Use All Cores by Default in Scanpy-Scripts

[anilthanki]

Scanpy can use all cores by default with setting sc.settings.n_jobs = -1. This setting is not configured in scanpy-scripts. Setting all cores by default would improve performance for computationally intensive tasks.

Impetus, see comment:
ebi-gene-expression-group/scxa-tertiary-workflow#1 (comment)

Proposed Solution
Update cli.py in scanpy-scripts to include an argument for setting sc.settings.n_jobs, where default is sc.settings.n_jobs = -1, ensuring all commands adopt the default.

[irisdianauy]

This is the block in scanpy-scripts where we can add the said argument, maybe name it as --default_njobs:

scanpy-scripts/scanpy_scripts/cli.py

Lines 43 to 74 in 6297be2

	@click.group(cls=NaturalOrderGroup)
	@click.option(
	"--debug",
	is_flag=True,
	default=False,
	help="Print debug information",
	)
	@click.option(
	"--verbosity",
	type=click.INT,
	default=3,
	help="Set scanpy verbosity",
	)
	@click.version_option(
	version="0.2.0",
	prog_name="scanpy",
	)
	def cli(debug=False, verbosity=3):
	"""
	Command line interface to [scanpy](https://github.com/theislab/scanpy)
	"""
	log_level = logging.DEBUG if debug else logging.INFO
	logging.basicConfig(
	level=log_level,
	format=(
	"%(asctime)s; %(levelname)s; %(filename)s; " "%(funcName)s(): %(message)s"
	),
	datefmt="%y-%m-%d %H:%M:%S",
	)
	logging.debug("debugging")
	sc.settings.verbosity = verbosity
	return 0

[irisdianauy]

We can apply this change once we've tested the sc tertiary pipeline on newer scanpy and scanpy-scripts versions.

[irisdianauy]

This PR addresses this issue.