[From nobody Mon Apr 13 07:21:07 2026 Received: (at submit) by bugs.debian.org; 16 Dec 2025 16:01:01 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-105.1 required=4.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FOURLA, FROMDEVELOPER,SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY, USER_IN_DKIM_WELCOMELIST,WEIRD_PORT autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 42; hammy, 150; neutral, 194; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <cjwatson@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:52326) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <cjwatson@debian.org>) id 1vVXTx-007RYx-2S for submit@bugs.debian.org; Tue, 16 Dec 2025 16:01:01 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Type:MIME-Version:Message-ID: Subject:To:From:Date:Reply-To:Cc:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=DOS8TE6Kqh0aLR8z8wVeF6DoFRTqVBDO6XP+nJ0IhK0=; b=UrmZbcffCSDfmcOgpG58Y6XAqI 3P6GPAj78/IigU8YVK3ApyGdv5mX8Uu0KaJ02owCKCx49h1a+0hWVJ9W0z4UwvQRyR8/fQ3eh3eDe 1QOc3In4kGXw8cokmx5bQhWfL88sy7EF90iWgPwbT3o75Zp3Da2Dd4BC1yDtxoEVZje5DV6NYVM4a hokqwbZaDNMGwzJLQhjaw5/McPZJ72p+dZ5ibb/D/jd8bNuRHSfKvuf7C1KZ/zw9Xy8NueLuZBy4y FYJTlY7Yl+ZSZB+B6KyNvLc/fbzbodd1W+uo+E5FUZ158ERiFDBKV2YkKGiDDK6Xj266be3dDPDar VK0zJ07g==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <cjwatson@debian.org>) id 1vVXTv-000wH2-J8 for submit@bugs.debian.org; Tue, 16 Dec 2025 16:01:00 +0000 Received: from camorr.wl.rosewood.vpn.ucam.org ([172.20.153.148] helo=camorr.rosewood.vpn.ucam.org) by riva.rosewood.vpn.ucam.org with esmtps (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.98.2) (envelope-from <cjwatson@debian.org>) id 1vVXTt-00000005S7q-31CP for submit@bugs.debian.org; Tue, 16 Dec 2025 16:00:57 +0000 Date: Tue, 16 Dec 2025 16:00:53 +0000 From: Colin Watson <cjwatson@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: pyensembl: FTBFS with Python 3.14 Message-ID: <aUGCNTlfTddPYj_Z@camorr.rosewood.vpn.ucam.org> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Reportbug-Version: 13.2.0 X-Debian-User: cjwatson Delivered-To: submit@bugs.debian.org Source: pyensembl Version: 2.3.13-3 Severity: serious Tags: ftbfs User: debian-python@lists.debian.org Usertags: python3.14 pyensembl fails to build in unstable with Python 3.14 as a supported Python version. Here's the relevant part of the build log: dh_auto_test -O--buildsystem=pybuild pybuild --test --test-pytest -i python{version} -p "3.14 3.13" I: pybuild base:317: cd /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.14_pyensembl/build; python3.14 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' ============================= test session starts ============================== platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 cachedir: .pytest_cache rootdir: /build/reproducible-path/pyensembl-2.3.13 plugins: typeguard-4.4.4 collecting ... collected 125 items / 1 error / 98 deselected / 27 selected ==================================== ERRORS ==================================== _ ERROR collecting .pybuild/cpython3_3.14_pyensembl/build/tests/test_shell.py __ tests/test_shell.py:1: in <module> from pyensembl.shell import parser, all_combinations_of_ensembl_genomes pyensembl/shell.py:74: in <module> release_group = root_group.add_argument_group() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /usr/lib/python3.14/argparse.py:1805: in add_argument_group raise ValueError('argument groups cannot be nested') E ValueError: argument groups cannot be nested =============================== warnings summary =============================== pyensembl/shell.py:43 /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.14_pyensembl/build/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ ERROR tests/test_shell.py - ValueError: argument groups cannot be nested !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! ================== 98 deselected, 1 warning, 1 error in 0.48s ================== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.14_pyensembl/build; python3.14 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' Thanks, -- Colin Watson (he/him) [cjwatson@debian.org] -- System Information: Debian Release: forky/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: arm64 Kernel: Linux 6.16.12+deb14+1-amd64 (SMP w/12 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB:en Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled ]