From d4cbf392af7bfcccedd3828f2ed97198f0edaea6 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Wed, 8 Jan 2025 16:14:13 +0000
Subject: [PATCH 1/3] Remove default C48_ATM case

---
 workflow/generate_workflows.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/workflow/generate_workflows.sh b/workflow/generate_workflows.sh
index a5615a8b0d..cc6cbad4b9 100755
--- a/workflow/generate_workflows.sh
+++ b/workflow/generate_workflows.sh
@@ -43,7 +43,6 @@ function _usage() {
        Run all valid SFS cases in the specified YAML directory.
 
     NOTES:
-         - Only one of -G -E or -S may be specified
          - Valid cases are determined by the experiment:system key as
            well as the skip_ci_on_hosts list in each YAML.
 
@@ -86,7 +85,7 @@ _specified_home=false
 _build=false
 _build_flags=""
 _update_submods=false
-declare -a _yaml_list=("C48_ATM")
+declare -a _yaml_list=("")
 _specified_yaml_list=false
 _yaml_dir=""  # Will be set based off of HOMEgfs if not specified explicitly
 _specified_yaml_dir=false

From ed7ad210f2d3be3394fa7d5805e12dc0d0b2f9a5 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Fri, 10 Jan 2025 14:09:02 +0000
Subject: [PATCH 2/3] Prevent duplicate tests when running generate_workflows

---
 workflow/generate_workflows.sh | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/workflow/generate_workflows.sh b/workflow/generate_workflows.sh
index cc6cbad4b9..7c98cf05c9 100755
--- a/workflow/generate_workflows.sh
+++ b/workflow/generate_workflows.sh
@@ -17,13 +17,13 @@ function _usage() {
        directory up from this script's residing directory.
 
     -b Run build_all.sh with default flags
-       (build the UFS, UPP, UFS_Utils, and GFS-utils only
+       (build the UFS, UPP, UFS_Utils, and GFS-utils only)
 
     -u Update submodules before building and/or generating experiments.
 
     -y "list of YAMLs to run"
        If this option is not specified, the default case (C48_ATM) will be
-       run.  This option is overidden by -G or -E (see below).
+       run.  This option is incompatible with -G, -E, or -S.
        Example: -y "C48_ATM C48_S2SW C96C48_hybatmDA"
 
     -Y /path/to/directory/with/YAMLs
@@ -85,7 +85,7 @@ _specified_home=false
 _build=false
 _build_flags=""
 _update_submods=false
-declare -a _yaml_list=("")
+declare -a _yaml_list=("C48_ATM")
 _specified_yaml_list=false
 _yaml_dir=""  # Will be set based off of HOMEgfs if not specified explicitly
 _specified_yaml_dir=false
@@ -222,6 +222,22 @@ else
    done
 fi
 
+# Empty the _yaml_list array if -G, -E, and/or -S were selected
+if [[ "${_run_all_gfs}" == "true" || \
+      "${_run_all_gefs}" == "true" || \
+      "${_run_all_sfs}" == "true" ]]; then
+
+   # Raise an error if the user specified a yaml list and any of -G -E -S
+   if [[ "${_specified_yaml_list}" == "true" ]]; then
+      echo "Ambiguous case selection."
+      echo "Please select which tests to run explicitly with -y (test list) or"
+      echo "by specifying -G (all GFS), -E (all GEFS), and/or -S (all SFS), but not both."
+      exit 3
+   fi
+
+   _yaml_list=()
+fi
+
 # If -S is specified, exit (for now).
 # TODO when SFS tests come online, enable this option.
 if [[ "${_run_all_sfs}" == "true" ]]; then

From 4f127de481f72e067bae4d578654e048594fe69a Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Fri, 10 Jan 2025 14:16:28 +0000
Subject: [PATCH 3/3] Clarify error message

---
 workflow/generate_workflows.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/generate_workflows.sh b/workflow/generate_workflows.sh
index 7c98cf05c9..dbd360fda2 100755
--- a/workflow/generate_workflows.sh
+++ b/workflow/generate_workflows.sh
@@ -230,7 +230,7 @@ if [[ "${_run_all_gfs}" == "true" || \
    # Raise an error if the user specified a yaml list and any of -G -E -S
    if [[ "${_specified_yaml_list}" == "true" ]]; then
       echo "Ambiguous case selection."
-      echo "Please select which tests to run explicitly with -y (test list) or"
+      echo "Please select which tests to run explicitly with -y \"list of tests\" or"
       echo "by specifying -G (all GFS), -E (all GEFS), and/or -S (all SFS), but not both."
       exit 3
    fi