere in_smoothwm: generic/file # type=file|default=: Input surface required when -q flag is not selected diff --git a/example-specs/interface/nipype/freesurfer/interfaces/spherical_average.yaml b/example-specs/interface/nipype/freesurfer/interfaces/spherical_average.yaml index 9d33d71a..91b2ac5a 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/spherical_average.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/spherical_average.yaml @@ -41,7 +41,7 @@ inputs: # passed to the field in the automatically generated unittests. in_orig: generic/file # type=file|default=: Original surface filename - in_surf: fileformats.medimage_freesurfer.Pial + in_surf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input surface file subjects_dir: generic/directory # type=directory|default=: subjects directory @@ -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_freesurfer.Out + out_file: fileformats.vendor.freesurfer.medimage.Out # type=file: Output label # type=file|default=: Output filename callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/tkregister_2.yaml b/example-specs/interface/nipype/freesurfer/interfaces/tkregister_2.yaml index 09eb8a0b..4038dcd6 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/tkregister_2.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/tkregister_2.yaml @@ -81,7 +81,7 @@ outputs: # type=file: FSL-style registration file lta_file: generic/file # type=file: LTA-style registration file - reg_file: fileformats.medimage_freesurfer.Dat + reg_file: fileformats.vendor.freesurfer.medimage.Dat # type=file: freesurfer-style registration file # type=file|default='register.dat': freesurfer-style registration file callables: diff --git a/example-specs/interface/nipype/freesurfer/interfaces/volume_mask.yaml b/example-specs/interface/nipype/freesurfer/interfaces/volume_mask.yaml index 48a4efb8..d1a59a32 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/volume_mask.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/volume_mask.yaml @@ -49,9 +49,9 @@ inputs: # type=file|default=: Implicit aseg.mgz segmentation. Specify a different aseg by using the 'in_aseg' input. in_aseg: generic/file # type=file|default=: Input aseg file for VolumeMask - lh_pial: fileformats.medimage_freesurfer.Pial + lh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input left pial surface - lh_white: fileformats.medimage_freesurfer.Pial + lh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input left white matter surface rh_pial: generic/file # type=file|default=: Implicit input right pial surface diff --git a/example-specs/interface/nipype/freesurfer/interfaces/watershed_skull_strip.yaml b/example-specs/interface/nipype/freesurfer/interfaces/watershed_skull_strip.yaml index 0d97e979..5dba26ee 100644 --- a/example-specs/interface/nipype/freesurfer/interfaces/watershed_skull_strip.yaml +++ b/example-specs/interface/nipype/freesurfer/interfaces/watershed_skull_strip.yaml @@ -49,7 +49,7 @@ inputs: # type=file|default=: input volume subjects_dir: generic/directory # type=directory|default=: subjects directory - transform: fileformats.medimage_freesurfer.Lta + transform: fileformats.vendor.freesurfer.medimage.Lta # type=file|default=: undocumented callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/example-specs/interface/nipype/fsl/interfaces/flameo.yaml b/example-specs/interface/nipype/fsl/interfaces/flameo.yaml index d651e82b..9da42ab5 100644 --- a/example-specs/interface/nipype/fsl/interfaces/flameo.yaml +++ b/example-specs/interface/nipype/fsl/interfaces/flameo.yaml @@ -53,7 +53,7 @@ inputs: # type=directory|default='stats': mask_file: generic/file # type=file|default=: mask file - t_con_file: fileformats.medimage_fsl.Con + t_con_file: fileformats.vendor.fsl.medimage.Con # type=file|default=: ascii matrix specifying t-contrasts var_cope_file: generic/file # type=file|default=: varcope weightings data file diff --git a/example-specs/interface/nipype/fsl/interfaces/melodic.yaml b/example-specs/interface/nipype/fsl/interfaces/melodic.yaml index 37627ea6..67e8db7d 100644 --- a/example-specs/interface/nipype/fsl/interfaces/melodic.yaml +++ b/example-specs/interface/nipype/fsl/interfaces/melodic.yaml @@ -54,13 +54,13 @@ inputs: # type=file|default=: file name of mask for thresholding mix: generic/file # type=file|default=: mixing matrix for mixture modelling / filtering - s_con: fileformats.medimage_fsl.Con + s_con: fileformats.vendor.fsl.medimage.Con # type=file|default=: t-contrast matrix across subject-domain s_des: generic/file # type=file|default=: design matrix across subject-domain smode: generic/file # type=file|default=: matrix of session modes for report generation - t_con: fileformats.medimage_fsl.Con + t_con: fileformats.vendor.fsl.medimage.Con # type=file|default=: t-contrast matrix across time-domain t_des: generic/file # type=file|default=: design matrix across time-domain diff --git a/example-specs/interface/nipype/fsl/interfaces/randomise.yaml b/example-specs/interface/nipype/fsl/interfaces/randomise.yaml index f1d1032f..a8064778 100644 --- a/example-specs/interface/nipype/fsl/interfaces/randomise.yaml +++ b/example-specs/interface/nipype/fsl/interfaces/randomise.yaml @@ -39,7 +39,7 @@ inputs: # type=file|default=: 4D input file mask: medimage/nifti1 # type=file|default=: mask image - tcon: fileformats.medimage_fsl.Con + tcon: fileformats.vendor.fsl.medimage.Con # type=file|default=: t contrasts file x_block_labels: generic/file # type=file|default=: exchangeability block labels file diff --git a/example-specs/pkg-gen/nipype.yaml b/example-specs/pkg-gen/nipype.yaml index fe1afe5b..1ffcab40 100644 --- a/example-specs/pkg-gen/nipype.yaml +++ b/example-specs/pkg-gen/nipype.yaml @@ -1,5 +1,5 @@ -afni: - target_version: v25_2_06 +nipype.interfaces.afni: + target_version: v25 interfaces: - nipype.interfaces.afni.model.Deconvolve - nipype.interfaces.afni.model.Remlfit @@ -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 @@ -279,11 +279,11 @@ 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 @@ -291,7 +291,7 @@ elastix: - 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 diff --git a/nipype2pydra/cli/pkg_gen.py b/nipype2pydra/cli/pkg_gen.py index fc0faba7..093a8b2c 100644 --- a/nipype2pydra/cli/pkg_gen.py +++ b/nipype2pydra/cli/pkg_gen.py @@ -308,7 +308,7 @@ def pkg_gen( for example_pkg_name in example_pkg_names: specs_dir = ( output_dir - / ("pydra-" + example_pkg_name) + / ("pydra-tasks-" + example_pkg_name) / "nipype-auto-conv" / "specs" ) diff --git a/nipype2pydra/interface/base.py b/nipype2pydra/interface/base.py index 0284c6fc..3b74740e 100644 --- a/nipype2pydra/interface/base.py +++ b/nipype2pydra/interface/base.py @@ -940,7 +940,7 @@ def create_doctests(self, input_fields, nonstd_types): if val is None and is_fileset(tp): val = f"{tp.__name__}.mock()" if val is not attrs.NOTHING: - doctest_str += f" >>> task.inputs.{nm} = {val}\n" + doctest_str += f" >>> task.{nm} = {val}\n" doctest_str += " >>> task.cmdline\n" doctest_str += f" '{doctest.cmdline}'" doctest_str += "\n\n\n" @@ -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 diff --git a/nipype2pydra/interface/shell.py b/nipype2pydra/interface/shell.py index d73524e2..5a8dc7c9 100644 --- a/nipype2pydra/interface/shell.py +++ b/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" ) diff --git a/nipype2pydra/package.py b/nipype2pydra/package.py index 7680cf15..2bab6f87 100644 --- a/nipype2pydra/package.py +++ b/nipype2pydra/package.py @@ -302,7 +302,7 @@ def nipype_module(self): @property 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\.mrtrix3.\w+\b", r"pydra.tasks.mrtrix3.v3_1"), ( r"nipype\.interfaces\.(?!base)(\w+)\b", r"pydra.tasks.\1." + self.target_version, @@ -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 @@ -1162,7 +1162,7 @@ def write_pkg_inits( from ._version import __version__ except ImportError: raise RuntimeError( - "pydra-{pkg} has not been properly installed, please run " + "pydra-tasks-{pkg} has not been properly installed, please run " f"`pip install -e {str(pkg_path)}` to install a development version" ) if "nipype" not in __version__: diff --git a/nipype2pydra/pkg_gen/__init__.py b/nipype2pydra/pkg_gen/__init__.py index 4e1a82ed..efe22bcf 100644 --- a/nipype2pydra/pkg_gen/__init__.py +++ b/nipype2pydra/pkg_gen/__init__.py @@ -611,7 +611,7 @@ def _fields_stub(cls, name, category_class, values=None): def download_tasks_template(output_path: Path): - """Downloads the latest pydra-template to the output path""" + """Downloads the latest pydra-tasks-template to the output path""" output_path.parent.mkdir(parents=True, exist_ok=True) release_url = ( diff --git a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-interface.yaml b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-interface.yaml index 47945bbb..a92f91e2 100644 --- a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-interface.yaml +++ b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-interface.yaml @@ -93,17 +93,17 @@ jobs: pushd $HOME pip install ${{ matrix.pydra }} popd - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - name: Install task package run: | pip install ${{ matrix.pip-flags }} "./related-packages/fileformats[dev]" pip install ${{ matrix.pip-flags }} "related-packages/fileformats-extras[dev]" pip install ${{ matrix.pip-flags }} ".[dev]" - python -c "import pydra.tasks.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import fileformats.medimage_CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import fileformats.extras.medimage_CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.tasks.CHANGEME.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import fileformats.vendor.CHANGEME.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import fileformats.extras.medimage_CHANGEME.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" test: needs: [nipype-conv] @@ -164,8 +164,8 @@ jobs: - name: Install task package run: | pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]" - python -c "import pydra.tasks.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.tasks.CHANGEME.