Pin Biopython 1.81

[victorlin]

Description of proposed changes

Issue linked in changes. Pin to an exact version which is known to be compatible.

Related issue(s)

• ancestral, translate: GFF parsing broken with Biopython >=1.82 augur#1373

Checklist

• Checks pass
• Add temporary commit reversion to show where CI would fail: d4a5dcb (CI)

[victorlin]

Merging this (see plan) so that future builds of the package don't expose effects of nextstrain/augur#1373, which are made apparent by the failing CI when testing without this change:

rsv

        python scripts/cut.py             --oldalignment results/a/G/sequences.aligned.fasta             --slicedalignment results/a/G/G_slicedalignment.fasta             --reference config/areference.gbk             --gene G
        
G
4645 5578 933
Traceback (most recent call last):
  File "/home/runner/work/conda-base/conda-base/scripts/cut.py", line 46, in <module>
    cut(args.oldalignment, args.slicedalignment, args.reference, args.gene, args.min_length)
  File "/home/runner/work/conda-base/conda-base/scripts/cut.py", line 24, in cut
    if len(newrecord.seq.ungap('-')) >= min_length:
AttributeError: 'Seq' object has no attribute 'ungap'
Traceback (most recent call last):
  File "/home/runner/work/conda-base/conda-base/scripts/cut.py", line 46, in <module>
    cut(args.oldalignment, args.slicedalignment, args.reference, args.gene, args.min_length)
  File "/home/runner/work/conda-base/conda-base/scripts/cut.py", line 24, in cut
F
5683 7585 1902
    if len(newrecord.seq.ungap('-')) >= min_length:
AttributeError: 'Seq' object has no attribute 'ungap'
Traceback (most recent call last):
  File "/home/runner/work/conda-base/conda-base/scripts/cut.py", line 46, in <module>
    cut(args.oldalignment, args.slicedalignment, args.reference, args.gene, args.min_length)
  File "/home/runner/work/conda-base/conda-base/scripts/cut.py", line 24, in cut
    if len(newrecord.seq.ungap('-')) >= min_length:
AttributeError: 'Seq' object has no attribute 'ungap'

seasonal-flu

Traceback (most recent call last):
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/augur/__init__.py", line 66, in run
    return args.__command__.run(args)
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/augur/ancestral.py", line 305, in run
    features = load_features(args.annotation, args.genes)
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/augur/utils.py", line 159, in load_features
    for rec in GFF.parse(in_handle, limit_info=limit_info):
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 793, in parse
    for rec in parser.parse_in_parts(gff_files, base_dict, limit_info,
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 337, in parse_in_parts
    cur_dict = self._results_to_features(cur_dict, results)
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 375, in _results_to_features
    (_, base) = self._add_toplevel_feature(base, feature)
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 582, in _add_toplevel_feature
    new_feature = self._get_feature(feature_dict)
  File "/home/runner/.nextstrain/runtimes/conda/env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 591, in _get_feature
    new_feature = SeqFeature.SeqFeature(location, feature_dict['type'],
TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'


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>