From 860830233201186361b204ffea368f6df22087cb Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Oct 2023 14:32:54 -0400
Subject: [PATCH 1/9] add a soca test

---
 ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml         | 18 ++++++++++++++++++
 ci/cases/{pr => pr_disable}/C48_ATM.yaml       |  2 +-
 ci/cases/{pr => pr_disable}/C48_S2SA_gefs.yaml |  0
 ci/cases/{pr => pr_disable}/C48_S2SW.yaml      |  2 +-
 .../{pr => pr_disable}/C96C48_hybatmDA.yaml    |  2 +-
 ci/cases/{pr => pr_disable}/C96_atm3DVar.yaml  |  2 +-
 ...ts_ci-updates.yaml => gfs_defaults_ci.yaml} |  0
 ci/platforms/soca_gfs_defaults_ci.yaml         |  6 ++++++
 parm/config/gefs/config.base.emc.dyn           |  6 +++---
 parm/config/gfs/config.base.emc.dyn            | 10 +++++-----
 parm/config/gfs/config.ocnanal                 |  9 ++++-----
 parm/config/gfs/yaml/defaults.yaml             | 18 ++++++++++--------
 workflow/setup_expt.py                         |  4 ----
 13 files changed, 50 insertions(+), 29 deletions(-)
 create mode 100644 ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
 rename ci/cases/{pr => pr_disable}/C48_ATM.yaml (75%)
 rename ci/cases/{pr => pr_disable}/C48_S2SA_gefs.yaml (100%)
 rename ci/cases/{pr => pr_disable}/C48_S2SW.yaml (75%)
 rename ci/cases/{pr => pr_disable}/C96C48_hybatmDA.yaml (81%)
 rename ci/cases/{pr => pr_disable}/C96_atm3DVar.yaml (80%)
 rename ci/platforms/{gfs_defaults_ci-updates.yaml => gfs_defaults_ci.yaml} (100%)
 create mode 100644 ci/platforms/soca_gfs_defaults_ci.yaml

diff --git a/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml b/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
new file mode 100644
index 0000000000..95f45b10a2
--- /dev/null
+++ b/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
@@ -0,0 +1,18 @@
+experiment:
+  type: gfs
+  mode: cycled
+
+arguments:
+  pslot: ${pslot}
+  app: S2S
+  resdet: 48
+  comrot: ${RUNTESTS}/COMROT
+  expdir: ${RUNTESTS}/EXPDIR
+  # icsdir: ${ICSDIR_ROOT}/C48cpldDA
+  icsdir: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/ICSDIR/C48O500"
+  idate: 2021032312
+  edate: 2021032400
+  nens: 0
+  gfs_cyc: 0
+  start: warm
+  yaml: ${HOMEgfs_PR}/ci/platforms/soca_gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C48_ATM.yaml b/ci/cases/pr_disable/C48_ATM.yaml
similarity index 75%
rename from ci/cases/pr/C48_ATM.yaml
rename to ci/cases/pr_disable/C48_ATM.yaml
index ccb001d296..1a6aef5e9d 100644
--- a/ci/cases/pr/C48_ATM.yaml
+++ b/ci/cases/pr_disable/C48_ATM.yaml
@@ -10,4 +10,4 @@ arguments:
   expdir: ${RUNTESTS}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci-updates.yaml
+  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C48_S2SA_gefs.yaml b/ci/cases/pr_disable/C48_S2SA_gefs.yaml
similarity index 100%
rename from ci/cases/pr/C48_S2SA_gefs.yaml
rename to ci/cases/pr_disable/C48_S2SA_gefs.yaml
diff --git a/ci/cases/pr/C48_S2SW.yaml b/ci/cases/pr_disable/C48_S2SW.yaml
similarity index 75%
rename from ci/cases/pr/C48_S2SW.yaml
rename to ci/cases/pr_disable/C48_S2SW.yaml
index aba66cb4f3..865d97469d 100644
--- a/ci/cases/pr/C48_S2SW.yaml
+++ b/ci/cases/pr_disable/C48_S2SW.yaml
@@ -10,4 +10,4 @@ arguments:
   expdir: ${RUNTESTS}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci-updates.yaml
+  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C96C48_hybatmDA.yaml b/ci/cases/pr_disable/C96C48_hybatmDA.yaml
similarity index 81%
rename from ci/cases/pr/C96C48_hybatmDA.yaml
rename to ci/cases/pr_disable/C96C48_hybatmDA.yaml
index 660291a3be..25abe81384 100644
--- a/ci/cases/pr/C96C48_hybatmDA.yaml
+++ b/ci/cases/pr_disable/C96C48_hybatmDA.yaml
@@ -15,4 +15,4 @@ arguments:
   nens: 2
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci-updates.yaml
+  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C96_atm3DVar.yaml b/ci/cases/pr_disable/C96_atm3DVar.yaml
similarity index 80%
rename from ci/cases/pr/C96_atm3DVar.yaml
rename to ci/cases/pr_disable/C96_atm3DVar.yaml
index f103f08d1f..e90ff53aaf 100644
--- a/ci/cases/pr/C96_atm3DVar.yaml
+++ b/ci/cases/pr_disable/C96_atm3DVar.yaml
@@ -14,4 +14,4 @@ arguments:
   nens: 0
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci-updates.yaml
+  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/platforms/gfs_defaults_ci-updates.yaml b/ci/platforms/gfs_defaults_ci.yaml
similarity index 100%
rename from ci/platforms/gfs_defaults_ci-updates.yaml
rename to ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/platforms/soca_gfs_defaults_ci.yaml b/ci/platforms/soca_gfs_defaults_ci.yaml
new file mode 100644
index 0000000000..244c235860
--- /dev/null
+++ b/ci/platforms/soca_gfs_defaults_ci.yaml
@@ -0,0 +1,6 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+base:
+  ACCOUNT: ${SLURM_ACCOUNT}
+  DOIAU: "NO"
+  DO_JEDIOCNVAR: "YES"
diff --git a/parm/config/gefs/config.base.emc.dyn b/parm/config/gefs/config.base.emc.dyn
index 7140ef477b..ed4efc2910 100644
--- a/parm/config/gefs/config.base.emc.dyn
+++ b/parm/config/gefs/config.base.emc.dyn
@@ -138,7 +138,7 @@ export DO_WAVE="NO"
 export DO_OCN="NO"
 export DO_ICE="NO"
 export DO_AERO="NO"
-export CCPP_SUITE="@CCPP_SUITE@"
+export CCPP_SUITE="FV3_GFS_v17_p8"
 export WAVE_CDUMP="" # When to include wave suite: gdas, gfs, or both
 export DOBNDPNT_WAVE="NO"
 export cplwav2atm=".false."
@@ -204,7 +204,7 @@ case "${APP}" in
     export DO_COUPLED="YES"
     export DO_OCN="YES"
     export DO_ICE="YES"
-    export CCPP_SUITE="FV3_GFS_v17_coupled_p8"
+    export CCPP_SUITE="FV3_GFS_v17_coupled_p8"  # TODO: Does this include FV3_GFS_v17_p8?  Can this be used instead of FV3_GFS_v17_p8 on L141
     export confignamevarfornems="cpld"
 
     if [[ "${APP}" =~ A$ ]]; then
@@ -264,7 +264,7 @@ export FLTFILEGFS="${PARMgfs}/post/postxconfig-NT-GEFS.txt"
 export FLTFILEGFSF00="${PARMgfs}/post/postxconfig-NT-GEFS-F00.txt"
 
 # Microphysics Options: 99-ZhaoCarr, 8-Thompson; 6-WSM6, 10-MG, 11-GFDL
-export imp_physics=@IMP_PHYSICS@
+export imp_physics=8
 
 # Shared parameters
 # DA engine
diff --git a/parm/config/gfs/config.base.emc.dyn b/parm/config/gfs/config.base.emc.dyn
index db4cd22e7f..713370d71e 100644
--- a/parm/config/gfs/config.base.emc.dyn
+++ b/parm/config/gfs/config.base.emc.dyn
@@ -146,14 +146,14 @@ export DO_WAVE="NO"
 export DO_OCN="NO"
 export DO_ICE="NO"
 export DO_AERO="NO"
-export CCPP_SUITE="@CCPP_SUITE@"
+export CCPP_SUITE="FV3_GFS_v17_p8"
 export WAVE_CDUMP="" # When to include wave suite: gdas, gfs, or both
 export DOBNDPNT_WAVE="NO"
 export cplwav2atm=".false."
 export FRAC_GRID=".true."
 
