add avaialble_diags output

payu/models/mom6.py

@@ -23,7 +23,7 @@
 from payu.models.mom_mixin import MomMixin
 from payu.git_utils import GitRepository
 
-MOM6_DOCS = "MOM_parameter_doc.*"
+MOM6_DOCS = ["MOM_parameter_doc.*","available_diags.*"]
 
 def mom6_add_parameter_files(model):
     """Add parameter files defined in input.nml to model configuration files.
@@ -53,19 +53,25 @@ def mom6_save_docs_files(model):
     mkdir_p(docs_folder)
 
     # copy everything that matches MOM_parameter_doc.* to the control dir
-    for f in glob(os.path.join(model.work_path, MOM6_DOCS)):
-        try:
-            shutil.copy(f, docs_folder)
-        except Exception as e:
-            warn(e)
+    for pattern in MOM6_DOCS:
+        for f in glob(os.path.join(model.work_path, pattern)):
+            try:
+                shutil.copy(f, docs_folder)
+            except Exception as e:
+                warn(e)
 
     if model.expt.runlog.enabled: #if runlog true, default to true
         # commit new files to the control dir
         repo = GitRepository(repo_path = model.control_path)
 
+        paths_to_commit = []
+        for pattern in MOM6_DOCS:
+            for i in glob(os.path.join(docs_folder, pattern)):
+                paths_to_commit.append(i)
+
         repo.commit(
             commit_message = "payu archive: documentation of MOM6 run-time configuration" ,
-            paths_to_commit = glob(os.path.join(docs_folder, MOM6_DOCS))
+            paths_to_commit = paths_to_commit
         )
 
 class Mom6(MomMixin, Fms):

test/models/test_mom6.py

@@ -152,7 +152,7 @@ def mom_parameter_doc(request):
 
 @pytest.mark.parametrize(
         "mom_parameter_doc", 
-        [["MOM_parameter_doc.all","MOM_parameter_doc.debug","MOM_parameter_docs.debug"]],
+        [["MOM_parameter_doc.all","MOM_parameter_doc.debug","MOM_parameter_docs.debug", "available_diags.000000"]],
         indirect=True
 )
 @pytest.mark.filterwarnings("error")
@@ -167,7 +167,7 @@ def test_mom6_save_doc_files(mom_parameter_doc):
     payu.models.mom6.mom6_save_docs_files(mom_parameter_doc)
 
     # Check MOM_parameter_doc.* are added to control_path
-    for file in ["MOM_parameter_doc.all","MOM_parameter_doc.debug"]:
+    for file in ["MOM_parameter_doc.all","MOM_parameter_doc.debug", "available_diags.000000"]:
         filename = os.path.join(mom_parameter_doc.control_path, "docs", file)
         assert os.path.isfile(filename)==True , "Payu did not move MOM_parameter_doc.* files into docs folder"
         os.remove(filename)