Relocate config templates to dev/ space in prep for EE2

dev/ci/cases/gfsv17/marine3dvar.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 
 base:
   DOIAU: "YES"

dev/ci/cases/gfsv17/marinehyb.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 
 base:
   DOIAU: "YES"

dev/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DO_JEDISNOWDA: "YES"
   DO_TEST_MODE: "NO"

dev/ci/cases/yamls/gefs_defaults_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gefs/yaml/defaults.yaml
 base:
   SFS_POST: "NO"
   FHOUT_GFS: 6

dev/ci/cases/yamls/gefs_replay_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gefs/yaml/defaults.yaml
 base:
   REPLAY_ICS: "YES"
   FCST_BREAKPOINTS: ""

dev/ci/cases/yamls/gfs_cyc_defaults_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DOIAU: "YES"
   DO_JEDIATMVAR: "NO"
@@ -18,11 +18,11 @@ base:
   EUPD_CYC: "both"
   INTERVAL_GFS: 6
   SDATE_GFS: 2021122018
-  NMEM_ENS_GFS: 2 
-  NMEM_ENS_GFS_OFFSET: 0 
+  NMEM_ENS_GFS: 2
+  NMEM_ENS_GFS_OFFSET: 0
   DO_TEST_MODE: "NO"
 
 marineanl:
   SOCA_NINNER: 1
 
-  
+

dev/ci/cases/yamls/gfs_defaults_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DO_TEST_MODE: "YES"
   FETCHDIR: "/NCEPDEV/emc-global/1year/David.Grumm/test_data"

dev/ci/cases/yamls/gfs_extended_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 
 base:
   DO_GOES: "YES"

dev/ci/cases/yamls/gfs_hyb_defaults_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DO_GSISOILDA: "YES"
   DO_TEST_MODE: "YES"

dev/ci/cases/yamls/gfs_metp_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DO_TEST_MODE: "NO"
   DO_METP: "YES"

dev/ci/cases/yamls/sfs_defaults.yaml

@@ -1,26 +1,13 @@
+defaults:
+  !INC {{ HOMEgfs }}/dev/parm/config/sfs/yaml/defaults.yaml
 base:
-  DO_JEDIATMVAR: "NO"
-  DO_JEDIATMENS: "NO"
-  DO_JEDIOCNVAR: "NO"
-  DO_JEDISNOWDA: "NO"
-  DO_MERGENSST: "NO"
-  DO_BUFRSND: "NO"
-  DO_GEMPAK: "NO"
-  DO_AWIPS: "NO"
-  KEEPDATA: "NO"
-  DO_EXTRACTVARS: "NO"
   FHMAX_GFS: 144
-  FHMAX_HF_GFS: 0
-  FHOUT_HF_GFS: 1
   FHOUT_GFS: 24
   FHOUT_OCN_GFS: 24
   FHOUT_ICE_GFS: 24
   FCST_BREAKPOINTS: "48,96"
-  REPLAY_ICS: "NO"
   USE_OCN_ENS_PERTURB_FILES: "YES"
   USE_ATM_ENS_PERTURB_FILES: "YES"
-  HPSSARCH: "NO"
-  LOCALARCH: "NO"
 fcst:
   TYPE: "hydro"
   MONO: "mono"

dev/ci/cases/yamls/sfs_full.yaml

@@ -1,26 +1,14 @@
+defaults:
+  !INC {{ HOMEgfs }}/dev/parm/config/sfs/yaml/defaults.yaml
 base:
-  DO_JEDIATMVAR: "NO"
-  DO_JEDIATMENS: "NO"
-  DO_JEDIOCNVAR: "NO"
-  DO_JEDISNOWDA: "NO"
-  DO_MERGENSST: "NO"
-  DO_BUFRSND: "NO"
-  DO_GEMPAK: "NO"
-  DO_AWIPS: "NO"
-  KEEPDATA: "NO"
-  DO_EXTRACTVARS: "NO"
   FHMAX_GFS: 2976
-  FHMAX_HF_GFS: 0
-  FHOUT_HF_GFS: 1
   FHOUT_GFS: 24
   FHOUT_OCN_GFS: 24
   FHOUT_ICE_GFS: 24
   FCST_BREAKPOINTS: ""
   REPLAY_ICS: "NO"
   USE_OCN_ENS_PERTURB_FILES: "YES"
   USE_ATM_ENS_PERTURB_FILES: "YES"
-  HPSSARCH: "NO"
-  LOCALARCH: "NO"
 fcst:
   TYPE: "hydro"
   MONO: "mono"