 # Set operational resolution
-export OPS_RES="C768" # Do not change
+export OPS_RES="C768" # Do not change # TODO: Why is this needed and where is it used?
 
 # Resolution specific parameters
 export LEVS=128
@@ -212,7 +212,7 @@ case "${APP}" in
     export DO_COUPLED="YES"
     export DO_OCN="YES"
     export DO_ICE="YES"
-    export CCPP_SUITE="FV3_GFS_v17_coupled_p8"
+    export CCPP_SUITE="FV3_GFS_v17_coupled_p8"  # TODO: Does this include FV3_GFS_v17_p8?  Can this be used instead of FV3_GFS_v17_p8 on L149
     export confignamevarfornems="cpld"
 
     if [[ "${APP}" =~ A$ ]]; then
@@ -284,7 +284,7 @@ export WRITE_DOPOST=".true." # WRITE_DOPOST=true, use inline POST
 export WRITE_NSFLIP=".true."
 
 # IAU related parameters
-export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
+export DOIAU="@DOIAU@"        # Enable 4DIAU for control with 3 increments
 export IAUFHRS="3,6,9"
 export IAU_FHROT=${IAUFHRS%%,*}
 export IAU_DELTHRS=6
@@ -302,7 +302,7 @@ export lobsdiag_forenkf=".true."
 # fi
 
 # Microphysics Options: 99-ZhaoCarr, 8-Thompson; 6-WSM6, 10-MG, 11-GFDL
-export imp_physics=@IMP_PHYSICS@
+export imp_physics=8
 
 # Shared parameters
 # DA engine
diff --git a/parm/config/gfs/config.ocnanal b/parm/config/gfs/config.ocnanal
index 36519c7f35..ec45ddd288 100644
--- a/parm/config/gfs/config.ocnanal
+++ b/parm/config/gfs/config.ocnanal
@@ -5,17 +5,16 @@
 
 echo "BEGIN: config.ocnanal"
 
-export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
+export OBS_YAML_DIR="${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config"
 export OBS_LIST=@SOCA_OBS_LIST@
-[[ -n "${OBS_LIST}" ]] || export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
-export OBS_YAML=${OBS_LIST}
-export FV3JEDI_STAGE_YAML=${HOMEgfs}/sorc/gdas.cd/test/soca/testinput/dumy.yaml
+export OBS_YAML="${OBS_LIST}"
+export FV3JEDI_STAGE_YAML="${HOMEgfs}/sorc/gdas.cd/test/soca/testinput/dumy.yaml"
 export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
 export SOCA_VARS=tocn,socn,ssh
 export SABER_BLOCKS_YAML=@SABER_BLOCKS_YAML@
 export SOCA_NINNER=@SOCA_NINNER@
 export CASE_ANL=@CASE_ANL@
-export DOMAIN_STACK_SIZE=116640000 #TODO: Make the stack size reolution dependent 
+export DOMAIN_STACK_SIZE=116640000  #TODO: Make the stack size resolution dependent
 export JEDI_BIN=${HOMEgfs}/sorc/gdas.cd/build/bin
 
 # R2D2
diff --git a/parm/config/gfs/yaml/defaults.yaml b/parm/config/gfs/yaml/defaults.yaml
index 202efc2270..112087bcbd 100644
--- a/parm/config/gfs/yaml/defaults.yaml
+++ b/parm/config/gfs/yaml/defaults.yaml
@@ -1,9 +1,11 @@
 base:
+  DOIAU: "YES"
   DO_JEDIATMVAR: "NO"
   DO_JEDIATMENS: "NO"
   DO_JEDIOCNVAR: "NO"
   DO_JEDILANDDA: "NO"
   DO_MERGENSST: "NO"
+
 aeroanl:
   IO_LAYOUT_X: 1
   IO_LAYOUT_Y: 1
@@ -13,13 +15,13 @@ landanl:
   IO_LAYOUT_Y: 1
 
 ocnanal:
-  SOCA_INPUT_FIX_DIR: '/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25'
-  CASE_ANL: 'C48'
-  SOCA_OBS_LIST: ''
-  COMIN_OBS: '/scratch2/NCEPDEV/marineda/r2d2'
-  SABER_BLOCKS_YAML: ''
-  SOCA_NINNER: 50
-  R2D2_OBS_SRC: 'gdas_marine'
-  R2D2_OBS_DUMP: 's2s_v1'
+  SOCA_INPUT_FIX_DIR: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25/soca"
+  CASE_ANL: "C48"
+  COMIN_OBS: "/scratch2/NCEPDEV/marineda/r2d2-v2-v3"
+  SOCA_OBS_LIST: "{{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml"
+  SOCA_NINNER: 100
+  R2D2_OBS_SRC: "gdas_marine"
+  R2D2_OBS_DUMP: "s2s_v1"
+  SABER_BLOCKS_YAML: ""
   NICAS_RESOL: 1
   NICAS_GRID_SIZE: 15000
diff --git a/workflow/setup_expt.py b/workflow/setup_expt.py
index c9aa9188f6..a9810ec3f2 100755
--- a/workflow/setup_expt.py
+++ b/workflow/setup_expt.py
@@ -343,10 +343,6 @@ def edit_baseconfig(host, inputs, yaml_dict):
         }
         tmpl_dict = dict(tmpl_dict, **extend_dict)
 
-    # All apps and modes now use the same physics and CCPP suite by default
-    extend_dict = {"@CCPP_SUITE@": "FV3_GFS_v17_p8", "@IMP_PHYSICS@": 8}
-    tmpl_dict = dict(tmpl_dict, **extend_dict)
-
     try:
         tmpl_dict = dict(tmpl_dict, **get_template_dict(yaml_dict['base']))
     except KeyError:

From eced3f4ade3ce9e7a6d7f5f686087582aa321f54 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Oct 2023 15:31:30 -0400
Subject: [PATCH 2/9] replace HOMEgfs_PR with HOMEgfs, and HOMEgfs with
 ROOT_DIR. ROOT_DIR is the location where the ci scripts live

---
 ci/cases/{pr_disable => pr}/C48_ATM.yaml |  2 +-
 ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml   |  4 +-
 ci/cases/pr_disable/C48_S2SA_gefs.yaml   |  2 +-
 ci/cases/pr_disable/C48_S2SW.yaml        |  2 +-
 ci/cases/pr_disable/C96C48_hybatmDA.yaml |  2 +-
 ci/cases/pr_disable/C96_atm3DVar.yaml    |  2 +-
 ci/scripts/check_ci.sh                   | 24 ++++-----
 ci/scripts/clone-build_ci.sh             |  4 +-
 ci/scripts/create_experiment.py          |  2 +-
 ci/scripts/driver.sh                     | 68 ++++++++++++------------
 ci/scripts/driver_weekly.sh              | 16 +++---
 ci/scripts/run_ci.sh                     | 14 ++---
 parm/config/gfs/yaml/defaults.yaml       |  4 +-
 13 files changed, 72 insertions(+), 74 deletions(-)
 rename ci/cases/{pr_disable => pr}/C48_ATM.yaml (77%)

