Fix string replacements in lreprstruct test

The previous logic caused problems if "GRAIN" appeared in two (or more)
strings, where one was a substring of the other. For example, in
LREPRSTRUCT_Ly1_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-ciso--clm-cropMonthOutput,
before this replacement, one line contained 'GRAINN_TO_FOOD' and a later
line contained (among other things) "'GRAINN_TO_FOOD_PERHARV',
'GRAINN_TO_FOOD_ANN'". This was problematic because the first
replacement of GRAINN_TO_FOOD incorrectly led to replacements in the
later strings as well.

This new logic should solve this issue.

Resolves #3313

Author: billsacks

cime_config/SystemTests/lreprstruct.py

@@ -16,6 +16,8 @@
 
 """
 
+import re
+
 from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
@@ -53,13 +55,16 @@ def _case_one_setup(self):
         user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
         with open(user_nl_clm_path) as f:
             user_nl_clm_text = f.read()
-        for grain_output in re.findall("GRAIN\w*", user_nl_clm_text):
-            user_nl_clm_text = user_nl_clm_text.replace(
-                grain_output,
+
+        def replace_grain(match):
+            grain_output = match.group()
+            return (
                 grain_output.replace("GRAIN", "REPRODUCTIVE1")
                 + "', '"
-                + grain_output.replace("GRAIN", "REPRODUCTIVE2"),
+                + grain_output.replace("GRAIN", "REPRODUCTIVE2")
             )
+
+        user_nl_clm_text = re.sub(r"GRAIN\w*", replace_grain, user_nl_clm_text)
         with open(user_nl_clm_path, "w") as f:
             f.write(user_nl_clm_text)