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)

• https://github.com/nextstrain/augur/issues/1373

Checklist

• [x] Checks pass
• [x] Add temporary commit reversion to show where CI would fail: d4a5dcb5562765a8a684ccd6ec646bf6f3013922 (CI)

[victorlin]

Merging this (see plan) so that future builds of the package don't expose effects of https://github.com/nextstrain/augur/issues/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 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 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 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: ```