[WIP] Refactoring of neon_site into tower_site, and neon_site

.gitignore

@@ -111,6 +111,7 @@ unit_test_build
 /tools/site_and_regional/????.ad/
 /tools/site_and_regional/????.postad/
 /tools/site_and_regional/????.transient/
+/tools/site_and_regional/archive/
 
 # build output
 *.o

cime_config/buildnml

@@ -144,8 +144,8 @@ def buildnml(case, caseroot, compname):
                 or clm_usrdat_name is "NEON.PRISM"
             ):
                 logger.warning(
-                    "WARNING: Do you have approriprate initial conditions for this simulation?"
-                    + " Check that the finidat file used in the lnd_in namelist is apprporiately spunup for your case"
+                    "WARNING: Do you have appropriate initial conditions for this simulation?"
+                    + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
                 )
 
     if comp_atm != "datm":

python/ctsm/site_and_regional/neon_site.py

@@ -15,6 +15,10 @@
 _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python"))
 sys.path.insert(1, _CTSM_PYTHON)
 
+# -- import local classes for this script
+# pylint: disable=wrong-import-position
+from ctsm.site_and_regional.tower_site import TowerSite
+
 # pylint: disable=wrong-import-position, import-error, unused-import, wrong-import-order
 from ctsm import add_cime_to_path
 from ctsm.path_utils import path_to_ctsm_root
@@ -27,126 +31,30 @@
 
 
 # pylint: disable=too-many-instance-attributes
-class NeonSite:
+class NeonSite(TowerSite):
     """
     A class for encapsulating neon sites.
     """
 
     def __init__(self, name, start_year, end_year, start_month, end_month, finidat):
-        self.name = name
-        self.start_year = int(start_year)
-        self.end_year = int(end_year)
-        self.start_month = int(start_month)
-        self.end_month = int(end_month)
-        self.cesmroot = path_to_ctsm_root()
-        self.finidat = finidat
+        super().__init__(name, start_year, end_year, start_month, end_month, finidat)
+        # self.name = name
+        # self.start_year = int(start_year)
+        # self.end_year = int(end_year)
+        # self.start_month = int(start_month)
+        # self.end_month = int(end_month)
+        # self.cesmroot = path_to_ctsm_root()
+        # self.finidat = finidat
 
     def build_base_case(
         self, cesmroot, output_root, res, compset, overwrite=False, setup_only=False
     ):
-        """
-        Function for building a base_case to clone.
-        To spend less time on building ctsm for the neon cases,
-        all the other cases are cloned from this case
-
-        Args:
-        self:
-            The NeonSite object
-        base_root (str):
-            root of the base_case CIME
-        res (str):
-            base_case resolution or gridname
-        compset (str):
-            base case compset
-        overwrite (bool) :
-            Flag to overwrite the case if exists
-        """
-        print("---- building a base case -------")
-        # pylint: disable=attribute-defined-outside-init
-        self.base_case_root = output_root
-        # pylint: enable=attribute-defined-outside-init
-        user_mods_dirs = [os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)]
-        if not output_root:
-            output_root = os.getcwd()
-        case_path = os.path.join(output_root, self.name)
-
-        logger.info("base_case_name : %s", self.name)
-        logger.info("user_mods_dir  : %s", user_mods_dirs[0])
-
-        if overwrite and os.path.isdir(case_path):
-            print("Removing the existing case at: {}".format(case_path))
-            shutil.rmtree(case_path)
-
-        with Case(case_path, read_only=False) as case:
-            if not os.path.isdir(case_path):
-                print("---- creating a base case -------")
-
-                case.create(
-                    case_path,
-                    cesmroot,
-                    compset,
-                    res,
-                    run_unsupported=True,
-                    answer="r",
-                    output_root=output_root,
-                    user_mods_dirs=user_mods_dirs,
-                    driver="nuopc",
-                )
-
-                print("---- base case created ------")
-
-                # --change any config for base_case:
-                # case.set_value("RUN_TYPE","startup")
-                print("---- base case setup ------")
-                case.case_setup()
-            else:
-                # For existing case check that the compset name is correct
-                existingcompname = case.get_value("COMPSET")
-                match = re.search("^HIST", existingcompname, flags=re.IGNORECASE)
-                if re.search("^HIST", compset, flags=re.IGNORECASE) is None:
-                    expect(
-                        match is None,
-                        """Existing base case is a historical type and should not be
-                        --rerun with the --overwrite option""",
-                    )
-                else:
-                    expect(
-                        match is not None,
-                        """Existing base case should be a historical type and is not
-                        --rerun with the --overwrite option""",
-                    )
-                # reset the case
-                case.case_setup(reset=True)
-            case_path = case.get_value("CASEROOT")
+        case_path = super().build_base_case(cesmroot, output_root, res, compset)
 
