Merge pull request #9 from effigies/fix/process_isolation

FIX: Isolate Nipype1Tasks by running interfaces in Node

Author: effigies

pydra/tasks/nipype1/tests/__init__.py

@@ -0,0 +1,23 @@
+import pytest
+import shutil
+from pkg_resources import resource_filename
+
+from nipype.interfaces import fsl
+from pydra.tasks.nipype1.utils import Nipype1Task
+
+
+@pytest.mark.skipif(fsl.Info.version() is None, reason="Test requires FSL")
+def test_isolation(tmp_path):
+    in_file = tmp_path / "orig/tpms_msk.nii.gz"
+    in_file.parent.mkdir()
+    shutil.copyfile(resource_filename("nipype", "testing/data/tpms_msk.nii.gz"), in_file)
+
+    out_dir = tmp_path / "output"
+    out_dir.mkdir()
+
+    slicer = Nipype1Task(fsl.Slice(), cache_dir=str(out_dir))
+    slicer.inputs.in_file = in_file
+
+    res = slicer()
+    assert res.output.out_files
+    assert all(fname.startswith(str(out_dir)) for fname in res.output.out_files)

pydra/tasks/nipype1/tests/test_nipype1task.py

@@ -68,5 +68,7 @@ def __init__(
 
     def _run_task(self):
         inputs = attr.asdict(self.inputs, filter=lambda a, v: v is not attr.NOTHING)
-        res = self._interface.run(**inputs)
+        node = nipype.Node(self._interface, base_dir=self.output_dir, name=self.name)
+        node.inputs.trait_set(**inputs)
+        res = node.run()
         self.output_ = res.outputs.get()