Thanks for digging into this @imatiach-msft ! Feel free to merge this or the other PR whenever you can verify it fixes it :)

@slundberg I was able to reproduce the issue when using the non-sklearn API from lightgbm. There might be other cases where this happens as well (maybe save/reload model?). I added more test coverage for the non-sklearn API. The current fix does seem to resolve the issue for non-sklearn API so I think it can be merged.

Hello! Is there a chance of reviving this Pull Request and merging with Shap? It'd be great to solve this bug, I just ran into this issue on my current project.

Any update on this @slundberg @imatiach-msft? This is a pretty SHAP-breaking bug for me.

We appreciate your contribution! This Pull Request has been inactive for two years, so it's been automatically marked as 'stale'.

Please leave a comment if you would still like the PR to remain open, and the 'stale' label will be removed.

Otherwise, if there is no activity in the next 90 days the PR will be closed.

This PR has been automatically closed due to a lack of recent activity.

We welcome your contributions! If your patch is still relevant, please don't hesitate to open a new PR.

I cannot reproduce the issue on the latest master but I don't see any harm in here and it adds more tests, which I think, is a plus. Therefore I'll merge this ;)

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 65.67%. Comparing base (11af84a) to head (ffcfd69).
⚠️ Report is 31 commits behind head on master.

@@           Coverage Diff           @@
##           master    #1063   +/-   ##
=======================================
  Coverage   65.67%   65.67%           
=======================================
  Files          94       94           
  Lines       13134    13134           
=======================================
  Hits         8626     8626           
  Misses       4508     4508           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.