Allow nogil for most types of methods.

This requires a change in conversion providers.
+Some other cleanups.

Author: jpfeuffer

CONTRIBUTING.md

@@ -4,6 +4,19 @@ This document is displayed because you either opened an issue or you want to pro
 When interacting with other developers, users or anyone else from our community, please adhere to
 [the OpenMS CODE OF CONDUCT](https://github.com/OpenMS/OpenMS/blob/develop/CODE_OF_CONDUCT.md)
 
+# Setting up dev environment
+Install conda/mamba (or use a venv).
+Install git.
+Install a C++ compiler.
+
+```bash
+git clone https://github.com/OpenMS/autowrap
+cd autowrap
+mamba create -n autowrap -f environment.yml
+python -m pytest
+```
+
+
 # Reporting an Issue:
 
 You most likely came here to:
@@ -18,10 +31,10 @@ If you found a bug, e.g. an autowrap tool crashes during code generation, it is
   - how you installed autowrap (e.g., from source, pip)
   - a description on how to reproduce the bug
   - relevant tool output (e.g., error messages)
-  - data to repoduce the bug (If possible as a GitHub gist. Other platforms like Dropbox, Google Drive links also work. If you can't share the data publicly please indicate this and we will contact you in private.)
+  - data to reproduce the bug (If possible as a GitHub gist. Other platforms like Dropbox, Google Drive links also work. If you can't share the data publicly please indicate this and we will contact you in private.)
 
-If you are an official OpenMS team meber:
-  - label your issue using github labels (e.g. as: question, defect) that indicate the type of issue and which components of autowrap (blue labels) are affected. The severity is usually assigned by OpenMS maintainers and used internally to e.g. indicate if a bug is a blocker for a new release.
+If you are an official OpenMS team member:
+  - label your issue using GitHub labels (e.g. as: question, defect) that indicate the type of issue and which components of autowrap (blue labels) are affected. The severity is usually assigned by OpenMS maintainers and used internally to e.g. indicate if a bug is a blocker for a new release.
 
 # Opening a Pull Request
 

README_DEVELOP

@@ -1113,18 +1113,22 @@ def _create_fun_decl_and_input_conversion(self, code, py_name, method, is_free_f
         call_args = []
         checks = []
         in_types = []
+        decls = []
+        decl_calls = []
         for arg_num, (t, n) in enumerate(args):
             # get new ConversionProvider using the converter registry
             converter = self.cr.get(t)
             converter.cr = self.cr
             py_type = converter.matching_python_type(t)
             py_typing_type = converter.matching_python_type_full(t)
-            conv_code, call_as, cleanup = converter.input_conversion(t, n, arg_num)
+            conv_code, call_as, cleanup, (decl, decl_call) = converter.input_conversion(t, n, arg_num)
             py_signature_parts.append("%s %s " % (py_type, n))
             py_typing_signature_parts.append("%s: %s " % (n, py_typing_type))
             input_conversion_codes.append(conv_code)
             cleanups.append(cleanup)
             call_args.append(call_as)
+            decls.append(decl)
+            decl_calls.append(decl_call)
             in_types.append(t)
             checks.append((n, converter.type_check_expression(t, n)))
 
@@ -1211,7 +1215,7 @@ def _create_fun_decl_and_input_conversion(self, code, py_name, method, is_free_f
         for conv_code in input_conversion_codes:
             code.add(conv_code)
 
-        return call_args, cleanups, in_types, stub
+        return call_args, cleanups, in_types, stub, decls, decl_calls
 
     def _create_wrapper_for_attribute(self, attribute):
         code = Code()
@@ -1228,7 +1232,7 @@ def _create_wrapper_for_attribute(self, attribute):
         converter = self.cr.get(t)
         py_type = converter.matching_python_type(t)
         py_typing_type = converter.matching_python_type_full(t)
-        conv_code, call_as, cleanup = converter.input_conversion(t, name, 0)
+        conv_code, call_as, cleanup, (decl, decl_call) = converter.input_conversion(t, name, 0)
 
         code.add(
             """
@@ -1323,7 +1327,7 @@ def _create_wrapper_for_attribute(self, attribute):
         code.add("        return py_result")
         return code, stubs
 