diff --git a/ci/cases/pr_disable/C48_ATM.yaml b/ci/cases/pr/C48_ATM.yaml
similarity index 77%
rename from ci/cases/pr_disable/C48_ATM.yaml
rename to ci/cases/pr/C48_ATM.yaml
index 1a6aef5e9d..d563c6fba9 100644
--- a/ci/cases/pr_disable/C48_ATM.yaml
+++ b/ci/cases/pr/C48_ATM.yaml
@@ -10,4 +10,4 @@ arguments:
   expdir: ${RUNTESTS}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml b/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
index 95f45b10a2..245a6a066d 100644
--- a/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
+++ b/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
@@ -9,10 +9,10 @@ arguments:
   comrot: ${RUNTESTS}/COMROT
   expdir: ${RUNTESTS}/EXPDIR
   # icsdir: ${ICSDIR_ROOT}/C48cpldDA
-  icsdir: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/ICSDIR/C48O500"
+  icsdir: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/ICSDIR/C48O500"  # TODO: make platform agnostic
   idate: 2021032312
   edate: 2021032400
   nens: 0
   gfs_cyc: 0
   start: warm
-  yaml: ${HOMEgfs_PR}/ci/platforms/soca_gfs_defaults_ci.yaml
+  yaml: ${HOMEgfs}/ci/platforms/soca_gfs_defaults_ci.yaml
diff --git a/ci/cases/pr_disable/C48_S2SA_gefs.yaml b/ci/cases/pr_disable/C48_S2SA_gefs.yaml
index 4d5f066858..50f8df1d55 100644
--- a/ci/cases/pr_disable/C48_S2SA_gefs.yaml
+++ b/ci/cases/pr_disable/C48_S2SA_gefs.yaml
@@ -14,4 +14,4 @@ arguments:
   icsdir: ${ICSDIR_ROOT}/C48C48mx500
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs_PR}/ci/platforms/gefs_ci_defaults.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gefs_ci_defaults.yaml
diff --git a/ci/cases/pr_disable/C48_S2SW.yaml b/ci/cases/pr_disable/C48_S2SW.yaml
index 865d97469d..63e175de80 100644
--- a/ci/cases/pr_disable/C48_S2SW.yaml
+++ b/ci/cases/pr_disable/C48_S2SW.yaml
@@ -10,4 +10,4 @@ arguments:
   expdir: ${RUNTESTS}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr_disable/C96C48_hybatmDA.yaml b/ci/cases/pr_disable/C96C48_hybatmDA.yaml
index 25abe81384..bd4810ebd1 100644
--- a/ci/cases/pr_disable/C96C48_hybatmDA.yaml
+++ b/ci/cases/pr_disable/C96C48_hybatmDA.yaml
@@ -15,4 +15,4 @@ arguments:
   nens: 2
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr_disable/C96_atm3DVar.yaml b/ci/cases/pr_disable/C96_atm3DVar.yaml
index e90ff53aaf..acd1a18690 100644
--- a/ci/cases/pr_disable/C96_atm3DVar.yaml
+++ b/ci/cases/pr_disable/C96_atm3DVar.yaml
@@ -14,4 +14,4 @@ arguments:
   nens: 0
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/scripts/check_ci.sh b/ci/scripts/check_ci.sh
index b2c8129d32..d5cf6a20bd 100755
--- a/ci/scripts/check_ci.sh
+++ b/ci/scripts/check_ci.sh
@@ -2,13 +2,13 @@
 set -eux
 #####################################################################################
 #
-# Script description: BASH script for checking for cases in a given PR and 
+# Script description: BASH script for checking for cases in a given PR and
 #                     running rocotostat on each to determine if the experiment has
 #                     succeeded or faild.  This script is intended
 #                     to run from within a cron job in the CI Managers account
 #####################################################################################
 
-HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
+ROOT_DIR="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
 scriptname=$(basename "${BASH_SOURCE[0]}")
 echo "Begin ${scriptname} at $(date -u)" || true
 export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
@@ -20,11 +20,11 @@ REPO_URL="https://github.com/NOAA-EMC/global-workflow.git"
 #  Set up runtime environment varibles for accounts on supproted machines
 #########################################################################
 
-source "${HOMEgfs}/ush/detect_machine.sh"
+source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
   hera | orion)
    echo "Running Automated Testing on ${MACHINE_ID}"
-   source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
+   source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
    ;;
  *)
    echo "Unsupported platform. Exiting with error."
@@ -32,8 +32,8 @@ case ${MACHINE_ID} in
    ;;
 esac
 set +x
-source "${HOMEgfs}/ush/module-setup.sh"
-module use "${HOMEgfs}/modulefiles"
+source "${ROOT_DIR}/ush/module-setup.sh"
+module use "${ROOT_DIR}/modulefiles"
 module load "module_gwsetup.${MACHINE_ID}"
 module list
 set -x
@@ -56,7 +56,7 @@ pr_list_dbfile="${GFS_CI_ROOT}/open_pr_list.db"
 
 pr_list=""
 if [[ -f "${pr_list_dbfile}" ]]; then
-  pr_list=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display | grep -v Failed | grep Running | awk '{print $1}') || true
+  pr_list=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display | grep -v Failed | grep Running | awk '{print $1}') || true
 fi
 if [[ -z "${pr_list+x}" ]]; then
   echo "no PRs open and ready to run cases on .. exiting"
@@ -85,7 +85,7 @@ for pr in ${pr_list}; do
     "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Running" --add-label "CI-${MACHINE_ID^}-Passed"
     sed -i "s/\`\`\`//2g" "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
     "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
-    "${HOMEgfs}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
     # Check to see if this PR that was opened by the weekly tests and if so close it if it passed on all platforms
     weekly_labels=$(${GH} pr view "${pr}" --repo "${REPO_URL}"  --json headRefName,labels,author --jq 'select(.author.login | contains("emcbot")) | select(.headRefName | contains("weekly_ci")) | .labels[].name ') || true
     if [[ -n "${weekly_labels}" ]]; then
@@ -103,8 +103,8 @@ for pr in ${pr_list}; do
     fi
     # Completely remove the PR and its cloned repo on sucess
     # of all cases on this platform
-    rm -Rf "${pr_dir}" 
-    continue 
+    rm -Rf "${pr_dir}"
+    continue
   fi
 
   for pslot_dir in "${pr_dir}/RUNTESTS/EXPDIR/"*; do
@@ -134,10 +134,10 @@ for pr in ${pr_list}; do
       {
        echo "Error logs:"
        echo "${error_logs}"
-      } >> "${GFS_CI_ROOT}/PR/${pr}/output_${id}" 
+      } >> "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
       sed -i "s/\`\`\`//2g" "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
       "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
-      "${HOMEgfs}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
+      "${ROOT_DIR}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
       for kill_cases in "${pr_dir}/RUNTESTS/"*; do
          pslot=$(basename "${kill_cases}")
          sacct --format=jobid,jobname%35,WorkDir%100,stat | grep "${pslot}" | grep "PR\/${pr}\/RUNTESTS" |  awk '{print $1}' | xargs scancel || true
diff --git a/ci/scripts/clone-build_ci.sh b/ci/scripts/clone-build_ci.sh
index 83f43ef54b..796e4b7014 100755
--- a/ci/scripts/clone-build_ci.sh
+++ b/ci/scripts/clone-build_ci.sh
@@ -9,8 +9,8 @@ usage() {
   echo
   echo "Usage: $0 -p <PR#> -d <directory> -o <output> -h"
   echo
-  echo "  -p  PR nunber to clone and build"
-  echo "  -d  Full path of <directory> of were to clone and build PR"
+  echo "  -p  PR number to clone and build"
+  echo "  -d  Full path of <directory> of where to clone and build PR"
   echo "  -o  Full path to output message file detailing results of CI tests"
   echo "  -h  display this message and quit"
   echo
diff --git a/ci/scripts/create_experiment.py b/ci/scripts/create_experiment.py
index 3c5096e875..47c1e1429f 100755
--- a/ci/scripts/create_experiment.py
+++ b/ci/scripts/create_experiment.py
@@ -62,7 +62,7 @@ def input_args():
                             formatter_class=ArgumentDefaultsHelpFormatter)
 
     parser.add_argument('--yaml', help='full path to yaml file describing the experiment configuration', type=str, required=True)
-    parser.add_argument('--dir', help='full path to global-workflow build', type=str, required=True)
+    parser.add_argument('--dir', help='full path to global-workflow', type=str, required=True)
 
     return parser.parse_args()
 
diff --git a/ci/scripts/driver.sh b/ci/scripts/driver.sh
index 0267d88e03..d2bffdd93a 100755
--- a/ci/scripts/driver.sh
+++ b/ci/scripts/driver.sh
@@ -10,9 +10,8 @@ set -eux
 #
 # This script uses GitHub CLI to check for Pull Requests with CI-Ready-${machine} tags on the
 # development branch for the global-workflow repo.  It then stages tests directories per
-# PR number and calls clone-build_ci.sh to perform a clone and full build from $(HOMEgfs)/sorc
-# of the PR. It then is ready to run a suite of regression tests with various
-# configurations with run_tests.py.
+# PR number and calls clone-build_ci.sh to perform a clone and full build from the PR.
+# It then is ready to run a suite of regression tests with various configurations
 #######################################################################################
 
