From ab7fc7b12e33e8dda33e1aa717aec10b57c3223d Mon Sep 17 00:00:00 2001
From: "kate.friedman" <kate.friedman@noaa.gov>
Date: Thu, 20 Oct 2022 19:47:56 +0000
Subject: [PATCH 1/7] Update gfs-utils ush script paths

- Update scripts that use gfs-utils ush scripts to point to new path
under /ush folder (used to be /util/ush).

Refs #1059
---
 gempak/ush/gempak_gfs_f00_gif.sh | 2 +-
 parm/config/config.gldas         | 2 +-
 scripts/exgfs_atmos_fbwind.sh    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/gempak/ush/gempak_gfs_f00_gif.sh b/gempak/ush/gempak_gfs_f00_gif.sh
index 172cb687a2..2a7cca5c9f 100755
--- a/gempak/ush/gempak_gfs_f00_gif.sh
+++ b/gempak/ush/gempak_gfs_f00_gif.sh
@@ -593,7 +593,7 @@ if [ $SENDCOM = YES ]; then
   export input=${COMOUT}/${hgttmp500dev}
   export HEADER=YES
   export OUTPATH=$DATA/gfs_500_hgt_tmp_nh_anl_${cyc}.tif
-  ${UTILgfs}/ush/make_tif.sh
+  ${USHgfs}/make_tif.sh
 fi 
 
    msg=" GEMPAK_GIF ${fhr} hour completed normally"
diff --git a/parm/config/config.gldas b/parm/config/config.gldas
index 8d503d0368..c51829d9fc 100755
--- a/parm/config/config.gldas
+++ b/parm/config/config.gldas
@@ -11,6 +11,6 @@ echo "BEGIN: config.gldas"
 export GLDASSH=$HOMEgfs/scripts/exgdas_atmos_gldas.sh
 export gldas_spinup_hours=72
 export CPCGAUGE=$DMPDIR
-export FINDDATE=$HOMEgfs/util/ush/finddate.sh
+export FINDDATE=$USHgfs/finddate.sh
 
 echo "END: config.gldas"
diff --git a/scripts/exgfs_atmos_fbwind.sh b/scripts/exgfs_atmos_fbwind.sh
index ee15e6c634..e7d0ff3d82 100755
--- a/scripts/exgfs_atmos_fbwind.sh
+++ b/scripts/exgfs_atmos_fbwind.sh
@@ -79,7 +79,7 @@ fi
 if test "$SENDDBN" = 'YES'
 then
 #    make_ntc_bull.pl WMOBH NONE KWNO NONE tran.fbwnd_pacific ${COMOUTwmo}/tran.fbwnd_pacific.$job_name
-   ${UTILgfs}/ush/make_ntc_bull.pl WMOBH NONE KWNO NONE tran.fbwnd_pacific ${COMOUTwmo}/tran.fbwnd_pacific.$job_name
+   ${USHgfs}/make_ntc_bull.pl WMOBH NONE KWNO NONE tran.fbwnd_pacific ${COMOUTwmo}/tran.fbwnd_pacific.$job_name
 fi
 
 #####################################################################

From 680c02944b2d83ab5dc021e2b0a92a80e3c2aebb Mon Sep 17 00:00:00 2001
From: "kate.friedman" <kate.friedman@noaa.gov>
Date: Thu, 20 Oct 2022 19:49:48 +0000
Subject: [PATCH 2/7] Update build_gfs_utils.sh for new repo home

Refs #1059
---
 sorc/build_gfs_utils.sh | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/sorc/build_gfs_utils.sh b/sorc/build_gfs_utils.sh
index 9bceedb733..06e70c01ed 100755
--- a/sorc/build_gfs_utils.sh
+++ b/sorc/build_gfs_utils.sh
@@ -1,10 +1,9 @@
 #! /usr/bin/env bash
 set -eux
 
-function _usage() {
+function usage() {
   cat << EOF
-Builds all of the global-workflow components by calling the individual build
-  scripts in sequence.
+Builds the GFS utility programs.
 
 Usage: ${BASH_SOURCE[0]} [-d][-h][-v]
   -d:
@@ -24,6 +23,9 @@ while getopts ":dv" option; do
   case "${option}" in
     d) export BUILD_TYPE="DEBUG";;
     v) export BUILD_VERBOSE="YES";;
+    h)
+      usage
+      ;;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
@@ -31,11 +33,13 @@ while getopts ":dv" option; do
     *)
       echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
       usage
-      ;;    
+      ;;
   esac
 done
 shift $((OPTIND-1))
 
-"${cwd}/gfs_utils.fd/sorc/build_gfs_utils.sh"
+BUILD_TYPE=${BUILD_TYPE:-"Release"} \
+BUILD_VERBOSE=${BUILD_VERBOSE:-"NO"} \
+${cwd}/gfs_utils.fd/ush/build.sh
 
-exit
\ No newline at end of file
+exit

From 45732567cbb0d821d37905e90842c072ad5a39c1 Mon Sep 17 00:00:00 2001
From: "kate.friedman" <kate.friedman@noaa.gov>
Date: Thu, 20 Oct 2022 19:50:28 +0000
Subject: [PATCH 3/7] Update link_workflow.sh for new gfs-utils repo

- Update machine detection.
- Update gfs-utils exec symlink location.
- Add gfs-utils ush scripts as symlinks.

