cookiecutter-scverse
cookiecutter-scverse copied to clipboard
scverse
Unified logging and settings
Should we propose a default mechanism for logging and settings?
Benefits IMO would be consistent behaviour for all ecosystem packages. Ideally there would be a way to set the logging level for all scverse packages globally.
This could either be implemented as
- a bunch of vendored code
- a separate "scverse-tools" package that can be imported as dependency.
In the long run, a "scverse-tools" package could make sense. We kinda have something like that already with scanpydoc, but could extend the scope to other helper functions.
Should include a function to get the session_info as in
scanpy.loggin.print_versions()
We should likely just use the standard logging module? We have a very basic setup with scvi-tools that uses rich to format the messages.
Another interesting alternative that looks easier to understand (less magic API) and just as easy to use while encouraging to attach data to your log entries: https://www.structlog.org/en/stable/getting-started.html
If you have rich or better-exceptions installed, exceptions will be rendered in colors and with additional helpful information.
It also promotes logging json by default if the stdlib isn’t a TTY which I really like: https://www.structlog.org/en/stable/logging-best-practices.html#pretty-printing-vs-structured-output
See here how it integrates with the stdlib: https://www.structlog.org/en/stable/getting-started.html#structlog-and-standard-library-s-logging
