bug fixes, updates, and modernization#46
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harmsm merged 64 commits intoharmslab:mainfrom Mar 20, 2026
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harmsm
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Jul 3, 2024
harmsm
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- Removed Biopython blast to avoid deprecation
- Code clean up, keeping up with deprecations in upcoming python release
- Fixed bug that pulled inappropriate proteome down from NCBI if many proteomes were found.
- Fixed tree api to work with toytree 2.0.x and pinned version in requirements.txt
- Pinned on numpy < 2.0 to avoid bug in toyplot
no longer use Biopython for blast; avoid deprecation
cleaned up deprecation warnings for topiary itself
updated for toytree 2.0.x api, pinned requirements.txt
This was referenced Mar 18, 2026
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