Refs #1059
---
 sorc/link_workflow.sh | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 15c09168d9..79dda2f63e 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -47,9 +47,9 @@ top_dir=$(cd "$(dirname "${script_dir}")" &> /dev/null && pwd)
 cd ${script_dir}
 
 # shellcheck disable=SC1091
-source gfs_utils.fd/ush/machine-setup.sh > /dev/null 2>&1
+source gfs_utils.fd/ush/detect_machine.sh  # (sets MACHINE_ID)
 # shellcheck disable=
-machine="${target:?}"
+machine=$(echo $MACHINE_ID | cut -d. -f1)
 
 #------------------------------
 #--model fix fields
@@ -139,6 +139,9 @@ cd "${top_dir}/ush" || exit 8
         emcsfc_snow.sh  fv3gfs_filter_topo.sh  global_cycle.sh  fv3gfs_make_grid.sh ; do
         ${LINK} "${script_dir}/ufs_utils.fd/ush/${file}" .
     done
+    for file in finddate.sh  make_ntc_bull.pl  make_NTC_file.pl  make_tif.sh  month_name.sh ; do
+        ${LINK} "${script_dir}/gfs_utils.fd/ush/${file}" .
+    done
 
 #-----------------------------------
 #--add gfs_wafs link if checked out
@@ -227,7 +230,7 @@ for utilexe in fbwndgfs.x gaussian_sfcanl.x gfs_bufr.x regrid_nemsio.x supvit.x
   syndat_maksynrc.x syndat_qctropcy.x tocsbufr.x enkf_chgres_recenter.x \
   enkf_chgres_recenter_nc.x fv3nc2nemsio.x tave.x vint.x reg2grb2.x ; do
     [[ -s "${utilexe}" ]] && rm -f "${utilexe}"
-    ${LINK} "${script_dir}/gfs_utils.fd/sorc/install/bin/${utilexe}" .
+    ${LINK} "${script_dir}/gfs_utils.fd/install/bin/${utilexe}" .
 done
 
 [[ -s "ufs_model.x" ]] && rm -f ufs_model.x

From 29ae2196b5c72873c973a5f9f0aac0d5fbf5f8db Mon Sep 17 00:00:00 2001
From: "kate.friedman" <kate.friedman@noaa.gov>
Date: Thu, 20 Oct 2022 20:04:24 +0000
Subject: [PATCH 4/7] Add h to getopts in build_gfs_utils.sh

Refs #1059
---
 sorc/build_gfs_utils.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sorc/build_gfs_utils.sh b/sorc/build_gfs_utils.sh
index 06e70c01ed..432e733d29 100755
--- a/sorc/build_gfs_utils.sh
+++ b/sorc/build_gfs_utils.sh
@@ -19,7 +19,7 @@ EOF
 cwd=$(pwd)
 
 OPTIND=1
-while getopts ":dv" option; do
+while getopts ":dvh" option; do
   case "${option}" in
     d) export BUILD_TYPE="DEBUG";;
     v) export BUILD_VERBOSE="YES";;

From 3467e864bb31f5da55d4b550315dd4989887a083 Mon Sep 17 00:00:00 2001
From: "kate.friedman" <kate.friedman@noaa.gov>
Date: Thu, 20 Oct 2022 20:18:42 +0000
Subject: [PATCH 5/7] Update gfs-utils hash to af933d3

Refs #1059
---
 Externals.cfg    | 2 +-
 sorc/checkout.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Externals.cfg b/Externals.cfg
index 3bc53ffe64..1bd2d4400d 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -8,7 +8,7 @@ protocol = git
 required = True
 
 [gfs-utils]
-hash = 7bf599f
+hash = af933d3
 local_path = sorc/gfs_utils.fd
 repo_url = https://github.com/NOAA-EMC/gfs-utils
 protocol = git
diff --git a/sorc/checkout.sh b/sorc/checkout.sh
index d6326e5da9..b53d43496e 100755
--- a/sorc/checkout.sh
+++ b/sorc/checkout.sh
@@ -151,7 +151,7 @@ mkdir -p "${logdir}"
 
 # The checkout version should always be a speciifc commit (hash or tag), not a branch
 errs=0
-checkout "gfs_utils.fd"    "https://github.com/NOAA-EMC/gfs-utils"              "7bf599f"          ; errs=$((errs + $?))
+checkout "gfs_utils.fd"    "https://github.com/NOAA-EMC/gfs-utils"              "af933d3"                    ; errs=$((errs + $?))
 checkout "ufs_model.fd"    "https://github.com/ufs-community/ufs-weather-model" "${ufs_model_hash:-3c3548d}" ; errs=$((errs + $?))
 checkout "ufs_utils.fd"    "https://github.com/ufs-community/UFS_UTILS.git"     "8b990c0"                    ; errs=$((errs + $?))
 checkout "verif-global.fd" "https://github.com/NOAA-EMC/EMC_verif-global.git"   "c267780"                    ; errs=$((errs + $?))

