Bring in some changes from develop to dev/gcafs.v1

dev/jobs/JGDAS_AERO_ANALYSIS_GENERATE_BMATRIX

@@ -5,6 +5,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlgenb" -c "base aeroanl aeroanl
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_AERO_ANALYSIS_FINALIZE

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlfinal" -c "base aeroanl aeroan
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_AERO_ANALYSIS_INITIALIZE

@@ -6,6 +6,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlinit" -c "base aeroanl aeroanl
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}

dev/jobs/JGLOBAL_AERO_ANALYSIS_VARIATIONAL

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlvar" -c "base aeroanl aeroanlv
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ANALYSIS_STATS

@@ -5,6 +5,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "anlstat" -c "base anlstat"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ARCHIVE_TARS

@@ -9,6 +9,10 @@ fi
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
     COMIN_ATMOS_ANLMON:COM_ATMOS_ANLMON_TMPL \

dev/jobs/JGLOBAL_ARCHIVE_VRFY

@@ -5,6 +5,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "arch_vrfy" -c "base arch_vrfy"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
     COMIN_ATMOS_GENESIS:COM_ATMOS_GENESIS_TMPL \

dev/jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE

@@ -7,6 +7,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlfinal" -c "base atmensanl at
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 GDUMP="gdas"
 GDUMP_ENS="enkf${GDUMP}"
 

dev/jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlfv3inc" -c "base atmensanl a
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE

@@ -6,6 +6,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlinit" -c "base atmensanl atm
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}

dev/jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlletkf" -c "base atmensanl at
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ATMENS_ANALYSIS_OBS

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlobs" -c "base atmensanl atme
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ATMENS_ANALYSIS_SOL

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlsol" -c "base atmensanl atme
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC

@@ -2,6 +2,10 @@
 
 source "${HOMEgfs}/ush/jjob_header.sh" -e "analcalc" -c "base anal analcalc"
 
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 ##############################################
 # Set variables used in the script
 ##############################################

dev/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC_FV3JEDI

@@ -8,6 +8,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "analcalc_fv3jedi" -c "base analcalc_f
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}

dev/jobs/JGLOBAL_ATMOS_UPP

@@ -5,6 +5,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "upp" -c "base upp"
 ##############################################
 # Set variables used in the exglobal script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlfinal" -c "base atmanl atmanlfi
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ATM_ANALYSIS_FV3_INCREMENT

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlfv3inc" -c "base atmanl atmanlf
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE

@@ -6,6 +6,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlinit" -c "base atmanl atmanlini
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}

dev/jobs/JGLOBAL_ATM_ANALYSIS_VARIATIONAL

@@ -7,6 +7,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlvar" -c "base atmanl atmanlvar"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_ENKF_ARCHIVE_TARS

@@ -5,6 +5,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "earc_tars" -c "base arch_tars earc_ta
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_ATMOS_ANALYSIS_ENSSTAT:COM_ATMOS_ANALYSIS_TMPL \
     COMIN_ATMOS_HISTORY_ENSSTAT:COM_ATMOS_HISTORY_TMPL \

dev/jobs/JGLOBAL_ENKF_ARCHIVE_VRFY

@@ -5,6 +5,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "earc_vrfy" -c "base earc_vrfy"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_ATMOS_ANALYSIS_ENSSTAT:COM_ATMOS_ANALYSIS_TMPL \
     COMIN_ATMOS_HISTORY_ENSSTAT:COM_ATMOS_HISTORY_TMPL \

dev/jobs/JGLOBAL_ENKF_ECEN_FV3JEDI

@@ -8,6 +8,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ecen_fv3jedi" -c "base ecen_fv3jedi"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}

dev/jobs/JGLOBAL_ENS_GLOBUS_ARCH

@@ -5,6 +5,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "globus_earc" -c "base globus earc_gro
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_CONF:COM_CONF_TMPL
 

dev/jobs/JGLOBAL_FETCH

@@ -2,6 +2,10 @@
 
 source "${HOMEgfs}/ush/jjob_header.sh" -e "fetch" -c "base fetch"
 
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # Execute fetching
 # Do not export shell opts to the bash scripts in the htar/hsi wrappers
 export -n SHELLOPTS

dev/jobs/JGLOBAL_FORECAST

@@ -10,6 +10,10 @@ else
     source "${HOMEgfs}/ush/jjob_header.sh" -e "fcst" -c "base fcst"
 fi
 
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # Create the directory to hold restarts and output from the model in stmp
 export DATArestart="${DATAjob}/restart"
 if [[ ! -d "${DATArestart}" ]]; then mkdir -p "${DATArestart}"; fi

dev/jobs/JGLOBAL_GLOBUS_ARCH

@@ -5,6 +5,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "globus_arch" -c "base globus"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_CONF:COM_CONF_TMPL
 

dev/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT

@@ -8,6 +8,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlchkpt" -c "base marineanl ma
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_MARINE_ANALYSIS_ECEN

@@ -9,6 +9,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlecen" -c "base marineanlecen
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")

dev/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE

@@ -8,6 +8,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlfinal" -c "base marineanl ma
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE

@@ -8,6 +8,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlinit" -c "base marineanl mar
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")

dev/jobs/JGLOBAL_MARINE_ANALYSIS_LETKF

@@ -11,6 +11,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlletkf" -c "base marineanllet
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")

dev/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL

@@ -9,6 +9,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlvar" -c "base marineanl mari
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_MARINE_BMAT

@@ -17,6 +17,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marinebmat" -c "base marinebmat"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}

dev/jobs/JGLOBAL_MARINE_BMAT_INITIALIZE

@@ -16,6 +16,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marinebmatinit" -c "base marinebmat m
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 gPDY=${GDATE:0:8}

dev/jobs/JGLOBAL_OCEANICE_PRODUCTS

@@ -2,6 +2,10 @@
 
 source "${HOMEgfs}/ush/jjob_header.sh" -e "oceanice_products" -c "base oceanice_products"
 
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################

dev/jobs/JGLOBAL_OFFLINE_ATMOS_ANALYSIS

@@ -6,6 +6,9 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "offlineanl" -c "base offlineanl"
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 ##############################################
 # Begin JOB SPECIFIC work

dev/jobs/JGLOBAL_PREP_EMISSIONS

@@ -5,6 +5,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "prep_emissions" -c "base prep_emissio
 ##############################################
 # Set variables used in the script
 ##############################################
+# Setup Python path for pygfs
+PYTHONPATH="${HOMEgfs}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
+
 # TODO: Set local variables used in this script e.g. GDATE may be needed for previous cycle
 
 ##############################################