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Reply-To: bug#77902 <77902@debbugs.gnu.org> Date: Thu, 12 Jun 2025 15:33:51 +0000 retitle 77902 [PATCH science-team 0/2] Update SuiteSparse. reassign 77902 guix-patches submitter 77902 Greg Hogan severity 77902 normal tag 77902 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 18 11:12:19 2025 Received: (at submit) by debbugs.gnu.org; 18 Apr 2025 15:12:19 +0000 Received: from localhost ([127.0.0.1]:52475 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u5nO1-00017Q-UD for submit@debbugs.gnu.org; Fri, 18 Apr 2025 11:12:18 -0400 Received: from lists.gnu.org ([2001:470:142::17]:52194) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u5nNt-00014D-AH for submit@debbugs.gnu.org; Fri, 18 Apr 2025 11:12:12 -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 1u5nNj-0004mN-LL for guix-patches@gnu.org; Fri, 18 Apr 2025 11:11:55 -0400 Received: from mail-qk1-x72c.google.com ([2607:f8b0:4864:20::72c]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u5nNU-0005Ly-NH for guix-patches@gnu.org; Fri, 18 Apr 2025 11:11:55 -0400 Received: by mail-qk1-x72c.google.com with SMTP id af79cd13be357-7c07cd527e4so184672285a.3 for ; Fri, 18 Apr 2025 08:11:37 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=greghogan-com.20230601.gappssmtp.com; s=20230601; t=1744989088; x=1745593888; darn=gnu.org; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=vu0HG9q9CgwNV0e2D9YoP4sJ4kFSl1vkyN5DjRK1Nxc=; b=XdZbd+mu2Pvfwj7D4d9nqxcPMlQUWT53qT9AVXAdf13AFZiRvA58lc+jlRifJTsO5N ASRazeQ0r2Dlsb7GxI0f8tQ4i03PfjvDNKsvztuSAmoYT1+3gBPBPsF2sDk8JrPQpbPa wNZzwRVmr95T6urMxk5un5C3kw5UkcfEAVNoPDse0NmbyhMuNOn7ekqui9wrMEwn6iQE yW09cv5fWVT+g8yGPFyFXFlfa1fyrv+GpsWIC61JGafgGJFralzCcUtG+XhMkK8anYgF AG+Msi3h6BYNd1p2eJeaMFZfiZpKL7r7E0xCvLN7W0QJ4AhBiJVbsArlTpV8xW+FtCaV MGJg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1744989088; x=1745593888; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=vu0HG9q9CgwNV0e2D9YoP4sJ4kFSl1vkyN5DjRK1Nxc=; b=Cf3e3mZdki4wdX2n/yzgl2uyx/HQkYwMsrza5sb4NYMcoeJUBFmFmQ0IQQAD8hLX9q olwjdoZ7GDQh6zHWaBC6wRZB31OyRFq949Dtc5Pr5Lhqwv9RNDRohIubVxLI31uAb9WM 9Nuy3yZpXQAXvCtWstiJ8lDl3ol0/QUcmP7VVbm4uSsIv9Ks1SlLDMrgI60HH6P1LWje V+jCKljQC1ace1VL8gNN5h6OoX9rsCus3ezwz+cK3ctuxt5r8JXYi3Jvly6B6aIgE6su tFyhRmCBG/Y1nRx10s4E9h563ZA2OgPSlWHoWcgj9RLRZ6mkuTE2fGHSD9HcNtr5K6r9 /uUw== X-Gm-Message-State: AOJu0YwJN+bzxIfSdO+gD22jP6ozSdtY5sTwPvRwL6Cx693yt66PWF2r E07/0L+5wcq9s65iLIpKLnpP/J8d6v0M1sxr5xDeffgoZw439VLwEXqahxvdSDLw8Sh+UabQW3V i X-Gm-Gg: ASbGnctQ5HVxIH0fPS2zUfrFumkRQDcff2b3wBmy4CCHtiwhUCF53cTZwFkYVOQ8IkC Muef/IeRhPYqQ+vUe0ewvHG0gqGDKfU17W4xV+5i3qWpOVnL79X84uCHoxhmYhog6QwYSI423r7 p+t+1dMAXzABOJfIEuyhZob/4lj0d6yAZdlAY4C1kETCHGGWhw3bvl4ysnWj0n9ZnHqp9lLw5L0 fxzKTa+VVcirbDTDstsDNJL5Uc9X7UrNCRvf35bDpJiVAEUSc9Az4aEhuYSfn4TGHVCDemo8cwt