Merge pull request #3414 from skoudoro/fix-3411

[FIX] Import error for nipype.interfaces.dipy.base

Author: effigies

nipype/info.py

@@ -162,7 +162,7 @@ def get_nipype_gitversion():
 EXTRA_REQUIRES = {
  "data": ["datalad"],
  "doc": [
- "dipy!=1.4.1",
+ "dipy",
  "ipython",
  "matplotlib",
  "nbsphinx",
@@ -172,7 +172,7 @@ def get_nipype_gitversion():
  "sphinxcontrib-napoleon",
  ],
  "duecredit": ["duecredit"],
- "nipy": ["nitime", "nilearn", "dipy!=1.4.1", "nipy", "matplotlib"],
+ "nipy": ["nitime", "nilearn", "dipy", "nipy", "matplotlib"],
  "profiler": ["psutil>=5.0"],
  "pybids": ["pybids>=0.7.0"],
  "specs": ["black"],

nipype/interfaces/dipy/base.py

@@ -27,23 +27,21 @@
 
 
 def no_dipy():
- """Check if dipy is available"""
+ """Check if dipy is available."""
  global HAVE_DIPY
  return not HAVE_DIPY
 
 
 def dipy_version():
- """Check dipy version"""
+ """Check dipy version."""
  if no_dipy():
  return None
 
  return dipy.__version__
 
 
 class DipyBaseInterface(LibraryBaseInterface):
- """
- A base interface for py:mod:`dipy` computations
- """
+ """A base interface for py:mod:`dipy` computations."""
 
  _pkg = "dipy"
 
@@ -57,9 +55,7 @@ class DipyBaseInterfaceInputSpec(BaseInterfaceInputSpec):
 
 
 class DipyDiffusionInterface(DipyBaseInterface):
- """
- A base interface for py:mod:`dipy` computations
- """
+ """A base interface for py:mod:`dipy` computations."""
 
  input_spec = DipyBaseInterfaceInputSpec
 
@@ -90,6 +86,24 @@ def _gen_filename(self, name, ext=None):
  return out_prefix + "_" + name + ext
 
 
+def get_default_args(func):
+ """Return optional arguments of a function.
+
+ Parameters
+ ----------
+ func: callable
+
+ Returns
+ -------
+ dict
+
+ """
+ signature = inspect.signature(func)
+ return {k: v.default for k, v in signature.parameters.items()
+ if v.default is not inspect.Parameter.empty
+ }
+
+
 def convert_to_traits_type(dipy_type, is_file=False):
  """Convert DIPY type to Traits type."""
  dipy_type = dipy_type.lower()
@@ -189,7 +203,7 @@ def dipy_to_nipype_interface(cls_name, dipy_flow, BaseClass=DipyBaseInterface):
  parser = IntrospectiveArgumentParser()
  flow = dipy_flow()
  parser.add_workflow(flow)
- default_values = inspect.getfullargspec(flow.run).defaults
+ default_values = list(get_default_args(flow.run).values())
  optional_params = [
  args + (val,) for args, val in zip(parser.optional_parameters, default_values)
  ]

nipype/interfaces/dipy/tests/test_base.py

@@ -1,4 +1,5 @@
 import pytest
+from packaging.version import Version
 from collections import namedtuple
 from ...base import traits, File, TraitedSpec, BaseInterfaceInputSpec
 from ..base import (
@@ -8,6 +9,8 @@
  DipyBaseInterface,
  no_dipy,
  get_dipy_workflows,
+ get_default_args,
+ dipy_version
 )
 
 
@@ -112,6 +115,32 @@ def test_create_interface_specs():
  assert "out_params" in current_params.keys()
 
 
+@pytest.mark.skipif(no_dipy() or Version(dipy_version()) < Version("1.4"),
+ reason="DIPY >=1.4 required")
+def test_get_default_args():
+ from dipy.utils.deprecator import deprecated_params
+
+ def test(dummy=11, x=3):
+ return dummy, x
+
+ @deprecated_params('x', None, '0.3', '0.5', alternative='test2.y')
+ def test2(dummy=11, x=3):
+ return dummy, x
+
+ @deprecated_params(['dummy', 'x'], None, '0.3', alternative='test2.y')
+ def test3(dummy=11, x=3):
+ return dummy, x
+
+ @deprecated_params(['dummy', 'x'], None, '0.3', '0.5',
+ alternative='test2.y')
+ def test4(dummy=11, x=3):
+ return dummy, x
+
+ expected_res = {'dummy': 11, 'x': 3}
+ for func in [test, test2, test3, test4]:
+ assert get_default_args(func) == expected_res
+
+
 @pytest.mark.skipif(no_dipy(), reason="DIPY is not installed")
 def test_dipy_to_nipype_interface():
  from dipy.workflows.workflow import Workflow
@@ -178,3 +207,4 @@ def test_get_dipy_workflows():
  test_convert_to_traits_type()
  test_create_interface_specs()
  test_dipy_to_nipype_interface()
+ test_get_default_args()