From f272e643ad5c2fa4c105732de7ce74a259dde41a Mon Sep 17 00:00:00 2001
From: "Kate.Friedman" <Kate.Friedman@noaa.gov>
Date: Thu, 20 Oct 2022 20:25:30 +0000
Subject: [PATCH 6/7] Address SC2086 and SC2250 linter warnings

Refs #1059
---
 sorc/build_gfs_utils.sh | 2 +-
 sorc/link_workflow.sh   | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/sorc/build_gfs_utils.sh b/sorc/build_gfs_utils.sh
index 432e733d29..f160caa0aa 100755
--- a/sorc/build_gfs_utils.sh
+++ b/sorc/build_gfs_utils.sh
@@ -40,6 +40,6 @@ shift $((OPTIND-1))
 
 BUILD_TYPE=${BUILD_TYPE:-"Release"} \
 BUILD_VERBOSE=${BUILD_VERBOSE:-"NO"} \
-${cwd}/gfs_utils.fd/ush/build.sh
+"${cwd}"/gfs_utils.fd/ush/build.sh
 
 exit
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 79dda2f63e..6aef3fb934 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -44,12 +44,12 @@ shift $((OPTIND-1))
 
 script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
 top_dir=$(cd "$(dirname "${script_dir}")" &> /dev/null && pwd)
-cd ${script_dir}
+cd "${script_dir}"
 
 # shellcheck disable=SC1091
 source gfs_utils.fd/ush/detect_machine.sh  # (sets MACHINE_ID)
 # shellcheck disable=
-machine=$(echo $MACHINE_ID | cut -d. -f1)
+machine=$(echo "${MACHINE_ID}" | cut -d. -f1)
 
 #------------------------------
 #--model fix fields
@@ -133,7 +133,7 @@ cd "${top_dir}/parm/post" || exit 1
     done
 
 cd "${top_dir}/scripts" || exit 8
-    $LINK "${script_dir}/ufs_utils.fd/scripts/exemcsfc_global_sfc_prep.sh" .
+    ${LINK} "${script_dir}/ufs_utils.fd/scripts/exemcsfc_global_sfc_prep.sh" .
 cd "${top_dir}/ush" || exit 8
     for file in emcsfc_ice_blend.sh  fv3gfs_driver_grid.sh  fv3gfs_make_orog.sh  global_cycle_driver.sh \
         emcsfc_snow.sh  fv3gfs_filter_topo.sh  global_cycle.sh  fv3gfs_make_grid.sh ; do
@@ -244,7 +244,7 @@ if [ -d "${script_dir}/gfs_wafs.fd" ]; then
           wafs_awc_wafavn.x  wafs_blending.x  wafs_blending_0p25.x \
           wafs_cnvgrib2.x  wafs_gcip.x  wafs_grib2_0p25.x \
           wafs_makewafs.x  wafs_setmissing.x; do
-        [[ -s $wafsexe ]] && rm -f $wafsexe
+        [[ -s ${wafsexe} ]] && rm -f ${wafsexe}
         ${LINK} "${script_dir}/gfs_wafs.fd/exec/${wafsexe}" .
     done
 fi

From ee871e974bd00b539497f5e3059e02c3c63855c4 Mon Sep 17 00:00:00 2001
From: "kate.friedman" <kate.friedman@noaa.gov>
Date: Fri, 21 Oct 2022 14:02:33 +0000
Subject: [PATCH 7/7] Slight quote change to build command in
 build_gfs_utils.sh

Refs #1059
---
 sorc/build_gfs_utils.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sorc/build_gfs_utils.sh b/sorc/build_gfs_utils.sh
index f160caa0aa..2a7a611239 100755
--- a/sorc/build_gfs_utils.sh
+++ b/sorc/build_gfs_utils.sh
@@ -40,6 +40,6 @@ shift $((OPTIND-1))
 
 BUILD_TYPE=${BUILD_TYPE:-"Release"} \
 BUILD_VERBOSE=${BUILD_VERBOSE:-"NO"} \
-"${cwd}"/gfs_utils.fd/ush/build.sh
+"${cwd}/gfs_utils.fd/ush/build.sh"
 
 exit