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - name: Test with pytest run: >- @@ -174,7 +174,7 @@ jobs: ./related-packages/fileformats ./related-packages/fileformats-extras --cov pydra.tasks.CHANGEME - --cov fileformats.medimage_CHANGEME + --cov fileformats.vendor.CHANGEME.medimage --cov fileformats.extras.medimage_CHANGEME --cov-report xml @@ -183,7 +183,7 @@ jobs: if: ${{ always() }} with: files: coverage.xml - name: pydra-CHANGEME + name: pydra-tasks-CHANGEME deploy-fileformats: @@ -391,7 +391,7 @@ jobs: if: github.event_name == 'release' || github.event_name == 'repository_dispatch' run: >- curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json" - "https://api.github.com/repos/nipype/pydra-CHANGEME/dispatches" + "https://api.github.com/repos/nipype/pydra-tasks-CHANGEME/dispatches" -d '{ "event_type": "progress-report", "client_payload": ${{ steps.generate-report.output.progress_report }} diff --git a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-workflow.yaml b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-workflow.yaml index 06127ff0..9212e7aa 100644 --- a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-workflow.yaml +++ b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-workflow.yaml @@ -92,13 +92,13 @@ jobs: pushd $HOME pip install ${{ matrix.pydra }} popd - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - name: Install task package run: | pip install ${{ matrix.pip-flags }} ".[dev]" - python -c "import pydra.tasks.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.tasks.CHANGEME.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" test: needs: [nipype-conv] @@ -159,8 +159,8 @@ jobs: - name: Install task package run: | pip install ".[test]" - python -c "import pydra.tasks.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.tasks.CHANGEME.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import pydra.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - name: Test with pytest run: >- @@ -174,7 +174,7 @@ jobs: if: ${{ always() }} with: files: coverage.xml - name: pydra-CHANGEME + name: pydra-tasks-CHANGEME deploy: diff --git a/nipype2pydra/pkg_gen/resources/templates/init.py b/nipype2pydra/pkg_gen/resources/templates/init.py index 700486e8..dfacd572 100644 --- a/nipype2pydra/pkg_gen/resources/templates/init.py +++ b/nipype2pydra/pkg_gen/resources/templates/init.py @@ -14,7 +14,7 @@ from ._version import __version__ except ImportError: raise RuntimeError( - "pydra-CHANGEME has not been properly installed, please run " + "pydra-tasks-CHANGEME has not been properly installed, please run " f"`pip install -e {str(pkg_path)}` to install a development version" ) if "post" not in __version__: diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/README.rst b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/README.rst index 4aa206c0..1772dfc7 100644 --- a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/README.rst +++ b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/README.rst @@ -5,7 +5,7 @@ FileFormats-medimage-CHANGEME Extras :target: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml -This is a extras module for the `fileformats-medimage-CHANGEME `__ +This is a extras module for the `fileformats-vendor-CHANGEME `__ fileformats extension package, which provides additional functionality to format classes (i.e. aside from basic identification and validation), such as conversion tools, metadata parsers, sample data generators, etc... @@ -16,7 +16,7 @@ Quick Installation This extension can be installed for Python 3 using *pip*:: - $ pip3 install fileformats-medimage-CHANGEME-extras + $ pip3 install fileformats-vendor-CHANGEME-extras This will install the package, base packages, and any other dependencies required to implement the extra functionality. diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/pyproject.toml b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/pyproject.toml index fbb1237e..dffb39f4 100644 --- a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/pyproject.toml +++ b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/pyproject.toml @@ -3,13 +3,13 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-CHANGEME-extras" +name = "fileformats-vendor-CHANGEME-extras" description = "Extensions to add functionality to tool-specific *fileformats* classes" readme = "README.rst" requires-python = ">=3.8" dependencies = [ "fileformats", - "fileformats-medimage-CHANGEME", + "fileformats-vendor-CHANGEME", "pydra >= 0.23.0a" ] license = {file = "LICENSE"} @@ -58,21 +58,21 @@ converters = [ ] [project.urls] -repository = "https://github.com/nipype/pydra-CHANGEME" +repository = "https://github.com/nipype/pydra-tasks-CHANGEME" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/extras/medimage_CHANGEME/_version.py" +version-file = "fileformats/extras/vendor/CHANGEME/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/extras/medimage_CHANGEME/_version.py" +exclude = "fileformats/extras/vendor/CHANGEME/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/README.rst b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/README.rst index 1d07e924..7e06a454 100644 --- a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/README.rst +++ b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/README.rst @@ -13,7 +13,7 @@ Quick Installation This extension can be installed for Python 3 using *pip*:: - $ pip3 install fileformats-medimage-CHANGEME + $ pip3 install fileformats-vendor-CHANGEME This will install the format extensions and dependent base packages. diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml index b070d1f8..dc43f744 100644 --- a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml +++ b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-CHANGEME" +name = "fileformats-vendor-CHANGEME" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-CHANGEME" +repository = "https://github.com/nipype/pydra-tasks-CHANGEME" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_CHANGEME/_version.py" +version-file = "fileformats/vendor/CHANGEME/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_CHANGEME/_version.py" +exclude = "fileformats/vendor/CHANGEME/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/nipype2pydra/statements/imports.py b/nipype2pydra/statements/imports.py index 208c5e75..92f682af 100644 --- a/nipype2pydra/statements/imports.py +++ b/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 [] diff --git a/nipype2pydra/tests/test_package.py b/nipype2pydra/tests/test_package.py index fbbebbbd..89a4f689 100644 --- a/nipype2pydra/tests/test_package.py +++ b/nipype2pydra/tests/test_package.py @@ -12,23 +12,23 @@ "niworkflows": [ "bids", "templateflow", - "pydra-ants", - "pydra-afni", + "pydra-tasks-ants", + "pydra-tasks-afni", ], "mriqc": [ "nipype2pydra", - "pydra-ants", - "pydra-afni", - "pydra-fsl", - "pydra-mrtrix3 >=3.0.3a0", - "fileformats-medimage-afni-extras", - "fileformats-medimage-mrtrix3-extras", - "fileformats-medimage-fsl-extras", + "pydra-tasks-ants", + "pydra-tasks-afni", + "pydra-tasks-fsl", + "pydra-tasks-mrtrix3 >=3.1.0a1", + "fileformats-vendor-afni-extras", + "fileformats-vendor-mrtrix3-extras", + "fileformats-vendor-fsl-extras", "statsmodels", "dipy", "bids", - "pydra-niworkflows", - "pydra-nireports", + "pydra-tasks-niworkflows", + "pydra-tasks-nireports", "matplotlib", "seaborn", "templateflow", @@ -67,7 +67,7 @@ def test_package_complete(package_spec, cli_runner, tmp_path, tasks_template_arg + tasks_template_args, ) assert result.exit_code == 0, show_cli_trace(result) - pkg_root = repo_output / f"pydra-{pkg_name}" + pkg_root = repo_output / f"pydra-tasks-{pkg_name}" assert pkg_root.exists() pyproject_fspath = pkg_root / "pyproject.toml" @@ -104,10 +104,10 @@ def test_package_complete(package_spec, cli_runner, tmp_path, tasks_template_arg pip_output = pip_output.decode("utf-8") assert ( not p.returncode - ), f"Failed to install package pydra-{pkg_name} with command:\n{' '.join(pip_cmd)}:\n\n{pip_output}" + ), f"Failed to install package pydra-tasks-{pkg_name} with command:\n{' '.join(pip_cmd)}:\n\n{pip_output}" p = sp.Popen([venv_pytest, str(pkg_root)], stderr=sp.PIPE, stdout=sp.STDOUT) pytest_output, _ = p.communicate() pytest_output = pytest_output.decode("utf-8") assert ( p.returncode - ), f"Tests for pydra-{pkg_name} package (\n{' '.join(pip_cmd)}) failed:\n\n{pytest_output}" + ), f"Tests for pydra-tasks-{pkg_name} package (\n{' '.join(pip_cmd)}) failed:\n\n{pytest_output}" diff --git a/nipype2pydra/workflow.py b/nipype2pydra/workflow.py index fff775e5..02791b32 100644 --- a/nipype2pydra/workflow.py +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index 36078141..b89d49df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "fileformats-medimage-extras", - "fileformats-medimage-afni", + "fileformats-vendor-afni", "niworkflows", # "mriqc", "nipy", diff --git a/required-fileformats/afni/pyproject.toml b/required-fileformats/afni/pyproject.toml index 7030aee2..371c04cd 100644 --- a/required-fileformats/afni/pyproject.toml +++ b/required-fileformats/afni/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-afni" +name = "fileformats-vendor-afni" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-afni" +repository = "https://github.com/nipype/pydra-tasks-afni" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_afni/_version.py" +version-file = "fileformats/vendor/afni/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_afni/_version.py" +exclude = "fileformats/vendor/afni/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/ants/pyproject.toml b/required-fileformats/ants/pyproject.toml index e75b3e6a..5ca043ad 100644 --- a/required-fileformats/ants/pyproject.toml +++ b/required-fileformats/ants/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-ants" +name = "fileformats-vendor-ants" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-ants-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-ants" +repository = "https://github.com/nipype/pydra-tasks-ants" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_ants/_version.py" +version-file = "fileformats/vendor/ants/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_ants/_version.py" +exclude = "fileformats/vendor/ants/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/brainsuite/pyproject.toml b/required-fileformats/brainsuite/pyproject.toml index 85d5c2a2..61380c62 100644 --- a/required-fileformats/brainsuite/pyproject.toml +++ b/required-fileformats/brainsuite/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-brainsuite" +name = "fileformats-vendor-brainsuite" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-brainsuite" +repository = "https://github.com/nipype/pydra-tasks-brainsuite" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_brainsuite/_version.py" +version-file = "fileformats/vendor/brainsuite/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_brainsuite/_version.py" +exclude = "fileformats/vendor/brainsuite/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/bru2nii/pyproject.toml b/required-fileformats/bru2nii/pyproject.toml