From unknown Sun Jun 22 11:45:49 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#64447] [PATCH] gnu: python-pymol: Fix launch script. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net, guix-patches@gnu.org Resent-Date: Mon, 03 Jul 2023 21:33:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 64447 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64447@debbugs.gnu.org Cc: David Elsing , andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net Received: via spool by submit@debbugs.gnu.org id=B.168841992224130 (code B ref -1); Mon, 03 Jul 2023 21:33:01 +0000 Received: (at submit) by debbugs.gnu.org; 3 Jul 2023 21:32:02 +0000 Received: from localhost ([127.0.0.1]:34570 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGR9N-0006H8-Vj for submit@debbugs.gnu.org; Mon, 03 Jul 2023 17:32:02 -0400 Received: from lists.gnu.org ([209.51.188.17]:55316) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGR9K-0006Gi-ET for submit@debbugs.gnu.org; Mon, 03 Jul 2023 17:32:01 -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 1qGR9F-0004TD-Hy for guix-patches@gnu.org; Mon, 03 Jul 2023 17:31:54 -0400 Received: from mout01.posteo.de ([185.67.36.65]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qGR9D-0006YF-7G for guix-patches@gnu.org; Mon, 03 Jul 2023 17:31:53 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 31E26240027 for ; Mon, 3 Jul 2023 23:31:49 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1688419909; bh=CAumRDTUoW2mQQM7ZRxlruxdMAzzaCVYWQC45bAVKFQ=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=psvb2YZuHZ8raLSJewDGKJHLV1yYWCYbdu5LSKluqCLVNFeUB65fR6plfHxzuhrXU etjs6QPoTfsqazOvQv0PCCqLmr0WFP0q09loaLO8ziO0CI9aQ/Bnvud7/hoZ7Mesoi qQyY+fAuP6kSUC+MxaSueuJPMtDP67cKXfDVhKdLbCrvjoadNALCQlQxIx1EDNE0m6 b7kzXngM3y0Ma3803XFHJWK10JrCgmS6AYDkcqvDwixhibuAInEe1UXZb4JbeeELeg ueJb2et6xfZkGLrXqj2iO79vlFQeI1cUFr2mdtw7ilcz1QiZWa+15Nk4B2FCEGrWtP Bw5s3rEvF+k6Q== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Qvzdc5xXYz9rxG; Mon, 3 Jul 2023 23:31:48 +0200 (CEST) From: David Elsing Date: Mon, 3 Jul 2023 21:31:10 +0000 Message-Id: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=david.elsing@posteo.net; helo=mout01.posteo.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, RCVD_IN_MSPIKE_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) 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: -2.3 (--) * gnu/packages/chemistry.scm (python-pymol)[#:phases]: Add ‘disable-unchroot’. [native-inputs]: Remove python-setuptools. --- gnu/packages/chemistry.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index cddccf8aea..1f8b051a85 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2021 Ricardo Wurmus -;;; Copyright © 2022 David Elsing +;;; Copyright © 2022, 2023 David Elsing ;;; ;;; This file is part of GNU Guix. ;;; @@ -554,6 +554,12 @@ (define-public python-pymol (assoc-ref inputs "libxml2") "/include/libxml2:" (getenv "CPLUS_INCLUDE_PATH"))))) + ;; Prevent deleting the leading / in the __init__.py path in the + ;; launch script. + (add-after 'unpack 'disable-unchroot + (lambda _ + (substitute* "setup.py" + (("self\\.unchroot") "")))) ;; The setup.py script does not support one of the Python build ;; system's default flags, "--single-version-externally-managed". (replace 'install @@ -572,8 +578,7 @@ (define-public python-pymol python-pyqt glm netcdf)) - (native-inputs - (list catch2 python-setuptools)) + (native-inputs (list catch2)) (home-page "https://pymol.org") (synopsis "Molecular visualization system") (description "PyMOL is a capable molecular viewer and renderer. It can be -- 2.40.1 From unknown Sun Jun 22 11:45:49 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: David Elsing Subject: bug#64447: closed (Re: [bug#64447] [PATCH] gnu: python-pymol: Fix launch script.) Message-ID: References: X-Gnu-PR-Message: they-closed 64447 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 64447@debbugs.gnu.org Date: Wed, 26 Jul 2023 14:18:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1690381082-6490-1" This is a multi-part message in MIME format... ------------=_1690381082-6490-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #64447: [PATCH] gnu: python-pymol: Fix launch script. 