run_neon --setup-only is ignored

[samsrabin]

Brief summary of bug

run_neon --setup-only option is ignored.

General bug information

CTSM version you are using: ctsm5.3.012

Does this bug cause significantly incorrect results in the model's science? No

Configurations affected: All

Details of bug

The following patch fixes it:

diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py
index 70414d9e5..ced4c4c64 100755
--- a/python/ctsm/site_and_regional/neon_site.py
+++ b/python/ctsm/site_and_regional/neon_site.py
@@ -47,7 +47,8 @@ class NeonSite(TowerSite):
             user_mods_dirs = [
                 os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
             ]
-        case_path = super().build_base_case(cesmroot, output_root, res, compset, user_mods_dirs)
+        case_path = super().build_base_case(cesmroot, output_root, res, compset, user_mods_dirs,
+                                            setup_only=setup_only)

         return case_path

Important details of your setup / configuration so we can reproduce the bug

Tested on Derecho.

# Running this continues through the build step, but --setup-only means it shouldn't
python tools/site_and_regional/run_neon --neon-sites ABBY --setup-only

Important output or errors that show the problem

---- building a base case -------
/glade/work/samrabin/ctsm_anping_lecture/ABBY
Removing the existing case at: /glade/work/samrabin/ctsm_anping_lecture/ABBY
---- creating a base case -------
---- base case created ------
---- base case setup ------
---- base case build ------
--- This may take a while and you may see WARNING messages ---
WARNING: No .input_data_list files found in dir 'Buildconf'
...

[ekluzek]

Ran into this again working on ctsm5.3.015. And I see a similar problem with overwrite as well.

[samsrabin]

I see a similar problem with overwrite as well.

Yep, that's #2884.