debugged workflows and spatial normalisation monster interface

Author: tclose

nipype2pydra/interface/base.py

@@ -45,6 +45,7 @@
     parse_imports,
     ExplicitImport,
     from_list_to_imports,
+    make_imports_absolute,
 )
 from fileformats.generic import File
 import nipype2pydra.package
@@ -1319,6 +1320,11 @@ def process_method_body(
                 )
             method_body = output_re.sub(r"\1", method_body)
         method_body = self.unwrap_nested_methods(method_body)
+        method_body = make_imports_absolute(
+            method_body,
+            super_base.__module__,
+            translations=self.package.all_import_translations,
+        )
         # method_body = self._misc_cleanups(method_body)
         return method_body
 

nipype2pydra/interface/function.py

@@ -16,6 +16,8 @@
 @attrs.define(slots=False)
 class FunctionInterfaceConverter(BaseInterfaceConverter):
 
+    converter_type = "function"
+
     @property
     def included_methods(self) -> ty.Tuple[str, ...]:
         return ("__init__", "_run_interface", "_list_outputs")
@@ -65,7 +67,7 @@ def types_to_names(spec_fields):
         used = UsedSymbols.find(
             self.nipype_module,
             self.referenced_local_functions,
-            omit_classes=self.package.omit_classes,  # + [BaseInterface, TraitedSpec],
+            omit_classes=self.package.omit_classes,
             omit_modules=self.package.omit_modules,
             omit_functions=self.package.omit_functions,
             omit_constants=self.package.omit_constants,
@@ -81,7 +83,7 @@ def types_to_names(spec_fields):
             method_used = UsedSymbols.find(
                 method_module,
                 [ref_method],
-                omit_classes=self.package.omit_classes,  #  + [BaseInterface, TraitedSpec],
+                omit_classes=self.package.omit_classes,
                 omit_modules=self.package.omit_modules,
                 omit_functions=self.package.omit_functions,
                 omit_constants=self.package.omit_constants,
@@ -153,7 +155,7 @@ def types_to_names(spec_fields):
             run_interface_used = UsedSymbols.find(
                 run_interface_class.__module__,
                 [run_interface_code],
-                omit_classes=self.package.omit_classes,  #  + [BaseInterface, TraitedSpec],
+                omit_classes=self.package.omit_classes,
                 omit_modules=self.package.omit_modules,
                 omit_functions=self.package.omit_functions,
                 omit_constants=self.package.omit_constants,
@@ -187,7 +189,7 @@ def types_to_names(spec_fields):
             list_outputs_used = UsedSymbols.find(
                 list_outputs_class.__module__,
                 [list_outputs_code],
-                omit_classes=self.package.omit_classes,  #  + [BaseInterface, TraitedSpec],
+                omit_classes=self.package.omit_classes,
                 omit_modules=self.package.omit_modules,
                 omit_functions=self.package.omit_functions,
                 omit_constants=self.package.omit_constants,
@@ -231,7 +233,14 @@ def types_to_names(spec_fields):
         spec_str += "\n\n# Nipype methods converted into functions\n\n"
 
         for m in sorted(self.referenced_methods, key=attrgetter("__name__")):
-            spec_str += "\n\n" + self.process_method(m, input_names, output_names)
+            spec_str += "\n\n" + self.process_method(
+                m,
+                input_names,
+                output_names,
+                super_base=find_super_method(
+                    self.nipype_interface, m.__name__, include_class=True
+                )[1],
+            )
 
         # Replace runtime attributes
         additional_imports = set()

nipype2pydra/statements/__init__.py

@@ -5,6 +5,7 @@
     GENERIC_PYDRA_IMPORTS,
     ExplicitImport,
     from_list_to_imports,
+    make_imports_absolute,
 )
 from .workflow_build import (  # noqa: F401
     AddNestedWorkflowStatement,

nipype2pydra/statements/imports.py

@@ -465,6 +465,39 @@ def collate(
         )
 
 
+def translate(
+    module_name: str, translations: ty.Sequence[ty.Tuple[str, str]]
+) -> ty.Optional[str]:
+    for from_pkg, to_pkg in translations:
+        if re.match(from_pkg, module_name):
+            return re.sub(
+                from_pkg,
+                to_pkg,
+                module_name,
+                count=1,
+                flags=re.MULTILINE | re.DOTALL,
+            )
+    return None
+
+
+def make_imports_absolute(
+    src: str, modulepath: str, translations: ty.Sequence[ty.Tuple[str, str]] = ()
+) -> str:
+    parts = modulepath.split(".")
+
+    def replacer(match) -> str:
+        levels = len(match.group(2))
+        assert levels < len(parts)
+        abs_modulepath = ".".join(parts[:-levels]) + "." + match.group(3)
+        if translations:
+            newpath = translate(abs_modulepath, translations)
+            if newpath:
+                abs_modulepath = newpath
+        return f"{match.group(1)}from {abs_modulepath}"
+
+    return re.sub(r"(\s*)from\s+(\.+)(\w+)", replacer, src)
+
+
 def parse_imports(
     stmts: ty.Union[str, ty.Sequence[str]],
     relative_to: ty.Union[str, ModuleType, None] = None,
@@ -497,18 +530,6 @@ def parse_imports(
             ".__init__" if relative_to.__file__.endswith("__init__.py") else ""
         )
 
-    def translate(module_name: str) -> ty.Optional[str]:
-        for from_pkg, to_pkg in translations:
-            if re.match(from_pkg, module_name):
-                return re.sub(
-                    from_pkg,
-                    to_pkg,
-                    module_name,
-                    count=1,
-                    flags=re.MULTILINE | re.DOTALL,
-                )
-        return None
-
     parsed = []
     for stmt in stmts:
         if isinstance(stmt, ImportStatement):
@@ -543,7 +564,7 @@ def translate(module_name: str) -> ty.Optional[str]:
             )
             if absolute:
                 import_stmt = import_stmt.absolute()
-            import_stmt.translation = translate(import_stmt.module_name)
+            import_stmt.translation = translate(import_stmt.module_name, translations)
             parsed.append(import_stmt)
 
         else:
@@ -554,7 +575,7 @@ def translate(module_name: str) -> ty.Optional[str]:
                     ImportStatement(
                         indent=match.group(1),
                         imported={imp.local_name: imp},
-                        translation=translate(imp.name),
+                        translation=translate(imp.name, translations),
                     )
                 )
     return parsed