index 1cfa63d8..237f3226 100644 --- a/required-fileformats/bru2nii/pyproject.toml +++ b/required-fileformats/bru2nii/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-bru2nii" +name = "fileformats-vendor-bru2nii" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-bru2nii" +repository = "https://github.com/nipype/pydra-tasks-bru2nii" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_bru2nii/_version.py" +version-file = "fileformats/vendor/bru2nii/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_bru2nii/_version.py" +exclude = "fileformats/vendor/bru2nii/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/c3/pyproject.toml b/required-fileformats/c3/pyproject.toml index f1dd6bca..687f8287 100644 --- a/required-fileformats/c3/pyproject.toml +++ b/required-fileformats/c3/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-c3" +name = "fileformats-vendor-c3" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-c3" +repository = "https://github.com/nipype/pydra-tasks-c3" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_c3/_version.py" +version-file = "fileformats/vendor/c3/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_c3/_version.py" +exclude = "fileformats/vendor/c3/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/camino/pyproject.toml b/required-fileformats/camino/pyproject.toml index 970e6b9a..0c349a87 100644 --- a/required-fileformats/camino/pyproject.toml +++ b/required-fileformats/camino/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-camino" +name = "fileformats-vendor-camino" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-camino" +repository = "https://github.com/nipype/pydra-tasks-camino" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_camino/_version.py" +version-file = "fileformats/vendor/camino/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_camino/_version.py" +exclude = "fileformats/vendor/camino/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/camino2trackvis/pyproject.toml b/required-fileformats/camino2trackvis/pyproject.toml index 76fbac2d..aa4840cd 100644 --- a/required-fileformats/camino2trackvis/pyproject.toml +++ b/required-fileformats/camino2trackvis/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-camino2trackvis" +name = "fileformats-vendor-camino2trackvis" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-camino2trackvis" +repository = "https://github.com/nipype/pydra-tasks-camino2trackvis" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_camino2trackvis/_version.py" +version-file = "fileformats/vendor/camino2trackvis/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_camino2trackvis/_version.py" +exclude = "fileformats/vendor/camino2trackvis/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/cat12/pyproject.toml b/required-fileformats/cat12/pyproject.toml index 93cc7e66..4eb081b5 100644 --- a/required-fileformats/cat12/pyproject.toml +++ b/required-fileformats/cat12/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-cat12" +name = "fileformats-vendor-cat12" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-cat12" +repository = "https://github.com/nipype/pydra-tasks-cat12" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_cat12/_version.py" +version-file = "fileformats/vendor/cat12/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_cat12/_version.py" +exclude = "fileformats/vendor/cat12/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/cmtk/pyproject.toml b/required-fileformats/cmtk/pyproject.toml index c9509df2..26a337a2 100644 --- a/required-fileformats/cmtk/pyproject.toml +++ b/required-fileformats/cmtk/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-cmtk" +name = "fileformats-vendor-cmtk" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-cmtk" +repository = "https://github.com/nipype/pydra-tasks-cmtk" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_cmtk/_version.py" +version-file = "fileformats/vendor/cmtk/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_cmtk/_version.py" +exclude = "fileformats/vendor/cmtk/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/dcmstack/pyproject.toml b/required-fileformats/dcmstack/pyproject.toml index 7ace73b7..e302fbef 100644 --- a/required-fileformats/dcmstack/pyproject.toml +++ b/required-fileformats/dcmstack/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-dcmstack" +name = "fileformats-vendor-dcmstack" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-dcmstack" +repository = "https://github.com/nipype/pydra-tasks-dcmstack" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_dcmstack/_version.py" +version-file = "fileformats/vendor/dcmstack/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_dcmstack/_version.py" +exclude = "fileformats/vendor/dcmstack/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/diffusion_toolkit/pyproject.toml b/required-fileformats/diffusion_toolkit/pyproject.toml index 1422da4c..45ada639 100644 --- a/required-fileformats/diffusion_toolkit/pyproject.toml +++ b/required-fileformats/diffusion_toolkit/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-diffusion_toolkit" +name = "fileformats-vendor-diffusion_toolkit" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-diffusion_toolkit" +repository = "https://github.com/nipype/pydra-tasks-diffusion_toolkit" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_diffusion_toolkit/_version.py" +version-file = "fileformats/vendor/diffusion_toolkit/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_diffusion_toolkit/_version.py" +exclude = "fileformats/vendor/diffusion_toolkit/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/dipy/pyproject.toml b/required-fileformats/dipy/pyproject.toml index f4415d7c..65686016 100644 --- a/required-fileformats/dipy/pyproject.toml +++ b/required-fileformats/dipy/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-dipy" +name = "fileformats-vendor-dipy" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-dipy" +repository = "https://github.com/nipype/pydra-tasks-dipy" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_dipy/_version.py" +version-file = "fileformats/vendor/dipy/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_dipy/_version.py" +exclude = "fileformats/vendor/dipy/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/dtitk/pyproject.toml b/required-fileformats/dtitk/pyproject.toml index 3748ff18..d12984a7 100644 --- a/required-fileformats/dtitk/pyproject.toml +++ b/required-fileformats/dtitk/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-dtitk" +name = "fileformats-vendor-dtitk" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-dtitk" +repository = "https://github.com/nipype/pydra-tasks-dtitk" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_dtitk/_version.py" +version-file = "fileformats/vendor/dtitk/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_dtitk/_version.py" +exclude = "fileformats/vendor/dtitk/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/dynamic_slicer/pyproject.toml b/required-fileformats/dynamic_slicer/pyproject.toml index f070ca42..733a6baf 100644 --- a/required-fileformats/dynamic_slicer/pyproject.toml +++ b/required-fileformats/dynamic_slicer/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-dynamic_slicer" +name = "fileformats-vendor-dynamic_slicer" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-dynamic_slicer" +repository = "https://github.com/nipype/pydra-tasks-dynamic_slicer" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_dynamic_slicer/_version.py" +version-file = "fileformats/vendor/dynamic_slicer/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_dynamic_slicer/_version.py" +exclude = "fileformats/vendor/dynamic_slicer/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/elastix/pyproject.toml b/required-fileformats/elastix/pyproject.toml index bcd3bf2d..71830ef6 100644 --- a/required-fileformats/elastix/pyproject.toml +++ b/required-fileformats/elastix/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-elastix" +name = "fileformats-vendor-elastix" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-elastix" +repository = "https://github.com/nipype/pydra-tasks-elastix" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_elastix/_version.py" +version-file = "fileformats/vendor/elastix/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_elastix/_version.py" +exclude = "fileformats/vendor/elastix/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/freesurfer/pyproject.toml b/required-fileformats/freesurfer/pyproject.toml index 6e30941e..c5bc7766 100644 --- a/required-fileformats/freesurfer/pyproject.toml +++ b/required-fileformats/freesurfer/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-freesurfer" +name = "fileformats-vendor-freesurfer" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-freesurfer" +repository = "https://github.com/nipype/pydra-tasks-freesurfer" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_freesurfer/_version.py" +version-file = "fileformats/vendor/freesurfer/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_freesurfer/_version.py" +exclude = "fileformats/vendor/freesurfer/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/fsl/pyproject.toml b/required-fileformats/fsl/pyproject.toml index f0b3af08..0c19d94d 100644 --- a/required-fileformats/fsl/pyproject.toml +++ b/required-fileformats/fsl/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-fsl" +name = "fileformats-vendor-fsl" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-fsl" +repository = "https://github.com/nipype/pydra-tasks-fsl" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_fsl/_version.py" +version-file = "fileformats/vendor/fsl/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_fsl/_version.py" +exclude = "fileformats/vendor/fsl/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/meshfix/pyproject.toml b/required-fileformats/meshfix/pyproject.toml index 0d748ac1..d80c3de3 100644 --- a/required-fileformats/meshfix/pyproject.toml +++ b/required-fileformats/meshfix/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-meshfix" +name = "fileformats-vendor-meshfix" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-meshfix" +repository = "https://github.com/nipype/pydra-tasks-meshfix" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_meshfix/_version.py" +version-file = "fileformats/vendor/meshfix/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_meshfix/_version.py" +exclude = "fileformats/vendor/meshfix/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/minc/pyproject.toml b/required-fileformats/minc/pyproject.toml index