Merge pull request #3273 from nipy/fix-unavailable-traits

handle unavailable traits due to version differences

Author: satra

nipype/interfaces/base/core.py

@@ -31,7 +31,7 @@
 
 from ...external.due import due
 
-from .traits_extension import traits, isdefined
+from .traits_extension import traits, isdefined, Undefined
 from .specs import (
     BaseInterfaceInputSpec,
     CommandLineInputSpec,
@@ -180,7 +180,16 @@ def __init__(
         if not self.input_spec:
             raise Exception("No input_spec in class: %s" % self.__class__.__name__)
 
-        self.inputs = self.input_spec(**inputs)
+        # Create input spec, disable any defaults that are unavailable due to
+        # version, and then apply the inputs that were passed.
+        self.inputs = self.input_spec()
+        unavailable_traits = self._check_version_requirements(
+            self.inputs, permissive=True
+        )
+        if unavailable_traits:
+            self.inputs.trait_set(**{k: Undefined for k in unavailable_traits})
+        self.inputs.trait_set(**inputs)
+
         self.ignore_exception = ignore_exception
 
         if resource_monitor is not None:
@@ -264,8 +273,12 @@ def _check_mandatory_inputs(self):
         ):
             self._check_requires(spec, name, getattr(self.inputs, name))
 
-    def _check_version_requirements(self, trait_object, raise_exception=True):
+    def _check_version_requirements(self, trait_object, permissive=False):
         """ Raises an exception on version mismatch
+
+        Set the ``permissive`` attribute to True to suppress warnings and exceptions.
+        This is currently only used in __init__ to silently identify unavailable
+        traits.
         """
         unavailable_traits = []
         # check minimum version
@@ -283,15 +296,16 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
                         f"Nipype cannot validate the package version {version!r} for "
                         f"{self.__class__.__name__}. Trait {name} requires version >={min_ver}."
                     )
-                    iflogger.warning(f"{msg}. Please verify validity.")
+                    if not permissive:
+                        iflogger.warning(f"{msg}. Please verify validity.")
                     if config.getboolean("execution", "stop_on_unknown_version"):
                         raise ValueError(msg) from err
                     continue
                 if too_old:
                     unavailable_traits.append(name)
                     if not isdefined(getattr(trait_object, name)):
                         continue
-                    if raise_exception:
+                    if not permissive:
                         raise Exception(
                             "Trait %s (%s) (version %s < required %s)"
                             % (name, self.__class__.__name__, version, min_ver)
@@ -311,15 +325,16 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
                         f"Nipype cannot validate the package version {version!r} for "
                         f"{self.__class__.__name__}. Trait {name} requires version <={max_ver}."
                     )
-                    iflogger.warning(f"{msg}. Please verify validity.")
+                    if not permissive:
+                        iflogger.warning(f"{msg}. Please verify validity.")
                     if config.getboolean("execution", "stop_on_unknown_version"):
                         raise ValueError(msg) from err
                     continue
                 if too_new:
                     unavailable_traits.append(name)
                     if not isdefined(getattr(trait_object, name)):
                         continue
-                    if raise_exception:
+                    if not permissive:
                         raise Exception(
                             "Trait %s (%s) (version %s > required %s)"
                             % (name, self.__class__.__name__, version, max_ver)

nipype/interfaces/base/tests/test_core.py

@@ -253,7 +253,7 @@ class input_spec(nib.TraitedSpec):
     assert len(caplog.records) == 2
 
 
-def test_input_version_missing_error():
+def test_input_version_missing_error(caplog):
     from nipype import config
 
     class DerivedInterface(nib.BaseInterface):
@@ -263,13 +263,55 @@ class input_spec(nib.TraitedSpec):
 
         _version = "misparsed-garbage"
 
-    with mock.patch.object(config, "getboolean", return_value=True):
-        obj = DerivedInterface(foo=1)
-        with pytest.raises(ValueError):
-            obj._check_version_requirements(obj.inputs)
-        obj = DerivedInterface(bar=1)
-        with pytest.raises(ValueError):
-            obj._check_version_requirements(obj.inputs)
+    obj1 = DerivedInterface(foo=1)
+    obj2 = DerivedInterface(bar=1)
+    with caplog.at_level(logging.WARNING, logger="nipype.interface"):
+        with mock.patch.object(config, "getboolean", return_value=True):
+            with pytest.raises(ValueError):
+                obj1._check_version_requirements(obj1.inputs)
+            with pytest.raises(ValueError):
+                obj2._check_version_requirements(obj2.inputs)
+    assert len(caplog.records) == 2
+
+
+def test_unavailable_input():
+    class WithInput(nib.BaseInterface):
+        class input_spec(nib.TraitedSpec):
+            foo = nib.traits.Int(3, usedefault=True, max_ver="0.5")
+
+        _version = "0.4"
+
+        def _run_interface(self, runtime):
+            return runtime
+
+    class WithoutInput(WithInput):
+        _version = "0.6"
+
+    has = WithInput()
+    hasnt = WithoutInput()
+    trying_anyway = WithoutInput(foo=3)
+    assert has.inputs.foo == 3
+    assert not nib.isdefined(hasnt.inputs.foo)
+    assert trying_anyway.inputs.foo == 3
+
+    has.run()
+    hasnt.run()
+    with pytest.raises(Exception):
+        trying_anyway.run()
+
+    # Still settable
+    has.inputs.foo = 4
+    hasnt.inputs.foo = 4
+    trying_anyway.inputs.foo = 4
+    assert has.inputs.foo == 4
+    assert hasnt.inputs.foo == 4
+    assert trying_anyway.inputs.foo == 4
+
+    has.run()
+    with pytest.raises(Exception):
+        hasnt.run()
+    with pytest.raises(Exception):
+        trying_anyway.run()
 
 
 def test_output_version():

nipype/interfaces/tests/test_io.py

@@ -465,7 +465,7 @@ def test_datasink_substitutions(tmpdir):
         files.append(f)
         open(f, "w")
     ds = nio.DataSink(
-        parametrization=False,
+        parameterization=False,
         base_directory=str(outdir),
         substitutions=[("ababab", "ABABAB")],
         # end archoring ($) is used to assure operation on the filename