Turn C96C48_ufs_hybatmDA and C48mx500_3DVarAOWCDA into a regression test

ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml

@@ -5,6 +5,7 @@ base:
   DO_JEDIATMVAR: "YES"
   DO_JEDIATMENS: "YES"
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"
 atmanl:
   LAYOUT_X_ATMANL: 4
   LAYOUT_Y_ATMANL: 4

parm/config/gfs/config.atmanl

@@ -6,6 +6,7 @@
 echo "BEGIN: config.atmanl"
 
 export JCB_ALGO_YAML_VAR=@JCB_ALGO_YAML_VAR@
+export JCB_ALGO_YAML_FV3INC=@JCB_ALGO_YAML_FV3INC@
 
 export STATICB_TYPE=@STATICB_TYPE@
 export LOCALIZATION_TYPE="bump"

parm/config/gfs/config.atmensanl

@@ -8,6 +8,7 @@ echo "BEGIN: config.atmensanl"
 export JCB_ALGO_YAML_LETKF=@JCB_ALGO_YAML_LETKF@
 export JCB_ALGO_YAML_OBS=@JCB_ALGO_YAML_OBS@
 export JCB_ALGO_YAML_SOL=@JCB_ALGO_YAML_SOL@
+export JCB_ALGO_YAML_FV3INC=@JCB_ALGO_YAML_FV3INC@
 
 export INTERP_METHOD='barycentric'
 

parm/config/gfs/yaml/defaults.yaml

@@ -25,6 +25,7 @@ base:
 
 atmanl:
   JCB_ALGO_YAML_VAR: "${PARMgfs}/gdas/atm/jcb-prototype_3dvar.yaml.j2"
+  JCB_ALGO_YAML_FV3INC: "${PARMgfs}/gdas/atm/jcb-prototype_3dvar-fv3inc.yaml.j2"
   STATICB_TYPE: "gsibec"
   LAYOUT_X_ATMANL: 8
   LAYOUT_Y_ATMANL: 8
@@ -35,6 +36,7 @@ atmensanl:
   JCB_ALGO_YAML_LETKF: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2"
   JCB_ALGO_YAML_OBS: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_observer.yaml.j2"
   JCB_ALGO_YAML_SOL: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_solver.yaml.j2"
+  JCB_ALGO_YAML_FV3INC: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf-fv3inc.yaml.j2"
   LAYOUT_X_ATMENSANL: 8
   LAYOUT_Y_ATMENSANL: 8
   IO_LAYOUT_X: 1

parm/gdas/atmanl_jedi_config.yaml.j2

@@ -10,4 +10,4 @@ atmanlfv3inc:
   exe_src: '{{ EXECgfs }}/fv3jedi_fv3inc.x'
   mpi_cmd: '{{ APRUN_ATMANLFV3INC }}'
   jcb_base_yaml: '{{ PARMgfs }}/gdas/atm/jcb-base.yaml.j2'
-  jcb_algo: fv3jedi_fv3inc_variational
+  jcb_algo_yaml: '{{ JCB_ALGO_YAML_FV3INC }}'

parm/gdas/atmensanl_jedi_config.yaml.j2

@@ -17,7 +17,7 @@ atmensanlfv3inc:
   exe_src: '{{ EXECgfs }}/fv3jedi_fv3inc.x'
   mpi_cmd: '{{ APRUN_ATMENSANLFV3INC }}'
   jcb_base_yaml: '{{ PARMgfs }}/gdas/atm/jcb-base.yaml.j2'
-  jcb_algo: fv3jedi_fv3inc_lgetkf
+  jcb_algo_yaml: '{{ JCB_ALGO_YAML_FV3INC }}'
 atmensanlletkf:
   rundir: '{{ DATA }}'
   exe_src: '{{ EXECgfs }}/gdas.x'

sorc/link_workflow.sh

@@ -242,7 +242,6 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
   cd "${HOMEgfs}/ush" || exit 1
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/soca"                              .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ufsda"                              .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/jediinc2fv3.py"                     .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_json.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_yaml.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.py"    .

ush/python/pygfs/task/marine_analysis.py

@@ -211,6 +211,8 @@ def _prep_variational_yaml(self: Task) -> None:
         envconfig_jcb['SOCA_NINNER'] = self.task_config.SOCA_NINNER
         envconfig_jcb['obs_list'] = ['adt_rads_all']
         envconfig_jcb['MOM6_LEVS'] = mdau.get_mom6_levels(str(self.task_config.OCNRES))
+        envconfig_jcb['HOMEgfs'] = self.task_config.HOMEgfs
+        envconfig_jcb['DO_TEST_MODE'] = self.task_config.DO_TEST_MODE
 
         # Write obs_list_short
         save_as_yaml(parse_obs_list_file(self.task_config.MARINE_OBS_LIST_YAML), 'obs_list_short.yaml')
@@ -220,12 +222,8 @@ def _prep_variational_yaml(self: Task) -> None:
         jcb_base_yaml = os.path.join(self.task_config.PARMsoca, 'marine-jcb-base.yaml')
         jcb_algo_yaml = os.path.join(self.task_config.PARMsoca, 'marine-jcb-3dfgat.yaml.j2')
 
-        jcb_base_config = YAMLFile(path=jcb_base_yaml)
-        jcb_base_config = Template.substitute_structure(jcb_base_config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig_jcb.get)
-        jcb_base_config = Template.substitute_structure(jcb_base_config, TemplateConstants.DOLLAR_PARENTHESES, envconfig_jcb.get)
-        jcb_algo_config = YAMLFile(path=jcb_algo_yaml)
-        jcb_algo_config = Template.substitute_structure(jcb_algo_config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig_jcb.get)
-        jcb_algo_config = Template.substitute_structure(jcb_algo_config, TemplateConstants.DOLLAR_PARENTHESES, envconfig_jcb.get)
+        jcb_base_config = parse_j2yaml(jcb_base_yaml, envconfig_jcb)
+        jcb_algo_config = parse_j2yaml(jcb_algo_yaml, envconfig_jcb)
 
         # Override base with the application specific config
         jcb_config = {**jcb_base_config, **jcb_algo_config}