Merge pull request #15 from nipype/formatter-fixes

manually fixed nipype2pydra converter issue where formatters are assigned as strings

Author: tclose

.github/workflows/auto-release.yaml

@@ -33,4 +33,4 @@ jobs:
               "draft": false,
               "prerelease": false
             }' \
-            "https://api.github.com/repos/nipype/pydra-#PACKAGE#/releases"
+            "https://api.github.com/repos/nipype/pydra-tasks-#PACKAGE#/releases"

.github/workflows/ci-cd.yaml

@@ -129,10 +129,10 @@ jobs:
     - name: Install task package
       run: |
         pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
-        python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import fileformats.vendor.afni.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test fileformats with pytest
       run: >-
-        pytest ./related-packages -sv --cov fileformats.medimage_afni
+        pytest ./related-packages -sv --cov fileformats.vendor.afni.medimage
         --cov fileformats.extras.medimage_afni --cov-report xml .
 
   deploy-fileformats:

docs/conf.py

@@ -17,7 +17,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "pydra-afni"
+project = "pydra-tasks-afni"
 copyright = "2020, Xihe Xie"
 author = "Xihe Xie"
 

nipype-auto-conv/requirements.txt

@@ -6,6 +6,6 @@ PyYAML>=6.0
 fileformats >=0.8
 fileformats-medimage >=0.4
 fileformats-datascience >= 0.1
-fileformats-medimage-afni
+fileformats-vendor-afni
 traits
 nipype2pydra

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

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

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

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

nipype-auto-conv/specs/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:

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

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

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

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

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

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