From 13b7fb8709921e5d90c725c43bd11b3594913435 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 12 Jan 2024 13:09:18 -0800
Subject: [PATCH 1/2] Don't support Biopython >=1.82

This is a follow-up to "Don't support Biopython 1.82" (ee35e7e71) which
only excludes 1.82. The newly released 1.83 also includes the same
breaking changes to bcbio-gff, so we can expect all future versions to
have the same effect.
---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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.*",

From cbe10df4e2f279ce1eab959758bc836c1a198e0a Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 12 Jan 2024 13:19:46 -0800
Subject: [PATCH 2/2] Update changelog

---
 CHANGES.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

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)