From unknown Sun Jun 22 04:07:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#66064] [PATCH] gnu: python-plastid: Patch it for python 3.10. 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Mon, 18 Sep 2023 05:40:02 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Mon, 18 Sep 2023 05:40:01 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 18 Sep 2023 05:39:20 +0200 Message-ID: <20230918033947.4556-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27882.004 X-TM-AS-Result: No-10--5.110000-5.000000 X-TMASE-MatchedRID: Dbk4bQCj7CbRTAZ5iUYfyQrcxrzwsv5uP3Y6Dcg5mW1XGTbsQqHbkr8F Hrw7frluf146W0iUu2tvedD3CYSjHQJW+jkd+3/uGqSG/c50XgPjmgMQ17h5699zZd3pUn7Ki3G OCGgGiOaGsZX0q3FpiOhAZQXEXXZu0N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jC24oEZ6SpSl2+n EixMccdpFOlJCK/1ftTg/F8SJNhCsoZIGIBy2E2dJzsDYDrU6iqLDv4G/Ae+Ouv/V/C2WBwNAbC zmxvXAh X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.110000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27882.004 X-TM-SNTS-SMTP: 61AF4293DA8197FB6FBEFCE34A7AF648BAEAB09752A50E46A5C580082235A3EA2000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, 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-plastid)[arguments]: Add new phase patch-for-python-3.10. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c78f017a24..d7a9697c6e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3787,6 +3787,13 @@ (define-public python-plastid "-xf" (assoc-ref inputs "test-data")) ;; This one requires bowtie-build (delete-file "plastid/test/functional/test_crossmap.py"))) + (add-after 'unpack 'patch-for-python-3.10 + (lambda _ + ;; Some classes were moved from collections to collections.abc + ;; in Python 3.10. + (substitute* "plastid/readers/bigbed.pyx" + ((", Iterable") + "\nfrom collections.abc import Iterable")))) (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. base-commit: 1d30ec935126f316187dfc26446347bc7de9868b -- 2.41.0 From unknown Sun Jun 22 04:07:32 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: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Subject: bug#66064: closed (Re: [bug#66064] [PATCH] gnu: python-plastid: Patch it for python 3.10.) Message-ID: References: <87led3yj6c.fsf@elephly.net> <20230918033947.4556-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 66064 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 66064@debbugs.gnu.org Date: Mon, 18 Sep 2023 08:35:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1695026101-28219-1" This is a multi-part message in MIME format... ------------=_1695026101-28219-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #66064: [PATCH] gnu: python-plastid: Patch it for python 3.10. 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 66064@debbugs.gnu.org. --=20 66064: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D66064 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1695026101-28219-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 66064-done) by debbugs.gnu.org; 18 Sep 2023 08:34:07 +0000 Received: from localhost ([127.0.0.1]:52026 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qi9hn-0007Jn-6R for submit@debbugs.gnu.org; Mon, 18 Sep 2023 04:34:07 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21711) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qi9hk-0007Jd-76 for 66064-done@debbugs.gnu.org; Mon, 18 Sep 2023 04:34:06 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1695026033; cv=none; d=zohomail.com; s=zohoarc; b=aeeZfgwdYvNUnICEWKJIYC9rNoJq4Qo9Ai+Go0LZKfDIs+VTP0NDi9COd+GrDiNnWGT3lLUDuVl4TlhvzwKkDc80xJ1msV/svh+Hn76BH1jSjVoDgj+Q7Nu+onRoDqy4lGWD6j7Q+Q9bDEYsSmLJ0/K3/mIHj3IGt4/rL+/U9bM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1695026033; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=AlKtSB4JhLu0k0UXDHLCau53BUARUc48G+XC8wGKMbk=; b=D/h+uhZFEiklJE1uSsFJAjgEHk5QFoNLoXUEyNEGibteJjDfG5ulgG3u3XTl0mwUsnOoJ8qqt0B9Yk3JFCaLITe4uPE3LO97krLN9E2NSvTmWgHLn51xbavCdNLn1mLfvyP0lRzJJaUpTejAG/rYGKIZfmlf8YdyERuU7S6sYMA= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1695026033; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=AlKtSB4JhLu0k0UXDHLCau53BUARUc48G+XC8wGKMbk=; b=TJd3fLx/RrUE6GLcRUHv9b490/UWRUVCn7TpGscnNdDpFK0ug4XpETI40xU/8FYz