First wave of linter fixes

First wave of linter fixes for removing gfs-utils code/fix reorg. Refs: NOAA-EMC#966
WalterKolczynski-NOAA · Oct 4, 2022 · 797dd70 · 797dd70
1 parent d7e1f29
commit 797dd70
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Showing 11 changed files with 343 additions and 331 deletions.
diff --git a/sorc/build_all.sh b/sorc/build_all.sh
@@ -16,7 +16,7 @@ function _usage() {
 Builds all of the global-workflow components by calling the individual build
   scripts in sequence.
 
-Usage: $BASH_SOURCE [-a UFS_app][-c build_config][-h][-v]
+Usage: ${BASH_SOURCE[0]} [-a UFS_app][-c build_config][-h][-v]
   -a UFS_app:
     Build a specific UFS app instead of the default
   -c build_config:
@@ -30,7 +30,7 @@ EOF
 }
 
 script_dir=$(cd $(dirname "${BASH_SOURCE[0]}") &> /dev/null && pwd)
-cd ${script_dir}
+cd "${script_dir}" || exit 1
 
 _build_ufs_opt=""
 _ops_opt=""
@@ -46,22 +46,22 @@ while getopts ":a:c:hov" option; do
     # s) _build_ufs_opt+="-s ${OPTARG} ";;
     v) _verbose_opt="-v";;
     \?)
-      echo "[$BASH_SOURCE]: Unrecognized option: ${option}"
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
       usage
       ;;
     :)
-      echo "[$BASH_SOURCE]: ${option} requires an argument"
+      echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
   esac
 done
 
 shift $((OPTIND-1))
 
-logs_dir=${script_dir}/logs
-if [ ! -d $logs_dir  ]; then
+logs_dir="${script_dir}/logs"
+if [ ! -d "${logs_dir}"  ]; then
   echo "Creating logs folder"
-  mkdir $logs_dir
+  mkdir "${logs_dir}" || exit 1
 fi
 
 # Check final exec folder exists
@@ -74,7 +74,9 @@ fi
 # GET MACHINE
 #------------------------------------
 target=""
+# shellcheck disable=SC1091
 source gfs_utils.fd/ush/machine-setup.sh > /dev/null 2>&1
+# shellcheck disable=
 if [[ -z "${target}" ]]; then
   echo "FATAL: Unable to determine target machine"
   exit 1
@@ -85,10 +87,9 @@ fi
 #------------------------------------
 source ./partial_build.sh $_verbose_opt $_partial_opt
 
-if [ $target = jet ]; then
-  Build_gldas=false
-  Build_gfs_util=false
-  Build_ww3_prepost=false
+if [[ ${target} == "jet" ]]; then
+  Build_gldas="false"
+  Build_ww3_prepost="false"
 fi
 
