Depreciation warnining

[tayllatheodoro]

The depreciation warning was added as a decorator before each function and class that are migrating to biahub.
To do:

• Tests

[ieivanov]

I find that the warnings.warn() message is not issued on the terminal as click filters our these warnings. Instead of using warnings.warn() you should modify the click command decorator to @click.command(deprecated=True). I've tested that this does issue a warning. With this syntax, you don't have an option to add a custom message (e.g. Use the function in biahub), but I think that's OK.

[ieivanov]

Let's move the tests in test_analysis to a new PR in biahub. I think the tests in test_cli are good.

[ieivanov]

I find that the warnings.warn() message is not issued on the terminal as click filters our these warnings. Instead of using warnings.warn() you should modify the click command decorator to @click.command(deprecated=True). I've tested that this does issue a warning. With this syntax, you don't have an option to add a custom message (e.g. Use the function in biahub), but I think that's OK.

@tayllatheodoro I think this comment is still not resolved. Once you've implemented the @click.command(deprecated=True) syntax I think we can merge this branch.

P.S. Also, you should pull main into this branch to resolve the merge conflicts.

[tayllatheodoro]

deprecated=True

Hii, I had understood it was a suggestion, but I just corrected it. Thank you