The pathogen-embed command uses argparse's ArgumentDefaultsHelpFormatter class to show default values in the help text, but this behavior does not extend to the subparsers associated with each embedding subcommand (e.g., pca, mds, etc.).
To display defaults for the subparser arguments, we have to pass the same ArgumentDefaultsHelpFormatter argument to each add_parser function call which accepts the same arguments as the ArgumentParser class.
The
pathogen-embedcommand uses argparse'sArgumentDefaultsHelpFormatterclass to show default values in the help text, but this behavior does not extend to the subparsers associated with each embedding subcommand (e.g.,pca,mds, etc.).To display defaults for the subparser arguments, we have to pass the same
ArgumentDefaultsHelpFormatterargument to eachadd_parserfunction call which accepts the same arguments as theArgumentParserclass.