Open ccbaumler opened 1 year ago
singular sounds good to me! however per semantic versioning we can't remove --abundances-from
without bumping the major version, we can only make --abundance-from
work (which should be as simple as adding it to the add_argument
call). so I'd suggest that.
note that a feature of argparse is that it does partial string matching, so --abund
would work as long as there's a single argument that starts with abund
. This means --track-abundance
would match --track-abundances
, etc - so really only --abundance-from
is suffering bigly from this ambiguity.
you might also remove the [WIP] from this as this is an issue not a PR :)
When attempting to intersect signature files with preserved abundance, I followed this documentation and found the following error/results.
At the
intersect
of main and intersect.py, the argument is namedabundances-from
. There is a further discrepancy between--ignore-abundance
in the documentation as well.I purpose all
--abundance
related commands be a uniform singular tense (E.g. --track-abundance, --ignore-abundance, --min-abundance, --max-abundance, --abundance-from, --with-abundance).