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Bump bcbio-gff to 0.7.1 #1400

Merged
merged 3 commits into from
Jan 29, 2024
Merged

Bump bcbio-gff to 0.7.1 #1400

merged 3 commits into from
Jan 29, 2024

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victorlin
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@victorlin victorlin commented Jan 29, 2024

Description of proposed changes

This new release supports Biopython version 1.82 and removes suppression of BiopythonDeprecationWarnings.

Changes: chapmanb/bcbb@bcbio-gff-v0.7.0...bcbio-gff-v0.7.1

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  • Checks pass
  • If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR

@victorlin victorlin self-assigned this Jan 29, 2024
This new release supports newer versions of Biopython and removes
suppression of BiopythonDeprecationWarnings. This exposes warnings which
are now suppressed on the Augur side to avoid unnecessary noise from a
dependency.

Changes: <chapmanb/bcbb@bcbio-gff-v0.7.0...bcbio-gff-v0.7.1>
SeqFeature.strand was wrongly removed in Biopython 1.82, and added back
in 1.83 with a deprecation warning. Switch to the preferred alternative.

<biopython/biopython@68f683b>
@victorlin victorlin requested a review from a team January 29, 2024 20:09
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Merging to have passing CI.

@victorlin victorlin merged commit 8f24d66 into master Jan 29, 2024
20 checks passed
@victorlin victorlin deleted the victorlin/bcbio-gff-v0.7.1 branch January 29, 2024 23:47
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