Linter fixes for fix dir reorg

Second wave of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966

sorc/build_all.sh

@@ -29,7 +29,7 @@ EOF
   exit 1
 }
 
-script_dir=$(cd $(dirname "${BASH_SOURCE[0]}") &> /dev/null && pwd)
+script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
 cd "${script_dir}" || exit 1
 
 _build_ufs_opt=""
@@ -45,14 +45,14 @@ while getopts ":a:c:hov" option; do
     o) _ops_opt+="-o";;
     # s) _build_ufs_opt+="-s ${OPTARG} ";;
     v) _verbose_opt="-v";;
-    \?)
-      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-      usage
-      ;;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
+    *)
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
+      usage
+      ;;
   esac
 done
 
@@ -76,7 +76,7 @@ fi
 target=""
 # shellcheck disable=SC1091
 source gfs_utils.fd/ush/machine-setup.sh > /dev/null 2>&1
-# shellcheck disable=
+# shellcheck enable=SC1091
 if [[ -z "${target}" ]]; then
   echo "FATAL: Unable to determine target machine"
   exit 1
@@ -85,6 +85,7 @@ fi
 #------------------------------------
 # INCLUDE PARTIAL BUILD
 #------------------------------------
+# shellcheck source-path=sorc/
 source ./partial_build.sh $_verbose_opt $_partial_opt
 
 if [[ ${target} == "jet" ]]; then

sorc/build_gfs_utils.sh

@@ -24,18 +24,18 @@ while getopts ":dv" option; do
   case "${option}" in
     d) export BUILD_TYPE="DEBUG";;
     v) export BUILD_VERBOSE="YES";;
-    \?)
-      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-      usage
-      ;;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
+    *)
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
+      usage
+      ;;    
   esac
 done
 shift $((OPTIND-1))
 
-${cwd}/gfs_utils.fd/sorc/build_gfs_utils.sh
+"${cwd}/gfs_utils.fd/sorc/build_gfs_utils.sh"
 
 exit

sorc/build_ww3prepost.sh

@@ -4,7 +4,9 @@ set -x
 script_dir=$(dirname "${BASH_SOURCE[0]}")
 cd "${script_dir}" || exit 1
 
+# shellcheck disable=SC1091
 source gfs_utils.fd/ush/machine-setup.sh > /dev/null 2>&1
+# shellcheck enable=SC1091
 
 # Default settings
 APP="S2SWA"
@@ -13,14 +15,14 @@ while getopts "a:v" option; do
   case "${option}" in
     a) APP="${OPTARG}" ;;
     v) BUILD_VERBOSE="YES";;
-    \?)
-      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-      usage
-      ;;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
+    *)
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
+      usage
+      ;;
   esac
 done
 
@@ -43,9 +45,7 @@ finalexecdir=$( pwd -P )/../exec
 #Determine machine and load modules
 set +x
 module use ../modulefiles
-# shellcheck disable=SC1091
 module load modulefile.ww3.${target}
-# shellcheck disable=
 set -x
 
 #Set WW3 directory, switch, prep and post exes 

sorc/checkout.sh

@@ -146,7 +146,7 @@ while getopts ":chgum:o" option; do
 done
 shift $((OPTIND-1))
 
-export topdir=$(cd $(dirname "${BASH_SOURCE[0]}") &> /dev/null && pwd)
+export topdir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
 export logdir="${topdir}/logs"
 mkdir -p "${logdir}
 "

ush/gfs_bufr.sh

@@ -66,7 +66,7 @@ while (( hh <= FEND )); do
           break
       fi
 
-      if (( $ic >= 360 )); then
+      if (( ic >= 360 )); then
          echo "FATAL: COULD NOT LOCATE logf${hh3} file AFTER 1 HOUR"
          exit 2
       fi

ush/gfs_bufr_netcdf.sh

@@ -111,7 +111,7 @@ ln -sf $PARMbufrsnd/bufr_gfs_${CLASS}.tbl fort.1
 ln -sf ${STNLIST:-$PARMbufrsnd/bufr_stalist.meteo.gfs} fort.8
 ln -sf $PARMbufrsnd/bufr_ij13km.txt fort.7
 
-${APRUN_POSTSND} ${EXECbufrsnd}/${pgm} < gfsparm > out_gfs_bufr_$FEND
+${APRUN_POSTSND} "${EXECbufrsnd}/${pgm}" < gfsparm > "out_gfs_bufr_${FEND}"
 export err=$?
 
 exit ${err}

ush/gfs_sndp.sh

@@ -47,8 +47,7 @@ cd $DATA/$m
 EOF
        # JY export err=$?; err_chk
        export err=$?; #err_chk
-       if [ $err -ne 0 ]
-       then
+       if (( err != 0 )); then
           echo "ERROR in $pgm"
           err_chk
        fi

ush/syndat_getjtbul.sh

@@ -185,6 +185,6 @@ fi
 
 echo "Leaving sub-shell syndat_getjtbul.sh to recover JTWC Bulletins" \
  >> $pgmout
-echo " " >> $pgmout
+echo " " >> "${pgmout}"
 
 exit

ush/syndat_qctropcy.sh

@@ -384,6 +384,6 @@ then
 fi
 
 #  Write JTWC/FNOC Tcvitals to /com path since not saved anywhere else
-[ $SENDCOM = YES ]  &&  cp fnoc ${COMSP}jtwc-fnoc.tcvitals.$tmmark
+[ $SENDCOM = YES ]  &&  cp fnoc "${COMSP}jtwc-fnoc.tcvitals.${tmmark}"
 
 exit