 #################################################################
@@ -22,9 +21,9 @@ export GH=${HOME}/bin/gh
 export REPO_URL=${REPO_URL:-"https://github.com/NOAA-EMC/global-workflow.git"}
 
 ################################################################
-# Setup the reletive paths to scripts and PS4 for better logging 
+# Setup the reletive paths to scripts and PS4 for better logging
 ################################################################
-HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
+ROOT_DIR="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
 scriptname=$(basename "${BASH_SOURCE[0]}")
 echo "Begin ${scriptname} at $(date -u)" || true
 export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
@@ -33,11 +32,11 @@ export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
 #  Set up runtime environment varibles for accounts on supproted machines
 #########################################################################
 
-source "${HOMEgfs}/ush/detect_machine.sh"
+source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
   hera | orion)
     echo "Running Automated Testing on ${MACHINE_ID}"
-    source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
+    source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
     ;;
   *)
     echo "Unsupported platform. Exiting with error."
@@ -49,8 +48,8 @@ esac
 # setup runtime env for correct python install and git
 ######################################################
 set +x
-source "${HOMEgfs}/ush/module-setup.sh"
-module use "${HOMEgfs}/modulefiles"
+source "${ROOT_DIR}/ush/module-setup.sh"
+module use "${ROOT_DIR}/modulefiles"
 module load "module_gwsetup.${MACHINE_ID}"
 set -x
 
@@ -61,45 +60,45 @@ set -x
 pr_list_dbfile="${GFS_CI_ROOT}/open_pr_list.db"
 
 if [[ ! -f "${pr_list_dbfile}" ]]; then
-  "${HOMEgfs}/ci/scripts/pr_list_database.py" --create --dbfile "${pr_list_dbfile}"
+  "${ROOT_DIR}/ci/scripts/pr_list_database.py" --create --dbfile "${pr_list_dbfile}"
 fi
 
 pr_list=$(${GH} pr list --repo "${REPO_URL}" --label "CI-${MACHINE_ID^}-Ready" --state "open" | awk '{print $1}') || true
 
 for pr in ${pr_list}; do
   pr_dir="${GFS_CI_ROOT}/PR/${pr}"
-  db_list=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --add_pr "${pr}" --dbfile "${pr_list_dbfile}")
+  db_list=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --add_pr "${pr}" --dbfile "${pr_list_dbfile}")
   pr_id=0
   #############################################################
-  # Check if a Ready labeled PR has changed back from once set   
+  # Check if a Ready labeled PR has changed back from once set
   # and in that case remove all previous jobs in scheduler and
   # and remove PR from filesystem to start clean
   #############################################################
   if [[ "${db_list}" == *"already is in list"* ]]; then
-    pr_id=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display "${pr}" | awk '{print $4}') || true
+    pr_id=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --display "${pr}" | awk '{print $4}') || true
     pr_id=$((pr_id+1))
-    "${HOMEgfs}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Ready "${pr_id}"
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Ready "${pr_id}"
     for cases in "${pr_dir}/RUNTESTS/"*; do
       if [[ -z "${cases+x}" ]]; then
          break
-      fi   
+      fi
       pslot=$(basename "${cases}")
       sacct --format=jobid,jobname%35,WorkDir%100,stat | grep "${pslot}" | grep "PR\/${pr}\/RUNTESTS" |  awk '{print $1}' | xargs scancel || true
     done
     rm -Rf "${pr_dir}"
-  fi  
+  fi
 done
 
 pr_list=""
 if [[ -f "${pr_list_dbfile}" ]]; then
-  pr_list=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --display --dbfile "${pr_list_dbfile}" | grep -v Failed | grep Open | grep Ready | awk '{print $1}') || true
+  pr_list=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display --dbfile "${pr_list_dbfile}" | grep -v Failed | grep Open | grep Ready | awk '{print $1}') || true
 fi
 if [[ -z "${pr_list+x}" ]]; then
   echo "no PRs open and ready for checkout/build .. exiting"
   exit 0
 fi
 
- 
+
 #############################################################
 # Loop throu all open PRs
 # Clone, checkout, build, creat set of cases, for each
@@ -107,12 +106,12 @@ fi
 
 for pr in ${pr_list}; do
   # Skip pr's that are currently Building for when overlapping driver scripts are being called from within cron
-  pr_building=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --display "${pr}" --dbfile "${pr_list_dbfile}" | grep Building) || true
+  pr_building=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "${pr}" --dbfile "${pr_list_dbfile}" | grep Building) || true
   if [[ -z "${pr_building+x}" ]]; then
       continue
   fi
   "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Ready" --add-label "CI-${MACHINE_ID^}-Building"
-  "${HOMEgfs}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Building
+  "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Building
   echo "Processing Pull Request #${pr}"
   pr_dir="${GFS_CI_ROOT}/PR/${pr}"
   rm -Rf "${pr_dir}"
@@ -120,7 +119,7 @@ for pr in ${pr_list}; do
   # call clone-build_ci to clone and build PR
   id=$("${GH}" pr view "${pr}" --repo "${REPO_URL}" --json id --jq '.id')
   set +e
-  "${HOMEgfs}/ci/scripts/clone-build_ci.sh" -p "${pr}" -d "${pr_dir}" -o "${pr_dir}/output_${id}"
+  "${ROOT_DIR}/ci/scripts/clone-build_ci.sh" -p "${pr}" -d "${pr_dir}" -o "${pr_dir}/output_${id}"
   ci_status=$?
   ##################################################################
   # Checking for special case when Ready label was updated
@@ -128,14 +127,14 @@ for pr in ${pr_list}; do
   # building so we force and exit 0 instead to does not get relabled
   #################################################################
   if [[ ${ci_status} -ne 0 ]]; then
-     pr_id_check=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --display "{pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}') || true
+     pr_id_check=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "{pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}') || true
      if [[ "${pr_id}" -ne "${pr_id_check}" ]]; then
         exit 0
-     fi   
+     fi
   fi
   set -e
   if [[ ${ci_status} -eq 0 ]]; then
-    "${HOMEgfs}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Built
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Built
     #setup space to put an experiment
     # export RUNTESTS for yaml case files to pickup
     export RUNTESTS="${pr_dir}/RUNTESTS"
@@ -145,18 +144,17 @@ for pr in ${pr_list}; do
     # loop over every yaml file in the PR's ci/cases
     # and create an run directory for each one for this PR loop
     #############################################################
-    HOMEgfs_PR="${pr_dir}/global-workflow"
-    export HOMEgfs_PR
-    cd "${HOMEgfs_PR}"
+    export HOMEgfs="${pr_dir}/global-workflow"
+    cd "${HOMEgfs}"
     pr_sha=$(git rev-parse --short HEAD)
 
-    for yaml_config in "${HOMEgfs_PR}/ci/cases/pr/"*.yaml; do
+    for yaml_config in "${HOMEgfs}/ci/cases/pr/"*.yaml; do
       case=$(basename "${yaml_config}" .yaml) || true
       pslot="${case}_${pr_sha}"
       rm -Rf "${STMP}/RUNDIRS/${pslot}"
       export pslot
       set +e
-      "${HOMEgfs_PR}/ci/scripts/create_experiment.py" --yaml "${HOMEgfs_PR}/ci/cases/pr/${case}.yaml" --dir "${HOMEgfs_PR}"
+      "${HOMEgfs}/ci/scripts/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml" --dir "${HOMEgfs}"
       ci_status=$?
       set -e
       if [[ ${ci_status} -eq 0 ]]; then
@@ -165,27 +163,27 @@ for pr in ${pr_list}; do
           echo "Case setup: Completed at $(date) for experiment ${pslot}" || true
         } >> "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
         "${GH}" pr edit --repo "${REPO_URL}" "${pr}" --remove-label "CI-${MACHINE_ID^}-Building" --add-label "CI-${MACHINE_ID^}-Running"
-        "${HOMEgfs}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Running
-      else 
+        "${ROOT_DIR}/ci/scripts/pr_list_database.py" --dbfile "${pr_list_dbfile}" --update_pr "${pr}" Open Running
+      else
         {
           echo "Failed to create experiment:  *FAIL* ${pslot}"
           echo "Experiment setup: failed at $(date) for experiment ${pslot}" || true
           echo ""
-          cat "${HOMEgfs_PR}/ci/scripts/"setup_*.std*
+          cat "${HOMEgfs}/ci/scripts/"setup_*.std*
         } >> "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
         "${GH}" pr edit "${pr}" --repo "${REPO_URL}" --remove-label "CI-${MACHINE_ID^}-Building" --add-label "CI-${MACHINE_ID^}-Failed"
-        "${HOMEgfs}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
+        "${ROOT_DIR}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
       fi
     done
 
