Refactoring run_neon for PLUMBER2 part1

python/ctsm/site_and_regional/neon_arg_parse.py

@@ -0,0 +1,240 @@
+"""
+Argument parser to use throughout run_neon.py
+"""
+
+import argparse
+import logging
+import os
+import sys
+
+# Get the ctsm util tools and then the cime tools.
+_CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python"))
+sys.path.insert(1, _CTSM_PYTHON)
+
+# pylint: disable=wrong-import-position, import-error, unused-import, wrong-import-order
+from ctsm import add_cime_to_path
+from ctsm.utils import parse_isoduration
+from CIME.utils import parse_args_and_handle_standard_logging_options
+from CIME.utils import setup_standard_logging_options
+
+
+def get_parser(args, description, valid_neon_sites):
+    """
+    Get parser object for this script.
+    """
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    setup_standard_logging_options(parser)
+
+    parser.print_usage = parser.print_help
+
+    parser.add_argument(
+        "--neon-sites",
+        help="4-letter neon site code.",
+        action="store",
+        required=False,
+        choices=valid_neon_sites + ["all"],
+        dest="neon_sites",
+        default=["OSBS"],
+        nargs="+",
+    )
+
+    parser.add_argument(
+        "--base-case",
+        help="""
+                Root Directory of base case build
+                [default: %(default)s]
+                """,
+        action="store",
+        dest="base_case_root",
+        type=str,
+        required=False,
+        default=None,
+    )
+
+    parser.add_argument(
+        "--output-root",
+        help="""
+                Root output directory of cases
+                [default: %(default)s]
+                """,
+        action="store",
+        dest="output_root",
+        type=str,
+        required=False,
+        default="CIME_OUTPUT_ROOT as defined in cime",
+    )
+
+    parser.add_argument(
+        "--overwrite",
+        help="""
+                overwrite existing case directories
+                [default: %(default)s]
+                """,
+        action="store_true",
+        dest="overwrite",
+        required=False,
+        default=False,
+    )
+
+    parser.add_argument(
+        "--setup-only",
+        help="""
+                Only setup the requested cases, do not build or run
+                [default: %(default)s]
+                """,
+        action="store_true",
+        dest="setup_only",
+        required=False,
+        default=False,
+    )
+
+    parser.add_argument(
+        "--rerun",
+        help="""
+                If the case exists but does not appear to be complete, restart it.
+                [default: %(default)s]
+                """,
+        action="store_true",
+        dest="rerun",
+        required=False,
+        default=False,
+    )
+
+    parser.add_argument(
+        "--no-batch",
+        help="""
+                Run locally, do not use batch queueing system (if defined for Machine)
+                [default: %(default)s]
+                """,
+        action="store_true",
+        dest="no_batch",
+        required=False,
+        default=False,
+    )
+
+    parser.add_argument(
+        "--run-type",
+        help="""
+                        Type of run to do
+                        [default: %(default)s]
+                        """,
+        choices=["ad", "postad", "transient"],  # , "sasu"],
+        default="transient",
+    )
+
+    parser.add_argument(
+        "--prism",
+        help="""
+                Uses the PRISM reanaylsis precipitation data for the site instead of the NEON data
+                (only available over Continental US)
+                """,
+        action="store_true",
+        dest="prism",
+        required=False,
+        default=False,
+    )
+
+    parser.add_argument(
+        "--experiment",
+        help="""
+                Appends the case name with string for model experiment
+                """,
+        action="store",
+        dest="experiment",
+        type=str,
+        required=False,
+        default=None,
+    )
+
+    parser.add_argument(
+        "--run-length",
+        help="""
+                How long to run (modified ISO 8601 duration)
+                [default: %(default)s]
+                """,
+        required=False,
+        type=str,
+        default="0Y",
+    )
+
+    parser.add_argument(
+        "--run-from-postad",
+        help="""
+                        For transient runs only - should we start from the postad spinup or finidat?
+                        By default start from finidat, if this flag is used the postad run must be available.
+                        """,
+        action="store_true",
+        required=False,
+        default=False,
+    )
+    parser.add_argument(
+        "--neon-version",
+        help="""
+                Neon data version to use for this simulation.
+                [default: use the latest data available]
+                """,
+        action="store",
+        dest="user_version",
+        required=False,
+        type=str,
+        choices=["v1", "v2", "v3"],
+    )
+
+    args = parse_args_and_handle_standard_logging_options(args, parser)
+
+    if "all" in args.neon_sites:
+        neon_sites = valid_neon_sites
+    else:
+        neon_sites = args.neon_sites
+        for site in neon_sites:
+            if site not in valid_neon_sites:
+                raise ValueError("Invalid site name {}".format(site))
+
+    if "CIME_OUTPUT_ROOT" in args.output_root:
+        args.output_root = None
+
+    if args.run_length == "0Y":
+        if args.run_type == "ad":
+            run_length = "100Y"
+        elif args.run_type == "postad":
+            run_length = "100Y"
+        else:
+            # The transient run length is set by cdeps atm buildnml to
+            # the last date of the available tower data
+            # this value is not used
+            run_length = "4Y"
+    else:
+        run_length = args.run_length
+
+    run_length = parse_isoduration(run_length)
+
+    base_case_root = None
+    if args.base_case_root:
+        base_case_root = os.path.abspath(args.base_case_root)
+        if not os.path.exists(base_case_root):
+            raise ValueError("Base case root does not exist: {}".format(base_case_root))
+
+    # Reduce output level for this script unless --debug or
+    # --verbose is provided on the command line
+    if not args.debug and not args.verbose:
+        root_logger = logging.getLogger()
+        root_logger.setLevel(logging.WARN)
+
+    return (
+        neon_sites,
+        args.output_root,
+        args.run_type,
+        args.experiment,
+        args.prism,
+        args.overwrite,
+        run_length,
+        base_case_root,
+        args.run_from_postad,
+        args.setup_only,
+        args.no_batch,
+        args.rerun,
+        args.user_version,
+    )