Merge pull request #1152 from nextstrain/pin-biopython

fix: Pin Biopython to <=1.80
nextstrain · Feb 17, 2023 · eef2a05 · eef2a05
2 parents 53fed2d + a89cccb
commit eef2a05
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diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,11 @@
 
 ## __NEXT__
 
+### Bug fixes
+
+* Constrain Biopython version to <=1.80 so that `augur translate` is not broken by a deprecation of `UnknownSeq` in 1.81. When running `augur translate` with Biopython 1.81, the user will receive an error starting with `ERROR: Package BCBio.GFF not found!` and ending with `TypeError: object of type 'NoneType' has no len()`. [#1152][] (@corneliusroemer)
+
+[#1152]: https://github.com/nextstrain/augur/pull/1152
 
 ## 21.0.0 (7 February 2023)
 

diff --git a/setup.py b/setup.py
@@ -52,7 +52,7 @@
     python_requires = '>={}'.format('.'.join(str(n) for n in py_min_version)),
     install_requires = [
         "bcbio-gff >=0.6.0, ==0.6.*",
-        "biopython >=1.67, !=1.77, !=1.78",
+        "biopython >=1.67, !=1.77, !=1.78, <=1.80",
         "cvxopt >=1.1.9, ==1.*",
         "isodate ==0.6.*",
         "jsonschema >=3.0.0, ==3.*",