Automatic naming of qsartuna-build output if not supplied by user

[shortydutchie]

Hi

I'd suggest addition of following to optbuild.py so that the best and merged models are named automatically as ..._best.pkl, ..._final.pkl etc. if not supplied by user. That way the results are always written and not lost.

def basename_from_config(nm: str) -> (pathlib.Path, str):
    """
    Basename for automatic naming purposes
    Returns:
       basepath, basename
    """
    p, n = os.path.split(nm)
    b, e = os.path.splitext(n)
    base = b[:]
    for repl in ["config_", "conf_"]:
        base = base.replace(repl, "")
        base = base.replace(repl.upper(), "")
    return pathlib.Path(p), base

def set_default_output_names(args) -> Union[str, bool]:
    """
    Set default output names based on the conf file name, where not supplied
    """

    if not args.config:
        return False

    if not os.path.exists(args.config):
        logger.critical(
            "\n!!! Please specify a valid configuration file, '%s' does not exist !!!\n"
            % args.config
        )
        return False

    basepath, basename = basename_from_config(args.config)

    if args.best_buildconfig_outpath is None:
        args.best_buildconfig_outpath = pathlib.Path(
            os.path.join(basepath, "model_%s_best.json" % basename)
        )
        logger.info(
            "best_buildconfig_outpath : set to %s based on config file name"
            % args.best_buildconfig_outpath
        )
    if args.best_model_outpath is None:
        args.best_model_outpath = pathlib.Path(
            os.path.join(basepath, "model_%s_best.pkl" % basename)
        )
        logger.info(
            "best_model_outpath       : set to %s based on config file name"
            % args.best_model_outpath
        )
    if args.merged_model_outpath is None:
        args.merged_model_outpath = pathlib.Path(
            os.path.join(basepath, "model_%s_final.pkl" % basename)
        )
        logger.info(
            "merged_model_outpath     : set to %s based on config file name"
            % args.merged_model_outpath
        )

    return basename

Call it right after args = parser.parse_args() as follows:

    args = parser.parse_args()
    basename = set_default_output_names(args)

Thanks!

[lewismervin1]

Thanks for the helpful suggestion @shortydutchie!

I incorporated your proposed suggestions into the branch https://github.com/MolecularAI/QSARtuna/tree/3.1.4_prep. It would be great if you could try it and see if it works as you expect.

[shortydutchie]

Thank you Lewis!
Yes that works, specifying only --conf automatically sets the output names.

> qsartuna-build --config test_Lasso.json
2024-10-03 08:46:37,282.282 INFO optbuild - set_default_output_names: best_buildconfig_outpath : set to model_test_Lasso_best.json based on config file name
2024-10-03 08:46:37,282.282 INFO optbuild - set_default_output_names: best_model_outpath       : set to model_test_Lasso_best.pkl based on config file name
2024-10-03 08:46:37,282.282 INFO optbuild - set_default_output_names: merged_model_outpath     : set to model_test_Lasso_final.pkl based on config file name

But I forgot - there's a minor issue with this bit (line 211 optbuild.py):

    if args.best_buildconfig_outpath:
        os.makedirs(os.path.dirname(args.best_buildconfig_outpath), exist_ok=True)
        ...
        ...

If the path name is supplied by user without a directory it will fail as dirname() returns "", which makedirs() does not like.
Couple of options -

• I've commented it out in my version, ie. user needs to create output directory themselves.
• should add "./" to the default names set in set_default_output_names() - my oversight, apologies

Thanks!

[lewismervin1]

Thanks @shortydutchie, I made some changes and incorporated them into 3.1.4