Support Python 3.12 and test in CI (#1678)

nextstrain · Nov 16, 2024 · 783f15e · 783f15e
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -45,11 +45,16 @@ jobs:
           - '3.9'
           - '3.10'
           - '3.11'
-        biopython-version:
-          # list of Biopython versions with support for a new Python version
-          # from https://github.com/biopython/biopython/blob/master/NEWS.rst
+          - '3.12'
+        biopython-version: 
+          # list of Biopython versions with support for a new Python version 
+          # from https://github.com/biopython/biopython/blob/master/NEWS.rst 
           - '1.80' # first to support Python 3.10 and 3.11
-          - ''     # latest
+          - '1.82' # first to support Python 3.12
+          - ''     # latest 
+        exclude: 
+          # some older Biopython versions are incompatible with later Python versions 
+          - { biopython-version: '1.80', python-version: '3.12' }
     defaults:
       run:
         shell: bash -l {0}

diff --git a/CHANGES.md b/CHANGES.md
@@ -4,14 +4,15 @@
 
 ### Features
 
-- support pandas v2. [#1671] (@corneliusroemer and @victorlin)
+- support Python 3.12 (@corneliusroemer)
+- support Pandas v2. [#1671] (@corneliusroemer and @victorlin)
 - curate: change output metadata to [RFC 4180 CSV-like TSVs][] to match the TSV format output by other Augur subcommands and the Nextstrain ecosystem as discussed in [#1566][]. [#1565][] (@joverlee521)
 
-
 [#1565]: https://github.com/nextstrain/augur/pull/1565
 [#1566]: https://github.com/nextstrain/augur/issues/1566
 [RFC 4180 CSV-like TSVs]: https://datatracker.ietf.org/doc/html/rfc4180
 [#1671]: https://github.com/nextstrain/augur/pull/1671
+[#1678]: https://github.com/nextstrain/augur/pull/1678
 
 ## 26.1.0 (12 November 2024)
 

diff --git a/setup.py b/setup.py
@@ -106,6 +106,7 @@
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     # Install an "augur" program which calls augur.__main__.main()
     #   https://setuptools.readthedocs.io/en/latest/setuptools.html#automatic-script-creation