debugging running tests

example-specs/interface/nipype/afni/a_boverlap.yaml

@@ -6,23 +6,23 @@
 # Docs
 # ----
 # Output (to screen) is a count of various things about how
-#     the automasks of datasets A and B overlap or don't overlap.
+# the automasks of datasets A and B overlap or don't overlap.
 # 
-#     For complete details, see the `3dABoverlap Documentation.
-#     <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dABoverlap.html>`_
+# For complete details, see the `3dABoverlap Documentation.
+# <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dABoverlap.html>`_
+# 
+# Examples
+# --------
+# >>> from nipype.interfaces import afni
+# >>> aboverlap = afni.ABoverlap()
+# >>> aboverlap.inputs.in_file_a = 'functional.nii'
+# >>> aboverlap.inputs.in_file_b = 'structural.nii'
+# >>> aboverlap.inputs.out_file =  'out.mask_ae_overlap.txt'
+# >>> aboverlap.cmdline
+# '3dABoverlap functional.nii structural.nii  |& tee out.mask_ae_overlap.txt'
+# >>> res = aboverlap.run()  # doctest: +SKIP
 # 
-#     Examples
-#     --------
-#     >>> from nipype.interfaces import afni
-#     >>> aboverlap = afni.ABoverlap()
-#     >>> aboverlap.inputs.in_file_a = 'functional.nii'
-#     >>> aboverlap.inputs.in_file_b = 'structural.nii'
-#     >>> aboverlap.inputs.out_file =  'out.mask_ae_overlap.txt'
-#     >>> aboverlap.cmdline
-#     '3dABoverlap functional.nii structural.nii  |& tee out.mask_ae_overlap.txt'
-#     >>> res = aboverlap.run()  # doctest: +SKIP
 # 
-#     
 task_name: ABoverlap
 nipype_name: ABoverlap
 nipype_module: nipype.interfaces.afni.utils
@@ -39,11 +39,8 @@ inputs:
   # passed to the field in the automatically generated unittests.
     in_file_a: medimage/nifti1
     # type=file|default=<undefined>: input file A
-    in_file_b: medimage/nifti1
+    in_file_b: generic/file
     # type=file|default=<undefined>: input file B
-    out_file: Path
-    # type=file: output file
-    # type=file|default=<undefined>: collect output to a file
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set as the `default` method of input fields
@@ -67,7 +64,7 @@ outputs:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set to the `callable` attribute of output fields
   templates:
-  # dict[str, str] - `output_file_template` values to be provided to output fields
+  # dict[str, str] - `path_template` values to be provided to output fields
   requirements:
   # dict[str, list[str]] - input fields that are required to be provided for the output field to be present
 tests:
@@ -96,7 +93,7 @@ tests:
     environ:
     # type=dict|default={}: Environment variables
   imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.statements.imports.explicitimport] - 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
@@ -115,13 +112,11 @@ tests:
   # (if not specified, will try to choose a sensible value)
     in_file_a:
     # type=file|default=<undefined>: input file A
-    in_file_b:
-    # type=file|default=<undefined>: input file B
     out_file: ' "out.mask_ae_overlap.txt"'
     # type=file: output file
     # type=file|default=<undefined>: collect output to a file
   imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.statements.imports.explicitimport] - 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
@@ -136,21 +131,19 @@ tests:
   # 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: 3dABoverlap functional.nii structural.nii |& tee out.mask_ae_overlap.txt
+- cmdline:
   # 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_a: '"functional.nii"'
     # type=file|default=<undefined>: input file A
-    in_file_b: '"structural.nii"'
-    # type=file|default=<undefined>: input file B
     out_file: ' "out.mask_ae_overlap.txt"'
     # type=file: output file
     # type=file|default=<undefined>: collect output to a file
   imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.statements.imports.explicitimport] - 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

