NOAA-EMC · DavidHuber-NOAA · Dec 19, 2025 · Dec 11, 2025 · Dec 11, 2025 · Dec 11, 2025
@@ -80,6 +80,7 @@ parm/post/post_tag_gfs128
 parm/post/gfs
 parm/post/gefs
 parm/post/sfs
+parm/post/gcafs
 parm/post/ocean.csv
 parm/post/ocean_gefs.csv
 parm/post/ocean_gfs.csv
@@ -96,9 +97,11 @@ parm/ufs/MOM6_data_table.IN
 parm/ufs/ice_in.IN
 parm/ufs/ufs.configure.*.IN
 parm/ufs/post_itag_gfs
+parm/ufs/post_itag_gcafs
 parm/ufs/ww3_shel.nml.IN
 parm/ufs/global_control.nml.IN
 parm/regrid_sfc
+parm/chem/nexus
 
 # Ignore sorc and logs folders from externals
 #--------------------------------------------

@@ -17,3 +17,6 @@ disable=SC2174
 
 # Disable warning of functions in test statements
 disable=SC2310
+
+# Disable masking of return codes from chained commands.  Use `set -o pipefail` to trap them.
+disable=SC2312
@@ -71,7 +71,6 @@ while true; do
 
     # Get job statistics
     echo "Gather Rocoto statistics"
-    # shellcheck disable=SC2312 # We want to use the exit code of the command
     full_state=$("${HOMEgfs}/dev/ci/scripts/utils/rocotostat.py" -w "${xml}" -d "${db}" -v)
     error_stat=$?
 

@@ -253,7 +253,6 @@ function delete_dataroot() {
     _runtests="${1}"
     _pslot="${2}"
 
-    # shellcheck disable=SC2312
     eval "$(
         PDY=0 cyc=0 source "${_runtests}/EXPDIR/${_pslot}/config.base" >&/dev/null
         echo _dataroot="${STMP}/RUNDIRS/${_pslot}"

@@ -74,11 +74,9 @@ if [[ ! -s "${COMINobsproc_PREV}/${GDUMP}.t${gcyc}z.updated.status.tm00.bufr_d"
     fi
 fi
 # exception handling to ensure no dead link
-# shellcheck disable=SC2312
 if [[ $(find "${COMOUT_OBS}" -xtype l | wc -l) -ge 1 ]]; then
     exit 9
 fi
-# shellcheck disable=SC2312
 if [[ $(find "${COMINobsproc_PREV}" -xtype l | wc -l) -ge 1 ]]; then
     exit 9
 fi
@@ -155,9 +153,10 @@ export COMSP=${COMSP:-"${COMIN_OBS}/${RUN_local}.t${cyc}z."}
 # Create or Copy prepbufr, prepbufr.acft_profiles, nsstbufr files
 # Do not fail on external errors
 if [[ ${MAKE_PREPBUFR:-"YES"} == "YES" ]]; then
-    set +eu
+    unset_strict
     "${HOMEobsproc}/jobs/JOBSPROC_GLOBAL_PREP" && true
     export err=$?
+    set_strict
     if [[ ${err} -ne 0 ]]; then
         err_exit "JOBSPROC_GLOBAL_PREP job failed, ABORT!"
     fi

@@ -34,15 +34,14 @@ export JYYYY=${PDY:0:4}
 ##############################################
 
 # Do not fail on errors or unassigned variables in external code
-set +eu
+unset_strict
 "${SCRIPTens_tracker}/exgfs_tc_genesis.sh" && true
 export err=$?
+set_strict
 if [[ ${err} -ne 0 ]]; then
     err_exit
 fi
 
-set_strict
-
 ##############################################
 # Final processing
 ##############################################

@@ -29,13 +29,16 @@ done
 if [[ "${RUN_GRID2GRID_STEP1}" == "YES" || "${RUN_GRID2OBS_STEP1}" == "YES" || "${RUN_PRECIP_STEP1}" == "YES" ]]; then
     # Override the -e in VERIF_GLOBALSH's shebang and un-export SHELLOPTS
     # TODO: clean up the verif-global script so it does not raise false-positive errors
-    set +eu
+    unset_strict
     export -n SHELLOPTS
     bash -x "${VERIF_GLOBALSH}"
     err=$?
+    set_strict
     if [[ ${err} -ne 0 ]]; then
         exit "${err}"
     fi
 fi
 
