From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id yE4RLYMjzmFjnAAAgWs5BA (envelope-from ) for ; Thu, 30 Dec 2021 22:24:19 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id gGyjKYMjzmH2iQAAauVa8A (envelope-from ) for ; Thu, 30 Dec 2021 22:24:19 +0100 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 300F859A2 for ; Thu, 30 Dec 2021 22:24:19 +0100 (CET) Received: from localhost ([::1]:60780 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n32uI-0001G6-7h for larch@yhetil.org; Thu, 30 Dec 2021 16:24:18 -0500 Received: from eggs.gnu.org ([209.51.188.92]:32770) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n32u2-0001EZ-Vk for bug-guix@gnu.org; Thu, 30 Dec 2021 16:24:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:43176) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n32u2-0000nM-Jd for bug-guix@gnu.org; Thu, 30 Dec 2021 16:24:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n32u2-0003CX-B4; Thu, 30 Dec 2021 16:24:02 -0500 X-Loop: help-debbugs@gnu.org Subject: bug#52906: python-biopython conflicts with python-numpy Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, bug-guix@gnu.org Resent-Date: Thu, 30 Dec 2021 21:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 52906 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 52906@debbugs.gnu.org X-Debbugs-Original-To: Bug Guix X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by submit@debbugs.gnu.org id=B.164089942112269 (code B ref -1); Thu, 30 Dec 2021 21:24:02 +0000 Received: (at submit) by debbugs.gnu.org; 30 Dec 2021 21:23:41 +0000 Received: from localhost ([127.0.0.1]:54720 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n32tg-0003Bp-OA for submit@debbugs.gnu.org; Thu, 30 Dec 2021 16:23:41 -0500 Received: from lists.gnu.org ([209.51.188.17]:33326) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n32te-0003Bh-Hz for submit@debbugs.gnu.org; Thu, 30 Dec 2021 16:23:39 -0500 Received: from eggs.gnu.org ([209.51.188.92]:60934) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n32te-0000cx-CC for bug-guix@gnu.org; Thu, 30 Dec 2021 16:23:38 -0500 Received: from [2a00:1450:4864:20::433] (port=35356 helo=mail-wr1-x433.google.com) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n32tc-0008AX-Fr for bug-guix@gnu.org; Thu, 30 Dec 2021 16:23:37 -0500 Received: by mail-wr1-x433.google.com with SMTP id j18so52693479wrd.2 for ; Thu, 30 Dec 2021 13:23:36 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:subject:date:message-id:mime-version; bh=/P9GwQT4NHOtcyuVg6o7fBximpKv4TnSznJRvT+HzWw=; b=RiPVuVwuWhV+Xiw2y4gWwfCYctdkmVNlD29SvQD13XuBGKVC2H6RT5jh14wvgNt8ke gScwga8kUDE9oFaFQh1wU7ZIrEfHYGijtX/nyhs8M91Xb/ueEpkopOjiucILWX7F3hHJ xH6DybQEwDs44x2Pc1UbBImAvEYy+C46ffoZiQOOzQa3ceJ9WLg7PZxvUFGORMjMCo77 mfubv6jEV7exEJXceJBwBxvFQMf3HATnBvxj+5FwZx4DCFKc0uVN0IeJu3SzqN5fvRlf W3d2Ub44BuR6fOZi7MDqhuvuJ9h1kWDDCsth8E3Q77RQhD1GQQZ6vZ4z0McBEMm6+VGu AfcA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:subject:date:message-id:mime-version; bh=/P9GwQT4NHOtcyuVg6o7fBximpKv4TnSznJRvT+HzWw=; b=NQ8LaTMx+cO9JcuQeGQ5hrl94+CcdIPVMClmRgotvblg3SKW3ZR2vQZaZi2qePsxdn zTEWQRPew2DbqWbH62ad/1z7Rds2JrXVP3u8FwuU7BAqb1pvqJO9RsKV57zIi3Gb50yN nlBjlzcAUJviBGtfz3Hzlv1Pl2xM0lcxZa72cmd3OpKoU0gpAMe5BccJKyfKZLgaVzc/ AoT3BCYyJLVNMI/hSrjMhpu2BoMnkEWij+9NBcYof/FHJRc7YOBrLv535t2MEAbEmOHg VKBHRClrTgQL/Cz47frfiwwgu0lR8pVGnd8nnTPAo9w251m/mHimbCzPeRjI0/5OmGzI T32g== X-Gm-Message-State: AOAM533UT5MAJA1X6E1g15vBnIOrTkutDGlq58FhbDUHl4navqNw1bAy 8kUGL3MkuNA/QJkGPVu/ItsapAGt8AE= X-Google-Smtp-Source: ABdhPJxXKK/E6Unf8kkbwHUaiRp3eSBqS/zIObs1Okxjl5Ns2z4cItP4wlOeQLHRKxtamtn/THFEfA== X-Received: by 2002:a05:6000:120c:: with SMTP id e12mr26729328wrx.6.1640899414896; Thu, 30 Dec 2021 13:23:34 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id k31sm25062038wms.21.2021.12.30.13.23.34 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 30 Dec 2021 13:23:34 -0800 (PST) From: zimoun Date: Thu, 30 Dec 2021 22:13:48 +0100 Message-ID: <86o84xpzhv.