Source code for gunz_cm.cli.main

import typer
from loguru import logger
import sys

from .converters import app as converters_app
from .loaders import app as loaders_app
from ..reconstructions.__main__ import app as reconstructions_app

app = typer.Typer(
    name="gunz-cm",
    help="CM Library - Collection of tools for advancing research in spatial organization of genomes",
    no_args_is_help=True
)

app.add_typer(converters_app, name="converters", help="Data format converters")
app.add_typer(loaders_app, name="loaders", help="Data loaders and inspectors")
app.add_typer(reconstructions_app, name="recon", help="3D reconstruction tools")



def setup_logging(verbose: bool):
    logger.remove()
    log_level = "DEBUG" if verbose else "INFO"
    logger.add(sys.stderr, level=log_level, format="<level>{message}</level>")




@app.callback()
def main(
    verbose: bool = typer.Option(False, "--verbose", "-v", help="Enable verbose logging.")
):
    """
    CM Library Main CLI
    """
    setup_logging(verbose)


if __name__ == "__main__":
    app()