Configure proper logging

[lanery]

          Yeah, agreed. FWIW, what I've done in the past is to define a `configure_logging` function somewhere that uses `logging.getLogger()` to get the root logger and configure it (e.g. specify formatters and default logging levels). This function can then be called from every public-facing entrypoint (e.g. CLI script). Example [here](https://github.com/czbiohub-sf/opencell-portal-pub/blob/3bd2e218c7af5bf9081c2e5e218f51c2b55e8f10/opencell/cli/utils.py#L34).

Originally posted by @keithchev in #9 (comment)