move JEDI executable link to analysis.py (NOAA-EMC#1313)

parm/config/config.aeroanl

@@ -18,7 +18,7 @@ export BERROR_DATE="20160630.000000"
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIVAREXE=${HOMEgfs}/exec/fv3jedi_var.x
+export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
 export crtm_VERSION="2.3.0"
 
 echo "END: config.aeroanl"

parm/config/config.atmanl

@@ -19,7 +19,7 @@ export layout_y=1
 export io_layout_x=1
 export io_layout_y=1
 
-export JEDIVAREXE=${HOMEgfs}/exec/fv3jedi_var.x
+export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
 export crtm_VERSION="2.3.0"
 
 echo "END: config.atmanl"

parm/config/config.atmensanl

@@ -17,7 +17,7 @@ export layout_y=1
 export io_layout_x=1
 export io_layout_y=1
 
-export JEDIENSEXE=${HOMEgfs}/exec/fv3jedi_letkf.x
+export JEDIEXE=${HOMEgfs}/exec/fv3jedi_letkf.x
 export crtm_VERSION="2.3.0"
 
 echo "END: config.atmensanl"

ush/python/pygfs/task/aero_analysis.py

@@ -68,7 +68,6 @@ def initialize(self: Analysis) -> None:
         - staging B error files
         - staging model backgrounds
         - generating a YAML file for the JEDI executable
-        - linking the JEDI executable (TODO make it copyable, requires JEDI fix)
         - creating output directories
         """
         super().initialize()
@@ -99,14 +98,6 @@ def initialize(self: Analysis) -> None:
         save_as_yaml(varda_yaml, self.task_config.fv3jedi_yaml)
         logger.info(f"Wrote variational YAML to: {self.task_config.fv3jedi_yaml}")
 
-        # link executable to DATA/ directory
-        exe_src = self.task_config['JEDIVAREXE']
-        logger.debug(f"Link executable {exe_src} to DATA/")  # TODO: linking is not permitted per EE2.  Needs work in JEDI to be able to copy the exec.
-        exe_dest = os.path.join(self.task_config['DATA'], os.path.basename(exe_src))
-        if os.path.exists(exe_dest):
-            rm_p(exe_dest)
-        os.symlink(exe_src, exe_dest)
-
         # need output dir for diags and anl
         logger.debug("Create empty output [anl, diags] directories to receive output from executable")
         newdirs = [

ush/python/pygfs/task/analysis.py

@@ -5,7 +5,7 @@
 from netCDF4 import Dataset
 from typing import List, Dict, Any
 
-from pygw.yaml_file import YAMLFile, parse_j2yaml
+from pygw.yaml_file import YAMLFile, parse_j2yaml, parse_yamltmpl
 from pygw.file_utils import FileHandler
 from pygw.template import Template, TemplateConstants
 from pygw.logger import logit
@@ -36,6 +36,9 @@ def initialize(self) -> None:
         bias_dict = self.get_bias_dict()
         FileHandler(bias_dict).sync()
 
+        # link jedi executable to run directory
+        self.link_jediexe()
+
     @logit(logger)
     def get_obs_dict(self: Task) -> Dict[str, Any]:
         """Compile a dictionary of observation files to copy
@@ -171,3 +174,28 @@ def get_berror_dict(self, config: Dict[str, Any]) -> Dict[str, List[str]]:
         """
         berror_dict = {'foo': 'bar'}
         return berror_dict
+
+    @logit(logger)
+    def link_jediexe(self: Task) -> None:
+        """Compile a dictionary of background error files to copy
+
+        This method links a JEDI executable to the run directory
+
+        Parameters
+        ----------
+        Task: GDAS task
+
+        Returns
+        ----------
+        None
+        """
+        exe_src = self.task_config.JEDIEXE
+
+        # TODO: linking is not permitted per EE2.  Needs work in JEDI to be able to copy the exec.
+        logger.debug(f"Link executable {exe_src} to DATA/")
+        exe_dest = os.path.join(self.task_config.DATA, os.path.basename(exe_src))
+        if os.path.exists(exe_dest):
+            rm_p(exe_dest)
+        os.symlink(exe_src, exe_dest)
+
+        return

ush/python/pygfs/task/atm_analysis.py

@@ -67,7 +67,6 @@ def initialize(self: Analysis) -> None:
         - staging B error files
         - staging model backgrounds
         - generating a YAML file for the JEDI executable
-        - linking the JEDI executable (TODO make it copyable, requires JEDI fix)
         - creating output directories
         """
         super().initialize()
@@ -98,14 +97,6 @@ def initialize(self: Analysis) -> None:
         save_as_yaml(varda_yaml, self.task_config.fv3jedi_yaml)
         logger.info(f"Wrote variational YAML to: {self.task_config.fv3jedi_yaml}")
 
-        # link executable to DATA/ directory
-        exe_src = self.task_config.JEDIVAREXE
-        logger.debug(f"Link executable {exe_src} to DATA/")  # TODO: linking is not permitted per EE2.  Needs work in JEDI to be able to copy the exec.
-        exe_dest = os.path.join(self.task_config.DATA, os.path.basename(exe_src))
-        if os.path.exists(exe_dest):
-            rm_p(exe_dest)
-        os.symlink(exe_src, exe_dest)
-
         # need output dir for diags and anl
         logger.debug("Create empty output [anl, diags] directories to receive output from executable")
         newdirs = [

ush/python/pygfs/task/atmens_analysis.py

@@ -67,7 +67,6 @@ def initialize(self: Analysis) -> None:
         - staging FV3-JEDI fix files
         - staging model backgrounds
         - generating a YAML file for the JEDI executable
-        - linking the JEDI executable (TODO make it copyable, requires JEDI fix)
         - creating output directories
 
         Parameters
@@ -101,14 +100,6 @@ def initialize(self: Analysis) -> None:
         save_as_yaml(ensda_yaml, self.task_config.fv3jedi_yaml)
         logger.info(f"Wrote ensemble da YAML to: {self.task_config.fv3jedi_yaml}")
 
-        # link executable to DATA/ directory
-        exe_src = self.task_config.JEDIENSEXE
-        logger.debug(f"Link executable {exe_src} to DATA/")  # TODO: linking is not permitted per EE2.  Needs work in JEDI to be able to copy the exec.
-        exe_dest = os.path.join(self.task_config.DATA, os.path.basename(exe_src))
-        if os.path.exists(exe_dest):
-            rm_p(exe_dest)
-        os.symlink(exe_src, exe_dest)
-
         # need output dir for diags and anl
         logger.debug("Create empty output [anl, diags] directories to receive output from executable")
         newdirs = [