Improve help text of CLI options

[victorlin]

Example: augur filter --group-by-weights

Rendered rST docs is formatted nicely:

CLI help text is not great:

  --group-by-weights FILE
                        TSV file defining weights for grouping. Requirements: (1) Lines starting
                        with '#' are treated as comment lines. (2) The first non-comment line must
                        be a header row. (3) There must be a numeric ``weight`` column (weights can
                        take on any non-negative values). (4) Other columns must be a subset of
                        columns used in ``--group-by``, with combinations of values covering all
                        combinations present in the metadata. (5) This option only applies when
                        ``--group-by`` and ``--subsample-max-sequences`` are provided. (6) This
                        option cannot be used with ``--no-probabilistic-sampling``. Notes: (1) Any
                        ``--group-by`` columns absent from this file will be given equal weighting
                        across all values *within* groups defined by the other weighted columns. (2)
                        An entry with the value ``default`` under all columns will be treated as the
                        default weight for specific groups present in the metadata but missing from
                        the weights file. If there is no default weight and the metadata contains
                        rows that are not covered by the given weights, augur filter will exit with
                        an error. (default: None)

Possible solutions

1. Ensure all help text is correctly formatted (e.g. wrapped if necessary) in the source code

   • filter: Improve help text #1430
   • (other subcommands)

2. Use help_formatter=argparse.RawTextHelpFormatter (doc)

3. Render the rST to plain text

Related PRs

• Update module docstring usage #1130

[jameshadfield]

Is this the same as #313?

[victorlin]

Oh yes, thanks! Closing this as duplicate.

[victorlin]

I've clarified the scope of #313 so this is no longer a duplicate.