dev/ci/cases/yamls/soca_gfs_defaults_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DO_JEDIOCNVAR: "YES"
   DO_METP: "NO"

dev/ci/cases/yamls/soca_hyb_gfs_defaults_ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DO_JEDIOCNVAR: "YES"
   DOHYBVAR_OCN: "YES"

dev/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml

@@ -1,5 +1,5 @@
 defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+  !INC {{ HOMEgfs }}/dev/parm/config/gfs/yaml/defaults.yaml
 base:
   DOIAU: "NO"
   DO_JEDIATMVAR: "YES"

dev/ci/scripts/unittests/test_create_experiment.py

@@ -23,6 +23,7 @@ def test_create_experiment():
         if case.endswith('.yaml'):
             env['pslot'] = os.path.splitext(case)[0]
             cmd_args = ['-y', f'{yaml_dir}/{case}']
+            print(f"Running create_experiment.py for {case}")
             create_experiment(*cmd_args, env=env)
             if create_experiment.returncode:
                 print(f"FATAL ERROR: Failed to create experiment for {case}")

parm/config/gfs/config.aerosol_init → dev/parm/config/gfs/config.aerosol_init

@@ -5,6 +5,6 @@
 echo "BEGIN: config.aerosol_init"
 
 # Get task specific resources
-source $EXPDIR/config.resources aerosol_init
+source "${EXPDIR}/config.resources" aerosol_init
 
 echo "END: config.aerosol_init"

parm/config/gfs/config.anal → dev/parm/config/gfs/config.anal

@@ -6,10 +6,10 @@
 echo "BEGIN: config.anal"
 
 # Get task specific resources
-. ${EXPDIR}/config.resources anal
+source "${EXPDIR}/config.resources" anal
 
 if [[ ${DONST} = "YES" ]]; then
-  . ${EXPDIR}/config.nsst
+  source "${EXPDIR}/config.nsst"
 fi
 
 if [[ "${RUN}" == "gfs" ]] ; then

parm/config/gfs/config.analcalc → dev/parm/config/gfs/config.analcalc

@@ -6,6 +6,6 @@
 echo "BEGIN: config.analcalc"
 
 # Get task specific resources
-. ${EXPDIR}/config.resources analcalc
+source "${EXPDIR}/config.resources" analcalc
 
 echo "END: config.analcalc"

parm/config/gfs/config.analdiag → dev/parm/config/gfs/config.analdiag

@@ -6,6 +6,6 @@
 echo "BEGIN: config.analdiag"
 
 # Get task specific resources
-. $EXPDIR/config.resources analdiag
+source "${EXPDIR}/config.resources" analdiag
 
 echo "END: config.analdiag"

parm/config/gfs/config.anlstat → dev/parm/config/gfs/config.anlstat

@@ -9,7 +9,7 @@ echo "BEGIN: config.anlstat"
 source "${EXPDIR}/config.resources" anlstat
 
 export JEDI_CONFIG_YAML="${PARMgfs}/gdas/anlstat_jedi_config.yaml.j2"
-export STAT_BASE_CONFIG_YAML="${PARMgfs}/config/gfs/yaml/stat_base_config.yaml.j2"
+export STAT_BASE_CONFIG_YAML="${PARMgfs}/gdas/stat_base_config.yaml.j2"
 export JCB_BASE_YAML="${PARMgfs}/gdas/stat/aero/jcb-base.yaml.j2"
 export JCB_ALGO_YAML="${PARMgfs}/gdas/jcb-algorithms/anlstat.yaml.j2"
 export JEDIEXE="${HOMEgfs}/sorc/gdas.cd/build/bin/ioda-stats.x"

parm/config/gfs/config.ecen → dev/parm/config/gfs/config.ecen

@@ -6,16 +6,17 @@
 echo "BEGIN: config.ecen"
 
