adapted to std dev

CMakeLists.txt

@@ -94,7 +94,7 @@ if(BUILD_GDASBUNDLE)
   endif()
   ecbuild_bundle( PROJECT gsw GIT "https://github.com/jcsda-internal/GSW-Fortran.git" BRANCH develop )
   ecbuild_bundle( PROJECT mom6 GIT "https://github.com/jcsda-internal/MOM6.git" BRANCH main-ecbuild RECURSIVE )
-  ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/hybrid-B )
+  ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" BRANCH develop )
 
 # Build IODA converters
   option(BUILD_IODA_CONVERTERS "Build IODA Converters" ON)

parm/soca/berror/saber_blocks.yaml

@@ -42,6 +42,7 @@ components:
         cicen_max: 0.5
         hicen_min: 0.0
         hicen_max: 0.0
+        standard deviation: true
 
       - linear variable change name: BalanceSOCA
 #        kst:

scripts/exgdas_global_marine_analysis_run.sh

@@ -39,6 +39,7 @@ function clean_yaml()
 
 ################################################################################
 # run 3DVAR FGAT
+cp var.yaml var_original.yaml
 clean_yaml var.yaml
 $APRUN_OCNANAL $JEDI_BIN/soca_var.x var.yaml
 export err=$?; err_chk

scripts/exgdas_global_marine_analysis_vrfy.py

@@ -303,7 +303,7 @@ def plot_zonal_slice(config):
 
 evadir = os.path.join(HOMEgfs, 'sorc', f'{RUN}.cd', 'ush', 'eva')
 marinetemplate = os.path.join(evadir, 'marine_gdas_plots.yaml')
-varyaml = os.path.join(comout, 'yaml', 'var.yaml')
+varyaml = os.path.join(comout, 'yaml', 'var_original.yaml')
 
 # it would be better to refrence the dirs explicitly with the comout path
 # but eva doesn't allow for specifying output directories

test/soca/gw/CMakeLists.txt

@@ -40,9 +40,8 @@ set(jjob_list "JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP"
 #              "JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT_VRFY"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT"
-#              "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST")
-#              "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY")
-)
+              "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST"
+              "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY")
 
 set(setup "")
 foreach(jjob ${jjob_list})

ush/diag_statistics.py

@@ -31,8 +31,13 @@ def get_diag_stats():
         zipfilename = diagfilename + '.gz'
         outfilename = 'cnvstat.' + var + '.gdas.' + pdy + cyc + '.csv'
 
-        with tarfile.open(os.path.join(comout, tarfilename), "r") as tf:
-            tf.extract(member=zipfilename)
+        try:
+            with tarfile.open(os.path.join(comout, tarfilename), "r") as tf:
+                tf.extract(member=zipfilename)
+        except FileNotFoundError:
+            print('WARNING: file', os.path.join(comout, tarfilename),
+                  'not found, this is expected in GDASApp ctests')
+            return
         with gzip.open(zipfilename, 'rb') as f_in:
             with open(diagfilename, 'wb') as f_out:
                 shutil.copyfileobj(f_in, f_out)

ush/soca/run_jjobs.py

@@ -138,8 +138,10 @@ def _conda_envs(self, jjob):
         """
         if self.machine != "container":
             if jjob in ENVS:
-                # TODO: This does nothing for now. Make the conda activate work!
-                self.f.write(f"# conda activate {ENVS[jjob]} \n")
+                # set +/-u is a workaround for an apparent conda bug
+                self.f.write(f"set +u \n")
+                self.f.write(f"conda activate {ENVS[jjob]} \n")
+                self.f.write(f"set -u \n")
 
     def precom(self, com, tmpl):
         cmd = f"RUN={self.RUN} YMD={self.gPDY} HH={self.gcyc} generate_com -xr {com}:{tmpl}"