fix: ensure io classes derived from IOBase but not in nipype allow appropriate connections

Author: satra

nipype/pipeline/engine/tests/test_engine.py

@@ -734,3 +734,37 @@ def test_deep_nested_write_graph_runs(tmpdir):
                 os.remove('graph_detailed.dot')
             except OSError:
                 pass
+
+
+def test_io_subclass():
+    """Ensure any io subclass allows dynamic traits"""
+    from nipype.interfaces.io import IOBase
+    from nipype.interfaces.base import DynamicTraitedSpec
+
+    class TestKV(IOBase):
+        _always_run = True
+        output_spec = DynamicTraitedSpec
+
+        def _list_outputs(self):
+            outputs = {}
+            outputs['test'] = 1
+            outputs['foo'] = 'bar'
+            return outputs
+
+    wf = pe.Workflow('testkv')
+
+    def testx2(test):
+        return test * 2
+
+    kvnode = pe.Node(TestKV(), name='testkv')
+    from nipype.interfaces.utility import Function
+    func = pe.Node(
+        Function(input_names=['test'], output_names=['test2'], function=testx2),
+        name='func')
+    exception_not_raised = True
+    try:
+        wf.connect(kvnode, 'test', func, 'test')
+    except Exception as e:
+        if 'Module testkv has no output called test' in e:
+            exception_not_raised = False
+    assert exception_not_raised

nipype/pipeline/engine/workflows.py

@@ -200,11 +200,16 @@ def connect(self, *args, **kwargs):
 connected.
 """ % (srcnode, source, destnode, dest, dest, destnode))
                 if not (hasattr(destnode, '_interface') and
-                        '.io' in str(destnode._interface.__class__)):
+                            ('.io' in str(destnode._interface.__class__) or
+                                any(['.io' in str(val) for val in
+                                     destnode._interface.__class__.__bases__]))
+                        ):
                     if not destnode._check_inputs(dest):
                         not_found.append(['in', destnode.name, dest])
                 if not (hasattr(srcnode, '_interface') and
-                        '.io' in str(srcnode._interface.__class__)):
+                            ('.io' in str(srcnode._interface.__class__)
+                             or any(['.io' in str(val) for val in
+                                     srcnode._interface.__class__.__bases__]))):
                     if isinstance(source, tuple):
                         # handles the case that source is specified
                         # with a function