 # Get task specific resources
-. $EXPDIR/config.resources ecen
+source "${EXPDIR}/config.resources" ecen
 
 # Number of concurrent ecen jobs [1 implies sequential]
 # Usually IAUFHRS_ENKF=3,6,9, so NECENGRP=3.  Scripting
 # below queries IAUFHRS_ENKF to determine NECENGRP
 export NECENGRP=1
-if [ $DOIAU_ENKF = "YES" ]; then
-   ngrps=$(grep -o ',' <<<"$IAUFHRS_ENKF" | grep -c .)
+if [[ ${DOIAU_ENKF} = "YES" ]]; then
+   # shellcheck disable=SC2312
+   ngrps=$(grep -o ',' <<<"${IAUFHRS_ENKF}" | grep -c .)
    ((ngrps++))
-   export NECENGRP=$ngrps
+   export NECENGRP=${ngrps}
 fi
 
 echo "END: config.ecen"

parm/config/gfs/config.echgres → dev/parm/config/gfs/config.echgres

@@ -6,6 +6,6 @@
 echo "BEGIN: config.echgres"
 
 # Get task specific resources
-. $EXPDIR/config.resources echgres
+source "${EXPDIR}/config.resources" echgres
 
 echo "END: config.echgres"

parm/config/gfs/config.ediag → dev/parm/config/gfs/config.ediag

@@ -6,6 +6,6 @@
 echo "BEGIN: config.ediag"
 
 # Get task specific resources
-. $EXPDIR/config.resources ediag
+source "${EXPDIR}/config.resources" ediag
 
 echo "END: config.ediag"

parm/config/gfs/config.eobs → dev/parm/config/gfs/config.eobs

@@ -6,7 +6,7 @@
 echo "BEGIN: config.eobs"
 
 # Get task specific resources
-. $EXPDIR/config.resources eobs
+source "${EXPDIR}/config.resources" eobs
 
 
 # GSI namelist options related to observer for EnKF

parm/config/gfs/config.epos → dev/parm/config/gfs/config.epos

@@ -6,11 +6,11 @@
 echo "BEGIN: config.epos"
 
 # Get task specific resources
-. $EXPDIR/config.resources epos
+source "${EXPDIR}/config.resources" epos
 
 # No. of concurrent epos jobs [1 implies sequential]
 export NEPOSGRP=7
-if [ $l4densvar = ".false." ]; then
+if [[ "${l4densvar}" == ".false." ]]; then
     export NEPOSGRP=3
 fi
 

parm/config/gfs/config.esfc → dev/parm/config/gfs/config.esfc

@@ -6,7 +6,7 @@
 echo "BEGIN: config.esfc"
 
 # Get task specific resources
-. $EXPDIR/config.resources esfc
+source "${EXPDIR}/config.resources" esfc
 
 # With IAU only need surface analysis at start of IAU window.
 # Set DOSFCANL_ENKF=NO to prevent creation of sfcanl at 

parm/config/gfs/config.eupd → dev/parm/config/gfs/config.eupd

@@ -6,7 +6,7 @@
 echo "BEGIN: config.eupd"
 
 # Get task specific resources
-. $EXPDIR/config.resources eupd
+source "${EXPDIR}/config.resources" eupd
 
 export ntasks_enkf=${ntasks}
 

parm/config/gfs/config.postsnd → dev/parm/config/gfs/config.postsnd

@@ -6,9 +6,9 @@
 echo "BEGIN: config.postsnd"
 
 # Get task specific resources
-. $EXPDIR/config.resources postsnd
+source "${EXPDIR}/config.resources" postsnd
 
 export ENDHOUR=180
-if [[ "$FHMAX_GFS" -lt "$ENDHOUR" ]] ; then export ENDHOUR=$FHMAX_GFS ; fi
+if [[ ${FHMAX_GFS} -lt ${ENDHOUR} ]] ; then export ENDHOUR=${FHMAX_GFS} ; fi
 
 echo "END: config.postsnd"

parm/config/gfs/config.prep → dev/parm/config/gfs/config.prep

@@ -6,7 +6,7 @@
 echo "BEGIN: config.prep"
 
 # Get task specific resources
-. $EXPDIR/config.resources prep
+source "${EXPDIR}/config.resources" prep
 
 export MAKE_PREPBUFR="YES"   # if NO, will copy prepbufr from globaldump
 export cdate10=${PDY}${cyc}
@@ -16,7 +16,7 @@ export PROCESS_TROPCY=${PROCESS_TROPCY:-NO}
 export TROPCYQCRELOSH="${SCRgfs}/exglobal_atmos_tropcy_qc_reloc.sh"
 
 export COMINtcvital=${COMINtcvital:-${DMPDIR}/${RUN}.${PDY}/${cyc}/atmos}
-export COMINsyn=${COMINsyn:-$(compath.py ${envir}/com/gfs/${gfs_ver})/syndat}
+export COMINsyn=${COMINsyn:-$(compath.py "${envir}/com/gfs/${gfs_ver}")/syndat}
 