-if [[ ${KEEPDATA:-"NO"} == "NO" ]]; then rm -rf "${DATAROOT}"; fi # TODO: This should be $DATA
+if [[ ${KEEPDATA:-"NO"} == "NO" ]]; then
+    rm -rf "${DATAROOT}" # TODO: This should be $DATA
+fi
@@ -80,17 +80,15 @@ fi
 # Run archive script
 ###############################################################
 
-set +eu
 # Do not export shell opts to the bash scripts in the htar/hsi wrappers
 export -n SHELLOPTS
+unset_strict
 ${GLOBALARCHIVESH:-${SCRgfs}/exglobal_archive_tars.py}
 export err=$?
-set +x
+set_strict
 if [[ ${err} -ne 0 ]]; then
     err_exit "failed to archive the COM structure"
 fi
-set_trace
-set_strict
 
 ##############################################
 # End JOB SPECIFIC work
@@ -106,10 +104,7 @@ fi
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd "${DATAROOT}" || (
-    echo "${DATAROOT} does not exist. ABORT!"
-    exit 1
-)
+cd "${DATAROOT}" || true
 if [[ "${KEEPDATA}" == "NO" ]]; then
     rm -rf "${DATA}"
 fi

@@ -45,13 +45,7 @@ fi
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd "${DATAROOT}" && true
-export err=$?
-set +e
-if [[ ${err} -ne 0 ]]; then
-    err_exit "${DATAROOT} does not exist, ABORT!"
-fi
-set_trace
+cd "${DATAROOT}" || true
 if [[ "${KEEPDATA}" == "NO" ]]; then
     rm -rf "${DATA}"
 fi

@@ -2,7 +2,6 @@
 
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
-# shellcheck disable=SC2312
 
 source "${HOMEgfs}/ush/jjob_header.sh" -e "analcalc_fv3jedi" -c "base analcalc_fv3jedi"
 

@@ -23,16 +23,14 @@ mkdir -p "${COMIN_CONF}"
 ###############################################################
 
 # Calls an external bash command; do not fail on unassigned/error
-set +eu
 export -n SHELLOPTS
+unset_strict
 "${SCRgfs}/exglobal_enkf_earc_tars.py"
 export err=$?
-set +x
+set_strict
 if [[ ${err} -ne 0 ]]; then
     err_exit "Failed to archive the ensemble COM structure"
 fi
-set_trace
-set_strict
 
 ###############################################################
 
@@ -50,10 +48,7 @@ fi
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd "${DATAROOT}" || (
-    echo "${DATAROOT} does not exist. ABORT!"
-    exit 1
-)
+cd "${DATAROOT}" || true
 if [[ "${KEEPDATA}" == "NO" ]]; then
     rm -rf "${DATA}"
 fi

@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
@@ -13,7 +13,6 @@ source "${EXPDIR}/config.resources" ecen
 # below queries IAUFHRS_ENKF to determine NECENGRP
 export NECENGRP=1
 if [[ ${DOIAU_ENKF} = "YES" ]]; then
-   # shellcheck disable=SC2312
    ngrps=$(grep -o ',' <<<"${IAUFHRS_ENKF}" | grep -c .)
    ((ngrps++))
    export NECENGRP=${ngrps}

@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
@@ -6,7 +6,6 @@
 export is_exclusive="True"
 unset memory
 
-# shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
 done
@@ -18,7 +18,7 @@
 ################################################################################
 
 # Do not exit on errors so that restricted data can be protected
-set +eu
+unset_strict
 
 if [[ ! -s "${radstat}" || ! -s "${biascr}" ]]; then
     export err=1
@@ -102,7 +102,6 @@ for type in ${SATYPE}; do
         netcdf=1
     fi
 
