diff --git a/CHANGES.md b/CHANGES.md index 734a2b83d..70eacda32 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -30,7 +30,7 @@ * separate VCF-only arguments into their own group * translate: Fixes a bug in the parsing behaviour of GFF files whereby the presence of the `--genes` command line argument would change how we read individual GFF lines. Issue [#1349][], PR [#1351][] (@jameshadfield) * If `TreeTimeError` is encountered Augur now exits with code 2 rather than 0. (This restores the original behaviour.) [#1367][] (@jameshadfield) -* ancestral, translate: Avoid incompatibilities with Biopython 1.82. [#1374][] (@victorlin) +* ancestral, translate: Avoid incompatibilities with Biopython >=1.82. [#1374][], [#1387][] (@victorlin) * ancestral, translate: Address Biopython deprecation warnings. [#1379][] (@victorlin) * ancestral: Previously, the help text for `--genes` falsely claimed that it could accept a file. Now, it can truly claim that. [#1353][] (@victorlin) * Deprecate `read_strains` from `augur.utils` and add it to the public API under `augur.io`. [#1353][] (@victorlin) @@ -46,6 +46,7 @@ [#1379]: https://github.com/nextstrain/augur/pull/1379 [#1352]: https://github.com/nextstrain/augur/pull/1352 [#1353]: https://github.com/nextstrain/augur/pull/1353 +[#1387]: https://github.com/nextstrain/augur/pull/1387 ## 23.1.1 (7 November 2023) diff --git a/setup.py b/setup.py index d6d536d55..f13cb136d 100644 --- a/setup.py +++ b/setup.py @@ -52,8 +52,8 @@ python_requires = '>={}'.format('.'.join(str(n) for n in py_min_version)), install_requires = [ "bcbio-gff >=0.7.0, ==0.7.*", - # Skip Biopython 1.82: https://github.com/nextstrain/augur/issues/1373 - "biopython >=1.67, !=1.77, !=1.78, !=1.82", + # Skip Biopython >=1.82: https://github.com/nextstrain/augur/issues/1373 + "biopython >=1.67, !=1.77, !=1.78, <1.82", "cvxopt >=1.1.9, ==1.*", "importlib_resources >=5.3.0; python_version < '3.11'", "isodate ==0.6.*",