-            if setup_only:
-                return case_path
-
-            print("---- base case build ------")
-            print("--- This may take a while and you may see WARNING messages ---")
-            # always walk through the build process to make sure it's up to date.
-            initial_time = time.time()
-            build.case_build(case_path, case=case)
-            end_time = time.time()
-            total = end_time - initial_time
-            print("Time required to building the base case: {} s.".format(total))
-            # update case_path to be the full path to the base case
         return case_path
 
-    # pylint: disable=no-self-use
     def get_batch_query(self, case):
-        """
-        Function for querying the batch queue query command for a case, depending on the
-        user's batch system.
-
-        Args:
-        case:
-            case object
-        """
-
-        if case.get_value("BATCH_SYSTEM") == "none":
-            return "none"
-        return case.get_value("batch_query")
+        return super().get_batch_query(case)
 
     # pylint: disable=too-many-statements
     def run_case(
@@ -321,50 +229,8 @@ def run_case(
                     print(f"Use {batch_query} to check its run status")
 
     def set_ref_case(self, case):
-        """
-        Set an existing case as the reference case, eg for use with spinup.
-        """
-        rundir = case.get_value("RUNDIR")
-        case_root = case.get_value("CASEROOT")
-        if case_root.endswith(".postad"):
-            ref_case_root = case_root.replace(".postad", ".ad")
-            root = ".ad"
-        else:
-            ref_case_root = case_root.replace(".transient", ".postad")
-            root = ".postad"
-        if not os.path.isdir(ref_case_root):
-            logger.warning(
-                "ERROR: spinup must be completed first, could not find directory %s", ref_case_root
-            )
-            return False
-
-        with Case(ref_case_root) as refcase:
-            refrundir = refcase.get_value("RUNDIR")
-        case.set_value("RUN_REFDIR", refrundir)
-        case.set_value("RUN_REFCASE", os.path.basename(ref_case_root))
-        refdate = None
-        for reffile in glob.iglob(refrundir + "/{}{}.clm2.r.*.nc".format(self.name, root)):
-            m_searched = re.search(r"(\d\d\d\d-\d\d-\d\d)-\d\d\d\d\d.nc", reffile)
-            if m_searched:
-                refdate = m_searched.group(1)
-            symlink_force(reffile, os.path.join(rundir, os.path.basename(reffile)))
-        logger.info("Found refdate of %s", refdate)
-        if not refdate:
-            logger.warning("Could not find refcase for %s", case_root)
-            return False
-
-        for rpfile in glob.iglob(refrundir + "/rpointer*"):
-            safe_copy(rpfile, rundir)
-        if not os.path.isdir(os.path.join(rundir, "inputdata")) and os.path.isdir(
-            os.path.join(refrundir, "inputdata")
-        ):
-            symlink_force(os.path.join(refrundir, "inputdata"), os.path.join(rundir, "inputdata"))
-
-        case.set_value("RUN_REFDATE", refdate)
-        if case_root.endswith(".postad"):
-            case.set_value("RUN_STARTDATE", refdate)
-        # NOTE: if start options are set, RUN_STARTDATE should be modified here
-        return True
+        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):
         """