[ENH] Use logging and let the user reduce the verbosity

[surchs]

Is there an existing issue for this?

• I have searched the existing issues

New feature

Right now we tell the user good news with a print statement, e.g:

bagel-cli/bagel/cli.py

Lines 70 to 74 in 0ed0e4d

	print(
	"Processing phenotypic annotations:\n"
	f" {'Tabular file (.tsv):' : <{space}} {pheno}\n"
	f" {'Data dictionary (.json):' : <{space}} {dictionary}\n"
	)

which means they can't turn that off if they'd prefer (e.g. when they run this thing a couple hundred times in a row).
We should instead use a logger (https://docs.python.org/3/library/logging.html).
This has other nice benefits such as:

• I can choose what level of "news" I'd like to see
• I can have it log to a file
• and probably others I forget

In short: let's do this.

Unclear documentation

No response

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[github-actions]

We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days.
We have applied the stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

[github-actions]

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