Preserve formatting of command descriptions

This is useful for commands such as `augur distance` which have
descriptions written in rST. The rST syntax is preserved and could be
removed with a custom formatter class (as done in Nextstrain CLI¹), but
simply using the built-in RawDescriptionHelpFormatter is an improvement
over the default behavior.

Note that this only applies to descriptions, not help text for options.

¹ https://github.com/nextstrain/cli/blob/d4a419626eb5dc64e6de08566e51c5b48814727d/nextstrain/cli/argparse.py#L53

Author: victorlin

augur/__init__.py

@@ -54,7 +54,7 @@ def make_parser():
     parser = argparse.ArgumentParser(
         prog            = "augur",
         description     = "Augur: A bioinformatics toolkit for phylogenetic analysis.",
-        formatter_class = argparse.ArgumentDefaultsHelpFormatter,
+        formatter_class = argparse.RawDescriptionHelpFormatter,
     )
 
     add_default_command(parser)