Merge pull request #1705: Add help text to clarify extend actions

CHANGES.md

@@ -10,9 +10,11 @@
 
 * ancestral, refine: Explicitly specify how the root and ambiguous states are handled during sequence reconstruction and mutation counting. [#1690][] (@rneher)
 * titers: Fix type errors in code associated with cross-validation of models. [#1688][] (@huddlej)
+* Add help text to clarify difference in behavior between options that override defaults (e.g. `--metadata-delimiters`) vs. options that extend existing defaults (e.g. `--expected-date-formats`). [#1705][] (@victorlin)
 
 [#1688]: https://github.com/nextstrain/augur/pull/1688
 [#1690]: https://github.com/nextstrain/augur/pull/1690
+[#1705]: https://github.com/nextstrain/augur/pull/1705
 
 ## 27.0.0 (9 December 2024)
 

augur/argparse_.py

@@ -1,25 +1,47 @@
 """
 Custom helpers for the argparse standard library.
 """
-from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser, _ArgumentGroup
+from argparse import Action, ArgumentParser, _ArgumentGroup, HelpFormatter, SUPPRESS, OPTIONAL, ZERO_OR_MORE, _ExtendAction
 from typing import Union
 from .types import ValidationMode
 
 
 # Include this in an argument help string to suppress the automatic appending
-# of the default value by argparse.ArgumentDefaultsHelpFormatter.  This works
-# because the automatic appending is conditional on the presence of %(default),
-# so we include it but then format it as a zero-length string .0s.  🙃
+# of the default value by CustomHelpFormatter.  This works because the
+# automatic appending is conditional on the presence of %(default), so we
+# include it but then format it as a zero-length string .0s.  🙃
 #
 # Another solution would be to add an extra attribute to the argument (the
-# argparse.Action instance) and then subclass ArgumentDefaultsHelpFormatter to
-# condition on that new attribute, but that seems more brittle.
+# argparse.Action instance) and then modify CustomHelpFormatter to condition
+# on that new attribute, but that seems more brittle.
 #
-# Copied from the Nextstrain CLI repo
+# Initially copied from the Nextstrain CLI repo
 # https://github.com/nextstrain/cli/blob/017c53805e8317951327d24c04184615cc400b09/nextstrain/cli/argparse.py#L13-L21
 SKIP_AUTO_DEFAULT_IN_HELP = "%(default).0s"
 
 
+class CustomHelpFormatter(HelpFormatter):
+    """Customize help text.
+
+    Initially copied from argparse.ArgumentDefaultsHelpFormatter.
+    """
+    def _get_help_string(self, action: Action):
+        help = action.help
+
+        if action.default is not None and action.default != []:
+            if isinstance(action, ExtendOverwriteDefault):
+                help += ' Specified values will override the default list.'
+            if isinstance(action, _ExtendAction):
+                help += ' Specified values will extend the default list.'
+
+        if '%(default)' not in action.help:
+            if action.default is not SUPPRESS:
+                defaulting_nargs = [OPTIONAL, ZERO_OR_MORE]
+                if action.option_strings or action.nargs in defaulting_nargs:
+                    help += ' (default: %(default)s)'
+        return help
+
+
 def add_default_command(parser):
     """
     Sets the default command to run when none is provided.
@@ -61,7 +83,7 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
 
         # Use the same formatting class for every command for consistency.
         # Set here to avoid repeating it in every command's register_parser().
-        subparser.formatter_class = ArgumentDefaultsHelpFormatter
+        subparser.formatter_class = CustomHelpFormatter
 
         if not subparser.description and command.__doc__:
             subparser.description = command.__doc__

docs/conf.py

@@ -132,9 +132,10 @@ def prose_list(items):
      ("py:class", "json.decoder.JSONDecodeError"),
      ("py:class", "json.encoder.JSONEncoder"),
 
-     # This class can't be referenced.
+     # These classes can't be referenced.
      # <https://github.com/python/cpython/issues/101503>
      ("py:class", "argparse._SubParsersAction"),
+     ("py:class", "argparse.HelpFormatter"),
 ]
 
 # -- Cross-project references ------------------------------------------------