Information about analysis mode ends up in --all-versions output and --aliases output

[KHajji]

This seems to me to be unintended behaviour. Especially if the output of these commands is considered to be valid yaml and json in e.g. pipelines.

pangolin/pangolin/command.py

Lines 143 to 157 in 663c6d2

	# Parsing analysis mode flags to return one of 'usher' or 'pangolearn'
	config[KEY_ANALYSIS_MODE] = set_up_analysis_mode(args.analysis_mode, config[KEY_ANALYSIS_MODE])
	print(green(f"****\nPangolin running in {config[KEY_ANALYSIS_MODE]} mode.\n****"))
	if config[KEY_ANALYSIS_MODE] == "scorpio":
	print(cyan(f"Warning: in `scorpio` mode only variants of concern (VOCs) defined in constellations can be assigned. `Version` column corresponds to constellation_version.\n"))
	snakefile = get_snakefile(thisdir,config[KEY_ANALYSIS_MODE])
	config[KEY_DESIGNATION_CACHE],config[KEY_ALIAS_FILE] = data_checks.find_designation_cache_and_alias(config[KEY_DATADIR],DESIGNATION_CACHE_FILE,ALIAS_FILE)
	if args.aliases:
	print_alias_file_exit(config[KEY_ALIAS_FILE])
	if args.all_versions:
	print_versions_exit(config)

[aineniamh]

Fixed now in v4.0.4!