 #------------------------------------
@@ -100,44 +101,44 @@ err=0
 #------------------------------------
 # build WW3 pre & post execs
 #------------------------------------
-$Build_ww3_prepost && {
+${Build_ww3_prepost} && {
   echo " .... Building WW3 pre and post execs .... "
-  ./build_ww3prepost.sh ${_verbose_opt} ${_build_ufs_opt} > $logs_dir/build_ww3_prepost.log 2>&1
+  ./build_ww3prepost.sh ${_verbose_opt} ${_build_ufs_opt} > ${logs_dir}/build_ww3_prepost.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building WW3 pre/post processing."
-    echo "The log file is in $logs_dir/build_ww3_prepost.log"
+    echo "The log file is in ${logs_dir}/build_ww3_prepost.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 
 #------------------------------------
 # build forecast model
 #------------------------------------
-$Build_ufs_model && {
+${Build_ufs_model} && {
   echo " .... Building forecast model .... "
-  ./build_ufs.sh $_verbose_opt ${_build_ufs_opt} > $logs_dir/build_ufs.log 2>&1
+  ./build_ufs.sh ${_verbose_opt} ${_build_ufs_opt} > ${logs_dir}/build_ufs.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building UFS model."
-    echo "The log file is in $logs_dir/build_ufs.log"
+    echo "The log file is in ${logs_dir}/build_ufs.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 
 #------------------------------------
 # build GSI and EnKF - optional checkout
 #------------------------------------
 if [ -d gsi_enkf.fd ]; then
-  $Build_gsi_enkf && {
+  ${Build_gsi_enkf} && {
   echo " .... Building gsi and enkf .... "
-  ./build_gsi_enkf.sh $_ops_opt $_verbose_opt > $logs_dir/build_gsi_enkf.log 2>&1
+  ./build_gsi_enkf.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_gsi_enkf.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building gsi_enkf."
-    echo "The log file is in $logs_dir/build_gsi_enkf.log"
+    echo "The log file is in ${logs_dir}/build_gsi_enkf.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 else
   echo " .... Skip building gsi and enkf .... "
@@ -147,15 +148,15 @@ fi
 # build gsi utilities
 #------------------------------------
 if [ -d gsi_utils.fd ]; then
-  $Build_gsi_utils && {
+  ${Build_gsi_utils} && {
   echo " .... Building gsi utilities .... "
-  ./build_gsi_utils.sh $_ops_opt $_verbose_opt > $logs_dir/build_gsi_utils.log 2>&1
+  ./build_gsi_utils.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_gsi_utils.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building gsi utilities."
-    echo "The log file is in $logs_dir/build_gsi_utils.log"
+    echo "The log file is in ${logs_dir}/build_gsi_utils.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 else
   echo " .... Skip building gsi utilities .... "
@@ -165,15 +166,15 @@ fi
 # build gdas - optional checkout
 #------------------------------------
 if [ -d gdas.cd ]; then
-  $Build_gdas  && {
+  ${Build_gdas}  && {
   echo " .... Building GDASApp  .... "
-  ./build_gdas.sh $_verbose_opt > $logs_dir/build_gdas.log 2>&1
+  ./build_gdas.sh ${_verbose_opt} > ${logs_dir}/build_gdas.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building GDASApp."
-    echo "The log file is in $logs_dir/build_gdas.log"
+    echo "The log file is in ${logs_dir}/build_gdas.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 else
   echo " .... Skip building GDASApp  .... "
@@ -183,62 +184,62 @@ fi
 # build gsi monitor
 #------------------------------------
 if [ -d gsi_monitor.fd ]; then
-  $Build_gsi_monitor && {
-  echo " .... Building gsi monitor .... "
-  ./build_gsi_monitor.sh $_ops_opt $_verbose_opt > $logs_dir/build_gsi_monitor.log 2>&1
-  rc=$?
-  if [[ $rc -ne 0 ]] ; then
-    echo "Fatal error in building gsi monitor."
-    echo "The log file is in $logs_dir/build_gsi_monitor.log"
-  fi
-  ((err+=$rc))
-}
+  ${Build_gsi_monitor} && {
+    echo " .... Building gsi monitor .... "
+    ./build_gsi_monitor.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_gsi_monitor.log 2>&1
+    rc=$?
+    if [[ ${rc} -ne 0 ]] ; then
+      echo "Fatal error in building gsi monitor."
+      echo "The log file is in ${logs_dir}/build_gsi_monitor.log"
+    fi
+    err=$((err + rc))
+  }
 else
   echo " .... Skip building gsi monitor .... "
 fi
 
 #------------------------------------
 # build UPP
 #------------------------------------
-$Build_upp && {
+${Build_upp} && {
   echo " .... Building UPP .... "
-  ./build_upp.sh $_ops_opt $_verbose_opt > $logs_dir/build_upp.log 2>&1
+  ./build_upp.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_upp.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building UPP."
-    echo "The log file is in $logs_dir/build_upp.log"
+    echo "The log file is in ${logs_dir}/build_upp.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 
 #------------------------------------
 # build ufs_utils
 #------------------------------------
-$Build_ufs_utils && {
+${Build_ufs_utils} && {
   echo " .... Building ufs_utils .... "
-  ./build_ufs_utils.sh $_verbose_opt > $logs_dir/build_ufs_utils.log 2>&1
+  ./build_ufs_utils.sh ${_verbose_opt} > ${logs_dir}/build_ufs_utils.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building ufs_utils."
-    echo "The log file is in $logs_dir/build_ufs_utils.log"
+    echo "The log file is in ${logs_dir}/build_ufs_utils.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 
 #------------------------------------
 # build gldas
 #------------------------------------
 if [ -d gldas.fd ]; then
-  $Build_gldas && {
-  echo " .... Building gldas .... "
-  ./build_gldas.sh $_verbose_opt > $logs_dir/build_gldas.log 2>&1
-  rc=$?
-  if [[ $rc -ne 0 ]] ; then
-    echo "Fatal error in building gldas."
-    echo "The log file is in $logs_dir/build_gldas.log"
-  fi
-  ((err+=$rc))
-}
+  ${Build_gldas} && {
+    echo " .... Building gldas .... "
+    ./build_gldas.sh ${_verbose_opt} > ${logs_dir}/build_gldas.log 2>&1
+    rc=$?
+    if [[ ${rc} -ne 0 ]] ; then
+      echo "Fatal error in building gldas."
+      echo "The log file is in ${logs_dir}/build_gldas.log"
+    fi
+    err=$((err + rc))
+  }
 else
   echo " .... Skip building gldas .... "
 fi
@@ -247,37 +248,37 @@ fi
 # build gfs_wafs - optional checkout
 #------------------------------------
 if [ -d gfs_wafs.fd ]; then
-  $Build_gfs_wafs  && {
-  echo " .... Building gfs_wafs  .... "
-  ./build_gfs_wafs.sh $_verbose_opt > $logs_dir/build_gfs_wafs.log 2>&1
-  rc=$?
-  if [[ $rc -ne 0 ]] ; then
-    echo "Fatal error in building gfs_wafs."
-    echo "The log file is in $logs_dir/build_gfs_wafs.log"
-  fi
-  ((err+=$rc))
-}
+  ${Build_gfs_wafs}  && {
+    echo " .... Building gfs_wafs  .... "
+    ./build_gfs_wafs.sh ${_verbose_opt} > ${logs_dir}/build_gfs_wafs.log 2>&1
+    rc=$?
+    if [[ ${rc} -ne 0 ]] ; then
+      echo "Fatal error in building gfs_wafs."
+      echo "The log file is in ${logs_dir}/build_gfs_wafs.log"
+    fi
+    err=$((err + rc))
+  }
 fi
 
