Initial commit of marine letkf stubs (#1090)

Adds stubs and ctest for marine LETKF task. Co-dependent on
global-workflow PR NOAA-EMC/global-workflow#2564

Addresses #1091

scripts/exgdas_global_marine_analysis_letkf.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# exgdas_global_marine_analysis_ecen.py
+# This script creates an MarineLETKF class
+# and runs the initialize, run, and finalize  methods
+# which currently are stubs
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+# TODO (AFE): change to from pygfs.task.marine_recenter import MarineLETKF
+from soca.marine_recenter import MarineLETKF
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Instantiate the aerosol analysis task
+    MarineLetkf = MarineLETKF(config)
+    MarineLetkf.initialize()
+    MarineLetkf.run()
+    MarineLetkf.finalize()

test/soca/gw/CMakeLists.txt

@@ -46,6 +46,7 @@ set(jjob_list "JGLOBAL_PREP_OCEAN_OBS"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_ECEN"
+#	      "JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST")
 # TODO(WaterPeople) Add back to the list of tested jobs once fixed

ush/soca/marine_letkf.py

@@ -0,0 +1,90 @@
+#!/usr/bin/env python3
+
+from datetime import datetime, timedelta
+import f90nml
+from logging import getLogger
+import os
+from soca import bkg_utils
+from typing import Dict
+import ufsda
+from ufsda.stage import soca_fix
+from wxflow import (AttrDict,
+                    chdir,
+                    Executable,
+                    FileHandler,
+                    logit,
+                    parse_j2yaml,
+                    Task,
+                    Template,
+                    TemplateConstants,
+                    WorkflowException,
+                    YAMLFile)
+
+logger = getLogger(__name__.split('.')[-1])
+
+
+class MarineLETKF(Task):
+    """
+    Class for global ocean analysis recentering task
+    """
+
+    @logit(logger, name="MarineLETKF")
+    def __init__(self, config: Dict) -> None:
+        """Constructor for ocean recentering task
+        Parameters:
+        ------------
+        config: Dict
+            configuration, namely evironment variables
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("init")
+        super().__init__(config)
+
+    @logit(logger)
+    def initialize(self):
+        """Method initialize for ocean recentering task
+        Parameters:
+        ------------
+        None
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("initialize")
+        RUN = self.runtime_config.RUN
+        gcyc = self.runtime_config.gcyc
+
+    @logit(logger)
+    def run(self):
+        """Method run for ocean recentering task
+        Parameters:
+        ------------
+        None
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("run")
+
+        chdir(self.runtime_config.DATA)
+
+    @logit(logger)
+    def finalize(self):
+        """Method finalize for ocean recentering task
+        Parameters:
+        ------------
+        None
+        Returns:
+        --------
+        None
+        """
+
+        logger.info("finalize")
+
+        RUN = self.runtime_config.RUN
+        cyc = self.runtime_config.cyc