-    def create_wrapper_for_nonoverloaded_method(self, cdcl, py_name, method):
+    def create_wrapper_for_nonoverloaded_method(self, cdcl, py_name, method: ResolvedMethod):
         L.info("   create wrapper for %s ('%s')" % (py_name, method))
         meth_code = Code()
 
@@ -1332,10 +1336,22 @@ def create_wrapper_for_nonoverloaded_method(self, cdcl, py_name, method):
             cleanups,
             in_types,
             stubs,
+            decls,
+            decl_calls
         ) = self._create_fun_decl_and_input_conversion(meth_code, py_name, method)
 
+        init = ""
+        c_call_args = []
+        for decl, decl_call in zip(decls, decl_calls):
+            init = init + decl + "\n"
+            c_call_args.append(decl_call)
+
         # call wrapped method and convert result value back to python
         cpp_name = method.cpp_decl.name
+
+        if method.with_nogil and init.strip("\n"):
+            call_args = c_call_args
+
         call_args_str = ", ".join(call_args)
         if method.is_static:
             cy_call_str = "%s.%s(%s)" % (
@@ -1348,13 +1364,15 @@ def create_wrapper_for_nonoverloaded_method(self, cdcl, py_name, method):
 
         res_t = method.result_type
         out_converter = self.cr.get(res_t)
-        full_call_stmt = out_converter.call_method(res_t, cy_call_str)
+        full_call_stmt = out_converter.call_method(res_t, cy_call_str, True, not method.with_nogil)
 
         if method.with_nogil:
             meth_code.add(
                 """
+              |    $init
               |    with nogil:
-              """
+              |
+              """, locals()
             )
             indented = Code()
         else:
@@ -1370,6 +1388,10 @@ def create_wrapper_for_nonoverloaded_method(self, cdcl, py_name, method):
         else:
             indented.add(full_call_stmt)
 
+        if method.with_nogil:
+            meth_code.add(indented)
+            indented = meth_code
+
         for cleanup in reversed(cleanups):
             if not cleanup:
                 continue
@@ -1385,9 +1407,6 @@ def create_wrapper_for_nonoverloaded_method(self, cdcl, py_name, method):
             indented.add(to_py_code)
             indented.add("    return py_result")
 
-        if method.with_nogil:
-            meth_code.add(indented)
-
         return meth_code, stubs
 
     def create_wrapper_for_free_function(self, decl: ResolvedFunction, out_codes: CodeDict) -> None:
@@ -1445,6 +1464,8 @@ def _create_wrapper_for_free_function(
             cleanups,
             in_types,
             stubs,
+            decls,
+            decl_calls
         ) = self._create_fun_decl_and_input_conversion(fun_code, name, decl, is_free_fun=True)
 
         call_args_str = ", ".join(call_args)
@@ -1552,6 +1573,8 @@ def create_wrapper_for_nonoverloaded_constructor(self, class_decl, py_name, cons
             cleanups,
             in_types,
             stubs,
+            decls,
+            decl_calls
         ) = self._create_fun_decl_and_input_conversion(cons_code, py_name, cons_decl)
 
         stub_code.extend(stubs)
@@ -1663,6 +1686,8 @@ def create_special_getitem_method(self, mdcl):
             cleanups,
             (in_type,),
             stubs,
+            decls,
+            decl_calls
         ) = self._create_fun_decl_and_input_conversion(meth_code, "__getitem__", mdcl)
 
         meth_code.add(
@@ -1790,7 +1815,7 @@ def create_special_setitem_method(self, mdcl):
         #  CppObject[ idx ] = value
         #
         cy_call_str = "deref(self.inst.get())[%s]" % call_arg
-        code, call_as, cleanup = out_converter.input_conversion(res_t, value_arg, 0)
+        code, call_as, cleanup, (decl, decl_call) = out_converter.input_conversion(res_t, value_arg, 0)
         meth_code.add(
             """
                  |    $cy_call_str = $call_as