scverse / scverse/PyDESeq2

Replace `print` to `logging`

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Dominant language
Python
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761
Forks
90
Avg merge
25m
Merged PRs (30d)
10

Description

Is your feature request related to a problem? Please describe.
When we build application like cli, web service, we often should suppress messages, send into stderr or record logs in files.
If we use print function for logging, it is not so easy to achieve these. logging is easy to suppress messages depend on the log level, and easy to send messages into stderr and files.

Describe the solution you'd like
replace print function to logging like following:

+ import logging
+ logger = logging.getLogger(__name__)

- print("INFO")
+ logger.info("INFO!") # or debug, warn, error

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Search the repository for print calls and inspect each caller to determine whether its message is informational, diagnostic, warning, or error output. Add module logging where needed and verify that messages use appropriate logging levels while preserving the intended output behavior; the issue names no specific files or tests.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Refactor
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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