deps: unpin biopython, pin bcbio-gff to 0.7* by corneliusroemer · Pull Request #1178 · nextstrain/augur (original) (raw)

Alright, I managed to reproduce the bug by installing bcbio-gff 0.6.9, biopython 1.81 and running:

❌2 ❯ augur translate --reference-sequence defaults/annotation.gff --tree builds/21L/tree.nwk --ancestral-sequences builds/21L/nt_muts.json --output-node-data test.json Validating schema of 'builds/21L/nt_muts.json'... Traceback (most recent call last): File "/Users/corneliusromer/code/augur/augur/init.py", line 67, in run return args.command.run(args) File "/Users/corneliusromer/code/augur/augur/translate.py", line 364, in run features = load_features(args.reference_sequence, genes) File "/Users/corneliusromer/code/augur/augur/utils.py", line 155, in load_features from BCBio import GFF File "/opt/homebrew/Caskroom/miniforge/base/envs/augur-dev/lib/python3.8/site-packages/BCBio/GFF/init.py", line 3, in from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple File "/opt/homebrew/Caskroom/miniforge/base/envs/augur-dev/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 34, in from Bio.Seq import UnknownSeq ImportError: cannot import name 'UnknownSeq' from 'Bio.Seq' (/opt/homebrew/Caskroom/miniforge/base/envs/augur-dev/lib/python3.8/site-packages/Bio/Seq.py)

An error occurred (see above) that has not been properly handled by Augur. To report this, please open a new issue including the original command and the error above: https://github.com/nextstrain/augur/issues/new/choose

I had to edit the setup.py to allow installation of these otherwise not-allowed version (by constraints).

When I installed bcbio-gff 0.7.0 the bug no longer occurred. So 0.7.0 seems to fix it indeed.

And running the same command that errors with this PR does not produce an error. So all looks good.