updated threed, oned formats to three-d, one-d

Author: tclose

nipype-auto-conv/specs/afn_ito_nifti.yaml

@@ -7,10 +7,10 @@
 # ----
 # Converts AFNI format files to NIFTI format. This can also convert 2D or
 #     1D data, which you can numpy.squeeze() to remove extra dimensions.
-# 
+#
 #     For complete details, see the `3dAFNItoNIFTI Documentation.
 #     <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dAFNItoNIFTI.html>`_
-# 
+#
 #     Examples
 #     --------
 #     >>> from nipype.interfaces import afni
@@ -20,8 +20,8 @@
 #     >>> a2n.cmdline
 #     '3dAFNItoNIFTI -prefix afni_output.nii afni_output.3D'
 #     >>> res = a2n.run()  # doctest: +SKIP
-# 
-#     
+#
+#
 task_name: AFNItoNIFTI
 nipype_name: AFNItoNIFTI
 nipype_module: nipype.interfaces.afni.utils
@@ -31,12 +31,12 @@ inputs:
   rename:
   # dict[str, str] - fields to rename in the Pydra interface
   types:
-  # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
-  # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
-  # 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: medimage-afni/threed
+    # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
+    # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
+    # 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: medimage-afni/three-d
     # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
     out_file: Path
     # type=file: output file
@@ -52,11 +52,11 @@ outputs:
   rename:
   # dict[str, str] - fields to rename in the Pydra interface
   types:
-  # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
-  # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
-  # 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.
+    # dict[str, type] - override inferred types (use "mime-like" string for file-format types,
+    # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred
+    # 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: medimage/nifti1
     # type=file: output file
     # type=file|default=<undefined>: output image file name
@@ -68,82 +68,82 @@ outputs:
   requirements:
   # dict[str, list[str]] - input fields that are required to be provided for the output field to be present
 tests:
-- inputs:
-  # dict[str, str] - values to provide to inputs fields in the task initialisation
-  # (if not specified, will try to choose a sensible value)
-    in_file:
-    # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
-    out_file:
-    # type=file: output file
-    # type=file|default=<undefined>: output image file name
-    pure:
-    # type=bool|default=False: Do NOT write an AFNI extension field into the output file. Only use this option if needed. You can also use the 'nifti_tool' program to strip extensions from a file.
-    denote:
-    # type=bool|default=False: When writing the AFNI extension field, remove text notes that might contain subject identifying information.
-    oldid:
-    # type=bool|default=False: Give the new dataset the input datasets AFNI ID code.
-    newid:
-    # type=bool|default=False: Give the new dataset a new AFNI ID code, to distinguish it from the input dataset.
-    num_threads:
-    # type=int|default=1: set number of threads
-    outputtype:
-    # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype
-    args:
-    # type=str|default='': Additional parameters to the command
-    environ:
-    # type=dict|default={}: Environment variables
-  imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
-  # consisting of 'module', 'name', and optionally 'alias' keys
-  expected_outputs:
-  # dict[str, str] - expected values for selected outputs, noting that tests will typically
-  # be terminated before they complete for time-saving reasons, and therefore
-  # these values will be ignored, when running in CI
-  timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
-  # successfully. Set to 0 to disable the timeout (warning, this could
-  # lead to the unittests taking a very long time to complete)
-  xfail: true
-  # bool - whether the unittest is expected to fail or not. Set to false
-  # when you are satisfied with the edits you have made to this file
-- inputs:
-  # dict[str, str] - values to provide to inputs fields in the task initialisation
-  # (if not specified, will try to choose a sensible value)
-    in_file:
-    # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
-    out_file: ' "afni_output.nii"'
-    # type=file: output file
-    # type=file|default=<undefined>: output image file name
-  imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
-  # consisting of 'module', 'name', and optionally 'alias' keys
-  expected_outputs:
-  # dict[str, str] - expected values for selected outputs, noting that tests will typically
-  # be terminated before they complete for time-saving reasons, and therefore
-  # these values will be ignored, when running in CI
-  timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
-  # successfully. Set to 0 to disable the timeout (warning, this could
-  # lead to the unittests taking a very long time to complete)