pHpCyXKQ8njV3qYIAss9y3YEIbsWuZ9yOGWv5+jpCkSJ4rWu1QIBkYy1QDnZU0HwJxK kivjZmGYX4SvDFowrmA0pe5z92c84237aC5O0iAQ= Received: from localhost (19-111-142-46.pool.kielnet.net [46.142.111.19]) by mx.zohomail.com with SMTPS id 1695026030665192.68943547411902; Mon, 18 Sep 2023 01:33:50 -0700 (PDT) References: <20230918033947.4556-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.10.5; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#66064] [PATCH] gnu: python-plastid: Patch it for python 3.10. Date: Mon, 18 Sep 2023 10:33:37 +0200 In-reply-to: <20230918033947.4556-1-madalinionel.patrascu@mdc-berlin.de> Message-ID: <87led3yj6c.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66064-done Cc: 66064-done@debbugs.gnu.org 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: -1.0 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add > new phase patch-for-python-3.10. Applied, thanks! --=20 Ricardo ------------=_1695026101-28219-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 18 Sep 2023 03:40:47 +0000 Received: from localhost ([127.0.0.1]:51751 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qi57u-0007PY-LE for submit@debbugs.gnu.org; Sun, 17 Sep 2023 23:40:46 -0400 Received: from lists.gnu.org ([2001:470:142::17]:47806) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qi57q-0007PC-0B for submit@debbugs.gnu.org; Sun, 17 Sep 2023 23:40:45 -0400 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 1qi57c-0004Jj-6G for guix-patches@gnu.org; Sun, 17 Sep 2023 23:40:28 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qi57Y-00046W-Pi for guix-patches@gnu.org; Sun, 17 Sep 2023 23:40:27 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1695008402; x=1696822803; bh=f6Wpkhuz83a9c6u bmrlnH8TeMBYzmtLAhESRIFWwE2g=; b=SlBLNrCPuvx67B4RekptY8QWRgdz8tn snorUCf0+Q3fBm9xkUHVLg9pD7qz/5vXzb3+/j9EGlx5/w1W56sBzYbc+q3vTvDC VQoZoKGhW5QM9Yba8YfxDdrMk9P1RCNLkY1U04LxC3blRwdQYsOyi9En8FItNi6X V41PoCUESSZs= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 9F675A0144 for ; Mon, 18 Sep 2023 05:40:02 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Mon, 18 Sep 2023 05:40:01 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: python-plastid: Patch it for python 3.10. Date: Mon, 18 Sep 2023 05:39:20 +0200 Message-ID: <20230918033947.4556-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27882.004 X-TM-AS-Result: No-10--5.110000-5.000000 X-TMASE-MatchedRID: Dbk4bQCj7CbRTAZ5iUYfyQrcxrzwsv5uP3Y6Dcg5mW1XGTbsQqHbkr8F Hrw7frluf146W0iUu2tvedD3CYSjHQJW+jkd+3/uGqSG/c50XgPjmgMQ17h5699zZd3pUn7Ki3G OCGgGiOaGsZX0q3FpiOhAZQXEXXZu0N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jC24oEZ6SpSl2+n EixMccdpFOlJCK/1ftTg/F8SJNhCsoZIGIBy2E2dJzsDYDrU6iqLDv4G/Ae+Ouv/V/C2WBwNAbC zmxvXAh X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.110000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27882.004 X-TM-SNTS-SMTP: 61AF4293DA8197FB6FBEFCE34A7AF648BAEAB09752A50E46A5C580082235A3EA2000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, 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 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-plastid)[arguments]: Add new phase patch-for-python-3.10. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c78f017a24..d7a9697c6e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3787,6 +3787,13 @@ (define-public python-plastid "-xf" (assoc-ref inputs "test-data")) ;; This one requires bowtie-build (delete-file "plastid/test/functional/test_crossmap.py"))) + (add-after 'unpack 'patch-for-python-3.10 + (lambda _ + ;; Some classes were moved from collections to collections.abc + ;; in Python 3.10. + (substitute* "plastid/readers/bigbed.pyx" + ((", Iterable") + "\nfrom collections.abc import Iterable")))) (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. base-commit: 1d30ec935126f316187dfc26446347bc7de9868b -- 2.41.0 ------------=_1695026101-28219-1--