example-specs/interface/nipype/afni/afn_ito_nifti.yaml

@@ -6,22 +6,22 @@
 # Docs
 # ----
 # Converts AFNI format files to NIFTI format. This can also convert 2D or
-#     1D data, which you can numpy.squeeze() to remove extra dimensions.
+# 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>`_
+# 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
+# >>> a2n = afni.AFNItoNIFTI()
+# >>> a2n.inputs.in_file = 'afni_output.3D'
+# >>> a2n.inputs.out_file =  'afni_output.nii'
+# >>> a2n.cmdline
+# '3dAFNItoNIFTI -prefix afni_output.nii afni_output.3D'
+# >>> res = a2n.run()  # doctest: +SKIP
 # 
-#     Examples
-#     --------
-#     >>> from nipype.interfaces import afni
-#     >>> a2n = afni.AFNItoNIFTI()
-#     >>> a2n.inputs.in_file = 'afni_output.3D'
-#     >>> a2n.inputs.out_file =  'afni_output.nii'
-#     >>> 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
@@ -36,11 +36,8 @@ 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: medimage-afni/three-d
+    in_file: fileformats.medimage_afni.ThreeD
     # type=file|default=<undefined>: input file to 3dAFNItoNIFTI
-    out_file: Path
-    # type=file: output file
-    # type=file|default=<undefined>: output image file name
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set as the `default` method of input fields
@@ -57,14 +54,14 @@ 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: medimage/nifti1
+    out_file: generic/file
     # type=file: output file
     # type=file|default=<undefined>: output image file name
   callables:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set to the `callable` attribute of output fields
   templates:
-  # dict[str, str] - `output_file_template` values to be provided to output fields
+  # dict[str, str] - `path_template` values to be provided to output fields
   requirements:
   # dict[str, list[str]] - input fields that are required to be provided for the output field to be present
 tests:
@@ -93,7 +90,7 @@ tests:
     environ:
     # type=dict|default={}: Environment variables
   imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.statements.imports.explicitimport] - 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
@@ -112,11 +109,8 @@ tests:
   # (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
+  # list[nipype2pydra.statements.imports.explicitimport] - 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
@@ -131,19 +125,16 @@ tests:
   # 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
+- cmdline:
   # 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: '"afni_output.3D"'
     # 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
+  # list[nipype2pydra.statements.imports.explicitimport] - 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

