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()