Fix Biopython deprecation warning #1102
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This also makes it easier to refactor.
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Codecov ReportBase: 63.36% // Head: 63.37% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #1102 +/- ##
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+ Coverage 63.36% 63.37% +0.01%
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Files 57 57
Lines 6635 6638 +3
Branches 1632 1632
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+ Hits 4204 4207 +3
Misses 2147 2147
Partials 284 284
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seq.ungap(gap) is deprecated as of biopython 1.80¹. try/except is used to support older Biopython versions. A bump to biopython>=1.79 would simplify this, but at the cost of narrowing Biopython support to versions released June 2021 and later. ¹ https://github.com/biopython/biopython/blob/dcf52bd4546410e1a60d39fbcd4c0041ec1e6fe6/DEPRECATED.rst#bioseqsequngap
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joverlee521
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Nov 29, 2022
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Ran into this in tests for another PR, glad I checked on GH before trying to fix it 😄
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Description of proposed changes
CI is failing with the latest Biopython release.
This PR applies the recommendation while retaining support for older Biopython versions.
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