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 64447@debbugs.gnu.org. --=20 64447: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D64447 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1690381082-6490-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 64447-done) by debbugs.gnu.org; 26 Jul 2023 14:17:08 +0000 Received: from localhost ([127.0.0.1]:49743 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qOfK4-0001fW-A7 for submit@debbugs.gnu.org; Wed, 26 Jul 2023 10:17:08 -0400 Received: from hera.aquilenet.fr ([2a0c:e300::1]:59442) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qOfJz-0001eu-2R for 64447-done@debbugs.gnu.org; Wed, 26 Jul 2023 10:17:03 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 5ACB01DF2; Wed, 26 Jul 2023 16:16:51 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id XtTSmlesrHGv; Wed, 26 Jul 2023 16:16:51 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id D6EAE1661; Wed, 26 Jul 2023 16:16:50 +0200 (CEST) Date: Wed, 26 Jul 2023 16:16:49 +0200 From: Andreas Enge To: David Elsing Subject: Re: [bug#64447] [PATCH] gnu: python-pymol: Fix launch script. Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 64447-done Cc: 64447-done@debbugs.gnu.org, efraim@flashner.co.il, bavier@posteo.net 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 (-) Applied, thanks! Andreas ------------=_1690381082-6490-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 Jul 2023 21:32:02 +0000 Received: from localhost ([127.0.0.1]:34570 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGR9N-0006H8-Vj for submit@debbugs.gnu.org; Mon, 03 Jul 2023 17:32:02 -0400 Received: from lists.gnu.org ([209.51.188.17]:55316) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGR9K-0006Gi-ET for submit@debbugs.gnu.org; Mon, 03 Jul 2023 17:32:01 -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 1qGR9F-0004TD-Hy for guix-patches@gnu.org; Mon, 03 Jul 2023 17:31:54 -0400 Received: from mout01.posteo.de ([185.67.36.65]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qGR9D-0006YF-7G for guix-patches@gnu.org; Mon, 03 Jul 2023 17:31:53 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 31E26240027 for ; Mon, 3 Jul 2023 23:31:49 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1688419909; bh=CAumRDTUoW2mQQM7ZRxlruxdMAzzaCVYWQC45bAVKFQ=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=psvb2YZuHZ8raLSJewDGKJHLV1yYWCYbdu5LSKluqCLVNFeUB65fR6plfHxzuhrXU etjs6QPoTfsqazOvQv0PCCqLmr0WFP0q09loaLO8ziO0CI9aQ/Bnvud7/hoZ7Mesoi qQyY+fAuP6kSUC+MxaSueuJPMtDP67cKXfDVhKdLbCrvjoadNALCQlQxIx1EDNE0m6 b7kzXngM3y0Ma3803XFHJWK10JrCgmS6AYDkcqvDwixhibuAInEe1UXZb4JbeeELeg ueJb2et6xfZkGLrXqj2iO79vlFQeI1cUFr2mdtw7ilcz1QiZWa+15Nk4B2FCEGrWtP Bw5s3rEvF+k6Q== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Qvzdc5xXYz9rxG; Mon, 3 Jul 2023 23:31:48 +0200 (CEST) From: David Elsing To: guix-patches@gnu.org Subject: [PATCH] gnu: python-pymol: Fix launch script. Date: Mon, 3 Jul 2023 21:31:10 +0000 Message-Id: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 X-Debbugs-Cc: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=david.elsing@posteo.net; helo=mout01.posteo.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, RCVD_IN_MSPIKE_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: David Elsing 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: -2.3 (--) * gnu/packages/chemistry.scm (python-pymol)[#:phases]: Add ‘disable-unchroot’. [native-inputs]: Remove python-setuptools. --- gnu/packages/chemistry.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index cddccf8aea..1f8b051a85 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2021 Ricardo Wurmus -;;; Copyright © 2022 David Elsing +;;; Copyright © 2022, 2023 David Elsing ;;; ;;; This file is part of GNU Guix. ;;; @@ -554,6 +554,12 @@ (define-public python-pymol (assoc-ref inputs "libxml2") "/include/libxml2:" (getenv "CPLUS_INCLUDE_PATH"))))) + ;; Prevent deleting the leading / in the __init__.py path in the + ;; launch script. + (add-after 'unpack 'disable-unchroot + (lambda _ + (substitute* "setup.py" + (("self\\.unchroot") "")))) ;; The setup.py script does not support one of the Python build ;; system's default flags, "--single-version-externally-managed". (replace 'install @@ -572,8 +578,7 @@ (define-public python-pymol python-pyqt glm netcdf)) - (native-inputs - (list catch2 python-setuptools)) + (native-inputs (list catch2)) (home-page "https://pymol.org") (synopsis "Molecular visualization system") (description "PyMOL is a capable molecular viewer and renderer. It can be -- 2.40.1 ------------=_1690381082-6490-1--