Inject mem_mb into existing resources

[victorlin]

Description of proposed changes

The trick with stack-walking --log-handler-script is a clever hack, but it relies on Snakemake's internal implementation.

Instead, parse the arguments for resources and either (1) update them in-place or (2) append the option at the end as done previously.

Related issue(s)

Addresses the removed TODO:

cli/nextstrain/cli/command/build.py

Lines 284 to 307 in 1867fd6

	# XXX TODO: Support parsing of --resources to see if "mem_mb" is
	# provided. If it's not, we could add our own "mem_mb" constraint
	# alongside the other values of --resources. Punting on this
	# because it's not as simple as appending an additional argument.
	# So for now, if folks are specifying their own --resources,
	# they'll also need to explicitly provide "mem_mb", which may mean
	# repeating a previous --memory argument they provided us.
	# -trs, 20 May 2020
	#
	# We might accomplish this TODO with a bit of a trick: using a
	# stack-walking --log-handler-script to get access to
	# Snakemake's in-process state and update --resources from
	# there. I wrote a proof of concept¹ when exploring options
	# around custom resources for an ncov PR², and it worked well
	# in manual testing.
	# -trs, 1 Feb 2023
	#
	# ¹ <https://gist.github.com/tsibley/6b3b5c37e651518d85810945a4140cde>
	# ² <https://github.com/nextstrain/ncov/pull/1045>
	warn(dedent("""
	Warning: The explicit %s option passed to Snakemake prevents
	the Nextstrain CLI from automatically providing a "mem_mb" resource
	based on its --memory option. This may or may not be what you expect.
	""" % (snakemake_opts["--resources"][0],)))

Checklist

• Checks pass
• Added doctests
• Update changelog