Merge pull request #1387: Don't support Biopython >=1.82

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)
 

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.*",