-    # shellcheck disable=SC2312
     if [[ $(find . -maxdepth 1 -type f -name "diag_${type}_ges.${PDY}${cyc}*.${Z}" | wc -l) -gt 0 ]]; then
         mv "diag_${type}_ges.${PDY}${cyc}"*".${Z}" "${type}.${Z}"
         ${UNCOMPRESS} "./${type}.${Z}"
@@ -111,7 +110,6 @@ for type in ${SATYPE}; do
     fi
 
     if [[ ${USE_ANL} -eq 1 ]]; then
-        # shellcheck disable=SC2312
         file_count=$(find . -maxdepth 1 -type f -name "diag_${type}_anl.${PDY}${cyc}*.${Z}" | wc -l)
         if [[ ${file_count} -gt 0 ]]; then
             mv "diag_${type}_anl.${PDY}${cyc}"*".${Z}" "${type}_anl.${Z}"

@@ -82,7 +82,6 @@ export opt28=' -new_grid_interpolation budget -fi '
 cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.t${cyc}z.pres_a.0p25.f${fcsthr}.grib2" "tmpfile2${fcsthr}"
 cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.t${cyc}z.pres_b.0p25.f${fcsthr}.grib2" "tmpfile2b${fcsthr}"
 cat "tmpfile2${fcsthr}" "tmpfile2b${fcsthr}" > "tmpfile${fcsthr}"
-# shellcheck disable=SC2312
 ${WGRIB2} "tmpfile${fcsthr}" | grep -F -f "${PARMgfs}/product/gfs_awips_parmlist_g2" |
     ${WGRIB2} -i -grib masterfile "tmpfile${fcsthr}" && true
 export err=$?
@@ -91,7 +90,6 @@ if [[ ${err} -ne 0 ]]; then
 fi
 
 ${WGRIB2} masterfile -match ":PWAT:entire atmosphere" -grib gfs_pwat.grb
-# shellcheck disable=SC2312
 ${WGRIB2} masterfile | grep -v ":PWAT:entire atmosphere" | ${WGRIB2} -i -grib temp_gfs masterfile
 ##################################################################
 #  Process to change PWAT from level 200 to 10 (Entire Atmosphere)
@@ -156,7 +154,6 @@ for GRID in conus ak prico pac 003; do
     # NOTE: numparm is the total of fields in grib2_awpgfs_20km_conusf000 file
     ###########################################################################
     numparm=247
-    # shellcheck disable=SC2312
     numrec=$(${WGRIB2} "awps_file_f${fcsthr}_${GRID}" | wc -l)
 
     if [[ ${numrec} -lt ${numparm} ]]; then

@@ -38,7 +38,6 @@ for fhr3 in 006 012 024; do
     cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.${cycle}.pres_a.0p25.f${fhr3}.grib2" "tmp_pgrb2_0p25${fhr3}"
     cpreq "${COMIN_ATMOS_GRIB_0p25}/gfs.${cycle}.pres_b.0p25.f${fhr3}.grib2" "tmp_pgrb2b_0p25${fhr3}"
     cat "tmp_pgrb2_0p25${fhr3}" "tmp_pgrb2b_0p25${fhr3}" > "tmp0p25filef${fhr3}"
-    # shellcheck disable=SC2312
     ${WGRIB2} "tmp0p25filef${fhr3}" | grep -F -f "${PARMgfs}/product/gfs_fbwnd_parmlist_g2" |
         ${WGRIB2} -i -grib "tmpfilef${fhr3}" "tmp0p25filef${fhr3}"
     ${CNVGRIB} -g21 "tmpfilef${fhr3}" "gfs.t${cyc}z.grbf${fhr3}_grb1"

@@ -49,15 +49,13 @@ while [[ ${fhr} -le ${fhend} ]]; do
 
     if [[ ${do_all} -eq 1 ]]; then
         do_all=0
-        # shellcheck disable=SC2312
         awk '{print $1}' "${HOMEgfs}/gempak/fix/gfs_meta" | envsubst > "poescript"
     else
         #
         #    Do not try to grep out 12, it will grab the 12 from 126.
         #    This will work as long as we don't need 12 fhr metafiles
         #
         if [[ ${fhr} -ne 12 ]]; then
-            # shellcheck disable=SC2312
             grep "${fhr}" "${HOMEgfs}/gempak/fix/gfs_meta" | awk -F" [0-9]" '{print $1}' | envsubst > "poescript"
         fi
     fi