-  else 
+  else
     {
       echo '```'
       echo "Failed on cloning and building global-workflowi PR: ${pr}"
       echo "CI on ${MACHINE_ID^} failed to build on $(date) for repo ${REPO_URL}" || true
     } >> "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
     "${GH}" pr edit "${pr}" --repo "${REPO_URL}" --remove-label "CI-${MACHINE_ID^}-Building" --add-label "CI-${MACHINE_ID^}-Failed"
-    "${HOMEgfs}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
+    "${ROOT_DIR}/ci/scripts/pr_list_database.py" --remove_pr "${pr}" --dbfile "${pr_list_dbfile}"
   fi
   sed -i "s/\`\`\`//2g" "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
   "${GH}" pr comment "${pr}" --repo "${REPO_URL}" --body-file "${GFS_CI_ROOT}/PR/${pr}/output_${id}"
diff --git a/ci/scripts/driver_weekly.sh b/ci/scripts/driver_weekly.sh
index 3650f75dfc..a52e5b1caa 100755
--- a/ci/scripts/driver_weekly.sh
+++ b/ci/scripts/driver_weekly.sh
@@ -8,13 +8,13 @@ set -eux
 #
 # Abstract:
 #
-# This script runs the high resolution cases found in $HOMEgfs/ci/cases/weekly
+# This script runs the high resolution cases found in ${HOMEgfs}/ci/cases/weekly
 # from the develop branch for the global-workflow repo that are intended to run on a weekly basis
 # from a cron job. When run it will clone and build a new branch from the EMC's global-workflow and
 # and create a pr using GitHub CLI by moving and replacing the yaml case files in
 # ${HOMEgfs}/ci/cases/weekly to {HOMEgfs}/ci/cases/pr.  Then the requisite labels are added
 # so that the current BASH CI framework can then run these cases.  Since this script
-# creates a PR with the CI-Ready labels, the BASH CI framework will automatically run these cases 
+# creates a PR with the CI-Ready labels, the BASH CI framework will automatically run these cases
 # from that point so it is only required to run this script once from a single machine.
 ##############################################################################################
 
@@ -27,7 +27,7 @@ export REPO_URL="ssh://git@ssh.github.com:443/NOAA-EMC/global-workflow.git"
 ################################################################
 # Setup the relative paths to scripts and PS4 for better logging
 ################################################################
-HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
+ROOT_DIR="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
 scriptname=$(basename "${BASH_SOURCE[0]}")
 echo "Begin ${scriptname} at $(date -u)" || true
 export PS4='+ $(basename ${BASH_SOURCE[0]})[${LINENO}]'
@@ -36,11 +36,11 @@ export PS4='+ $(basename ${BASH_SOURCE[0]})[${LINENO}]'
 # Set up runtime environment variables for accounts on supported machines
 #########################################################################
 
-source "${HOMEgfs}/ush/detect_machine.sh"
+source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
   hera | orion)
     echo "Running Automated Testing on ${MACHINE_ID}"
-    source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
+    source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
     ;;
   *)
     echo "Unsupported platform. Exiting with error."
@@ -52,8 +52,8 @@ esac
 # setup runtime env for correct python install and git
 ######################################################
 set +x
-source "${HOMEgfs}/ush/module-setup.sh"
-module use "${HOMEgfs}/modulefiles"
+source "${ROOT_DIR}/ush/module-setup.sh"
+module use "${ROOT_DIR}/modulefiles"
 module load "module_gwsetup.${MACHINE_ID}"
 set -x
 
@@ -71,7 +71,7 @@ cd global-workflow || exit 1
 git checkout -b "${branch}"
 
 ######################################################
-# move yaml files from ci/cases/weekly to ci/cases/pr 
+# move yaml files from ci/cases/weekly to ci/cases/pr
 # and push new branch for PR weekly CI tests to GitHub
 REPO_OWNER="emcbot"
 REPO_NAME="global-workflow"
diff --git a/ci/scripts/run_ci.sh b/ci/scripts/run_ci.sh
index 0ff3725be9..cdaafb337f 100755
--- a/ci/scripts/run_ci.sh
+++ b/ci/scripts/run_ci.sh
@@ -3,13 +3,13 @@ set -eux
 
 #####################################################################################
 #
-# Script description: BASH script for checking for cases in a given PR and 
+# Script description: BASH script for checking for cases in a given PR and
 #                     simply running rocotorun on each.  This script is intended
 #                     to run from within a cron job in the CI Managers account
 # Abstract TODO
 #####################################################################################
 
-HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
+ROOT_DIR="$(cd "$(dirname  "${BASH_SOURCE[0]}")/../.." >/dev/null 2>&1 && pwd )"
 scriptname=$(basename "${BASH_SOURCE[0]}")
 echo "Begin ${scriptname} at $(date -u)" || true
 export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
@@ -18,11 +18,11 @@ export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
 #  Set up runtime environment varibles for accounts on supproted machines
 #########################################################################
 
-source "${HOMEgfs}/ush/detect_machine.sh"
+source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
   hera | orion)
    echo "Running Automated Testing on ${MACHINE_ID}"
-   source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
+   source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
    ;;
  *)
    echo "Unsupported platform. Exiting with error."
@@ -30,8 +30,8 @@ case ${MACHINE_ID} in
    ;;
 esac
 set +x
-source "${HOMEgfs}/ush/module-setup.sh"
-module use "${HOMEgfs}/modulefiles"
+source "${ROOT_DIR}/ush/module-setup.sh"
+module use "${ROOT_DIR}/modulefiles"
 module load "module_gwsetup.${MACHINE_ID}"
 module list
 set -eux
@@ -47,7 +47,7 @@ pr_list_dbfile="${GFS_CI_ROOT}/open_pr_list.db"
 
 pr_list=""
 if [[ -f "${pr_list_dbfile}" ]]; then
-  pr_list=$("${HOMEgfs}/ci/scripts/pr_list_database.py" --display --dbfile "${pr_list_dbfile}" | grep -v Failed | grep Open | grep Running | awk '{print $1}' | head -"${max_concurrent_pr}") || true
+  pr_list=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display --dbfile "${pr_list_dbfile}" | grep -v Failed | grep Open | grep Running | awk '{print $1}' | head -"${max_concurrent_pr}") || true
 fi
 if [[ -z "${pr_list}" ]]; then
   echo "no open and built PRs that are ready for the cases to advance with rocotorun .. exiting"
diff --git a/parm/config/gfs/yaml/defaults.yaml b/parm/config/gfs/yaml/defaults.yaml
index 112087bcbd..8c2b4ff22b 100644
--- a/parm/config/gfs/yaml/defaults.yaml
+++ b/parm/config/gfs/yaml/defaults.yaml
@@ -15,9 +15,9 @@ landanl:
   IO_LAYOUT_Y: 1
 
 ocnanal:
-  SOCA_INPUT_FIX_DIR: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25/soca"
+  SOCA_INPUT_FIX_DIR: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25/soca"  # TODO: These need to go to glopara fix space. @guillaumevernieres will open an issue
   CASE_ANL: "C48"
-  COMIN_OBS: "/scratch2/NCEPDEV/marineda/r2d2-v2-v3"
+  COMIN_OBS: "/scratch2/NCEPDEV/marineda/r2d2-v2-v3"  # TODO: make platform agnostic
   SOCA_OBS_LIST: "{{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml"
   SOCA_NINNER: 100
   R2D2_OBS_SRC: "gdas_marine"