-  xfail: true
-  # bool - whether the unittest is expected to fail or not. Set to false
-  # when you are satisfied with the edits you have made to this file
+  - inputs:
+      # dict[str, str] - values to provide to inputs fields in the task initialisation
+      # (if not specified, will try to choose a sensible value)
+      in_file:
+      # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
+      out_file:
+      # type=file: output file
+      # type=file|default=<undefined>: output image file name
+      pure:
+      # type=bool|default=False: Do NOT write an AFNI extension field into the output file. Only use this option if needed. You can also use the 'nifti_tool' program to strip extensions from a file.
+      denote:
+      # type=bool|default=False: When writing the AFNI extension field, remove text notes that might contain subject identifying information.
+      oldid:
+      # type=bool|default=False: Give the new dataset the input datasets AFNI ID code.
+      newid:
+      # type=bool|default=False: Give the new dataset a new AFNI ID code, to distinguish it from the input dataset.
+      num_threads:
+      # type=int|default=1: set number of threads
+      outputtype:
+      # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype
+      args:
+      # type=str|default='': Additional parameters to the command
+      environ:
+      # type=dict|default={}: Environment variables
+    imports:
+    # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+    # consisting of 'module', 'name', and optionally 'alias' keys
+    expected_outputs:
+    # dict[str, str] - expected values for selected outputs, noting that tests will typically
+    # be terminated before they complete for time-saving reasons, and therefore
+    # these values will be ignored, when running in CI
+    timeout: 10
+    # int - the value to set for the timeout in the generated test,
+    # after which the test will be considered to have been initialised
+    # successfully. Set to 0 to disable the timeout (warning, this could
+    # lead to the unittests taking a very long time to complete)
+    xfail: true
+    # bool - whether the unittest is expected to fail or not. Set to false
+    # when you are satisfied with the edits you have made to this file
+  - inputs:
+      # dict[str, str] - values to provide to inputs fields in the task initialisation
+      # (if not specified, will try to choose a sensible value)
+      in_file:
+      # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
+      out_file: ' "afni_output.nii"'
+      # type=file: output file
+      # type=file|default=<undefined>: output image file name
+    imports:
+    # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+    # consisting of 'module', 'name', and optionally 'alias' keys
+    expected_outputs:
+    # dict[str, str] - expected values for selected outputs, noting that tests will typically
+    # be terminated before they complete for time-saving reasons, and therefore
+    # these values will be ignored, when running in CI
+    timeout: 10
+    # int - the value to set for the timeout in the generated test,
+    # after which the test will be considered to have been initialised
+    # successfully. Set to 0 to disable the timeout (warning, this could
+    # lead to the unittests taking a very long time to complete)
+    xfail: true
+    # bool - whether the unittest is expected to fail or not. Set to false
+    # when you are satisfied with the edits you have made to this file
 doctests:
-- cmdline: 3dAFNItoNIFTI -prefix afni_output.nii afni_output.3D
-  # str - the expected cmdline output
-  inputs:
-  # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
-  # If the field is of file-format type and the value is None, then the
-  # '.mock()' method of the corresponding class is used instead.
-    in_file:
-    # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
-    out_file: ' "afni_output.nii"'
-    # type=file: output file
-    # type=file|default=<undefined>: output image file name
-  imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
-  # consisting of 'module', 'name', and optionally 'alias' keys
-  directive:
-  # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS
+  - cmdline: 3dAFNItoNIFTI -prefix afni_output.nii afni_output.3D
+    # str - the expected cmdline output
+    inputs:
+      # dict[str, str] - name-value pairs for inputs to be provided to the doctest.
+      # If the field is of file-format type and the value is None, then the
+      # '.mock()' method of the corresponding class is used instead.
+      in_file:
+      # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
+      out_file: ' "afni_output.nii"'
+      # type=file: output file
+      # type=file|default=<undefined>: output image file name
+    imports:
+    # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+    # consisting of 'module', 'name', and optionally 'alias' keys
+    directive:
+    # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS