From unknown Thu Aug 14 22:19:31 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#75558] [PATCH] gnu: python-cyvcf2: Update to 0.31.1 Resent-From: Alexis Simon Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Tue, 14 Jan 2025 16:14:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 75558 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 75558@debbugs.gnu.org Cc: Alexis Simon , rekado@elephly.net X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.17368712401326 (code B ref -1); Tue, 14 Jan 2025 16:14:02 +0000 Received: (at submit) by debbugs.gnu.org; 14 Jan 2025 16:14:00 +0000 Received: from localhost ([127.0.0.1]:55421 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tXjYG-0000LK-9q for submit@debbugs.gnu.org; Tue, 14 Jan 2025 11:14:00 -0500 Received: from lists.gnu.org ([2001:470:142::17]:38848) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tXjYD-0000Kh-VN for submit@debbugs.gnu.org; Tue, 14 Jan 2025 11:13:58 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tXjY8-0001TU-0i for guix-patches@gnu.org; Tue, 14 Jan 2025 11:13:52 -0500 Received: from mailtransmit04.runbox.com ([2a0c:5a00:149::25]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tXjY5-0003rf-4y for guix-patches@gnu.org; Tue, 14 Jan 2025 11:13:51 -0500 Received: from mailtransmit03.runbox ([10.9.9.163] helo=aibo.runbox.com) by mailtransmit04.runbox.com with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (Exim 4.93) (envelope-from ) id 1tXjXy-00GsWz-2j for guix-patches@gnu.org; Tue, 14 Jan 2025 17:13:42 +0100 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=runbox.com; s=selector2; h=Content-Transfer-Encoding:MIME-Version:Message-ID:Date: Subject:Cc:To:From; bh=2HarW/Bv9ugji0P3jil5fAkpnxVh424/WkESFtqSpZc=; b=T5nfNH bHJBZV6o9Zv1tx2GPLqiU8DtFZjRe2gitX/kjBTtgaVVu/Y1V0jtINFO1QIqBmUtNOBbxQjXAf0Ei 2Bu+mNpGopbXaKXEfOMpiyt0+WpEz5W2q4+KrbEVzs1dAVnRCB0dYRaklO/Ff2nbbqSOvei/4Az+A P6EyrblXQWNMjNuKjK/0uKjTA9IvOPR1tQrYir8a1QFPV0tOjRpigQdPF/DotQytBBkXc9y+mSOdm 6USrVAUuvHlzdGZO36MsRaf/yN5Iiw9NWze9ktEAfNsqYONSHfhT/qwXLFzcabPMKxHnaqk/95Kbv chob5Amzw/4a4yeuI9nJm4Zy1Djg==; Received: from [10.9.9.73] (helo=submission02.runbox) by mailtransmit03.runbox with esmtp (Exim 4.86_2) (envelope-from ) id 1tXjXw-0006wV-GH for guix-patches@gnu.org; Tue, 14 Jan 2025 17:13:41 +0100 Received: by submission02.runbox with esmtpsa [Authenticated ID (1174703)] (TLS1.2:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.93) id 1tXjXl-003XZB-6q; Tue, 14 Jan 2025 17:13:29 +0100 From: Alexis Simon Date: Tue, 14 Jan 2025 17:13:01 +0100 Message-ID: <5cca5fa72a4b9c00561e5f0ea34c3a790013ff25.1736871181.git.alexis.simon@runbox.com> X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a0c:5a00:149::25; envelope-from=alexis.simon@runbox.com; helo=mailtransmit04.runbox.com X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (python-cyvcf2): Update to 0.31.1 and fix build failure. Change-Id: Icc5057cf9f5e6ba141e6e29e8f4db657cd04c1d2 --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 34a39a48f1..35f1a76fb1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2357,7 +2357,7 @@ (define-public python-cmseq (define-public python-cyvcf2 (package (name "python-cyvcf2") - (version "0.30.28") + (version "0.31.1") (source (origin (method git-fetch) @@ -2366,7 +2366,7 @@ (define-public python-cyvcf2 (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk")) + (base32 "02x7ic2q4x3sfwx9n2sxg0a79iifjal0a68fqp9ljsfvdx4b7nq5")) (modules '((guix build utils))) (snippet ;; Delete bundled library @@ -2395,7 +2395,7 @@ (define-public python-cyvcf2 (setenv "CYTHONIZE" "1") (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL")))))) (inputs (list curl htslib libdeflate openssl zlib)) - (native-inputs (list python-cython python-pytest)) + (native-inputs (list python-cython python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-click python-coloredlogs base-commit: d663d4b6cae2289bcdd8bdcd02d58ed30769f1e2 -- 2.45.2 From unknown Thu Aug 14 22:19:31 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Alexis Simon Subject: bug#75558: closed (Re: [PATCH] gnu: python-cyvcf2: Update to 0.31.1) Message-ID: References: <87ed1422ha.fsf@dismail.de> <5cca5fa72a4b9c00561e5f0ea34c3a790013ff25.1736871181.git.alexis.simon@runbox.com> X-Gnu-PR-Message: they-closed 75558 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 75558@debbugs.gnu.org Date: Wed, 15 Jan 2025 03:15:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1736910902-7585-1" This is a multi-part message in MIME format... ------------=_1736910902-7585-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #75558: [PATCH] gnu: python-cyvcf2: Update to 0.31.1 which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 75558@debbugs.gnu.org. --=20 75558: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D75558 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1736910902-7585-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 75558-done) by debbugs.gnu.org; 15 Jan 2025 03:14:10 +0000 Received: from localhost ([127.0.0.1]:56443 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tXtr8-0001wz-KO for submit@debbugs.gnu.org; Tue, 14 Jan 2025 22:14:10 -0500 Received: from mx2.dismail.de ([159.69.191.136]:19592) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tXtr4-0001wD-1f for 75558-done@debbugs.gnu.org; Tue, 14 Jan 2025 22:14:07 -0500 Received: from mx2.dismail.de (localhost [127.0.0.1]) by mx2.dismail.de (OpenSMTPD) with ESMTP id 6a54a196; Wed, 15 Jan 2025 04:13:58 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed; d=dismail.de; h=from:to:cc :subject:in-reply-to:date:message-id:mime-version:content-type; s=20190914; bh=cq2jtlxl9rb1i1oKs3BLrL83L8p7q8tuJLd0JNToRk8=; b= Ho60+zW41hL+eFIGdjdH0aMhfQ1lI+5kBBRLx89ksP2oypGNJpUtP+t2VpC6UpUY lQnkIb6H+EOo6gUTvJ3jGh65H4COioNVSxEinmm/jn4wM7Xa0t8rDEgSrWgwB3oC 4L3RhyyzWVurhTXofax4YTXJBILP8mSsdWeElZqpuBjgEMOnmu1vaW4C0zPu0wfN WLFrPgqlMCBxwcVT1AUoiHIgAyy6I8CIk5svuYPL6kMGO5ac5Rz8cZbxBJCMQZsP uPiFVxrMOT7kJYbCo4eosV00lP1rFSW2aUUKonBbVlp31jeBaHwfdiCk4RQ1+l0u ehWtkioUWGfoppQjdyNYTA== Received: from smtp2.dismail.de ( [10.240.26.12]) by mx2.dismail.de (OpenSMTPD) with ESMTP id 3866246a; Wed, 15 Jan 2025 04:13:58 +0100 (CET) Received: from smtp2.dismail.de (localhost [127.0.0.1]) by smtp2.dismail.de (OpenSMTPD) with ESMTP id 24aa4e0b; Wed, 15 Jan 2025 04:13:58 +0100 (CET) Received: by dismail.de (OpenSMTPD) with ESMTPSA id 25eed9d5 (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Wed, 15 Jan 2025 04:13:57 +0100 (CET) From: jgart To: 75558-done@debbugs.gnu.org Subject: Re: [PATCH] gnu: python-cyvcf2: Update to 0.31.1 In-Reply-To: <5cca5fa72a4b9c00561e5f0ea34c3a790013ff25.1736871181.git.alexis.simon@runbox.com> Date: Tue, 14 Jan 2025 21:13:53 -0600 Message-ID: <87ed1422ha.fsf@dismail.de> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 75558-done Cc: Alexis Simon X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Thanks! Applied. -- all the best, jgart ------------=_1736910902-7585-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 14 Jan 2025 16:14:00 +0000 Received: from localhost ([127.0.0.1]:55421 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tXjYG-0000LK-9q for submit@debbugs.gnu.org; Tue, 14 Jan 2025 11:14:00 -0500 Received: from lists.gnu.org ([2001:470:142::17]:38848) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tXjYD-0000Kh-VN for submit@debbugs.gnu.org; Tue, 14 Jan 2025 11:13:58 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tXjY8-0001TU-0i for guix-patches@gnu.org; Tue, 14 Jan 2025 11:13:52 -0500 Received: from mailtransmit04.runbox.com ([2a0c:5a00:149::25]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tXjY5-0003rf-4y for guix-patches@gnu.org; Tue, 14 Jan 2025 11:13:51 -0500 Received: from mailtransmit03.runbox ([10.9.9.163] helo=aibo.runbox.com) by mailtransmit04.runbox.com with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (Exim 4.93) (envelope-from ) id 1tXjXy-00GsWz-2j for guix-patches@gnu.org; Tue, 14 Jan 2025 17:13:42 +0100 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=runbox.com; s=selector2; h=Content-Transfer-Encoding:MIME-Version:Message-ID:Date: Subject:Cc:To:From; bh=2HarW/Bv9ugji0P3jil5fAkpnxVh424/WkESFtqSpZc=; b=T5nfNH bHJBZV6o9Zv1tx2GPLqiU8DtFZjRe2gitX/kjBTtgaVVu/Y1V0jtINFO1QIqBmUtNOBbxQjXAf0Ei 2Bu+mNpGopbXaKXEfOMpiyt0+WpEz5W2q4+KrbEVzs1dAVnRCB0dYRaklO/Ff2nbbqSOvei/4Az+A P6EyrblXQWNMjNuKjK/0uKjTA9IvOPR1tQrYir8a1QFPV0tOjRpigQdPF/DotQytBBkXc9y+mSOdm 6USrVAUuvHlzdGZO36MsRaf/yN5Iiw9NWze9ktEAfNsqYONSHfhT/qwXLFzcabPMKxHnaqk/95Kbv chob5Amzw/4a4yeuI9nJm4Zy1Djg==; Received: from [10.9.9.73] (helo=submission02.runbox) by mailtransmit03.runbox with esmtp (Exim 4.86_2) (envelope-from ) id 1tXjXw-0006wV-GH for guix-patches@gnu.org; Tue, 14 Jan 2025 17:13:41 +0100 Received: by submission02.runbox with esmtpsa [Authenticated ID (1174703)] (TLS1.2:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.93) id 1tXjXl-003XZB-6q; Tue, 14 Jan 2025 17:13:29 +0100 From: Alexis Simon To: guix-patches@gnu.org Subject: [PATCH] gnu: python-cyvcf2: Update to 0.31.1 Date: Tue, 14 Jan 2025 17:13:01 +0100 Message-ID: <5cca5fa72a4b9c00561e5f0ea34c3a790013ff25.1736871181.git.alexis.simon@runbox.com> X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a0c:5a00:149::25; envelope-from=alexis.simon@runbox.com; helo=mailtransmit04.runbox.com X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Alexis Simon X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (python-cyvcf2): Update to 0.31.1 and fix build failure. Change-Id: Icc5057cf9f5e6ba141e6e29e8f4db657cd04c1d2 --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 34a39a48f1..35f1a76fb1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2357,7 +2357,7 @@ (define-public python-cmseq (define-public python-cyvcf2 (package (name "python-cyvcf2") - (version "0.30.28") + (version "0.31.1") (source (origin (method git-fetch) @@ -2366,7 +2366,7 @@ (define-public python-cyvcf2 (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk")) + (base32 "02x7ic2q4x3sfwx9n2sxg0a79iifjal0a68fqp9ljsfvdx4b7nq5")) (modules '((guix build utils))) (snippet ;; Delete bundled library @@ -2395,7 +2395,7 @@ (define-public python-cyvcf2 (setenv "CYTHONIZE" "1") (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL")))))) (inputs (list curl htslib libdeflate openssl zlib)) - (native-inputs (list python-cython python-pytest)) + (native-inputs (list python-cython python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-click python-coloredlogs base-commit: d663d4b6cae2289bcdd8bdcd02d58ed30769f1e2 -- 2.45.2 ------------=_1736910902-7585-1--