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CLI Module

Command line interface.

alienbio.cli

Bio CLI: Command-line interface for Bio operations.

Usage

bio Run scenario and create report (default) bio build Build spec (resolve includes, refs, defaults) bio cd Print current DAT path bio cd Set current DAT path bio expand Show processed spec (same as build) bio fetch Fetch and display a spec bio hydrate Fully evaluate spec (resolve all placeholders) bio report Run scenario and create Excel report bio run Debug: run entity, print result dict bio store Store data from stdin to spec path bio --help Show help bio --version Show version

Examples:

bio catalog/jobs/hardcoded_test # Create and open Excel report bio cd data/experiments/run1 # Set current DAT bio fetch catalog/scenarios/mutualism # Display spec as YAML bio hydrate catalog/jobs/test --seed 42 # Evaluate with seed echo '{name: test}' | bio store ./test # Store data to relative path

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

    parser = argparse.ArgumentParser(
        prog="bio",
        description="Bio CLI: Run scenarios and create reports",
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog="""
Commands:
  build <path>    Build spec (resolve includes, refs, defaults)
  cd              Print current DAT path
  cd <path>       Set current DAT path
  expand <path>   Show processed spec (same as build)
  fetch <spec>    Fetch and display a spec (--raw, --json)
  hydrate <path>  Fully evaluate spec (resolve all placeholders)
  report <path>   Run scenario and create Excel report (default)
  run <path>      Debug: run entity, print result dict
  store <spec>    Store data from stdin to spec path (--raw)

Examples:
  bio cd data/experiments/run1          # Set current DAT
  bio fetch catalog/scenarios/mutualism # Display spec as YAML
  bio hydrate catalog/jobs/test --seed 42  # Evaluate with seed
  echo '{key: val}' | bio store ./test  # Store to relative path
  bio catalog/jobs/hardcoded_test       # Create and open Excel report
""",
    )
    parser.add_argument(
        "command",
        nargs="?",
        help="Command (report, run, expand) or path to run as report",
    )
    parser.add_argument(
        "args",
        nargs="*",
        help="Command arguments",
    )
    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)

    # Otherwise, treat as path and run report (default behavior)
    return COMMANDS["report"]([args.command] + args.args, verbose=args.verbose)