 # Adjust observation error for GFS v16 parallels
 #
@@ -27,7 +27,7 @@ export PRVT=${FIXgfs}/gsi/prepobs_errtable.global
 
 
 # Set prepobs.errtable.global for GFS v16 retrospective parallels
-if [[ $RUN_ENVIR == "emc" ]]; then
+if [[ ${RUN_ENVIR} == "emc" ]]; then
   if [[ "${PDY}${cyc}" -ge "2019021900" && "${PDY}${cyc}" -lt "2019110706" ]]; then
     export PRVT=${FIXgfs}/gsi/gfsv16_historical/prepobs_errtable.global.2019021900
   fi

parm/config/gfs/config.sfcanl → dev/parm/config/gfs/config.sfcanl

@@ -6,7 +6,7 @@
 echo "BEGIN: config.sfcanl"
 
 # Get task specific resources
-. $EXPDIR/config.resources sfcanl
+source "${EXPDIR}/config.resources" sfcanl
 
 # Turn off NST in JEDIATMVAR
 if [[ "${DO_JEDIATMVAR}" == "YES" ]]; then

parm/config/gfs/config.waveawipsbulls → dev/parm/config/gfs/config.waveawipsbulls

@@ -6,6 +6,6 @@
 echo "BEGIN: config.waveawipsbulls"
 
 # Get task specific resources
-. $EXPDIR/config.resources waveawipsbulls
+source "${EXPDIR}/config.resources" waveawipsbulls
 
 echo "END: config.waveawipsbulls"

parm/config/gfs/config.waveawipsgridded → dev/parm/config/gfs/config.waveawipsgridded

@@ -6,7 +6,7 @@
 echo "BEGIN: config.waveawipsgridded"
 
 # Get task specific resources
-. $EXPDIR/config.resources waveawipsgridded
+source "${EXPDIR}/config.resources" waveawipsgridded
 
 export GEMPAK_GRIDS=${GEMPAK_GRIDS:-ak_10m at_10m ep_10m wc_10m glo_30m}
 # export GEMPAK_GRIDS=${GEMPAK_GRIDS:-ao_9km at_10m ep_10m wc_10m glo_30m}

parm/config/gfs/config.wavegempak → dev/parm/config/gfs/config.wavegempak

@@ -6,7 +6,7 @@
 echo "BEGIN: config.wavegempak"
 
 # Get task specific resources
-. $EXPDIR/config.resources wavegempak
+source "${EXPDIR}/config.resources" wavegempak
 
 #export GEMPAK_GRIDS=${GEMPAK_GRIDS:-'glo_30m at_10m ep_10m wc_10m ao_9km'} #Interpolated grids
 export GEMPAK_GRIDS=${GEMPAK_GRIDS:-${waveinterpGRD:-'glo_30m'}}

parm/config/gfs/config.waveinit → dev/parm/config/gfs/config.waveinit

@@ -6,7 +6,7 @@
 echo "BEGIN: config.waveinit"
 
 # Get task specific resources
-. $EXPDIR/config.resources waveinit
+source "${EXPDIR}/config.resources" waveinit
 
 # Step label
 export sigMODE=${sigMODE:-init}

parm/config/gfs/config.waveprep → dev/parm/config/gfs/config.waveprep

@@ -6,7 +6,7 @@
 echo "BEGIN: config.waveprep"
 
 # Get task specific resources
-. $EXPDIR/config.resources waveprep
+source "${EXPDIR}/config.resources" waveprep
 
 # Step label
 export sigMODE=${sigMODE:-prep}
@@ -20,7 +20,7 @@ export WAV_CUR_CDO_SMOOTH="NO"
 # Location of CDO module
 export CDO_ROOT=${CDO_ROOT:-/usrx/local/dev/packages/cdo/1.9.8}
 
-if [ "${WW3ICEINP}" = "YES" ]; then
+if [[ "${WW3ICEINP}" == "YES" ]]; then
   export WAVICEFILE=${RUN}.t${cyc}z.seaice.5min.grib2
 fi