From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id aC12IV4w8WJTLgAAbAwnHQ (envelope-from ) for ; Mon, 08 Aug 2022 17:48:46 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id aDRgIV4w8WLR9QAAauVa8A (envelope-from ) for ; Mon, 08 Aug 2022 17:48:46 +0200 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 4F187EB6C for ; Mon, 8 Aug 2022 17:48:46 +0200 (CEST) Received: from localhost ([::1]:49446 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oL4zl-0001Oy-DW for larch@yhetil.org; Mon, 08 Aug 2022 11:48:45 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41172) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oL4z9-0000Ju-4G for guix-patches@gnu.org; Mon, 08 Aug 2022 11:48:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:52007) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oL4z8-0006mq-RD for guix-patches@gnu.org; Mon, 08 Aug 2022 11:48:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oL4z8-000696-MZ for guix-patches@gnu.org; Mon, 08 Aug 2022 11:48:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56729] [RFC PATCH v2 00/29] Add sagemath. Resent-From: vicvbcun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Aug 2022 15:48:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56729 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 56729@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge Received: via spool by 56729-submit@debbugs.gnu.org id=B56729.165997365323227 (code B ref 56729); Mon, 08 Aug 2022 15:48:06 +0000 Received: (at 56729) by debbugs.gnu.org; 8 Aug 2022 15:47:33 +0000 Received: from localhost ([127.0.0.1]:41697 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oL4yZ-00062F-Fg for submit@debbugs.gnu.org; Mon, 08 Aug 2022 11:47:32 -0400 Received: from mo4-p05-ob.smtp.rzone.de ([85.215.255.130]:35317) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oL4yQ-00060P-JP for 56729@debbugs.gnu.org; Mon, 08 Aug 2022 11:47:27 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; t=1659973638; s=strato-dkim-0002; d=ikherbers.com; h=References:In-Reply-To:Message-Id:Date:Subject:Cc:To:From:Cc:Date: From:Subject:Sender; bh=Hd+z01vdnoNaPvOZEHNKAkiYZYLZSUrQt0c8V37h864=; b=A6cGsphJ8Jcz08pmpWECJu/MBTSWNqHmTz/GJTdU0Zk8ayvVLH6H65EBwvRa+KA7Vl jcVMxJVMFxTD1o3vQAulfFfoxjFaCNJugk5dfw2WEV2aq9NIUi6eZlhS/eifzSVb4XJO /OnApIUIzpPtUBsnTFHC4IqSOK8H79nAwfyiTjO92oqeJp+mkmPz0Kum7mfAC5NnMALi nXeUQHf9nav8h+smTIqGzTCLd3G1oPf7KB/cJedPlZfa8EpwLDpTCNyrqUIr2SMjNDs/ fB9AmK2741Lc0SIpY+/DgrROoGmgX281c72O2rgSgEDpdJusS85JkpHXduKdNy08PTBX 1uQQ== X-RZG-AUTH: ":IUwNfkitaf3qOWm2b/jA5tveVwUUcwH3PkiYp6DPxTDDEo4xO9ymAEzKSWlvmNAhIG6s" X-RZG-CLASS-ID: mo05 Received: from lambda.localdomain by smtp.strato.de (RZmta 47.47.0 DYNA|AUTH) with ESMTPSA id 0cac6cy78FlHoRC (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256 bits)) (Client did not present a certificate); Mon, 8 Aug 2022 17:47:17 +0200 (CEST) From: vicvbcun Date: Mon, 8 Aug 2022 17:45:35 +0200 Message-Id: X-Mailer: git-send-email 2.37.