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CLI Module

Command line interface.

alienbio.cli

Bio CLI — the bio front door.

bio <command> [args...] hands everything after the command to that command's own parser (each has --help). The commands are the :data:alienbio.commands.COMMANDS registry; bio --help lists them from it, so this page cannot drift from what runs (T051 box 4 found it documenting eight verbs that no longer existed).

main(argv=None)

Main entry point for bio CLI.

Parameters:

Name Type Description Default
argv list[str] | None

Command line arguments (defaults to sys.argv[1:])

 None

Returns:

Type Description
int

Exit code (0 for success, non-zero for failure)
Source code in src/alienbio/cli.py 
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def main(argv: list[str] | None = None) -> int:
    """Main entry point for bio CLI.

    Args:
        argv: Command line arguments (defaults to sys.argv[1:])

    Returns:
        Exit code (0 for success, non-zero for failure)
    """
    from alienbio import __version__
    from alienbio.commands import COMMANDS

    commands = "\n".join(f"  {name:<12} {_summary(fn)}" for name, fn in sorted(COMMANDS.items()))
    parser = argparse.ArgumentParser(
        prog="bio",
        description="bio — the Alien Biology framework CLI",
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog=f"""
Commands (each takes --help):
{commands}

Examples:
  bio suite run catalog/experiments/exp04-zero.yaml --dry
  bio suite run catalog/examples/ecosystem/ecosystem.yaml
  bio test-matrix --check
""",
    )
    parser.add_argument(
        "command",
        nargs="?",
        help=f"one of {', '.join(sorted(COMMANDS))}",
    )
    parser.add_argument(
        "args",
        nargs=argparse.REMAINDER,
        help="Command arguments (everything after the command, flags included, "
        "is handed to the subcommand verbatim; put -v/--version BEFORE the command)",
    )
    parser.add_argument(
        "--version",
        action="version",
        version=f"%(prog)s {__version__}",
    )
    parser.add_argument(
        "-v", "--verbose",
        action="store_true",
        help="Enable verbose output",
    )

    args = parser.parse_args(argv)

    if not args.command:
        parser.print_help()
        return 1

    # Check if command is a registered command
    if args.command in COMMANDS:
        return COMMANDS[args.command](args.args, verbose=args.verbose)

    print(f"bio: unknown command {args.command!r}; one of {sorted(COMMANDS)}", file=sys.stderr)
    return 2