nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
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merge: Avoid overwriting the output id column with non-id columns #1593

Closed tsibley closed 1 month ago

tsibley commented 1 month ago

This edge case occurs when an input table has an id column used for joining (in tests, literally "id", but any valid id column name) and also another, non-id column that matches the output id column name (in tests, literally "strain").

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codecov[bot] commented 1 month ago

Codecov Report

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

Project coverage is 71.03%. Comparing base (d662698) to head (232698b). Report is 6 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #1593 +/- ## ======================================= Coverage 71.02% 71.03% ======================================= Files 79 79 Lines 8256 8258 +2 Branches 2003 2004 +1 ======================================= + Hits 5864 5866 +2 Misses 2101 2101 Partials 291 291 ```

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tsibley commented 1 month ago

The linkcheck step in CI has now failed twice in different ways: first reporting a 403 Forbidden for http://www.microbesonline.org/fasttree/ and then reporting 406 Unacceptable for https://github.com/nextstrain/augur/commit/4859b5d70e77cc9a0bb99e741fefb29952058b71. Third time was the charm. The only thing I did was re-run the job.