debugged N4BiasFieldCorrection

Author: tclose

nipype2pydra/task.py

@@ -311,8 +311,8 @@ def types_to_names(spec_fields):
         spec_str += f"    output_spec = {self.task_name}_output_spec\n"
         spec_str += f"    executable='{self.nipype_interface._cmd}'\n"
 
-        for tp_repl in self.TYPE_REPLACE:
-            spec_str = spec_str.replace(*tp_repl)
+        # for tp_repl in self.TYPE_REPLACE:
+        #     spec_str = spec_str.replace(*tp_repl)
 
         spec_str_black = black.format_file_contents(
             spec_str, fast=False, mode=black.FileMode()

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+addopts = -s

tests/test_task.py

@@ -5,6 +5,16 @@
 from nipype2pydra.utils import import_module_from_path
 
 
+INBUILT_NIPYPE_TRAIT_NAMES = [
+    "__all__",
+    "args",
+    "trait_added",
+    "trait_modified",
+    "environ",
+    "environ_items",
+]
+
+
 def test_task_conversion(task_spec_file, cli_runner, work_dir):
 
     with open(task_spec_file) as f:
@@ -27,4 +37,15 @@ def test_task_conversion(task_spec_file, cli_runner, work_dir):
         import_module(task_spec["nipype_module"]), task_spec["task_name"]
     )
 
-    assert sorted(f[0] for f in pydra_task.input_spec.fields) == sorted(nipype_interface.input_spec().all_trait_names())
+    nipype_trait_names = nipype_interface.input_spec().all_trait_names()
+
+    assert sorted(f[0] for f in pydra_task.input_spec.fields) == sorted(
+        n
+        for n in nipype_trait_names
+        if not (
+            n in INBUILT_NIPYPE_TRAIT_NAMES
+            or (n.endswith("_items") and n[:-len("_items")] in nipype_trait_names)
+        )
+    )
+
+    # TODO: More detailed tests needed here