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

[joverlee521]

Nice to tackle this longstanding TODO! I'm not sure --resources concurrent_deploys=2 is the way we want work around setdefault described in nextstrain/public#37, but good to have it as a fallback option.

[joverlee521]

The "explicit inline resource option" seems vague. Would it be possible to include the explicit option that was passed in the warning output so that the user knows what to modify?