From a80b61bf3cd7cebc68dd342e1a4fdba789fbc78d Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Oct 2023 15:40:26 -0400
Subject: [PATCH 3/9] update type to system

---
 ci/cases/pr/C48_ATM.yaml                 | 2 +-
 ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml   | 4 ++--
 ci/cases/pr_disable/C48_S2SA_gefs.yaml   | 2 +-
 ci/cases/pr_disable/C48_S2SW.yaml        | 2 +-
 ci/cases/pr_disable/C96C48_hybatmDA.yaml | 2 +-
 ci/cases/pr_disable/C96_atm3DVar.yaml    | 2 +-
 ci/cases/weekly/C384C192_hybatmda.yaml   | 4 ++--
 ci/cases/weekly/C384_S2SWA.yaml          | 4 ++--
 ci/cases/weekly/C384_atm3DVar.yaml       | 4 ++--
 ci/scripts/create_experiment.py          | 2 +-
 10 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/ci/cases/pr/C48_ATM.yaml b/ci/cases/pr/C48_ATM.yaml
index d563c6fba9..01a328873f 100644
--- a/ci/cases/pr/C48_ATM.yaml
+++ b/ci/cases/pr/C48_ATM.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: forecast-only
 
 arguments:
diff --git a/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml b/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
index 245a6a066d..51bfc817b2 100644
--- a/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
+++ b/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: cycled
 
 arguments:
@@ -9,7 +9,7 @@ arguments:
   comrot: ${RUNTESTS}/COMROT
   expdir: ${RUNTESTS}/EXPDIR
   # icsdir: ${ICSDIR_ROOT}/C48cpldDA
-  icsdir: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/ICSDIR/C48O500"  # TODO: make platform agnostic
+  icsdir: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/ICSDIR/C48O500" # TODO: make platform agnostic
   idate: 2021032312
   edate: 2021032400
   nens: 0
diff --git a/ci/cases/pr_disable/C48_S2SA_gefs.yaml b/ci/cases/pr_disable/C48_S2SA_gefs.yaml
index 50f8df1d55..156683ae28 100644
--- a/ci/cases/pr_disable/C48_S2SA_gefs.yaml
+++ b/ci/cases/pr_disable/C48_S2SA_gefs.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gefs
+  system: gefs
   mode: forecast-only
 
 arguments:
diff --git a/ci/cases/pr_disable/C48_S2SW.yaml b/ci/cases/pr_disable/C48_S2SW.yaml
index 63e175de80..4c4cf4f147 100644
--- a/ci/cases/pr_disable/C48_S2SW.yaml
+++ b/ci/cases/pr_disable/C48_S2SW.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: forecast-only
 
 arguments:
diff --git a/ci/cases/pr_disable/C96C48_hybatmDA.yaml b/ci/cases/pr_disable/C96C48_hybatmDA.yaml
index bd4810ebd1..4844ee3c9b 100644
--- a/ci/cases/pr_disable/C96C48_hybatmDA.yaml
+++ b/ci/cases/pr_disable/C96C48_hybatmDA.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: cycled
 
 arguments:
diff --git a/ci/cases/pr_disable/C96_atm3DVar.yaml b/ci/cases/pr_disable/C96_atm3DVar.yaml
index acd1a18690..02aff389c4 100644
--- a/ci/cases/pr_disable/C96_atm3DVar.yaml
+++ b/ci/cases/pr_disable/C96_atm3DVar.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: cycled
 
 arguments:
diff --git a/ci/cases/weekly/C384C192_hybatmda.yaml b/ci/cases/weekly/C384C192_hybatmda.yaml
index ca62c4e8f9..1d3c94017c 100644
--- a/ci/cases/weekly/C384C192_hybatmda.yaml
+++ b/ci/cases/weekly/C384C192_hybatmda.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: cycled
 
 arguments:
@@ -15,4 +15,4 @@ arguments:
   nens: 2
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci-updates.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/weekly/C384_S2SWA.yaml b/ci/cases/weekly/C384_S2SWA.yaml
index d494efb44b..2978e87c95 100644
--- a/ci/cases/weekly/C384_S2SWA.yaml
+++ b/ci/cases/weekly/C384_S2SWA.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: forecast-only
 
 arguments:
@@ -10,4 +10,4 @@ arguments:
   expdir: ${RUNTESTS}/EXPDIR
   idate: 2016070100
   edate: 2016070100
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci-updates.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/weekly/C384_atm3DVar.yaml b/ci/cases/weekly/C384_atm3DVar.yaml
index 99f302b9ca..a754ed0ee0 100644
--- a/ci/cases/weekly/C384_atm3DVar.yaml
+++ b/ci/cases/weekly/C384_atm3DVar.yaml
@@ -1,5 +1,5 @@
 experiment:
-  type: gfs
+  system: gfs
   mode: cycled
 
 arguments:
@@ -15,4 +15,4 @@ arguments:
   nens: 0
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs_PR}/ci/platforms/gfs_defaults_ci-updates.yaml
+  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/scripts/create_experiment.py b/ci/scripts/create_experiment.py
index 47c1e1429f..fd65e042d1 100755
--- a/ci/scripts/create_experiment.py
+++ b/ci/scripts/create_experiment.py
@@ -75,7 +75,7 @@ def input_args():
     experiment_dir = Path.absolute(Path.joinpath(Path(testconf.arguments.expdir), Path(testconf.arguments.pslot)))
 
     # Create a list of arguments to setup_expt.py
-    setup_expt_args = [testconf.experiment.type, testconf.experiment.mode]  # TODO: rename 'type' as 'system' in case.yaml
+    setup_expt_args = [testconf.experiment.system , testconf.experiment.mode]
     for kk, vv in testconf.arguments.items():
         setup_expt_args.append(f"--{kk}")
         setup_expt_args.append(str(vv))

From 0715d149a805d913d8604072d5af4c669ea121cc Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Oct 2023 15:44:05 -0400
Subject: [PATCH 4/9] move create_experiment.py to workflow/

---
 ci/scripts/driver.sh                          |  2 +-
 {ci/scripts => workflow}/create_experiment.py | 14 ++++----------
 2 files changed, 5 insertions(+), 11 deletions(-)
 rename {ci/scripts => workflow}/create_experiment.py (89%)

diff --git a/ci/scripts/driver.sh b/ci/scripts/driver.sh
index d2bffdd93a..25682fd1aa 100755
--- a/ci/scripts/driver.sh
+++ b/ci/scripts/driver.sh
@@ -154,7 +154,7 @@ for pr in ${pr_list}; do
       rm -Rf "${STMP}/RUNDIRS/${pslot}"
       export pslot
       set +e
-      "${HOMEgfs}/ci/scripts/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml" --dir "${HOMEgfs}"
+      "${HOMEgfs}/workflow/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml" --dir "${HOMEgfs}"
       ci_status=$?
       set -e
       if [[ ${ci_status} -eq 0 ]]; then
diff --git a/ci/scripts/create_experiment.py b/workflow/create_experiment.py
similarity index 89%
rename from ci/scripts/create_experiment.py
rename to workflow/create_experiment.py
index fd65e042d1..ebef94a9e6 100755
--- a/ci/scripts/create_experiment.py
+++ b/workflow/create_experiment.py
@@ -17,25 +17,19 @@
 with an error code of 0 upon success.
 """
 
-import os
-import sys
 from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
 from pathlib import Path
 
 from wxflow import YAMLFile, Logger, logit
 
-
-_here = os.path.dirname(__file__)
-_top = os.path.abspath(os.path.join(os.path.abspath(_here), '../..'))
-logger = Logger(level='DEBUG', colored_log=True)
-
-
-# TODO: move create_experiment.py to workflow/ and remove this sys.path.insert business
-sys.path.insert(0, os.path.join(_top, 'workflow'))
 import setup_expt
 import setup_xml
 
 
+# Setup the logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
 @logit(logger)
 def input_args():
     """

From e64ae94e1dcbe785cfd96d579b3d205f74d03b62 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Oct 2023 15:45:54 -0400
Subject: [PATCH 5/9] fix pycodestyle error

