renamed references to pydra-* to pydra-tasks-*

.github/workflows/ci-cd.yaml

@@ -129,11 +129,11 @@ jobs:
     - name: Install task package
       run: |
         pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
-        python -c "import fileformats.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import fileformats.vendor.freesurfer.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test fileformats with pytest
       run: >-
-        pytest ./related-packages -sv --cov fileformats.medimage_freesurfer
-        --cov fileformats.extras.medimage_freesurfer --cov-report xml .
+        pytest ./related-packages -sv --cov fileformats.vendor.freesurfer.medimage
+        --cov fileformats.extras.vendor.freesurfer.medimage --cov-report xml .
 
   deploy-fileformats:
     needs: [build, test, fileformats-test]

.gitignore

@@ -156,6 +156,6 @@ cython_debug/
 
 # Generated files
 /pydra/tasks/freesurfer/_version.py
-/related-packages/fileformats/fileformats/medimage_freesurfer/_version.py
-/related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/_version.py
+/related-packages/fileformats/fileformats/vendor/freesurfer/_version.py
+/related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/_version.py
 /pydra/tasks/freesurfer/auto

docs/source/conf.py

@@ -8,7 +8,7 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "pydra-freesurfer"
+project = "pydra-tasks-freesurfer"
 author = "Pydra Developers"
 copyright = f"2022-2023, {author}"
 release = __version__

nipype-auto-conv/specs/interfaces/aparc_2_aseg.yaml

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

nipype-auto-conv/specs/interfaces/concatenate_lta.yaml

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

nipype-auto-conv/specs/interfaces/contrast.yaml

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

nipype-auto-conv/specs/interfaces/curvature.yaml

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

nipype-auto-conv/specs/interfaces/curvature_stats.yaml

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

nipype-auto-conv/specs/interfaces/em_register.yaml

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

nipype-auto-conv/specs/interfaces/euler_number.yaml

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

nipype-auto-conv/specs/interfaces/extract_main_component.yaml

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

nipype-auto-conv/specs/interfaces/fix_topology.yaml

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

nipype-auto-conv/specs/interfaces/gtmpvc.yaml

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

nipype-auto-conv/specs/interfaces/jacobian.yaml

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

nipype-auto-conv/specs/interfaces/label_2_label.yaml

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

nipype-auto-conv/specs/interfaces/label_2_vol.yaml

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

nipype-auto-conv/specs/interfaces/make_surfaces.yaml

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

nipype-auto-conv/specs/interfaces/mr_is_ca_label.yaml

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

nipype-auto-conv/specs/interfaces/mr_is_calc.yaml

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

nipype-auto-conv/specs/interfaces/mr_is_expand.yaml

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

nipype-auto-conv/specs/interfaces/mr_is_inflate.yaml

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

nipype-auto-conv/specs/interfaces/paint.yaml

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

nipype-auto-conv/specs/interfaces/parcellation_stats.yaml

@@ -61,9 +61,9 @@ inputs:
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/lh.pial
     lh_white: generic/file
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/lh.white
-    rh_pial: fileformats.medimage_freesurfer.Pial
+    rh_pial: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/rh.pial
-    rh_white: fileformats.medimage_freesurfer.White
+    rh_white: fileformats.vendor.freesurfer.medimage.White
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/rh.white
     ribbon: medimage/mgh-gz
     # type=file|default=<undefined>: Input file must be <subject_id>/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=<undefined>: Output annotation files's colortable to text file
     out_table: generic/file

nipype-auto-conv/specs/interfaces/register.yaml

@@ -36,9 +36,9 @@ inputs:
   # passed to the field in the automatically generated unittests.
     in_smoothwm: generic/file
     # type=file|default=<undefined>: Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm 
-    in_sulc: fileformats.medimage_freesurfer.Pial
+    in_sulc: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: 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=<undefined>: Surface to register, often {hemi}.sphere
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: 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=<undefined>: Output surface file to capture registration
   callables:

nipype-auto-conv/specs/interfaces/relabel_hypointensities.yaml

@@ -35,7 +35,7 @@ inputs:
   # passed to the field in the automatically generated unittests.
     aseg: generic/file
     # type=file|default=<undefined>: Input aseg file
-    lh_white: fileformats.medimage_freesurfer.Pial
+    lh_white: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Implicit input file must be lh.white
     rh_white: generic/file
     # type=file|default=<undefined>: Implicit input file must be rh.white

nipype-auto-conv/specs/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=<undefined>: Input file for RemoveIntersection
     subjects_dir: generic/directory
     # type=directory|default=<undefined>: subjects directory

nipype-auto-conv/specs/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=<undefined>: Segmentation stats summary table file
   callables:

nipype-auto-conv/specs/interfaces/seg_stats_recon_all.yaml

@@ -80,11 +80,11 @@ inputs:
     # type=file|default=<undefined>: Compensate for partial voluming
     presurf_seg: medimage/mgh-gz
     # type=file|default=<undefined>: Input segmentation volume
-    rh_orig_nofix: fileformats.medimage_freesurfer.Pial
+    rh_orig_nofix: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input rh.orig.nofix
-    rh_pial: fileformats.medimage_freesurfer.Pial
+    rh_pial: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/rh.pial
-    rh_white: fileformats.medimage_freesurfer.Pial
+    rh_white: fileformats.vendor.freesurfer.medimage.Pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/rh.white
     ribbon: medimage/mgh-gz
     # type=file|default=<undefined>: 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=<undefined>: Segmentation stats summary table file
   callables: