move collapsed_nested_matches into yaml load from prepare_schism

Author: lily-tomkovic-DWR

schimpy/prepare_schism.py

@@ -642,14 +642,6 @@ def update_temporal_inputs(s, inputs):
             print(l)
 
 
-def check_nested_match(node):
-    for key, item in node.items():
-        if isinstance(item, dict):
-            if key in item.keys():
-                node[key] = item[key]
-            check_nested_match(item)
-
-
 def item_exist(inputs, name):
     return True if name in inputs else False
 
@@ -667,11 +659,13 @@ def setup_logger(outdir):
 
 
 @click.command()
-@click.argument('main_inputfile', type=click.Path(exists=True))
+@click.argument("main_inputfile", type=click.Path(exists=True))
 def prepare_schism_cli(main_inputfile):
     """Prepare SCHISM input files."""
+
     class Args:
         pass
+
     args = Args()
     args.main_inputfile = main_inputfile
     prepare_schism(args)
@@ -758,9 +752,6 @@ def process_prepare_yaml(in_fname, use_logging=True, write_echo=True):
     logger.info("Processing the top level...")
     check_and_suggest(list(inputs.keys()), keys_top_level, logger)
 
-    logger.info("Checking for matching nested keys...")
-    check_nested_match(inputs)
-
     if write_echo:
         out_fname = (
             os.path.splitext(in_fname)[0] + "_echo" + os.path.splitext(in_fname)[1]

schimpy/schism_yaml.py

@@ -264,7 +264,15 @@ def check_unsubstituted_vars(data, path=None, found=None):
     return found
 
 
-def load(stream, envvar=None):
+def collapsed_nested_matches(node):
+    for key, item in node.items():
+        if isinstance(item, dict):
+            if key in item.keys():
+                node[key] = item[key]
+            collapsed_nested_matches(item)
+
+
+def load(stream, envvar=None, collapse_nested=True):
     """Load a schism YAML"""
     # First round to get environmental variables
     loader = RawLoader(stream)
@@ -294,6 +302,8 @@ def load(stream, envvar=None):
                 msg.append(f"  {path}: {matches}")
             msg.append(r"This could be an issue of using {var} instead of ${var}")
             warnings.warn("\n".join(msg))
+            
+        collapsed_nested_matches(data)
         return data
     finally:
         loader.dispose()