Merge develop into main for pre-release preparation

README.md

@@ -22,6 +22,7 @@ It currently supports the following sources and standards:
 | Standard                                                                                                                   | Source                                                            | .nc/OPeNDAP/.cdl | SOS                             |
 | ----------------------------------------------------------------------------------------------------                       | -----------                                                       | ------           | ------------------------------- |
 | [ACDD (1.1, 1.3)](https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery_1-3)                                    | Built-in                                                          | X                | -                               |
+| [CF (1.9)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.9/cf-conventions.html)                            | Built-in                                                          | X                | -                               |
 | [CF (1.8)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html)                            | Built-in                                                          | X                | -                               |
 | [CF (1.7)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html)                            | Built-in                                                          | X                | -                               |
 | [CF (1.6)](http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html)                                             | Built-in                                                          | X                | -                               |

cchecker.py

@@ -22,21 +22,25 @@ def _print_checker_name_header(checker_str):
 
 def parse_options(opts):
     """
-    Helper function to parse possible options.  Splits option after the first
-    colon to split into key/value pairs.
+    Helper function to parse possible options. Splits option into key/value
+    pairs and optionally a value for the checker option. The separator
+    is a colon.
 
     :param opts: Iterable of strings with options
     :rtype: dict
-    :return: Dictionary with keys as checker type (i.e. "cf", "acdd")
+    :return: Dictionary with keys as checker type (i.e. "cf", "acdd").
+             Each value is a dictionary where keys are checker options and values
+             are checker option values or None if not provided.
     """
-    options_dict = defaultdict(set)
+    options_dict = defaultdict(dict)
     for opt_str in opts:
         try:
-            checker_type, checker_opt = opt_str.split(":", 1)
+            checker_type, checker_opt, *checker_val = opt_str.split(":", 2)
+            checker_val = checker_val[0] if checker_val else None
         except ValueError:
             warnings.warn(f"Could not split option {opt_str}, ignoring", stacklevel=2)
         else:
-            options_dict[checker_type].add(checker_opt)
+            options_dict[checker_type][checker_opt] = checker_val
     return options_dict
 
 
@@ -174,8 +178,9 @@ def main():
                                     checkers.  Multiple options can be specified
                                     via multiple invocations of this switch.
                                     Options should be prefixed with a the
-                                    checker name followed by the option, e.g.
-                                    '<checker>:<option_name>'
+                                    checker name followed by the option,
+                                    potentially followed by a value, e.g.
+                                    '<checker>:<option_name>[:<option_value>]'
 
                                     Available options:
                                     'cf:enable_appendix_a_checks' - Allow check
@@ -235,7 +240,7 @@ def main():
         print(f"IOOS compliance checker version {__version__}")
         sys.exit(0)
 
-    options_dict = parse_options(args.option) if args.option else defaultdict(set)
+    options_dict = parse_options(args.option) if args.option else defaultdict(dict)
 
     if args.describe_checks:
         error_stat = 0

compliance_checker/base.py

@@ -157,7 +157,7 @@ def setup(self, ds):
     def __init__(self, options=None):
         self._defined_results = defaultdict(lambda: defaultdict(dict))
         if options is None:
-            self.options = set()
+            self.options = {}
         else:
             self.options = options
 

compliance_checker/suite.py

@@ -401,7 +401,7 @@ def run_all(self, ds, checker_names, include_checks=None, skip_checks=None):
             #       use some kind of checker object with checker type and
             #       version baked in
             checker_type_name = checker_name.split(":")[0]
-            checker_opts = self.options.get(checker_type_name, set())
+            checker_opts = self.options.get(checker_type_name, {})
 
             # instantiate a Checker object
             try:

compliance_checker/tests/test_cf.py

@@ -240,7 +240,7 @@ def test_appendix_a(self):
         dataset = self.load_dataset(STATIC_FILES["bad_data_type"])
         # Ordinarily, options would be specified in the checker constructor, but
         # we set them manually here so we don't have to monkey patch `setUp`
-        self.cf.options = {"enable_appendix_a_checks"}
+        self.cf.options = {"enable_appendix_a_checks": None}
         new_check = copy.deepcopy(self.cf)
         self.cf.setup(dataset)
         aa_results = self.cf.check_appendix_a(dataset)

compliance_checker/tests/test_cli.py

@@ -10,6 +10,9 @@
 import subprocess
 import sys
 from argparse import Namespace
+from collections import defaultdict
+import importlib.util
+from importlib.machinery import SourceFileLoader
 
 import pytest
 
@@ -268,3 +271,28 @@ def test_nczarr_pass_through(self, zarr_url):
             output_format="text",
         )
         assert not errors
+
+
+def test_parse_options():
+    """Test the option parser of cchecker.py"""
+    # Load cchecker.py
+    cchecker_file_path = os.path.join(os.path.dirname(__file__), "..", "..",
+                                      "cchecker.py")
+    spec = importlib.util.spec_from_file_location("cchecker",
+                                                  cchecker_file_path)
+    module = importlib.util.module_from_spec(spec)
+    SourceFileLoader(spec.name, spec.origin).exec_module(module)
+    # Simple test checker_type:checker_opt
+    opt_dict = module.parse_options(["cf:enable_appendix_a_checks"])
+    assert opt_dict == defaultdict(dict, {"cf": {"enable_appendix_a_checks": None}})
+    # Test case checker_type:checker_opt:checker_val
+    opt_dict = module.parse_options(
+        ["type:opt:val", "type:opt2:val:2", "cf:enable_appendix_a_checks"],
+    )
+    assert opt_dict == defaultdict(
+        dict,
+        {
+            "type": {"opt": "val", "opt2": "val:2"},
+            "cf": {"enable_appendix_a_checks": None},
+        },
+    )