f2d8e35e..f2e38742 100644 --- a/required-fileformats/minc/pyproject.toml +++ b/required-fileformats/minc/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-minc" +name = "fileformats-vendor-minc" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-minc" +repository = "https://github.com/nipype/pydra-tasks-minc" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_minc/_version.py" +version-file = "fileformats/vendor/minc/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_minc/_version.py" +exclude = "fileformats/vendor/minc/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/mipav/pyproject.toml b/required-fileformats/mipav/pyproject.toml index 5af708db..e2e9419c 100644 --- a/required-fileformats/mipav/pyproject.toml +++ b/required-fileformats/mipav/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-mipav" +name = "fileformats-vendor-mipav" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-mipav" +repository = "https://github.com/nipype/pydra-tasks-mipav" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_mipav/_version.py" +version-file = "fileformats/vendor/mipav/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_mipav/_version.py" +exclude = "fileformats/vendor/mipav/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/niftyfit/pyproject.toml b/required-fileformats/niftyfit/pyproject.toml index 049bb251..036bdc31 100644 --- a/required-fileformats/niftyfit/pyproject.toml +++ b/required-fileformats/niftyfit/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-niftyfit" +name = "fileformats-vendor-niftyfit" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-niftyfit" +repository = "https://github.com/nipype/pydra-tasks-niftyfit" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_niftyfit/_version.py" +version-file = "fileformats/vendor/niftyfit/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_niftyfit/_version.py" +exclude = "fileformats/vendor/niftyfit/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/niftyreg/pyproject.toml b/required-fileformats/niftyreg/pyproject.toml index 1ffe69c8..aa7aac95 100644 --- a/required-fileformats/niftyreg/pyproject.toml +++ b/required-fileformats/niftyreg/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-niftyreg" +name = "fileformats-vendor-niftyreg" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-niftyreg" +repository = "https://github.com/nipype/pydra-tasks-niftyreg" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_niftyreg/_version.py" +version-file = "fileformats/vendor/niftyreg/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_niftyreg/_version.py" +exclude = "fileformats/vendor/niftyreg/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/niftyseg/pyproject.toml b/required-fileformats/niftyseg/pyproject.toml index 7c9caafc..92d3bc34 100644 --- a/required-fileformats/niftyseg/pyproject.toml +++ b/required-fileformats/niftyseg/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-niftyseg" +name = "fileformats-vendor-niftyseg" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-niftyseg" +repository = "https://github.com/nipype/pydra-tasks-niftyseg" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_niftyseg/_version.py" +version-file = "fileformats/vendor/niftyseg/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_niftyseg/_version.py" +exclude = "fileformats/vendor/niftyseg/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/nilearn/pyproject.toml b/required-fileformats/nilearn/pyproject.toml index 2e86d5f3..433c6998 100644 --- a/required-fileformats/nilearn/pyproject.toml +++ b/required-fileformats/nilearn/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-nilearn" +name = "fileformats-vendor-nilearn" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-nilearn" +repository = "https://github.com/nipype/pydra-tasks-nilearn" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_nilearn/_version.py" +version-file = "fileformats/vendor/nilearn/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_nilearn/_version.py" +exclude = "fileformats/vendor/nilearn/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/nitime/pyproject.toml b/required-fileformats/nitime/pyproject.toml index bf9a3ffa..92a00133 100644 --- a/required-fileformats/nitime/pyproject.toml +++ b/required-fileformats/nitime/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-nitime" +name = "fileformats-vendor-nitime" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-nitime" +repository = "https://github.com/nipype/pydra-tasks-nitime" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_nitime/_version.py" +version-file = "fileformats/vendor/nitime/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_nitime/_version.py" +exclude = "fileformats/vendor/nitime/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/petpvc/pyproject.toml b/required-fileformats/petpvc/pyproject.toml index 8a549cee..a478e37c 100644 --- a/required-fileformats/petpvc/pyproject.toml +++ b/required-fileformats/petpvc/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-petpvc" +name = "fileformats-vendor-petpvc" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-petpvc" +repository = "https://github.com/nipype/pydra-tasks-petpvc" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_petpvc/_version.py" +version-file = "fileformats/vendor/petpvc/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_petpvc/_version.py" +exclude = "fileformats/vendor/petpvc/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/quickshear/pyproject.toml b/required-fileformats/quickshear/pyproject.toml index 2efe1956..9e5dc362 100644 --- a/required-fileformats/quickshear/pyproject.toml +++ b/required-fileformats/quickshear/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-quickshear" +name = "fileformats-vendor-quickshear" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-quickshear" +repository = "https://github.com/nipype/pydra-tasks-quickshear" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_quickshear/_version.py" +version-file = "fileformats/vendor/quickshear/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_quickshear/_version.py" +exclude = "fileformats/vendor/quickshear/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/robex/pyproject.toml b/required-fileformats/robex/pyproject.toml index 8e26dff6..74ffd8fe 100644 --- a/required-fileformats/robex/pyproject.toml +++ b/required-fileformats/robex/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-robex" +name = "fileformats-vendor-robex" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-robex" +repository = "https://github.com/nipype/pydra-tasks-robex" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_robex/_version.py" +version-file = "fileformats/vendor/robex/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_robex/_version.py" +exclude = "fileformats/vendor/robex/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/semtools/pyproject.toml b/required-fileformats/semtools/pyproject.toml index f1352036..645ed572 100644 --- a/required-fileformats/semtools/pyproject.toml +++ b/required-fileformats/semtools/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-semtools" +name = "fileformats-vendor-semtools" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-semtools" +repository = "https://github.com/nipype/pydra-tasks-semtools" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_semtools/_version.py" +version-file = "fileformats/vendor/semtools/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_semtools/_version.py" +exclude = "fileformats/vendor/semtools/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/slicer/pyproject.toml b/required-fileformats/slicer/pyproject.toml index 87c95a8a..026e70c1 100644 --- a/required-fileformats/slicer/pyproject.toml +++ b/required-fileformats/slicer/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-slicer" +name = "fileformats-vendor-slicer" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-slicer" +repository = "https://github.com/nipype/pydra-tasks-slicer" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_slicer/_version.py" +version-file = "fileformats/vendor/slicer/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_slicer/_version.py" +exclude = "fileformats/vendor/slicer/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/spm/pyproject.toml b/required-fileformats/spm/pyproject.toml index cb29880b..fa75e58b 100644 --- a/required-fileformats/spm/pyproject.toml +++ b/required-fileformats/spm/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-spm" +name = "fileformats-vendor-spm" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-spm" +repository = "https://github.com/nipype/pydra-tasks-spm" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_spm/_version.py" +version-file = "fileformats/vendor/spm/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_spm/_version.py" +exclude = "fileformats/vendor/spm/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/vista/pyproject.toml b/required-fileformats/vista/pyproject.toml index 4e3bc882..e506fa36 100644 --- a/required-fileformats/vista/pyproject.toml +++ b/required-fileformats/vista/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-vista" +name = "fileformats-vendor-vista" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-vista" +repository = "https://github.com/nipype/pydra-tasks-vista" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_vista/_version.py" +version-file = "fileformats/vendor/vista/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_vista/_version.py" +exclude = "fileformats/vendor/vista/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/required-fileformats/workbench/pyproject.toml b/required-fileformats/workbench/pyproject.toml index 1c446a5e..b3c182ea 100644 --- a/required-fileformats/workbench/pyproject.toml +++ b/required-fileformats/workbench/pyproject.toml @@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-workbench" +name = "fileformats-vendor-workbench" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" requires-python = ">=3.8" @@ -51,25 +51,25 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-CHANGME-extras", + "fileformats-vendor-CHANGEME-extras", ] [project.urls] -repository = "https://github.com/nipype/pydra-workbench" +repository = "https://github.com/nipype/pydra-tasks-workbench" [tool.hatch.version] source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_workbench/_version.py" +version-file = "fileformats/vendor/workbench/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_workbench/_version.py" +exclude = "fileformats/vendor/workbench/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords"