fixed up parsing of doctest strings split over multiple paras

Author: tclose

nipype-interfaces-to-import.yaml

@@ -472,7 +472,6 @@ interfaces:
   - FEAT
   - FEATModel
   - FILMGLS
-  - FEATRegister
   - FLAMEO
   - ContrastMgr
   - L2Model

nipype2pydra/task.py

@@ -871,9 +871,14 @@ def write_tests(self, filename_test, input_fields, nonstd_types, run=False):
         )
         spec_str = "\n".join(imports) + "\n\n" + spec_str
 
-        spec_str_black = black.format_file_contents(
-            spec_str, fast=False, mode=black.FileMode()
-        )
+        try:
+            spec_str_black = black.format_file_contents(
+                spec_str, fast=False, mode=black.FileMode()
+            )
+        except black.parsing.InvalidInput as e:
+            raise RuntimeError(
+                f"Black could not parse generated code: {e}\n\n{spec_str}"
+            )
 
         with open(filename_test, "w") as f:
             f.write(spec_str_black)

scripts/pkg_gen/create_packages.py

@@ -204,10 +204,10 @@ def fields_stub(name, category_class, values=None):
                 doctest_blocks = []
                 for para in doc_str.split("\n\n"):
                     if "cmdline" in para:
-                        doctest_blocks.append(prev_block + para)
+                        doctest_blocks.append(prev_block + "\n" + para)
                         prev_block = ""
-                    else:
-                        prev_block += para
+                    elif ">>>" in para:
+                        prev_block += "\n" + para
 
                 doctests: ty.List[DocTestGenerator] = []
                 tests: ty.List[TestGenerator] = [
@@ -591,23 +591,26 @@ def parse_nipype_interface(
             if isinstance(inpt.trait_type, nipype.interfaces.base.core.traits.Enum):
                 inpt_mdata += f"|allowed[{','.join(sorted(repr(v) for v in inpt.trait_type.values))}]"
             input_helps[inpt_name] = f"{inpt_mdata}: {inpt_desc}"
+            trait_type_name = type(inpt.trait_type).__name__
             if inpt.genfile:
                 genfile_outputs.append(inpt_name)
-            elif type(inpt.trait_type).__name__ == "File":
+            elif trait_type_name == "File":
                 file_inputs.append(inpt_name)
-            elif type(inpt.trait_type).__name__ == "Directory":
+            elif trait_type_name == "Directory":
                 dir_inputs.append(inpt_name)
-            elif type(inpt.trait_type).__name__ == "InputMultiObject":
-                if inpt.trait_type.item_trait and inpt.trait_type.item_trait.trait_type._is_dir:
+            elif trait_type_name == "InputMultiObject":
+                inner_trait_type_name = type(inpt.trait_type.item_trait.trait_type).__name__
+                if inner_trait_type_name == "Directory":
                     dir_inputs.append(inpt_name)
-                else:
+                elif inner_trait_type_name == "File":
                     file_inputs.append(inpt_name)
                 multi_inputs.append(inpt_name)
             elif (
                 type(inpt.trait_type).__name__ == "List"
                 and type(inpt.trait_type.inner_traits()[0].handler).__name__ in ("File", "Directory")
             ):
-                if type(inpt.trait_type.inner_traits()[0].handler).__name__ == "File":
+                item_type_name = type(inpt.trait_type.inner_traits()[0].handler).__name__
+                if item_type_name == "File":
                     file_inputs.append(inpt_name)
                 else:
                     dir_inputs.append(inpt_name)

scripts/pkg_gen/fsl-only.yaml

@@ -2,5 +2,5 @@ packages:
 - fsl
 interfaces:
   fsl:
-  - AccuracyTester
+  - FNIRT