deps: unpin biopython, pin bcbio-gff to 0.7*

[corneliusroemer]

Biopython was pinned to <=1.80 in #1152 because bcbio-gff <=0.6.9 requires deprecated Biopython functionality that was removed in 1.81

A fix to bcbio-gff was released as 0.7.0, see chapmanb/bcbb#137 chapmanb/bcbb#136 So now we can pin bcbio-gff to >=0.7.0 and remove the pin of Biopython

Note added in #1170 can hence be removed

Testing

We need to check that bcbio-gff actually works without problems

I think the error with bcbio-gff occured in translate, so we should test that part in particular, to make sure there are no regressions in bcbio-gff==0.7.0

Checklist

• Add a message in CHANGES.md summarizing the changes in this PR that are end user focused. Keep headers and formatting consistent with the rest of the file.

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (8b2dfc5) 68.25% compared to head (bbd53e5) 68.25%.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1178   +/-   ##
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  Coverage   68.25%   68.25%           
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  Files          63       63           
  Lines        6772     6772           
  Branches     1659     1659           
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  Hits         4622     4622           
  Misses       1841     1841           
  Partials      309      309           

Impacted Files	Coverage Δ
augur/__version__.py	100.00% <100.00%> (ø)

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[corneliusroemer]

Rebased on current master, automatic and manual tests augur translate pass. I think this should be ready to be merged if no one objects.

[victorlin]

I didn't test anything (not sure how to reproduce #1151), but the changes look good.

[corneliusroemer]

The bug happened whenever one ran augur translate with biopython 1.81 and any bcbio-gff.

I tested with biopython 1.81 and bcbio-gff 0.7.0 and didn't get an error, so seems to be good.

[corneliusroemer]

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 <module>
    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 <module>
    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.