debugging mriqc and qsmxt conversions

Author: tclose

example-specs/pkg-gen/qsmxt.yaml

@@ -45,4 +45,5 @@ qsmxt:
   - qsmxt.workflows.qsm.get_matching_files
   - qsmxt.workflows.qsm.init_qsm_workflow
   - qsmxt.workflows.qsm.qsm_workflow
-  - qsmxt.workflows.template.init_template_workflow
+  - qsmxt.workflows.template.init_template_workflow
+  - qsmxt.scripts.antsBuildTemplate.ANTSTemplateBuildSingleIterationWF

nipype2pydra/interface/base.py

@@ -735,7 +735,9 @@ def pydra_type_converter(self, field, spec_type, name):
                 pydra_type = MultiOutputObj
         elif isinstance(trait_tp, (traits.trait_types.List, traits.trait_types.Tuple)):
             seq_type = list if isinstance(trait_tp, traits.trait_types.List) else tuple
-            if isinstance(field.inner_traits[0].trait_type, traits_extension.File):
+            if not field.inner_traits:
+                pydra_type = seq_type[ty.Any]
+            elif isinstance(field.inner_traits[0].trait_type, traits_extension.File):
                 if spec_type == "input":
                     pydra_type = seq_type[File]
                 else:

nipype2pydra/statements/workflow_build.py

@@ -285,15 +285,20 @@ def parse(
             conns = [args]
         conn_stmts = []
         for conn in conns:
-            src, tgt, field_conns_str = extract_args(conn)[1]
-            if (
-                field_conns_str.startswith("(")
-                and len(extract_args(field_conns_str)[1]) == 1
-            ):
-                field_conns_str = extract_args(field_conns_str)[1][0]
-            field_conns = extract_args(field_conns_str)[1]
-            for field_conn in field_conns:
-                out, in_ = extract_args(field_conn)[1]
+            if isinstance(conn, str):
+                src, tgt, field_conns_str = extract_args(conn)[1]
+                if (
+                    field_conns_str.startswith("(")
+                    and len(extract_args(field_conns_str)[1]) == 1
+                ):
+                    field_conns_str = extract_args(field_conns_str)[1][0]
+                field_conns = [
+                    extract_args(c)[1] for c in extract_args(field_conns_str)[1]
+                ]
+            else:
+                src, out, tgt, in_ = conn
+                field_conns = [ (out, in_ ) ]
+            for out, in_ in field_conns:
                 pre, args, post = extract_args(out)
                 if args is not None:
                     varname, callable_str = args
@@ -525,7 +530,7 @@ def parse(
         indent = match.group(1)
         varname = match.group(2)
         args = extract_args(statement)[1]
-        node_kwargs = match_kwargs(args, AddInterfaceStatement.SIGNATURE)
+        node_kwargs = match_kwargs([a.replace("\n", "") for a in args], AddInterfaceStatement.SIGNATURE)
         intf_name, intf_args, intf_post = extract_args(node_kwargs["interface"])
         if "iterables" in node_kwargs:
             iterables = [
@@ -829,7 +834,7 @@ class WorkflowInitStatement:
     workflow_converter: "WorkflowConverter"
 
     match_re = re.compile(
-        r"\s+(\w+)\s*=.*\bWorkflow\(.*name\s*=\s*([^,=\)]+)",
+        r"\s+(\w+)\s*=.*\bWorkflow\((?:|.*name\s*=)\s*([^,=\)]+)",
         flags=re.MULTILINE,
     )
 
@@ -887,6 +892,9 @@ def match_kwargs(args: ty.List[str], sig: ty.List[str]) -> ty.Dict[str, str]:
             kwargs[key] = val
         else:
             if found_kw:
+                if arg.startswith("#"):
+                    # Ignore comments
+                    continue
                 raise ValueError(
                     f"Non-keyword arg '{arg}' found after keyword arg in {args}"
                 )