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1659973726; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=Hd+z01vdnoNaPvOZEHNKAkiYZYLZSUrQt0c8V37h864=; b=PleUY8Pw8fDaIKf3IizGXWC4MNs+ldQFczseIa1Pd6vTYnKHqrNeAF4jpAH08C2om1z8Rc 66syLtTu9VfDW2BFzHx7YcI+tU/fBhevLXAu2WpkBY/r1x5BDSEumakyb46Ecpegk/LpaZ kED+940hE1qu7oJpLV59kLc0yUCYe3RtR3tGoWxas/lYIMvR30IgzG/1JVrCxniAbLBHai OsUKXTqGvDektQR3VhkTBgzZ+Olod9B+YwHgXMdcPhfKoSjAYYXRXQlvV/2RT+plkpsYn7 iuBhc5YmvNzxR1SKlfhr9NAO+xve4RoPKefINL4cHxDBvF64/j67YpeJEKmohw== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1659973726; a=rsa-sha256; cv=none; b=othD6X/Oh7UVo1i/89KkcY6Sx+aTOxlkxZf4Lchk2pTvXkEr2k7eLgr46pSMQPpro9Pdoi FF+9QXyNgRHDGc9IRv7iI43EoXVeYmleXlKrbkC6k2oRqo/N01/yyoRKnHgjxnwX3C6dct h+rsEyX2mT7+By/GngbJ76HpTKMl3kZOu0uUzbxHZMg1PZxDAmWn5UsfVgR1wiA6xE6lII WG/i95MNoEsWV4hHL0JTuStU4fPoKs5nyiH2zYdawdY6QbCK6jW240N8pgmflypfT1XU5v nAoTgu6VUL272QNdpbJE3SCVFIj9CizqMdONOIzJdnnNYTgopwmeuoZ/DD1Hog== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=ikherbers.com header.s=strato-dkim-0002 header.b=A6cGsphJ; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 1.81 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=ikherbers.com header.s=strato-dkim-0002 header.b=A6cGsphJ; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 4F187EB6C X-Spam-Score: 1.81 X-Migadu-Scanner: scn0.migadu.com X-TUID: xLWUPsoKGLmC Hello guix! This is a second try, hopefully this time without silly errors. The packaging of sagemath is for now structured as follows: - `sagemath-just-build' builds everything using the minimal set of dependecies to avoid rebuilding where possible. As runtime dependencies are missing, this is useless on its own. - `sagemath-with-dependencies' adds all remaining dependencies as propagated-inputs. This should work, if we set a few additional environment variables. - `sagemath-tests' simply runs the tests. If I interpret the output correctly, these are the tests that are still failing: > sage/calculus/calculus.py # 6 doctests failed > sage/categories/primer.py # 1 doctest failed > sage/doctest/control.py # 3 doctests failed > sage/doctest/sources.py # 1 doctest failed > sage/doctest/test.py # 1 doctest failed > sage/env.py # 4 doctests failed > sage/doctest/forker.py # 1 doctest failed > sage/functions/exp_integral.py # 1 doctest failed > sage/interfaces/gap_workspace.py # 2 doctests failed > sage/interfaces/maxima_abstract.py # 2 doctests failed > sage/interfaces/maxima_lib.py # 2 doctests failed > sage/lfunctions/sympow.py # 10 doctests failed > sage/libs/eclib/interface.py # 7 doctests failed > sage/misc/package_dir.py # 1 doctest failed > sage/modular/abvar/abvar.py # 1 doctest failed > sage/modular/hecke/submodule.py # 1 doctest failed > sage/plot/plot3d/tachyon.py # 2 doctests failed > sage/repl/display/jsmol_iframe.py # 11 doctests failed > sage/repl/display/formatter.py # 4 doctests failed > sage/repl/ipython_kernel/install.py # 1 doctest failed > sage/repl/ipython_tests.py # 2 doctests failed > sage/repl/rich_output/backend_ipython.py # 1 doctest failed > sage/repl/rich_output/output_graphics.py # 25 doctests failed > sage/repl/rich_output/output_graphics3d.py # 34 doctests failed > sage/repl/rich_output/output_video.py # 14 doctests failed > sage/repl/rich_output/backend_doctest.py # 17 doctests failed > sage/schemes/elliptic_curves/ell_rational_field.py # 14 doctests failed > sage/symbolic/integration/integral.py # 1 doctest failed > sage/symbolic/relation.py # 1 doctest failed > sage/tests/gap_packages.py # 1 doctest failed > sage/tests/cmdline.py # 14 doctests failed Some of these seem harmless, others seem