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-Host-Lookup-Failed: Reverse DNS lookup failed for 2a00:1450:4864:20::433 (failed) Received-SPF: pass client-ip=2a00:1450:4864:20::433; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x433.google.com X-Spam_score_int: 6 X-Spam_score: 0.6 X-Spam_bar: / X-Spam_report: (0.6 / 5.0 requ) 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_NONE=-0.0001, RDNS_NONE=0.793, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Ricardo Wurmus Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1640899459; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:list-id:list-help:list-unsubscribe:list-subscribe: list-post:dkim-signature; bh=/P9GwQT4NHOtcyuVg6o7fBximpKv4TnSznJRvT+HzWw=; b=Fdx1LALLaVUqAbGxqkwqWNbeDyhu8gvqGv74EITchHI2G/lFc7P8nRmO0fKLSWAr0wLvqV eaoXpscpDDMcYsETxqdhe4WDyWhy3SlcCIqGoY00ZTdSEWlDph/U9f879KYefNELYeS7Md NBysba+90NzRrnbh1No2FULGRDvWH8l08yKbdAwsDF1HJPZjSCJtf5H4bKq1mnJCnB1lkB uHVasiJtjj/k/JZTDAg7JQy0ZrCkK0AQrj1U1Jz7pyZA6OvllK8qtiEO4EZqRk548nmq+S ezoafVQkMKFTSXU8madDwQM6wWC+7xEri4xY/9GmFLNmosHz83QmxGZ65OIqwA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1640899459; a=rsa-sha256; cv=none; b=sweM4OExD+JEBnpXlldFleV5Y1qRN6sVnY90OFigCT+RC89cWVXXSpbAcfEnvI1+uTwF9I ukqs74ZpzKCwUZY3Gh4Udo5CjnvNUm8lYkCuY6EFlzIcPgYlZj4dqDqYmkj+5RrOtm2yiq kpCLhNIOzusFkrkCLcTqWVQecUJ09QDApvd9fMKZ0Hn3Cv4bH5svAkbwpYWmzSLWwFwcyT KyUgZppsq/h8RnDVhC9tjlKPM2MZkPbOXBSSMaQY5a039PY067zcjWki7N+YOuwhS2kfuV ZuBxR/h0e9Xa7+lFPQtbQaaAzqQbvUK1o2mz/xZQVQIGcZEpWQ9gfJuWadWudw== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=RiPVuVwu; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: -2.17 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=RiPVuVwu; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 300F859A2 X-Spam-Score: -2.17 X-Migadu-Scanner: scn1.migadu.com X-TUID: h58g/7+di6vI --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi, Using 7022eb6, the package =E2=80=99python-biopython=E2=80=99 propagates =E2=80=99python-numpy=E2=80=99, i.e., python-numpy@1.20.3. However, because Guix installs by default the last version and: --8<---------------cut here---------------start------------->8--- $ guix package -A | grep 'python-numpy ' | cut -f1,2 python-numpy 1.21.3=20=20=20=20=20=20=20=20=20=20=20=20=20=20 python-numpy 1.20.3=20=20=20=20=20=20=20=20=20=20=20=20=20=20 --8<---------------cut here---------------end--------------->8--- then this manifests.scm leads to an error, --8<---------------cut here---------------start------------->8--- $ cat /tmp/manifest.scm (specifications->manifest (list "python-numpy" "python-biopython")) $ guix package -m /tmp/manifest.scm -p /tmp/fail The following packages will be installed: python-biopython 1.76 python-numpy 1.21.3 guix package: error: profile contains conflicting entries for python-numpy guix package: error: first entry: python-numpy@1.21.3 /gnu/store/ggrkk9l6= 7fjn1cj7alr8vx40xv08a6h0-python-numpy-1.21.3 guix package: error: second entry: python-numpy@1.20.3 /gnu/store/wgsmkn6= 8q8h178sqc7ywjcdr330z9rb6-python-numpy-1.20.3 guix package: error: ... propagated from python-biopython@1.76 hint: Try upgrading both `python-numpy' and `python-biopython', or remove o= ne of them from the profile. --8<---------------cut here---------------end--------------->8--- which is annoying. I propose to refer as name =E2=80=9Cpython-numpy=E2=80=9D the symbol python= -numpy which leads to a consistent scientific Python stack. And to refer as name =E2=80=9Cpython-numpy-next=E2=80=9D the symbol python-numpy-next. For instance, it is already the case for emacs-next or for the Bioconductor package r-cistopic. Doing so, adventurous people can use python-numpy-next (or recompile all the scientific Python stack using it), or update it directly on master (for testing say) without going to a core-update cycle. WDYT? Attached a proposed patch. Cheers, simon --=-=-= Content-Type: text/x-diff Content-Disposition: inline; filename=0001-gnu-Rename-last-python-numpy-as-python-numpy-next.patch Content-Description: patch.patch >From 962d942ffcba7893ab15c30dc602e51462d9b09a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 30 Dec 2021 22:04:49 +0100 Subject: [PATCH] gnu: Rename last 'python-numpy' as 'python-numpy-next'. * gnu/packages/python-xyz.scm (python-numpy-next): Rename. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7ca0b1668d..047bb4cbb8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5366,11 +5366,9 @@ (define-public python2-cython "")) #t))))))))) -;; NOTE: when upgrading numpy please make sure that python-pandas and -;; python-scipy still build, as these three packages are often used together. (define-public python-numpy-next (package - (name "python-numpy") + (name "python-numpy-next") (version "1.21.3") (source (origin @@ -5481,6 +5479,8 @@ (define-public python-numpy-1.20 (substitute-keyword-arguments (package-arguments python-numpy-next) ((#:tests? _ #t) #f))))) +;; NOTE: when upgrading numpy please make sure that python-pandas and +;; python-scipy still build, as these three packages are often used together. (define-public python-numpy python-numpy-1.20) ;; NOTE: NumPy 1.8 is packaged only for Python 2 because it is of base-commit: 002442b2209b0953dd209e6219696a8758ceceb2 -- 2.34.0 --=-=-=--