Final fixes

scripts/exglobal_atmens_analysis_fv3_increment.py

@@ -6,7 +6,7 @@
 import os
 
 from wxflow import Logger, cast_strdict_as_dtypedict
-from pygfs.task.atmens_analysis_fv3inc import AtmEnsAnalysis
+from pygfs.task.atmens_analysis_fv3inc import AtmEnsAnalysisFV3Inc
 
 # Initialize root logger
 logger = Logger(level='DEBUG', colored_log=True)
@@ -18,7 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnlFV3Inc = AtmEnsAnalysis(config)
+    AtmEnsAnlFV3Inc = AtmEnsAnalysisFV3Inc(config)
     AtmEnsAnlFV3Inc.initialize()
     AtmEnsAnlFV3Inc.execute(config.APRUN_ATMENSANLFV3INC)
     AtmEnsAnlFV3Inc.finalize()

ush/python/pygfs/task/atm_analysis.py

@@ -8,7 +8,7 @@
 
 from wxflow import (AttrDict,
                     FileHandler,
-                    add_to_datetime, to_timedelta, to_YMDH,
+                    add_to_datetime, to_fv3time, to_timedelta, to_YMDH,
                     parse_j2yaml,
                     logit)
 from pygfs.task.jedi import JEDI

ush/python/pygfs/task/atm_analysis_fv3inc.py

@@ -19,6 +19,7 @@ class AtmAnalysisFV3Inc(AtmAnalysis):
     """
     @logit(logger, name="AtmAnalysisFV3Inc")
     def __init__(self, config):
+        # Inherit task_config from AtmAnalysis class
         super().__init__(config)
 
     @logit(logger)

ush/python/pygfs/task/atmens_analysis_fv3inc.py

@@ -2,8 +2,9 @@
 
 import os
 from logging import getLogger
-from wxflow import FileHandler, to_fv3time, Template, TemplateConstants
+from wxflow import logit
 
+from pygfs.task.jedi import JEDI
 from pygfs.task.atmens_analysis import AtmEnsAnalysis
 
 logger = getLogger(__name__.split('.')[-1])
@@ -18,6 +19,7 @@ class AtmEnsAnalysisFV3Inc(AtmEnsAnalysis):
     """
     @logit(logger, name="AtmEnsAnalysisFV3Inc")
     def __init__(self, config):
+        # Inherit task_config from AtmEnsAnalysis class
         super().__init__(config)
 
     @logit(logger)
@@ -26,11 +28,11 @@ def initialize(self) -> None:
 
     @logit(logger)
     def execute(self, aprun_cmd: str) -> None:
-        JEDI.execute(aprun_cmd)
+        JEDI.execute(self, aprun_cmd)
 
     @logit(logger)
     def finalize(self) -> None:
-        JEDI.finalize()
+        JEDI.finalize(self)
 
     def clean(self):
-        JEDI.clean()
+        JEDI.clean(self)

ush/python/pygfs/task/jedi.py

@@ -227,72 +227,72 @@ def get_bias_dict(self) -> Dict[str, Any]:
         }
         return bias_dict
 
-    @logit(logger)
-    def find_value_in_nested_dict(nested_dict: Dict, target_key: str) -> Any:
-        """
-        Recursively search through a nested dictionary and return the value for the target key.
-        This returns the first target key it finds.  So if a key exists in a subsequent
-        nested dictionary, it will not be found.
-
-        Parameters
-        ----------
-        nested_dict : Dict
-            Dictionary to search
-        target_key : str
-            Key to search for
-
-        Returns
-        -------
-        Any
-            Value of the target key
-
-        Raises
-        ------
-        KeyError
-            If key is not found in dictionary
-
-        TODO: if this gives issues due to landing on an incorrect key in the nested
-        dictionary, we will have to implement a more concrete method to search for a key
-        given a more complete address.  See resolved conversations in PR 2387
-
-        # Example usage:
-        nested_dict = {
-            'a': {
-                'b': {
-                    'c': 1,
-                    'd': {
-                        'e': 2,
-                        'f': 3
-                    }
-                },
-                'g': 4
-            },
-            'h': {
-                'i': 5
+@logit(logger)
+def find_value_in_nested_dict(nested_dict: Dict, target_key: str) -> Any:
+    """
+    Recursively search through a nested dictionary and return the value for the target key.
+    This returns the first target key it finds.  So if a key exists in a subsequent
+    nested dictionary, it will not be found.
+
+    Parameters
+    ----------
+    nested_dict : Dict
+        Dictionary to search
+    target_key : str
+        Key to search for
+
+    Returns
+    -------
+    Any
+        Value of the target key
+
+    Raises
+    ------
+    KeyError
+        If key is not found in dictionary
+
+    TODO: if this gives issues due to landing on an incorrect key in the nested
+    dictionary, we will have to implement a more concrete method to search for a key
+    given a more complete address.  See resolved conversations in PR 2387
+
+    # Example usage:
+    nested_dict = {
+        'a': {
+            'b': {
+                'c': 1,
+                'd': {
+                    'e': 2,
+                    'f': 3
+                }
             },
-            'j': {
-                'k': 6
-            }
+            'g': 4
+        },
+        'h': {
+            'i': 5
+        },
+        'j': {
+            'k': 6
         }
+    }
 
-        user_key = input("Enter the key to search for: ")
-        result = find_value_in_nested_dict(nested_dict, user_key)
-        """
+    user_key = input("Enter the key to search for: ")
+    result = find_value_in_nested_dict(nested_dict, user_key)
+    """
 
-        if not isinstance(nested_dict, dict):
-            raise TypeError(f"Input is not of type(dict)")
+    if not isinstance(nested_dict, dict):
+        raise TypeError(f"Input is not of type(dict)")
 
-        result = nested_dict.get(target_key)
-        if result is not None:
-            return result
+    result = nested_dict.get(target_key)
+    if result is not None:
+        return result
 
-        for value in nested_dict.values():
-            if isinstance(value, dict):
-                try:
-                    result = find_value_in_nested_dict(value, target_key)
-                    if result is not None:
-                        return result
-                except KeyError:
-                    pass
+    for value in nested_dict.values():
+        if isinstance(value, dict):
+            try:
+                result = find_value_in_nested_dict(value, target_key)
+                if result is not None:
+                    return result
+            except KeyError:
+                pass
 
-        raise KeyError(f"Key '{target_key}' not found in the nested dictionary")
+    raise KeyError(f"Key '{target_key}' not found in the nested dictionary")