 #------------------------------------
 # build gfs_utils
 #------------------------------------
-$Build_gfs_utils && {
+${Build_gfs_utils} && {
   echo " .... Building gfs_utils .... "
-  target=$target ./build_gfs_utils.sh $_verbose_opt > $logs_dir/build_gfs_utils.log 2>&1
+  target=$target ./build_gfs_utils.sh ${_verbose_opt} > ${logs_dir}/build_gfs_utils.log 2>&1
   rc=$?
-  if [[ $rc -ne 0 ]] ; then
+  if [[ ${rc} -ne 0 ]] ; then
     echo "Fatal error in building gfs_utils."
-    echo "The log file is in $logs_dir/build_gfs_utils.log"
+    echo "The log file is in ${logs_dir}/build_gfs_utils.log"
   fi
-  ((err+=$rc))
+  err=$((err + rc))
 }
 
 #------------------------------------
 # Exception Handling
 #------------------------------------
-[[ $err -ne 0 ]] && echo "FATAL BUILD ERROR: Please check the log file for detail, ABORT!"
-$ERRSCRIPT || exit $err
+[[ ${err} -ne 0 ]] && echo "FATAL BUILD ERROR: Please check the log file for detail, ABORT!"
+${ERRSCRIPT} || exit ${err}
 
 echo;echo " .... Build system finished .... "
 

diff --git a/sorc/build_gdas.sh b/sorc/build_gdas.sh
@@ -1,12 +1,14 @@
 #! /usr/bin/env bash
 set -eux
 
-script_dir=$(dirname ${BASH_SOURCE[0]})
-cd ${script_dir}
+script_dir=$(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 disable=
 
-export BUILD_TARGET=$target
+export BUILD_TARGET="${target}"
 
 # use more build jobs if on NOAA HPC
 build_jobs=4
@@ -22,7 +24,7 @@ if [ ! -d "../exec" ]; then
 fi
 
 cd gdas.cd
-BUILD_JOBS=$build_jobs ./build.sh -t $BUILD_TARGET
+BUILD_JOBS="${build_jobs}" ./build.sh -t "${BUILD_TARGET}"
 
 exit
 
diff --git a/sorc/build_gfs_utils.sh b/sorc/build_gfs_utils.sh
@@ -1,19 +1,35 @@
 #! /usr/bin/env bash
 set -eux
 
+function _usage() {
+  cat << EOF
+Builds all of the global-workflow components by calling the individual build
+  scripts in sequence.
+
+Usage: ${BASH_SOURCE[0]} [-d][-h][-v]
+  -d:
+    Build with debug options
+  -h:
+    Print this help message and exit
+  -v:
+    Turn on verbose output
+EOF
+  exit 1
+}
+
 cwd=$(pwd)
 
 OPTIND=1
-while getopts ":dov" option; do
+while getopts ":dv" option; do
   case "${option}" in
     d) export BUILD_TYPE="DEBUG";;
     v) export BUILD_VERBOSE="YES";;
     \?)
-      echo "[$BASH_SOURCE]: Unrecognized option: ${option}"
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
       usage
       ;;
     :)
-      echo "[$BASH_SOURCE]: ${option} requires an argument"
+      echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
   esac

diff --git a/sorc/build_gfs_wafs.sh b/sorc/build_gfs_wafs.sh
@@ -1,8 +1,8 @@
 #! /usr/bin/env bash
 set -eux
 
-script_dir=$(dirname ${BASH_SOURCE[0]})
-cd ${script_dir}
+script_dir=$(dirname "${BASH_SOURCE[0]}")
+cd "${script_dir}" || exit 1
 
 # Check final exec folder exists
 if [ ! -d "../exec" ]; then