fix argument errors

TeaganKing · Feb 13, 2024 · f48bb75 · f48bb75
1 parent 68f6957
commit f48bb75
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Showing 3 changed files with 29 additions and 22 deletions.
diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py
@@ -3,13 +3,9 @@
 """
 
 # Import libraries
-import glob
 import logging
 import os
-import re
-import shutil
 import sys
-import time
 
 # Get the ctsm util tools and then the cime tools.
 _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python"))
@@ -36,21 +32,28 @@ class NeonSite(TowerSite):
     A class for encapsulating neon sites.
     """
 
-    def __init__(self, name, start_year, end_year, start_month, end_month, finidat):
-        super().__init__(name, start_year, end_year, start_month, end_month, finidat)
-
     def build_base_case(
-        self, cesmroot, output_root, res, compset, overwrite=False, setup_only=False
+        self,
+        cesmroot,
+        output_root,
+        res,
+        compset,
+        user_mods_dirs=None,
+        overwrite=False,
+        setup_only=False,
     ):
-        user_mods_dirs = [
-            os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
-        ]
+        if user_mods_dirs is None:
+            user_mods_dirs = [
+                os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
+            ]
+            print("in neonsite adding usermodsdirs")
+        print("usermodsdirs: {}".format(user_mods_dirs))
         case_path = super().build_base_case(cesmroot, output_root, res, compset, user_mods_dirs)
 
         return case_path
 
-    def get_batch_query(self, case):
-        return super().get_batch_query(case)
+    # def get_batch_query(self, case):
+    #    return super().get_batch_query(case)
 
     # pylint: disable=too-many-statements
     def run_case(
@@ -60,6 +63,8 @@ def run_case(
         prism,
         run_length,
         user_version,
+        tower_type=None,
+        user_mods_dirs=None,
         overwrite=False,
         setup_only=False,
         no_batch=False,
@@ -97,17 +102,18 @@ def run_case(
         ]
         tower_type = "NEON"
         super().run_case(
-            base_case_root, run_type, prism, run_length, tower_type, user_mods_dirs, user_version
+            base_case_root, run_type, prism, run_length, user_version, tower_type, user_mods_dirs
         )
 
     def set_ref_case(self, case):
         super().set_ref_case(case)
         return True  ### Check if super returns false, if this will still return True?
 
-    def modify_user_nl(self, case_root, run_type, rundir):
+    def modify_user_nl(self, case_root, run_type, rundir, site_lines=None):
         # TODO: include neon-specific user namelist lines, using this as just an example currently
-        site_lines = [
-            """hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC',
+        if site_lines is None:
+            site_lines = [
+                """hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC',
                                  'TOTVEGN', 'TLAI', 'GPP', 'CPOOL', 'NPP', 'TWS', 'H2OSNO',"""
-        ]
+            ]
         super().modify_user_nl(case_root, run_type, rundir, site_lines)
diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py
@@ -220,8 +220,9 @@ def main(description):
             if run_from_postad:
                 neon_site.finidat = None
             if not base_case_root:
+                user_mods_dirs = None
                 base_case_root = neon_site.build_base_case(
-                    cesmroot, output_root, res, compset, overwrite, setup_only
+                    cesmroot, output_root, res, compset, user_mods_dirs, overwrite, setup_only
                 )
             logger.info("-----------------------------------")
             logger.info("Running CTSM for neon site : %s", neon_site.name)

diff --git a/python/ctsm/site_and_regional/tower_site.py b/python/ctsm/site_and_regional/tower_site.py
@@ -171,7 +171,7 @@ def get_batch_query(self, case):
             return "none"
         return case.get_value("batch_query")
 
-    def modify_user_nl(self, case_root, run_type, rundir, site_lines):
+    def modify_user_nl(self, case_root, run_type, rundir, site_lines=None):
         """
         Modify user namelist. If transient, include finidat in user_nl;
         Otherwise, adjust user_nl to include different mfilt, nhtfrq, and variables in hist_fincl1.
@@ -249,9 +249,9 @@ def run_case(
         run_type,
         prism,
         run_length,
+        user_version,
         tower_type,
         user_mods_dirs,
-        user_version,
         overwrite=False,
         setup_only=False,
         no_batch=False,
@@ -399,7 +399,7 @@ def run_case(
             if not rundir:
                 rundir = case.get_value("RUNDIR")
 
-            self.modify_user_nl(case_root, run_type, rundir)
+            self.modify_user_nl(case_root, run_type, rundir)  # TODO: add site_lines argument?
 
             case.create_namelists()
             # explicitly run check_input_data