types/ArgparseEnum: add argtype method

Intended to be used as the type converter method for argparse options
that use the enum values as choices.

It raises a custom `argparse.ArgumentTypeError` so that we can provide
a helpful error message that lists all of the valid enum values.

augur/filter/__init__.py

@@ -71,7 +71,7 @@ def register_arguments(parser):
     output_group.add_argument('--output-log', help="tab-delimited file with one row for each filtered strain and the reason it was filtered. Keyword arguments used for a given filter are reported in JSON format in a `kwargs` column.")
     output_group.add_argument(
         '--empty-results-reporting',
-        type=EmptyResultsReportingMethod,
+        type=EmptyResultsReportingMethod.argtype,
         choices=list(EmptyResultsReportingMethod),
         default=EmptyResultsReportingMethod.ERROR,
         help="How should empty filter results be reported.")

augur/types.py

@@ -1,3 +1,4 @@
+from argparse import ArgumentTypeError
 import enum
 
 
@@ -19,6 +20,22 @@ def __str__(self) -> str:
         """
         return self.value
 
+    @classmethod
+    def argtype(cls, input_string):
+        """
+        Intended to be used as the argument type converter for argparse options
+        that use the enum values as inputs.
+
+        Raises a custom `argparse.ArgumentTypeError` so that the error
+        message can include a helpful list of the valid enum values.
+        """
+        try:
+            return cls(input_string)
+        except ValueError:
+            choices = ", ".join(map(str, cls))
+            raise ArgumentTypeError(
+                f"invalid choice: {input_string!r} (choose from {choices})")
+
 
 @enum.unique
 class DataErrorMethod(ArgparseEnum):