example-specs/interface/nipype/afni/align_epi_anat_py.yaml

@@ -7,55 +7,55 @@
 # ----
 # Align EPI to anatomical datasets or vice versa.
 # 
-#     This Python script computes the alignment between two datasets, typically
-#     an EPI and an anatomical structural dataset, and applies the resulting
-#     transformation to one or the other to bring them into alignment.
+# This Python script computes the alignment between two datasets, typically
+# an EPI and an anatomical structural dataset, and applies the resulting
+# transformation to one or the other to bring them into alignment.
 # 
-#     This script computes the transforms needed to align EPI and
-#     anatomical datasets using a cost function designed for this purpose. The
-#     script combines multiple transformations, thereby minimizing the amount of
-#     interpolation applied to the data.
+# This script computes the transforms needed to align EPI and
+# anatomical datasets using a cost function designed for this purpose. The
+# script combines multiple transformations, thereby minimizing the amount of
+# interpolation applied to the data.
 # 
-#     Basic Usage::
+# Basic Usage::
 # 
-#         align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 5
+#     align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 5
 # 
-#     The user must provide :abbr:`EPI (echo-planar imaging)` and anatomical datasets
-#     and specify the EPI sub-brick to use as a base in the alignment.
+# The user must provide :abbr:`EPI (echo-planar imaging)` and anatomical datasets
+# and specify the EPI sub-brick to use as a base in the alignment.
 # 
-#     Internally, the script always aligns the anatomical to the EPI dataset,
-#     and the resulting transformation is saved to a 1D file.
-#     As a user option, the inverse of this transformation may be applied to the
-#     EPI dataset in order to align it to the anatomical data instead.
+# Internally, the script always aligns the anatomical to the EPI dataset,
+# and the resulting transformation is saved to a 1D file.
+# As a user option, the inverse of this transformation may be applied to the
+# EPI dataset in order to align it to the anatomical data instead.
 # 
-#     This program generates several kinds of output in the form of datasets
-#     and transformation matrices which can be applied to other datasets if
-#     needed. Time-series volume registration, oblique data transformations and
-#     Talairach (standard template) transformations will be combined as needed
-#     and requested (with options to turn on and off each of the steps) in
-#     order to create the aligned datasets.
+# This program generates several kinds of output in the form of datasets
+# and transformation matrices which can be applied to other datasets if
+# needed. Time-series volume registration, oblique data transformations and
+# Talairach (standard template) transformations will be combined as needed
+# and requested (with options to turn on and off each of the steps) in
+# order to create the aligned datasets.
 # 
-#     Examples
-#     --------
-#     >>> from nipype.interfaces import afni
-#     >>> al_ea = afni.AlignEpiAnatPy()
-#     >>> al_ea.inputs.anat = "structural.nii"
-#     >>> al_ea.inputs.in_file = "functional.nii"
-#     >>> al_ea.inputs.epi_base = 0
-#     >>> al_ea.inputs.epi_strip = '3dAutomask'
-#     >>> al_ea.inputs.volreg = 'off'
-#     >>> al_ea.inputs.tshift = 'off'
-#     >>> al_ea.inputs.save_skullstrip = True
-#     >>> al_ea.cmdline # doctest: +ELLIPSIS
-#     'python2 ...align_epi_anat.py -anat structural.nii -epi_base 0 -epi_strip 3dAutomask -epi functional.nii -save_skullstrip -suffix _al -tshift off -volreg off'
-#     >>> res = allineate.run()  # doctest: +SKIP
+# Examples
+# --------
+# >>> from nipype.interfaces import afni
+# >>> al_ea = afni.AlignEpiAnatPy()
+# >>> al_ea.inputs.anat = "structural.nii"
+# >>> al_ea.inputs.in_file = "functional.nii"
+# >>> al_ea.inputs.epi_base = 0
+# >>> al_ea.inputs.epi_strip = '3dAutomask'
+# >>> al_ea.inputs.volreg = 'off'
+# >>> al_ea.inputs.tshift = 'off'
+# >>> al_ea.inputs.save_skullstrip = True
+# >>> al_ea.cmdline # doctest: +ELLIPSIS
+# 'python2 ...align_epi_anat.py -anat structural.nii -epi_base 0 -epi_strip 3dAutomask -epi functional.nii -save_skullstrip -suffix _al -tshift off -volreg off'
+# >>> res = al_ea.run()  # doctest: +SKIP
+# 
+# See Also
+# --------
+# For complete details, see the `align_epi_anat.py documentation.
+# <https://afni.nimh.nih.gov/pub/dist/doc/program_help/align_epi_anat.py.html>`__.
 # 
-#     See Also
-#     --------
-#     For complete details, see the `align_epi_anat.py documentation.
-#     <https://afni.nimh.nih.gov/pub/dist/doc/program_help/align_epi_anat.py.html>`__.
 # 
-#     
 task_name: AlignEpiAnatPy
 nipype_name: AlignEpiAnatPy
 nipype_module: nipype.interfaces.afni.preprocess
@@ -72,7 +72,7 @@ inputs:
   # passed to the field in the automatically generated unittests.
     anat: medimage/nifti1
     # type=file|default=<undefined>: name of structural dataset
-    in_file: medimage/nifti1
+    in_file: generic/file
     # type=file|default=<undefined>: EPI dataset to align
   callable_defaults:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
@@ -114,7 +114,7 @@ outputs:
   # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
   # to set to the `callable` attribute of output fields
   templates:
-  # dict[str, str] - `output_file_template` values to be provided to output fields
+  # dict[str, str] - `path_template` values to be provided to output fields
   requirements:
   # dict[str, list[str]] - input fields that are required to be provided for the output field to be present
 tests:
@@ -150,7 +150,7 @@ tests:
     environ:
     # type=dict|default={}: Environment variables
   imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.statements.imports.explicitimport] - 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
@@ -169,20 +169,14 @@ tests:
   # (if not specified, will try to choose a sensible value)
     anat:
     # type=file|default=<undefined>: name of structural dataset
-    in_file:
-    # type=file|default=<undefined>: EPI dataset to align
     epi_base: '0'
     # type=traitcompound|default=None: the epi base used in alignmentshould be one of (0/mean/median/max/subbrick#)
-    epi_strip: '"3dAutomask"'
-    # type=enum|default='3dSkullStrip'|allowed['3dAutomask','3dSkullStrip','None']: method to mask brain in EPI datashould be one of[3dSkullStrip]/3dAutomask/None)
     volreg: '"off"'
     # type=enum|default='on'|allowed['off','on']: do volume registration on EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on'
-    tshift: '"off"'
-    # type=enum|default='on'|allowed['off','on']: do time shifting of EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on'
     save_skullstrip: 'True'
     # type=bool|default=False: save skull-stripped (not aligned)
   imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.statements.imports.explicitimport] - 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
@@ -197,28 +191,22 @@ tests:
   # 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: python2 ...align_epi_anat.py -anat structural.nii -epi_base 0 -epi_strip 3dAutomask -epi functional.nii -save_skullstrip -suffix _al -tshift off -volreg off
+- cmdline:
   # 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.
     anat: '"structural.nii"'
     # type=file|default=<undefined>: name of structural dataset
-    in_file: '"functional.nii"'
-    # type=file|default=<undefined>: EPI dataset to align
     epi_base: '0'
     # type=traitcompound|default=None: the epi base used in alignmentshould be one of (0/mean/median/max/subbrick#)
-    epi_strip: '"3dAutomask"'
-    # type=enum|default='3dSkullStrip'|allowed['3dAutomask','3dSkullStrip','None']: method to mask brain in EPI datashould be one of[3dSkullStrip]/3dAutomask/None)
     volreg: '"off"'
     # type=enum|default='on'|allowed['off','on']: do volume registration on EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on'
-    tshift: '"off"'
-    # type=enum|default='on'|allowed['off','on']: do time shifting of EPI dataset before alignmentshould be 'on' or 'off', defaults to 'on'
     save_skullstrip: 'True'
     # type=bool|default=False: save skull-stripped (not aligned)
   imports:
-  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.statements.imports.explicitimport] - 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