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Don't support Biopython >=1.82 #1387

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Jan 12, 2024
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Don't support Biopython >=1.82 #1387

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Don't support Biopython >=1.82
victorlin Jan 12, 2024
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Update changelog
victorlin Jan 12, 2024
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3 changes: 2 additions & 1 deletion CHANGES.md
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Expand Up @@ -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)
Expand All @@ -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)

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4 changes: 2 additions & 2 deletions setup.py
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Expand Up @@ -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.*",
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