Fix up autopygen type annotation

planemo/autopygen/source_file_parsing/local_module_parsing.py

@@ -36,7 +36,7 @@ def __init__(self, unknown: Set[str]):
 
     # currently able to resolve add_argument calls containing unknown names,
     # and list comprehension assignment
-    def _reach_top(self, node: ast.Name) -> Tuple[ast.Call, ast.AST]:
+    def _reach_top(self, node: ast.Name) -> Tuple[ast.Call, ast.Name]:
         current = node
         parent = current.parent  # type: ignore
 
@@ -99,14 +99,14 @@ def visit_Name(self, node: ast.Name) -> Any:
             )
 
 
-def handle_local_module_names(actions: List[ast.AST], unknown_names: Set[str]) -> ast.Module:
+def handle_local_module_names(actions: List[ast.stmt], unknown_names: Set[str]) -> ast.Module:
     """
     Function used to remove assignments and list comprehensions which can't be
     resolved
 
     Parameters
     ----------
-    actions: List[ast.AST]
+    actions: List[ast.stmt]
       list of actions extracted so far
     unknown_names:
       set of unknown names that have to be extracted

planemo/autopygen/source_file_parsing/parser_discovery_and_init.py

@@ -48,7 +48,7 @@ class ImportDiscovery(Discovery):
     Class responsible for discovery and extraction of import statements
     """
 
-    def __init__(self, actions: List[ast.AST]):
+    def __init__(self, actions: List[ast.stmt]):
         super(ImportDiscovery, self).__init__(actions)
         self.argparse_module_alias: Optional[str] = None
         self.argument_parser_alias: Optional[str] = None
@@ -80,7 +80,7 @@ def visit_ImportFrom(self, node: ast.ImportFrom) -> Any:
                     if name == ARGPARSE_MODULE_NAME and item.name == ARGUMENT_PARSER_CLASS_NAME:
                         self.argument_parser_alias = alias
 
-    def report_findings(self) -> Tuple[List[ast.AST], Optional[str], Optional[str], Set[str]]:
+    def report_findings(self) -> Tuple[List[ast.stmt], Optional[str], Optional[str], Set[str]]:
         if self.argparse_module_alias is None and self.argument_parser_alias is None:
             raise ArgParseImportNotFound("No argparse import found")
 
@@ -95,7 +95,7 @@ class SimpleParserDiscoveryAndReplacement(Discovery):
     """
 
     def __init__(
-        self, actions: List[ast.AST], argparse_alias: str, argument_parser_alias: str, custom_parser_def: ast.ClassDef
+        self, actions: List[ast.stmt], argparse_alias: str, argument_parser_alias: str, custom_parser_def: ast.ClassDef
     ):
         self.argument_parser_alias = argument_parser_alias
         self.argparse_module_alias = argparse_alias
@@ -179,7 +179,7 @@ class GroupAndSubparsersDiscovery(Discovery):
     groups and subparsers
     """
 
-    def __init__(self, actions: List[ast.AST], known_names: Set[str], main_name: str):
+    def __init__(self, actions: List[ast.stmt], known_names: Set[str], main_name: str):
         self.main_name = main_name
         self.known_names = known_names
         super(GroupAndSubparsersDiscovery, self).__init__(actions)
@@ -205,7 +205,7 @@ class ArgumentCreationDiscovery(Discovery):
     and on the argument groups extracted by GroupDiscovery
     """
 
-    def __init__(self, actions: List[ast.AST], main_name: str):
+    def __init__(self, actions: List[ast.stmt], main_name: str):
         self.main_name = main_name
         super(ArgumentCreationDiscovery, self).__init__(actions)
 
@@ -219,11 +219,11 @@ def visit_Call(self, node: ast.Call) -> Any:
 
         self.generic_visit(node)
 
-    def report_findings(self) -> Tuple[List[ast.AST]]:
+    def report_findings(self) -> Tuple[List[ast.stmt]]:
         return (self.actions,)
 
 
-def get_parser_init_and_actions(source: ast.Module) -> Tuple[List[ast.AST], str, Set[str]]:
+def get_parser_init_and_actions(source: ast.Module) -> Tuple[List[ast.stmt], str, Set[str]]:
     """
     Function used to extract necessary imports, parser and argument creation
      function calls
@@ -239,7 +239,7 @@ def get_parser_init_and_actions(source: ast.Module) -> Tuple[List[ast.AST], str,
     section names
     """
 
-    actions: List[ast.AST] = []
+    actions: List[ast.stmt] = []
     custom_parser_class_def = obtain_class_def()
 
     if custom_parser_class_def is None:

planemo/autopygen/source_file_parsing/parsing_commons.py

@@ -11,7 +11,7 @@
 )
 
 
-class CustomAST(ast.AST):
+class CustomAST(ast.stmt):
     def __init__(self, *args: Any, **kwargs: Any):
         super().__init__(*args, **kwargs)
         self.parent = None
@@ -22,13 +22,13 @@ class CustomVisitor(ast.NodeVisitor, abc.ABC):
     def report_findings(self) -> Tuple:
         pass
 
-    def visit_and_report(self, source: ast.AST):
+    def visit_and_report(self, source: ast.Module):
         self.visit(source)
         return self.report_findings()
 
 
 class Discovery(CustomVisitor, abc.ABC):
-    def __init__(self, actions: List[ast.AST]):
+    def __init__(self, actions: List[ast.stmt]):
         self.actions = actions
 
 

planemo/autopygen/source_file_parsing/unknown_names_discovery.py

@@ -77,7 +77,7 @@ def report_findings(self) -> Tuple:
         return self.variable_definitions, self.class_definitions, self.new_known_names
 
 
-def _insert_into_actions(actions: List[ast.AST], assignments: List[ast.Assign], class_defs: List[ast.ClassDef]):
+def _insert_into_actions(actions: List[ast.stmt], assignments: List[ast.Assign], class_defs: List[ast.ClassDef]):
     def find_end_of_imports():
         index = 0
         for item in actions:
@@ -111,8 +111,8 @@ def find_end_of_assignments(start: int):
 
 
 def initialize_variables_in_module(
-    original_module: ast.Module, parser_name: str, actions: List[ast.AST], imported_names: Set[str]
-) -> Tuple[List[ast.AST], Set[str]]:
+    original_module: ast.Module, parser_name: str, actions: List[ast.stmt], imported_names: Set[str]
+) -> Tuple[List[ast.stmt], Set[str]]:
     """
     Function used to initialize variables that have constant values
 
@@ -123,7 +123,7 @@ def initialize_variables_in_module(
      AST of the original source file
     parser_name : str
      default name of the parser
-    actions : List[ast.AST]
+    actions : List[ast.stmt]
      list of actions extracted so far
     imported_names : Set[str]
      list of names imported from modules