@@ -21,8 +21,7 @@ done
 NAGRIB_TABLE="${HOMEgfs}/gempak/fix/nagrib.tbl"
 NAGRIB="${GEMEXE}/nagrib2"
 
-# shellcheck disable=SC2312
-entry=$(grep "^${RUN2} " "${NAGRIB_TABLE}" | awk 'index($1,"#") != 1 {print $0}')
+entry=$(grep "^${RUN2} " "${NAGRIB_TABLE}" | awk 'index($1,"#") != 1 {print $0}' || echo "")
 
 if [[ "${entry}" != "" ]]; then
     cpyfil=$(echo "${entry}" | awk 'BEGIN {FS="|"} {print $2}')
@@ -61,7 +60,7 @@ startmsg
 
 ${NAGRIB} << EOF
 GBFILE   = grib${fhr3}
-INDXFL   = 
+INDXFL   =
 GDOUTF   = ${GEMGRD}
 PROJ     = ${proj}
 GRDAREA  = ${grdarea}
@@ -71,7 +70,7 @@ CPYFIL   = ${cpyfil}
 GAREA    = ${garea}
 OUTPUT   = ${output}
 GBTBLS   = ${gbtbls}
-GBDIAG   = 
+GBDIAG   =
 PDSEXT   = ${pdsext}
 l
 r

@@ -110,7 +110,6 @@ for ((fhr = SHOUR; fhr <= FHOUR; fhr = fhr + FHINC)); do
     cpreq "${COMIN_ATMOS_GRIB_0p50}/gfs.t${cyc}z.pres_a.0p50.f${fhr3}.grib2" tmpfile2
     cpreq "${COMIN_ATMOS_GRIB_0p50}/gfs.t${cyc}z.pres_b.0p50.f${fhr3}.grib2" tmpfile2b
     cat tmpfile2 tmpfile2b > tmpfile
-    # shellcheck disable=SC2312
     ${WGRIB2} tmpfile | grep -F -f "${paramlist}" | ${WGRIB2} -i -grib pgb2file tmpfile && true
     export err=$?
     if [[ ${err} -ne 0 ]]; then

@@ -86,15 +86,13 @@ if [[ -f "${PARMgfs}/wave/wave_${NET}.buoys" ]]; then
     cpreq -f "${PARMgfs}/wave/wave_${NET}.buoys" buoy.loc.temp
     if [[ "${DOBNDPNT_WAV}" == "YES" ]]; then
         #only do boundary points
-        # shellcheck disable=SC2312
         sed -n '/^\$.*/!p' buoy.loc.temp | grep IBP > buoy.loc || {
             echo "WARNING: No boundary points found in buoy file ${PARMgfs}/wave/wave_${NET}.buoys"
             echo "         Ending job without doing anything."
             exit 0
         }
     else
         #exclude boundary points
-        # shellcheck disable=SC2312
         sed -n '/^\$.*/!p' buoy.loc.temp | grep -v IBP > buoy.loc
     fi
 fi
@@ -182,7 +180,6 @@ if [[ ${err} -ne 0 && ! -f buoy_log.ww3 ]]; then
 fi
 
 # Create new buoy_log.ww3
-# shellcheck disable=SC2312
 awk '{print $3}' buoy.loc | sed 's/'\''//g' > ibp_tags
 grep -F -f ibp_tags buoy_log.ww3 > buoy_log.tmp
 rm -f buoy_log.dat
@@ -199,7 +196,6 @@ fi
 
 # 1.f Data summary
 
-# shellcheck disable=SC2312
 cat << EOF
 
 Input files read and processed at : $(date)
@@ -219,11 +215,8 @@ EOF
 
 echo '   Making command file for wave post points '
 
-# shellcheck disable=SC2312
 grep -F -f ibp_tags buoy_log.dat | awk '{ print $2 }' > buoys
-# shellcheck disable=SC2312
 grep -F -f buoys buoy_log.ww3 | awk '{ print $1 }' > points
-# shellcheck disable=SC2312
 points=$(awk '{print $0 "\\n"}' points | tr -d '\n')
 rm -f buoys