Merge pull request #21 from nipype/pydra-tasks-rename

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

Author: tclose

.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