Update ush scripts to comply with bash static code checkers

.github/workflows/bash_code_analysis.yaml

@@ -32,11 +32,12 @@ jobs:
       #   with:
       #     filter_mode: nofilter
       #     level: warning
+      #     reporter: github-pr-review
 
       - name: Install shfmt
         uses: mfinelli/setup-shfmt@v4
       - name: shfmt scan
-        run: shfmt -d dev/jobs jobs scripts
+        run: shfmt -d dev/jobs dev/ush jobs scripts ush
 
   shellcheck:
     runs-on: ubuntu-22.04
@@ -57,10 +58,13 @@ jobs:
         with:
           filter_mode: nofilter
           level: warning
+          reporter: github-pr-review
           path: |
             dev/jobs
+            dev/ush
             jobs
             scripts
+            ush
           pattern: |
             config.*
             J*
@@ -88,6 +92,7 @@ jobs:
         with:
           filter_mode: added
           level: warning
+          reporter: github-pr-review
           check_all_files_with_shebangs: true
           pattern: |
             config.*

dev/ush/get_warm_s2sw_restart_tarballs.sh

@@ -33,9 +33,9 @@ fi
 
 cd "${untar_dir}"
 
-ptargets=( "enkfgdas_restartb_grp1.tar" "enkfgdas_restartb_grp2.tar" "enkfgdas_restartb_grp3.tar" "enkfgdas_restartb_grp4.tar" "enkfgdas_restartb_grp5.tar" "enkfgdas_restartb_grp6.tar" "enkfgdas_restartb_grp7.tar" "enkfgdas_restartb_grp8.tar" "gdas_restartb.tar" "gdasocean_restart.tar" "gdaswave_restart.tar" )
+ptargets=("enkfgdas_restartb_grp1.tar" "enkfgdas_restartb_grp2.tar" "enkfgdas_restartb_grp3.tar" "enkfgdas_restartb_grp4.tar" "enkfgdas_restartb_grp5.tar" "enkfgdas_restartb_grp6.tar" "enkfgdas_restartb_grp7.tar" "enkfgdas_restartb_grp8.tar" "gdas_restartb.tar" "gdasocean_restart.tar" "gdaswave_restart.tar")
 
-targets=( "enkfgdas_restarta_grp1.tar" "enkfgdas_restarta_grp2.tar" "enkfgdas_restarta_grp3.tar" "enkfgdas_restarta_grp4.tar" "enkfgdas_restarta_grp5.tar" "enkfgdas_restarta_grp6.tar" "enkfgdas_restarta_grp7.tar" "enkfgdas_restarta_grp8.tar" "gdas_restarta.tar" "gdasocean_analysis.tar")
+targets=("enkfgdas_restarta_grp1.tar" "enkfgdas_restarta_grp2.tar" "enkfgdas_restarta_grp3.tar" "enkfgdas_restarta_grp4.tar" "enkfgdas_restarta_grp5.tar" "enkfgdas_restarta_grp6.tar" "enkfgdas_restarta_grp7.tar" "enkfgdas_restarta_grp8.tar" "gdas_restarta.tar" "gdasocean_analysis.tar")
 
 # This is all specific to Gaea C6
 clusters="es"
@@ -48,7 +48,7 @@ tasks=1
 
 # Construct a wrapper script in a loop to submit to the sbatch system
 for tarball in "${targets[@]}"; do
-  sbatch << EOF
+    sbatch << EOF
 #!/bin/bash
 #SBATCH --job-name=get_retro_${tarball}
 #SBATCH --output=get_retro_${tarball}.out
@@ -81,7 +81,7 @@ done
 
 # Now do the same for the previous cycle tarballs
 for tarball in "${ptargets[@]}"; do
-  sbatch << EOF
+    sbatch << EOF
 #!/bin/bash
 #SBATCH --job-name=get_retro_${tarball}
 #SBATCH --output=get_retro_${tarball}.out

dev/ush/gw_setup.sh

@@ -11,10 +11,10 @@
 # Determine if HOMEgfs is already set
 unset_homegfs=NO
 if [[ -z "${HOMEgfs+x}" ]]; then
-  script_dir="$(cd "$(dirname  "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd )"
-  HOMEgfs=$(cd "${script_dir}" && git rev-parse --show-toplevel)
-  export HOMEgfs
-  unset_homegfs=YES
+    script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" > /dev/null 2>&1 && pwd)"
+    HOMEgfs=$(cd "${script_dir}" && git rev-parse --show-toplevel)
+    export HOMEgfs
+    unset_homegfs=YES
 fi
 source "${HOMEgfs}/ush/detect_machine.sh"
 source "${HOMEgfs}/ush/module-setup.sh"
@@ -23,18 +23,16 @@ module use "${HOMEgfs}/modulefiles"
 module load "gw_setup.${MACHINE_ID}"
 err=$?
 if [[ "${err}" -ne 0 ]]; then
-  echo "FATAL ERROR: Failed to load module_gwsetup.${MACHINE_ID}"
-  exit 1
+    echo "FATAL ERROR: Failed to load module_gwsetup.${MACHINE_ID}"
+    exit 1
 fi
 
 # Set up the PYTHONPATH to include wxflow from HOMEgfs
 if [[ -d "${HOMEgfs}/sorc/wxflow/src" ]]; then
-  PYTHONPATH="${HOMEgfs}/sorc/wxflow/src${PYTHONPATH:+:${PYTHONPATH}}"
-  export PYTHONPATH
+    PYTHONPATH="${HOMEgfs}/sorc/wxflow/src${PYTHONPATH:+:${PYTHONPATH}}"
+    export PYTHONPATH
 fi
 
-
 if [[ ${unset_homegfs} == "YES" ]]; then
-  unset HOMEgfs
+    unset HOMEgfs
 fi
-