resolve early further reading and copy/check the version between gene…

…ral and setup in early stages

src/esm_parser/esm_parser.py

@@ -2834,6 +2834,8 @@ class GeneralConfig(dict):  # pragma: no cover
     def __init__(self, model, version, user_config):
         super(dict, self).__init__()
 
+        self.check_user_defined_versions(user_config)
+
         if os.path.isfile(model + "-" + version):
             config_path = model + "-" + version
         elif os.path.isfile(model):
@@ -2851,6 +2853,14 @@ def __init__(self, model, version, user_config):
             self.config = yaml_file_to_dict(include_path)
         else:
             self.config = include_path
+
+        resolve_choose_with_var(
+            "further_reading",
+            self.config,
+            model_config={model: self.config},
+            user_config=user_config,
+        )
+
         for attachment in CONFIGS_TO_ALWAYS_ATTACH_AND_REMOVE:
             attach_to_config_and_remove(self.config, attachment, all_config=None)
 
@@ -2980,8 +2990,6 @@ def _config_init(self, user_config):
 
         del self.config
 
-        self.check_user_defined_versions(user_config, setup_config)
-
         setup_config["general"].update(
             {
                 "esm_function_dir": CONFIG_PATH,
@@ -3099,10 +3107,10 @@ def _config_init(self, user_config):
         # pprint_config(self.config)
         # sys.exit(0)
 
-    def check_user_defined_versions(self, user_config={}, setup_config={}):
+    def check_user_defined_versions(self, user_config):
         """
-        When running a standalone model, checks whether the users has defined the
-        variable ``version`` in more than one section and if that's the case
+        Checks whether the user has defined the variable ``version`` in both the
+        main model/coupled setup section and in ``general`` and if that's the case
         throws and error. If ``version`` is only defined in the ``general`` section
         it creates a ``version`` with the same value in the model section, ensuring
         that the user can arbitrarily define ``version`` in either ``general`` or
@@ -3122,26 +3130,23 @@ def check_user_defined_versions(self, user_config={}, setup_config={}):
             If something goes wrong with the user's version choices it exits the code
             with a ``esm_parser.user_error``
         """
-        if "general" in self:
-            user_config = setup_config = self
-        if (
-            setup_config["general"].get("standalone")
-            and user_config["general"].get("run_or_compile", "runtime") == "runtime"
-        ):
-            version_in_runscript_general = user_config["general"].get("version")
-            model_name = user_config["general"]["setup_name"]
-            version_in_runscript_model = user_config.get(model_name, {}).get("version")
-            if version_in_runscript_general and version_in_runscript_model:
-                user_error(
-                    "Version",
-                    "You have defined the ``version`` variable both in the "
-                    f"``general`` and ``{model_name}`` sections of your runscript. "
-                    "This is not supported for ``standalone`` simulations. Please "
-                    "define ``only one version`` in one of the two sections.",
-                )
-            elif version_in_runscript_general and not version_in_runscript_model:
-                if model_name in user_config:
-                    user_config[model_name]["version"] = version_in_runscript_general
+        version_in_runscript_general = user_config["general"].get("version")
+        model_name = user_config["general"]["setup_name"]
+        version_in_runscript_model = user_config.get(model_name, {}).get("version")
+        if version_in_runscript_general and version_in_runscript_model:
+            user_error(
+                "Version",
+                "You have defined the ``version`` variable both in the "
+                f"``general`` and ``{model_name}`` sections of your runscript. "
+                "This is not supported as it is redundant information. Please "
+                "define ``only one version`` in one of the two sections.",
+            )
+        elif version_in_runscript_general and not version_in_runscript_model:
+            if model_name in user_config:
+                user_config[model_name]["version"] = version_in_runscript_general
+        elif version_in_runscript_model and not version_in_runscript_general:
+            if "general" in user_config:
+                user_config["general"]["version"] = version_in_runscript_model
 
     def finalize(self):
         self.run_recursive_functions(self)