Fix how yaml model config options are update

We treat config options from files (with sections) differently
from replacement options provided in a dictionary in code.

polaris/model_step.py

@@ -658,30 +658,28 @@ def _process_yaml(self, quiet):
         if not self.model_config_data:
             return
 
-        replacements = dict()
+        if self._yaml is None:
+            raise ValueError('Trying to update a yaml object but it was '
+                             'never created.')
+
+        if not quiet:
+            print(f'Warning: replacing yaml options in {self.yaml}')
 
         for entry in self.model_config_data:
             if 'namelist' in entry:
                 raise ValueError('Cannot generate a yaml config from an MPAS '
                                  'namelist file.')
 
             if 'options' in entry:
-                # this is a dictionary of replacement namelist options
+                # this is a dictionary of replacement model config options
                 options = entry['options']
+                self._yaml.update(options=options, quiet=quiet)
             else:
                 yaml = PolarisYaml.read(filename=entry['yaml'],
                                         package=entry['package'],
                                         replacements=entry['replacements'])
-                options = yaml.configs
-            replacements.update(options)
-
-        if not quiet:
-            print(f'Warning: replacing yaml options in {self.yaml}')
 
-        if self._yaml is None:
-            raise ValueError('Trying to update a yaml object but it was '
-                             'never created.')
-        self._yaml = self._yaml.update(replacements, quiet=quiet)
+                self._yaml.update(configs=yaml.configs, quiet=quiet)
 
 
 def make_graph_file(mesh_filename, graph_filename='graph.info',

polaris/yaml.py

@@ -89,23 +89,30 @@ def read(cls, filename, package=None, replacements=None):
         yaml.configs = configs
         return yaml
 
-    def update(self, configs, quiet=True):
+    def update(self, configs=None, options=None, quiet=True):
         """
         Add config options from a dictionary
 
         Parameters
         ----------
-        configs : dict
+        configs : dict, optional
             A nested dictionary of config sections, options and values
 
+        options : dict, optional
+            A flat dictionary of options and values
+
         quiet : bool, optional
             Whether or not to print the updated config options as they are
             replaced
         """
-        if self.model in configs:
-            # we want one layer deeper
-            configs = configs[self.model]
-        _update_section(configs, self.configs, quiet)
+        if configs is not None:
+            if self.model in configs:
+                # we want one layer deeper
+                configs = configs[self.model]
+            _update_section(configs, self.configs, quiet)
+
+        if options is not None:
+            _update_options(options, self.configs, quiet)
 
     def write(self, filename):
         """
@@ -275,6 +282,41 @@ def _update_section(src, dst, quiet, print_section=None):
             dst[name] = src[name]
 
 
+def _update_options(src, dst, quiet):
+    """
+    Update config options by searching in the destination nested dictionary
+    """
+    for name in src:
+        success = _update_option(name, src[name], dst, quiet)
+        if not success:
+            raise ValueError(
+                f'Attempting to modify a nonexistent config '
+                f'options: {name}')
+
+
+def _update_option(option, value, dst, quiet, print_section=None):
+    """
+    Recursively attempt to find and replace the value of the
+    given option
+    """
+    for name in dst:
+        if isinstance(dst[name], (dict, OrderedDict)):
+            if print_section is not None:
+                print_subsection = f'{print_section}: {name}'
+            else:
+                print_subsection = name
+            success = _update_option(option, value, dst[name], quiet,
+                                     print_subsection)
+            if success:
+                return True
+        elif name == option:
+            dst[name] = value
+            if not quiet:
+                print(f'  {print_section}: {name} = {value}')
+            return True
+    return False
+
+
 def _read_namelist(namelist_template, namelist_filename):
     """ Read the defaults file """
     record_map = _read_namelist_template(namelist_template)