Don't support Biopython 1.82 #1374
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Biopython 1.82 was released a few hours ago¹ and has an undocumented breaking change in the SeqFeature API which is used indirectly in augur translate (through bcbio-gff). It's possible that this should be a hard ceiling instead of a one-off exclusion, but make it the latter for now. Fixing compatibility requires upstream changes in bcbio-gff which is out of our control. ¹ <https://github.com/biopython/biopython/blob/biopython-182/NEWS.rst>
3 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
Biopython 1.82 was released a few hours ago¹ and has an undocumented breaking change in the SeqFeature API which is used indirectly in augur translate (through bcbio-gff).
It's possible that this should be a hard ceiling instead of a one-off exclusion, but make it the latter for now. Fixing compatibility requires upstream changes in bcbio-gff which is out of our control.
¹ https://github.com/biopython/biopython/blob/biopython-182/NEWS.rst
Related issue(s)
Checklist