---
 workflow/create_experiment.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/create_experiment.py b/workflow/create_experiment.py
index ebef94a9e6..6e8dde0446 100755
--- a/workflow/create_experiment.py
+++ b/workflow/create_experiment.py
@@ -69,7 +69,7 @@ def input_args():
     experiment_dir = Path.absolute(Path.joinpath(Path(testconf.arguments.expdir), Path(testconf.arguments.pslot)))
 
     # Create a list of arguments to setup_expt.py
-    setup_expt_args = [testconf.experiment.system , testconf.experiment.mode]
+    setup_expt_args = [testconf.experiment.system, testconf.experiment.mode]
     for kk, vv in testconf.arguments.items():
         setup_expt_args.append(f"--{kk}")
         setup_expt_args.append(str(vv))

From 22ae19b842a74602be6cc8421bc97c93a2a92832 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Oct 2023 16:00:51 -0400
Subject: [PATCH 6/9] disable the soca test

---
 ci/cases/{pr_disable => pr}/C48_S2SA_gefs.yaml         | 0
 ci/cases/{pr_disable => pr}/C48_S2SW.yaml              | 0
 ci/cases/{pr_disable => pr}/C96C48_hybatmDA.yaml       | 0
 ci/cases/{pr_disable => pr}/C96_atm3DVar.yaml          | 0
 ci/cases/{pr => pr_disable}/C48_atm3DVar_ocnhybDA.yaml | 0
 5 files changed, 0 insertions(+), 0 deletions(-)
 rename ci/cases/{pr_disable => pr}/C48_S2SA_gefs.yaml (100%)
 rename ci/cases/{pr_disable => pr}/C48_S2SW.yaml (100%)
 rename ci/cases/{pr_disable => pr}/C96C48_hybatmDA.yaml (100%)
 rename ci/cases/{pr_disable => pr}/C96_atm3DVar.yaml (100%)
 rename ci/cases/{pr => pr_disable}/C48_atm3DVar_ocnhybDA.yaml (100%)

diff --git a/ci/cases/pr_disable/C48_S2SA_gefs.yaml b/ci/cases/pr/C48_S2SA_gefs.yaml
similarity index 100%
rename from ci/cases/pr_disable/C48_S2SA_gefs.yaml
rename to ci/cases/pr/C48_S2SA_gefs.yaml
diff --git a/ci/cases/pr_disable/C48_S2SW.yaml b/ci/cases/pr/C48_S2SW.yaml
similarity index 100%
rename from ci/cases/pr_disable/C48_S2SW.yaml
rename to ci/cases/pr/C48_S2SW.yaml
diff --git a/ci/cases/pr_disable/C96C48_hybatmDA.yaml b/ci/cases/pr/C96C48_hybatmDA.yaml
similarity index 100%
rename from ci/cases/pr_disable/C96C48_hybatmDA.yaml
rename to ci/cases/pr/C96C48_hybatmDA.yaml
diff --git a/ci/cases/pr_disable/C96_atm3DVar.yaml b/ci/cases/pr/C96_atm3DVar.yaml
similarity index 100%
rename from ci/cases/pr_disable/C96_atm3DVar.yaml
rename to ci/cases/pr/C96_atm3DVar.yaml
diff --git a/ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml b/ci/cases/pr_disable/C48_atm3DVar_ocnhybDA.yaml
similarity index 100%
rename from ci/cases/pr/C48_atm3DVar_ocnhybDA.yaml
rename to ci/cases/pr_disable/C48_atm3DVar_ocnhybDA.yaml

From beeaf3289d4ca14b0d01a9412006ad630f621e41 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Oct 2023 16:43:23 -0400
Subject: [PATCH 7/9] remove soca tests

---
 ci/cases/pr_disable/C48_atm3DVar_ocnhybDA.yaml | 18 ------------------
 ci/platforms/soca_gfs_defaults_ci.yaml         |  6 ------
 2 files changed, 24 deletions(-)
 delete mode 100644 ci/cases/pr_disable/C48_atm3DVar_ocnhybDA.yaml
 delete mode 100644 ci/platforms/soca_gfs_defaults_ci.yaml

diff --git a/ci/cases/pr_disable/C48_atm3DVar_ocnhybDA.yaml b/ci/cases/pr_disable/C48_atm3DVar_ocnhybDA.yaml
deleted file mode 100644
index 51bfc817b2..0000000000
--- a/ci/cases/pr_disable/C48_atm3DVar_ocnhybDA.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-experiment:
-  system: gfs
-  mode: cycled
-
-arguments:
-  pslot: ${pslot}
-  app: S2S
-  resdet: 48
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
-  # icsdir: ${ICSDIR_ROOT}/C48cpldDA
-  icsdir: "/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/ICSDIR/C48O500" # TODO: make platform agnostic
-  idate: 2021032312
-  edate: 2021032400
-  nens: 0
-  gfs_cyc: 0
-  start: warm
-  yaml: ${HOMEgfs}/ci/platforms/soca_gfs_defaults_ci.yaml
diff --git a/ci/platforms/soca_gfs_defaults_ci.yaml b/ci/platforms/soca_gfs_defaults_ci.yaml
deleted file mode 100644
index 244c235860..0000000000
--- a/ci/platforms/soca_gfs_defaults_ci.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-defaults:
-  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
-base:
-  ACCOUNT: ${SLURM_ACCOUNT}
-  DOIAU: "NO"
-  DO_JEDIOCNVAR: "YES"

From 758db445ff943e9bad6e5a9816a7cb11c8c5b135 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon, 16 Oct 2023 10:47:50 -0400
Subject: [PATCH 8/9] detect HOMEgfs in create_experiment.py based on location.
  update to use jinja templates in the cases

---
 ci/cases/pr/C48_ATM.yaml               |  8 +++----
 ci/cases/pr/C48_S2SA_gefs.yaml         | 10 ++++-----
 ci/cases/pr/C48_S2SW.yaml              |  8 +++----
 ci/cases/pr/C96C48_hybatmDA.yaml       | 10 ++++-----
 ci/cases/pr/C96_atm3DVar.yaml          |  8 +++----
 ci/cases/weekly/C384C192_hybatmda.yaml | 10 ++++-----
 ci/cases/weekly/C384_S2SWA.yaml        |  8 +++----
 ci/cases/weekly/C384_atm3DVar.yaml     | 10 ++++-----
 ci/scripts/driver.sh                   |  2 +-
 workflow/create_experiment.py          | 30 ++++++++++++++++++--------
 10 files changed, 58 insertions(+), 46 deletions(-)

