[Feature request]: Add Standardized Dry Run And Verbose Flags To All flepimop CLI Actions

[TimothyWillard]

Label

enhancement, cli

Priority Label

medium priority

Is your feature request related to a problem? Please describe.

Dry run and verbose flags provide developers/users a way to debug/diagnose issues using a CLI tool and a way to control the level of output from a tool. Furthermore, a dry run flag provides a way to painlessly test/experiment with a tool without unintended side effects. These are missing from flepiMoP's CLI interface.

Is your feature request related to a new application, scenario round, pathogen? Please describe.

No response

Describe the solution you'd like

An existing example of these features can be found in GH-394. See this for an example of verbosity:

flepiMoP/flepimop/gempyor_pkg/src/gempyor/batch.py

Lines 1084 to 1112 in ad11fae

	# Generic setup
	now = datetime.now(timezone.utc)
	logger = get_script_logger(__name__, kwargs["verbosity"])
	log_cli_inputs(kwargs)
	cfg = parse_config_files(config, ctx, **kwargs)
	# Job name/run id
	name = cfg["name"].get(str) if cfg["name"].exists() else None
	job_name = _job_name(name, now)
	logger.info("Assigning job name of '%s'", job_name)
	if kwargs["run_id"] is None:
	kwargs["run_id"] = run_id(now)
	logger.info("Using a run id of '%s'", kwargs["run_id"])
	# Determine inference method
	inference_method = (
	cfg["inference"]["method"].as_str()
	if cfg["inference"].exists() and cfg["inference"]["method"].exists()
	else None
	)
	inference_method = (
	inference_method if inference_method is None else inference_method.lower()
	)
	if kwargs["reset_chimerics"] and inference_method is not None:
	logger.warning(
	"The inference method is '%s', which does not support "
	"the reset chimerics on global accept flag.",
	inference_method,
	)

Which leverages logging infrastructure from the now merged into dev GH-447. See this for an example of dry run:

flepiMoP/flepimop/gempyor_pkg/src/gempyor/batch.py

Lines 489 to 510 in ad11fae

	if dry_run:
	if verbosity is not None:
	logger.info(
	"If not dry mode would have executed script with: %s",
	" ".join(cmd_args),
	)
	return
	if verbosity is not None:
	logger.info("Executing script with: %s", " ".join(cmd_args))
	process = subprocess.run(cmd_args, capture_output=True)
	stdout = process.stdout.decode().strip()
	stderr = process.stderr.decode().strip()
	if verbosity is not None:
	if process.returncode != 0:
	logger.critical(
	"Received non-zero exit code, %u, from executed script.", process.returncode
	)
	if stdout:
	logger.debug("Captured stdout from executed script: %s", stdout)
	if stderr:
	logger.error("Captured stderr from executed script: %s", stderr)

This issue is about extracting the verbose and dry run options as they exist in GH-394 and integrating them into other commands:

flepiMoP/flepimop/gempyor_pkg/src/gempyor/shared_cli.py

Lines 130 to 143 in ad11fae

	verbosity_options = {
	"verbosity": click.Option(
	param_decls=["-v", "--verbose", "verbosity"],
	count=True,
	help="The verbosity level to use for this command.",
	),
	"dry_run": click.Option(
	param_decls=["--dry-run", "dry_run"],
	type=bool,
	default=False,
	is_flag=True,
	help="Should this command be run using dry run?",
	),
	}