laminlabs / lamindb

A data framework for biology.
https://docs.lamin.ai
Apache License 2.0
129 stars 12 forks source link

✨ Truncate standardization output #2103

Closed Zethson closed 3 weeks ago

Zethson commented 1 month ago
codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 92.53%. Comparing base (57fbd29) to head (caf9755). Report is 6 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #2103 +/- ## ======================================= Coverage 92.53% 92.53% ======================================= Files 55 55 Lines 6467 6468 +1 ======================================= + Hits 5984 5985 +1 Misses 483 483 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

github-actions[bot] commented 1 month ago

🚀 Deployed on https://672a1b231f41fc9d52029e15--lamindb-qnwk.netlify.app

sunnyosun commented 3 weeks ago

Hmm, auto-saving doesn’t look right to me, .standardize is meant to be a non-write operation, similar to .validate and .inspect. The user pattern is expected to be:

standardized_names = bt.Gene.standardize(names)
records = bt.Gene.from_values(standardized_names)
ln.save(records)

I wouldn’t make un-explicit save calls in low-level API. I think it’s OK in Curator because that’s a high-level class. For standardize I don’t think we should do it.