augur curate --help raises ValueError

[joverlee521]

augur curate --help raises a ValueError:

$ augur curate --help
Traceback (most recent call last):
  File "/usr/local/bin/augur", line 33, in <module>
    sys.exit(load_entry_point('nextstrain-augur', 'console_scripts', 'augur')())
  File "/nextstrain/augur/augur/__main__.py", line 30, in main
    return augur.run( argv[1:] )
  File "/nextstrain/augur/augur/__init__.py", line 68, in run
    args = make_parser().parse_args(argv)
  File "/usr/local/lib/python3.10/argparse.py", line 1833, in parse_args
    args, argv = self.parse_known_args(args, namespace)
  File "/usr/local/lib/python3.10/argparse.py", line 1866, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
  File "/usr/local/lib/python3.10/argparse.py", line 2061, in _parse_known_args
    positionals_end_index = consume_positionals(start_index)
  File "/usr/local/lib/python3.10/argparse.py", line 2038, in consume_positionals
    take_action(action, args)
  File "/usr/local/lib/python3.10/argparse.py", line 1943, in take_action
    action(self, namespace, argument_values, option_string)
  File "/usr/local/lib/python3.10/argparse.py", line 1221, in __call__
    subnamespace, arg_strings = parser.parse_known_args(arg_strings, None)
  File "/usr/local/lib/python3.10/argparse.py", line 1866, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
  File "/usr/local/lib/python3.10/argparse.py", line 2079, in _parse_known_args
    start_index = consume_optional(start_index)
  File "/usr/local/lib/python3.10/argparse.py", line 2019, in consume_optional
    take_action(action, args, option_string)
  File "/usr/local/lib/python3.10/argparse.py", line 1943, in take_action
    action(self, namespace, argument_values, option_string)
  File "/usr/local/lib/python3.10/argparse.py", line 1106, in __call__
    parser.print_help()
  File "/usr/local/lib/python3.10/argparse.py", line 2567, in print_help
    self._print_message(self.format_help(), file)
  File "/usr/local/lib/python3.10/argparse.py", line 2551, in format_help
    return formatter.format_help()
  File "/usr/local/lib/python3.10/argparse.py", line 283, in format_help
    help = self._root_section.format_help()
  File "/usr/local/lib/python3.10/argparse.py", line 214, in format_help
    item_help = join([func(*args) for func, args in self.items])
  File "/usr/local/lib/python3.10/argparse.py", line 214, in <listcomp>
    item_help = join([func(*args) for func, args in self.items])
  File "/usr/local/lib/python3.10/argparse.py", line 214, in format_help
    item_help = join([func(*args) for func, args in self.items])
  File "/usr/local/lib/python3.10/argparse.py", line 214, in <listcomp>
    item_help = join([func(*args) for func, args in self.items])
  File "/usr/local/lib/python3.10/argparse.py", line 553, in _format_action
    parts.append(self._format_action(subaction))
  File "/usr/local/lib/python3.10/argparse.py", line 540, in _format_action
    help_text = self._expand_help(action)
  File "/usr/local/lib/python3.10/argparse.py", line 637, in _expand_help
    return self._get_help_string(action) % params
ValueError: unsupported format character 'Y' (0x59) at index 198

[joverlee521]

Tracked down first bad commit to 3401422, which updates the docstring for curate/format_dates.py. I can run augur curate format-dates -h without any issues 🤔

[joverlee521]

From python/cpython#60027 (comment):

The problem is the timeformat. % codes are used to include data into the strings, so if you want a literal % in the help string, you need to double it.

This makes me even more confused why augur curate format-dates -h doesn't raise an error...

---

I don't think we want to double % in this case because then the rendered docs will have %%Y instead of %Y.

[victorlin]

I don't think we want to double % in this case because then the rendered docs will have %%Y instead of %Y.

I'd think that formatting should be prioritized for the CLI help text, and that we should somehow work around the %% in the docs rendering.

[joverlee521]

This makes me even more confused why augur curate format-dates -h doesn't raise an error...

Ah, the %Y is in the description for augur curate format-dates -h, but is in the help message for augur curate -h resulting in the error.

I've worked around this for now in #1755 to only include the first line as the help message.

[joverlee521]

I'd think that formatting should be prioritized for the CLI help text, and that we should somehow work around the %% in the docs rendering.

I'm going to push back here because I just realized the %%Y shows up in the description for the subcommand 🤦‍♀

So I think the correct solution is to exclude the % from the first line of the docstring which is used in the help message. It then shows up correctly in the CLI description.

[victorlin]

%%Y renders differently in augur curate -h and augur curate format-dates -h? This sounds like an argparse bug... but I think what you have in the PR now is looking good.

[joverlee521]

%%Y renders differently in augur curate -h and augur curate format-dates -h? This sounds like an argparse bug...

It's the different treatment of the string in help (augur curate -h) vs description (augur curate format-dates -h).

We are automatically adding the description to the subparsers in Augur:

augur/augur/argparse_.py

Lines 67 to 68 in e6df775

	if not subparser.description and command.__doc__:
	subparser.description = command.__doc__