diff --git a/ci/cases/pr/C48_ATM.yaml b/ci/cases/pr/C48_ATM.yaml
index 01a328873f..fc0b729af6 100644
--- a/ci/cases/pr/C48_ATM.yaml
+++ b/ci/cases/pr/C48_ATM.yaml
@@ -3,11 +3,11 @@ experiment:
   mode: forecast-only
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: ATM
   resdet: 48
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C48_S2SA_gefs.yaml b/ci/cases/pr/C48_S2SA_gefs.yaml
index 156683ae28..927a979b13 100644
--- a/ci/cases/pr/C48_S2SA_gefs.yaml
+++ b/ci/cases/pr/C48_S2SA_gefs.yaml
@@ -3,15 +3,15 @@ experiment:
   mode: forecast-only
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: S2SA
   resdet: 48
   resens: 48
   nens: 2
   gfs_cyc: 1
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
-  icsdir: ${ICSDIR_ROOT}/C48C48mx500
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48C48mx500
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs}/ci/platforms/gefs_ci_defaults.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gefs_ci_defaults.yaml
diff --git a/ci/cases/pr/C48_S2SW.yaml b/ci/cases/pr/C48_S2SW.yaml
index 4c4cf4f147..f4b50ead22 100644
--- a/ci/cases/pr/C48_S2SW.yaml
+++ b/ci/cases/pr/C48_S2SW.yaml
@@ -3,11 +3,11 @@ experiment:
   mode: forecast-only
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: S2SW
   resdet: 48
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C96C48_hybatmDA.yaml b/ci/cases/pr/C96C48_hybatmDA.yaml
index 4844ee3c9b..c3aa6e8892 100644
--- a/ci/cases/pr/C96C48_hybatmDA.yaml
+++ b/ci/cases/pr/C96C48_hybatmDA.yaml
@@ -3,16 +3,16 @@ experiment:
   mode: cycled
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: ATM
   resdet: 96
   resens: 48
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
-  icsdir: ${ICSDIR_ROOT}/C96C48
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
   idate: 2021122018
   edate: 2021122106
   nens: 2
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C96_atm3DVar.yaml b/ci/cases/pr/C96_atm3DVar.yaml
index 02aff389c4..5215cb0d90 100644
--- a/ci/cases/pr/C96_atm3DVar.yaml
+++ b/ci/cases/pr/C96_atm3DVar.yaml
@@ -3,15 +3,15 @@ experiment:
   mode: cycled
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: ATM
   resdet: 96
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: ${ICSDIR_ROOT}/C96C48
   idate: 2021122018
   edate: 2021122106
   nens: 0
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/weekly/C384C192_hybatmda.yaml b/ci/cases/weekly/C384C192_hybatmda.yaml
index 1d3c94017c..4c14018e2d 100644
--- a/ci/cases/weekly/C384C192_hybatmda.yaml
+++ b/ci/cases/weekly/C384C192_hybatmda.yaml
@@ -3,16 +3,16 @@ experiment:
   mode: cycled
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: ATM
   resdet: 384
   resens: 192
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
-  icsdir: ${ICSDIR_ROOT}/C384C192
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
   idate: 2023040118
   edate: 2023040200
   nens: 2
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/weekly/C384_S2SWA.yaml b/ci/cases/weekly/C384_S2SWA.yaml
index 2978e87c95..6c624f5698 100644
--- a/ci/cases/weekly/C384_S2SWA.yaml
+++ b/ci/cases/weekly/C384_S2SWA.yaml
@@ -3,11 +3,11 @@ experiment:
   mode: forecast-only
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: S2SWA
   resdet: 384
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2016070100
   edate: 2016070100
-  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/cases/weekly/C384_atm3DVar.yaml b/ci/cases/weekly/C384_atm3DVar.yaml
index a754ed0ee0..e7986ef097 100644
--- a/ci/cases/weekly/C384_atm3DVar.yaml
+++ b/ci/cases/weekly/C384_atm3DVar.yaml
@@ -3,16 +3,16 @@ experiment:
   mode: cycled
 
 arguments:
-  pslot: ${pslot}
+  pslot: {{ 'pslot' | getenv }}
   app: ATM
   resdet: 384
   resens: 192
-  comrot: ${RUNTESTS}/COMROT
-  expdir: ${RUNTESTS}/EXPDIR
-  icsdir: ${ICSDIR_ROOT}/C384C192
+  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
   idate: 2023040118
   edate: 2023040200
   nens: 0
   gfs_cyc: 1
   start: cold
-  yaml: ${HOMEgfs}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
diff --git a/ci/scripts/driver.sh b/ci/scripts/driver.sh
index 25682fd1aa..267a93922e 100755
--- a/ci/scripts/driver.sh
+++ b/ci/scripts/driver.sh
@@ -154,7 +154,7 @@ for pr in ${pr_list}; do
       rm -Rf "${STMP}/RUNDIRS/${pslot}"
       export pslot
       set +e
-      "${HOMEgfs}/workflow/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml" --dir "${HOMEgfs}"
+      "${HOMEgfs}/workflow/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml"
       ci_status=$?
       set -e
       if [[ ${ci_status} -eq 0 ]]; then
diff --git a/workflow/create_experiment.py b/workflow/create_experiment.py
index 6e8dde0446..c343f1d798 100755
--- a/workflow/create_experiment.py
+++ b/workflow/create_experiment.py
@@ -3,7 +3,7 @@
 """
 Basic python script to create an experiment directory on the fly from a given
 yaml file for the arguments to the two scripts below in ${HOMEgfs}/workflow
-where ${HOMEgfs} is specified within the input yaml file.
+where ${HOMEgfs} is determined from the location of this script.
 
  ${HOMEgfs}/workflow/setup_expt.py
  ${HOMEgfs}/workflow/setup_xml.py
@@ -17,17 +17,22 @@
 with an error code of 0 upon success.
 """
 
+import os
+
 from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
 from pathlib import Path
 
-from wxflow import YAMLFile, Logger, logit
+from wxflow import AttrDict, parse_j2yaml, Logger, logit
 
 import setup_expt
 import setup_xml
 
 
+_here = os.path.dirname(__file__)
+_top = os.path.abspath(os.path.join(os.path.abspath(_here), '..'))
+
 # Setup the logger
-logger = Logger(level='DEBUG', colored_log=True)
+logger = Logger(level=os.environ.get("LOGGING_LEVEL", "INFO"), colored_log=True)
 
 
 @logit(logger)
@@ -55,8 +60,8 @@ def input_args():
     parser = ArgumentParser(description=description,
                             formatter_class=ArgumentDefaultsHelpFormatter)
 
-    parser.add_argument('--yaml', help='full path to yaml file describing the experiment configuration', type=str, required=True)
-    parser.add_argument('--dir', help='full path to global-workflow', type=str, required=True)
+    parser.add_argument(
+        '--yaml', help='full path to yaml file describing the experiment configuration', type=Path, required=True)
 
     return parser.parse_args()
 
@@ -64,9 +69,11 @@ def input_args():
 if __name__ == '__main__':
 
     user_inputs = input_args()
-    HOMEgfs = Path.absolute(Path(user_inputs.dir))
-    testconf = YAMLFile(path=user_inputs.yaml)
-    experiment_dir = Path.absolute(Path.joinpath(Path(testconf.arguments.expdir), Path(testconf.arguments.pslot)))
+
+    # Create a dictionary to pass to parse_j2yaml for parsing the yaml file
+    data = AttrDict(HOMEgfs=_top)
+    data.update(os.environ)
+    testconf = parse_j2yaml(path=user_inputs.yaml, data=data)
 
     # Create a list of arguments to setup_expt.py
     setup_expt_args = [testconf.experiment.system, testconf.experiment.mode]
@@ -74,11 +81,16 @@ def input_args():
         setup_expt_args.append(f"--{kk}")
         setup_expt_args.append(str(vv))
 
-    logger.info(f'Call: setup_expt.main()')
+    logger.info(f"Call: setup_expt.main()")
+    logger.debug(f"setup_expt.py {' '.join(setup_expt_args)}")
     setup_expt.main(setup_expt_args)
 
     # Create a list of arguments to setup_xml.py
+    experiment_dir = Path.absolute(Path.joinpath(
+        Path(testconf.arguments.expdir), Path(testconf.arguments.pslot)))
+
     setup_xml_args = [str(experiment_dir)]
 
     logger.info(f"Call: setup_xml.main()")
+    logger.debug(f"setup_xml.py {' '.join(setup_xml_args)}")
     setup_xml.main(setup_xml_args)

From e4933f7cc5a174149a6902e2efa10df40cedcf95 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon, 16 Oct 2023 15:50:11 -0400
Subject: [PATCH 9/9] remove export of HOMEgfs from driver.sh

---
 ci/scripts/driver.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/ci/scripts/driver.sh b/ci/scripts/driver.sh
index 267a93922e..a79ecfd6cf 100755
--- a/ci/scripts/driver.sh
+++ b/ci/scripts/driver.sh
@@ -144,15 +144,15 @@ for pr in ${pr_list}; do
     # loop over every yaml file in the PR's ci/cases
     # and create an run directory for each one for this PR loop
     #############################################################
-    export HOMEgfs="${pr_dir}/global-workflow"
+    HOMEgfs="${pr_dir}/global-workflow"
     cd "${HOMEgfs}"
     pr_sha=$(git rev-parse --short HEAD)
 
     for yaml_config in "${HOMEgfs}/ci/cases/pr/"*.yaml; do
       case=$(basename "${yaml_config}" .yaml) || true
-      pslot="${case}_${pr_sha}"
+      # export pslot for yaml case files to pickup
+      export pslot="${case}_${pr_sha}"
       rm -Rf "${STMP}/RUNDIRS/${pslot}"
-      export pslot
       set +e
       "${HOMEgfs}/workflow/create_experiment.py" --yaml "${HOMEgfs}/ci/cases/pr/${case}.yaml"
       ci_status=$?