From bd69a96393f3e6ddbf93054299e6197cecc60bfb Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 14 Nov 2024 13:10:34 +0100 Subject: [PATCH 1/5] Support Python 3.12, test 3.12 and 3.13 in CI --- .github/workflows/ci.yaml | 2 ++ setup.py | 1 + 2 files changed, 3 insertions(+) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 30768b362..77ed0099f 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -45,6 +45,8 @@ jobs: - '3.9' - '3.10' - '3.11' + - '3.12' + - '3.13' biopython-version: # list of Biopython versions with support for a new Python version # from https://github.com/biopython/biopython/blob/master/NEWS.rst diff --git a/setup.py b/setup.py index 863e67fa0..81aad167d 100644 --- 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 From 9822cf19c9143bdd14831e7acf13350ed43763a4 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 14 Nov 2024 13:13:17 +0100 Subject: [PATCH 2/5] Python 3.13 is blocked on biopython support --- .github/workflows/ci.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 77ed0099f..c77f9244f 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -46,7 +46,6 @@ jobs: - '3.10' - '3.11' - '3.12' - - '3.13' biopython-version: # list of Biopython versions with support for a new Python version # from https://github.com/biopython/biopython/blob/master/NEWS.rst From 56219904c6183e443621696e97d7ee4472f927ee Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 14 Nov 2024 13:25:59 +0100 Subject: [PATCH 3/5] Update minimum biopython version in CI to first that supports Python 3.12 --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index c77f9244f..6938337c8 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -49,7 +49,7 @@ jobs: 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 + - '1.82' # first to support Python 3.10 and 3.11 - '' # latest defaults: run: From d4da44cf8f4539f421416c29b491c66b92ebdab6 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 14 Nov 2024 13:47:20 +0100 Subject: [PATCH 4/5] fix comment --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 6938337c8..ba47391bd 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -49,7 +49,7 @@ jobs: biopython-version: # list of Biopython versions with support for a new Python version # from https://github.com/biopython/biopython/blob/master/NEWS.rst - - '1.82' # first to support Python 3.10 and 3.11 + - '1.82' # first to support Python 3.12 - '' # latest defaults: run: From 248535942976f3c875289af961de51b614266c7a Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 14 Nov 2024 20:02:08 +0100 Subject: [PATCH 5/5] Still test for biopython 1.80 --- .github/workflows/ci.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index ba47391bd..39998f2f4 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -46,11 +46,15 @@ jobs: - '3.10' - '3.11' - '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 + 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 - '1.82' # first to support Python 3.12 - - '' # latest + - '' # 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}