more concerning (including segmentation faults), some due to still missing dependencies. Some Notes: - We need to set some environment variables, so that sage can find all dependencies (see `sagemath-tests'). I suppose we could wrap the `sage' command, but this would of course add them as dependencies. - For the `sagemath-data-*' packages, I couldn't find explicit Licenses. In Sage's COPYING.txt it just says "None (database)" for license. - How should we handle test failures? Given errors such as the ones below, it seems delusional to expect every test to succeed. > Failed example: > solve_ineq_fourier([x+y<9,x-y>4],[y,x]) > Expected: > [[y < min(x - 4, -x + 9)]] > Got: > [[y < min(-x + 9, x - 4)]] > Failed example: > FDS.basename > Expected: > 'sage.rings.integer' > Got: > '/gnu/store/.../lib/python3.9/site-packages/sage/rings/integer.pyx' - `python-cython' is build-time dependency but may be needed at runtime. This could cause issues when cross-compiling, right? I think its path is only in the wrappers in bin/*. vicvbcun (29): gnu: Remove ecl-16. gnu: edge-addition-planarity-suite: Update to 3.0.2.0. gnu: gap: Update to 4.11.1. gnu: cliquer: Update to 1.22. gnu: lcalc: Update to 2.0.5. gnu: ntl: Update to 11.5.1. gnu: eclib: Update to 20220621. gnu: lrcalc: Update to 2.1. gnu: maxima: Update to 5.46.0. gnu: python-sympy: Update to 1.10.1. gnu: cddlib: Update to 0.94m. gnu: Add python-memory-allocator. gnu: Add python-pplpy. gnu: Add primecount. gnu: Add python-primecountpy. gnu: Add python-lrcalc. gnu: Add palp. gnu: Add gfan. gnu: Add flintqs. gnu: Add tachyon. gnu: Add sagemath-data-conway-polynomials. gnu: Add sagemath-data-elliptic-curves. gnu: Add sagemath-data-combinatorial-designs. gnu: Add sagemath-data-graphs. gnu: Add sagemath-data-poytopes-db. gnu: Add pari-galdata. gnu: Add sagemath-just-build. gnu: Add sagemath-with-dependencies. gnu: Add sagemath-tests. gnu/local.mk | 9 +- gnu/packages/algebra.scm | 203 +++-- gnu/packages/graph.scm | 4 +- gnu/packages/maths.scm | 31 +- .../ecl-16-format-directive-limit.patch | 83 -- .../ecl-16-ignore-stderr-write-error.patch | 17 - gnu/packages/patches/ecl-16-libffi.patch | 16 - .../patches/lcalc-default-parameters-1.patch | 26 - .../patches/lcalc-default-parameters-2.patch | 58 -- gnu/packages/patches/lcalc-lcommon-h.patch | 13 - .../patches/lcalc-using-namespace-std.patch | 43 - gnu/packages/patches/lrcalc-includes.patch | 92 --- gnu/packages/patches/tachyon-make-arch.patch | 13 + gnu/packages/python-xyz.scm | 4 +- gnu/packages/sagemath.scm | 780 ++++++++++++++++-- 15 files changed, 833 insertions(+), 559 deletions(-) delete mode 100644 gnu/packages/patches/ecl-16-format-directive-limit.patch delete mode 100644 gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch delete mode 100644 gnu/packages/patches/ecl-16-libffi.patch delete mode 100644 gnu/packages/patches/lcalc-default-parameters-1.patch delete mode 100644 gnu/packages/patches/lcalc-default-parameters-2.patch delete mode 100644 gnu/packages/patches/lcalc-lcommon-h.patch delete mode 100644 gnu/packages/patches/lcalc-using-namespace-std.patch delete mode 100644 gnu/packages/patches/lrcalc-includes.patch create mode 100644 gnu/packages/patches/tachyon-make-arch.patch base-commit: f6904c0b19c2fcca41bbf1400c738bd833fec9a8 -- 2.37.0