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Preserve small Newick branch lengths#5243
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peterjc merged 1 commit intoJun 22, 2026
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Thanks for the fix! It looks like the CircleCI+CodeCov failure was due to an auth issue when uploading from the CircleCI pipeline to CodeCov, not any unit test failure. I don't know why CodeCov is reporting a big drop in test coverage; that seems implausible. Code LGTM. OK to merge? |
etal
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Jun 22, 2026
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I think any apparent coverage drop is from the missing CircleCI upload. I don't see that we've opened an issue for fixing that... |
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Closes #5184
This PR updates the default Newick branch length format from
%1.5fto%1.8g.The previous default could silently round small nonzero branch lengths to
0.00000when writing Newick trees, which can lose biologically meaningful distance information. Using significant digits preserves small values such as0.000001while avoiding unnecessarily long fixed-width decimal output for all branch lengths.Changes included:
format_branch_lengthused by the Newick writer.Testing:
cd Tests python -m pytest test_Phylo.py python -m pre_commit run --files Bio/Phylo/NewickIO.py Tests/test_Phylo.py Result: 39 passed, 1 warning pre-commit passed