From 4748ca8b73a9bd1d0e7e236b159947587273ae33 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue, 22 Nov 2022 12:10:11 -0500
Subject: [PATCH 1/4] disable cloning GSI recursively.  Link GSI fix files from
 central space

---
 sorc/checkout.sh      | 21 ++++++++++++---------
 sorc/link_workflow.sh | 15 ++++-----------
 2 files changed, 16 insertions(+), 20 deletions(-)

diff --git a/sorc/checkout.sh b/sorc/checkout.sh
index dc58f19253..89f7176284 100755
--- a/sorc/checkout.sh
+++ b/sorc/checkout.sh
@@ -19,7 +19,7 @@ Usage: ${BASH_SOURCE[0]} [-c][-h][-m ufs_hash][-o]
     Check out this UFS hash instead of the default
   -o:
     Check out operational-only code (GTG and WAFS)
-  -g: 
+  -g:
     Check out GSI for GSI-based DA
   -u:
     Check out GDASApp for UFS-based DA
@@ -50,6 +50,7 @@ function checkout() {
   dir="$1"
   remote="$2"
   version="$3"
+  recursive=${4:-"YES"}
 
   name=$(echo "${dir}" | cut -d '.' -f 1)
   echo "Performing checkout of ${name}"
@@ -89,13 +90,15 @@ function checkout() {
     echo
     return "${status}"
   fi
-  git submodule update --init --recursive >> "${logfile}" 2>&1
-  echo "|-- Updating submodules (if any)"
-  status=$?
-  if ((status > 0)); then
-    echo "    WARNING: Error while updating submodules of ${name}"
-    echo
-    return "${status}"
+  if [[ "${recursive}" == "YES" ]]; then
+    git submodule update --init --recursive >> "${logfile}" 2>&1
+    echo "|-- Updating submodules (if any)"
+    status=$?
+    if ((status > 0)); then
+      echo "    WARNING: Error while updating submodules of ${name}"
+      echo
+      return "${status}"
+    fi
   fi
   echo
   return 0
@@ -158,7 +161,7 @@ checkout "ufs_utils.fd"    "https://github.com/ufs-community/UFS_UTILS.git"
 checkout "verif-global.fd" "https://github.com/NOAA-EMC/EMC_verif-global.git"   "c267780"                    ; errs=$((errs + $?))
 
 if [[ ${checkout_gsi} == "YES" ]]; then
-  checkout "gsi_enkf.fd"     "https://github.com/NOAA-EMC/GSI.git"         "48d8676"; errs=$((errs + $?))
+  checkout "gsi_enkf.fd" "https://github.com/NOAA-EMC/GSI.git" "48d8676" "NO"; errs=$((errs + $?))
 fi
 
 if [[ ${checkout_gdas} == "YES" ]]; then
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 36dd448cb9..25e083a1f0 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -27,7 +27,7 @@ OPTIND=1
 while getopts ":ho" option; do
   case "${option}" in
     h) usage ;;
-    o) 
+    o)
       echo "-o option received, configuring for NCO"
       RUN_ENVIR="nco";;
     :)
@@ -98,7 +98,8 @@ for dir in aer \
             sfc_climo \
             ugwd \
             verif \
-            wave
+            wave \
+            gsi
             do
     if [[ -d "${dir}" ]]; then
       [[ "${RUN_ENVIR}" == "nco" ]] && chmod -R 755 "${dir}"
@@ -108,6 +109,7 @@ for dir in aer \
     ${LINK} "${FIX_DIR}/${dir}/${!fix_ver}" "${dir}"
 done
 
+
 if [[ -d "${script_dir}/ufs_utils.fd" ]]; then
   cd "${script_dir}/ufs_utils.fd/fix" || exit 1
   ./link_fixdirs.sh "${RUN_ENVIR}" "${machine}" 2> /dev/null
@@ -163,15 +165,6 @@ if [[ -d "${script_dir}/gfs_wafs.fd" ]]; then
 fi
 
 
-#------------------------------
-#--add GSI fix directory
-#------------------------------
-if [[ -d "${script_dir}/gsi_enkf.fd" ]]; then
-  cd "${top_dir}/fix" || exit 1
-    [[ -d gsi ]] && rm -rf gsi
-    ${LINK} "${script_dir}/gsi_enkf.fd/fix"  gsi
-fi
-
 #------------------------------
 #--add GDASApp fix directory
 #------------------------------

From 9b867c1c1113e964b0bb021a85c3f69be6f1ca36 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon, 28 Nov 2022 10:53:13 -0500
Subject: [PATCH 2/4] add `gsi_ver` variable in fix.ver

---
 versions/fix.ver | 1 +
 1 file changed, 1 insertion(+)

diff --git a/versions/fix.ver b/versions/fix.ver
index 43da6ac1c6..6754f8e74f 100644
--- a/versions/fix.ver
+++ b/versions/fix.ver
@@ -21,3 +21,4 @@ export sfc_climo_ver=20220805
 export ugwd_ver=20220805
 export verif_ver=20220805
 export wave_ver=20220805
+export gsi_ver=20221128

From e11d4f9bc544a9ef356dcf3cd439fb084ed74387 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon, 28 Nov 2022 14:04:55 -0500
Subject: [PATCH 3/4] move gsi up

---
 sorc/link_workflow.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 25e083a1f0..ebee40b17e 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -91,6 +91,7 @@ for dir in aer \
             cpl \
             datm \
             gldas \
+            gsi \
             lut \
             mom6 \
             orog \
@@ -98,8 +99,7 @@ for dir in aer \
             sfc_climo \
             ugwd \
             verif \
-            wave \
-            gsi
+            wave
             do
     if [[ -d "${dir}" ]]; then
       [[ "${RUN_ENVIR}" == "nco" ]] && chmod -R 755 "${dir}"

From 62ecd5c2447fc6bd6f56535f81fc6b678fe7708f Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon, 28 Nov 2022 14:13:55 -0500
Subject: [PATCH 4/4] move gsi_ver up

---
 versions/fix.ver | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/versions/fix.ver b/versions/fix.ver
index 6754f8e74f..256d8efc5a 100644
--- a/versions/fix.ver
+++ b/versions/fix.ver
@@ -13,6 +13,7 @@ export gdas_fv3jedi_ver=20220805
 export gdas_gsibec_ver=20221031
 export gldas_ver=20220920
 export glwu_ver=20220805
+export gsi_ver=20221128
 export lut_ver=20220805
 export mom6_ver=20220805
 export orog_ver=20220805
@@ -21,4 +22,3 @@ export sfc_climo_ver=20220805
 export ugwd_ver=20220805
 export verif_ver=20220805
 export wave_ver=20220805
-export gsi_ver=20221128