uL1iQxzb9zdFUP6qKtFlnE0eU84eBWjE5yHjc/DVePZ5YN/55y8rM/03pVxYNJR3hr9zBVeukyj 0CiwXzx+tH/oaXqT1Sah16t1gZEPzgSAc80vl8Knl X-Google-Smtp-Source: AGHT+IEEv45yiFGxJPko7iRmD1jqQQ//X2MwBW9Q5yz0u42oADpOMy3UWmlXvQzRUw9pXkegwOUsWQ== X-Received: by 2002:a05:620a:bc8:b0:7c9:1335:633e with SMTP id af79cd13be357-7c927f6b658mr465847285a.1.1744989088233; Fri, 18 Apr 2025 08:11:28 -0700 (PDT) Received: from ip-10-117-149-49.evoforge.org (ec2-52-70-167-183.compute-1.amazonaws.com. [52.70.167.183]) by smtp.gmail.com with ESMTPSA id af79cd13be357-7c925ac5472sm116166585a.63.2025.04.18.08.11.27 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 18 Apr 2025 08:11:27 -0700 (PDT) From: Greg Hogan To: guix-patches@gnu.org Subject: [PATCH science-team 0/2] Update SuiteSparse. Date: Fri, 18 Apr 2025 15:11:09 +0000 Message-ID: X-Mailer: git-send-email 2.49.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: none client-ip=2607:f8b0:4864:20::72c; envelope-from=code@greghogan.com; helo=mail-qk1-x72c.google.com X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_NONE=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: submit Cc: Greg Hogan 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 (-) The component suitesparse packages have no other dependents. igraph has 26 dependent packages. Switch igraph to the suitesparse dependency as the newer CXSparse breaks the build (igraph vendors CXSparse from SuiteSparse 5.12.0). Greg Hogan (2): gnu: Add %suitesparse-package-versions. gnu: igraph: Update to 0.10.15. gnu/local.mk | 1 - gnu/packages/graph.scm | 7 +- gnu/packages/maths.scm | 64 +++++++++++-------- gnu/packages/patches/gklib-suitesparse.patch | 6 +- .../igraph-fix-varargs-integer-size.patch | 39 ----------- 5 files changed, 45 insertions(+), 72 deletions(-) delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch base-commit: ffc8a07ba45503014cc0647c5dd0613829999f98 -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 18 11:15:04 2025 Received: (at 77902) by debbugs.gnu.org; 18 Apr 2025 15:15:05 +0000 Received: from localhost ([127.0.0.1]:52481 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u5nQi-0001cE-37 for submit@debbugs.gnu.org; Fri, 18 Apr 2025 11:15:04 -0400 Received: from mail-qv1-xf30.google.com ([2607:f8b0:4864:20::f30]:48538) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.84_2) (envelope-from ) id 1u5nQZ-0001ZB-Co for 77902@debbugs.gnu.org; Fri, 18 Apr 2025 11:14:56 -0400 Received: by mail-qv1-xf30.google.com with SMTP id 6a1803df08f44-6f0ad74483fso22345596d6.1 for <77902@debbugs.gnu.org>; Fri, 18 Apr 2025 08:14:51 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=greghogan-com.20230601.gappssmtp.com; s=20230601; t=1744989284; x=1745594084; darn=debbugs.gnu.org; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:from:to:cc:subject:date :message-id:reply-to; bh=j48hDdxDEJk1ah0EPJXxOtAXU2VoTCbr49Jf+bt65LI=; b=sobfARwJ2roMxA1O7gsnf/g8Ylu4OKIhoK1UOG+yXkV1LlWKn7Bp9fWbB7q3GYQqgL InFQ0ZwX8DXKN1CT/rK2XWpIX1ROT5v0NwSCzz+D7EIWMem0LSrFekmHxuYuxq6Zi9L7 BP9Ae6xf4UwrT+Ko2ef4f6daTW2fJ1mguK5V22Vo15lBqIeFXjz6Z8Uc+3RrH3DqNnwI FPYiszxY070Gjsk+cDys4eFzUMHPRpONQtDAMzgRMiF5xp5fsmoqFRDD2DZeHdmuyHeQ 7oyfaA/SQysZEhb8lPYs1RRJotxMKN3yVskhh0IvKLtX3URbawscJtlERizEC/270MOK ftmg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1744989284; x=1745594084; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=j48hDdxDEJk1ah0EPJXxOtAXU2VoTCbr49Jf+bt65LI=; b=mg5n+JX9ucoWnczXRjBFOMLkIULxA3hrKbzn3CFbqiQM5pmVt0ixB17ao/D68eCUOk fYCyraK9VNyQSwYp/Oug0YUeDIDEBA6x6W5MX1QGlL3SWhyIfgtU9Faklcvls4vgEEEv i5t8Cr5sNvPUI9Heba/qmQVPczSfYHWKpM65n/KHRNVdH1wEa8GfISzlaWxcyUHynuG2 zVIvOR5yPd/Rnch/CfStwgsml9nmXPoRP5hqcsIrpyZfw5i4qnx26rO4D6ZMXGz7eJwe SobGG9Bj1ZUSNXIh1PPAgj2rl6jj138OtbR0k+ya5DHnnJo+xD0rG+fGALKwfEXNaCZZ SySA== X-Gm-Message-State: AOJu0YwFsejMvINJP1ank9lDFGMKx3dP6Z1YlbC7WdSnkPRlUQFRfR6r nkU4c/UW+Jf2dHeRLRTRoHGL9Dd65Ha65PM4iX2rXH3UjDYEBID671yF9oS5C4AP9/0MQ76wv2J a X-Gm-Gg: ASbGncue4raCFncnZ6C5GYtCVPsKr0/Ycao83cXRdpby3oerduTsMwbRMshb2yRXSoN omcO1cmS+0is6R/5uzLH4akLpLQLbiYh+Lzi4oV2wzikqZYyKrduQux/DgzcW2We4kV3zO6nKE6 edS42BvEJS8CMP48dw98zGMkXoUQKReiCbrGbebgIEVH4amreps9MoHFmgUosm95LiurgEDKzRU tnNzVCXgCaX5+URMNopv8u6DJcaQKbVHmAsu80hNA4Kl219FlFgf/pu1cnxLrViF+xk0D2YesRV OWhNzOZjSdzTidie7JzxkLWF6BL8SlWvRQjADbRB7nhsrhs3PRxsIVU+7Vi8BwbYIgEwycX3fp0 TsqSPR/98hSnyDokqn1Ylz5a+N6Iu9pGCxsG2ib+9 X-Google-Smtp-Source: AGHT+IF+3EMp3ZIl6as9xwbrXnCjLWiAE3mbLHG5GTzaoZ01sRJ/aMzCp6wWu7zSkULy/jPjHe7x1w== X-Received: by 2002:a05:6214:410e:b0:6d8:80e8:d567 with SMTP id 6a1803df08f44-6f2c4546bcamr49588976d6.18.1744989284180; Fri, 18 Apr 2025 08:14:44 -0700 (PDT) Received: from ip-10-117-149-49.evoforge.org (ec2-52-70-167-183.compute-1.amazonaws.com. [52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f2c2b0f80asm11563896d6.45.2025.04.18.08.14.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 18 Apr 2025 08:14:43 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH science-team 2/2] gnu: igraph: Update to 0.10.15. Date: Fri, 18 Apr 2025 15:14:10 +0000 Message-ID: <4765db19bd76943e2303a04eae2f77f2a43b445b.1744988258.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/graph.scm (igraph): Update to 0.10.15. [source]: Remove patches. [inputs]: Replace suitesparse-cxsparse with suitesparse. * gnu/packages/patches/igraph-fix-varargs-integer-size.patch: Delete. * gnu/local.mk (dist_patch_DATA): Update accordingly. Change-Id: Iffbfdc83b347f9abf82891f5b97954903d3df3dd --- gnu/local.mk | 1 - gnu/packages/graph.scm | 7 ++-- .../igraph-fix-varargs-integer-size.patch | 39 ------------------- 3 files changed, 3 insertions(+), 44 deletions(-) delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch diff --git a/gnu/local.mk b/gnu/local.mk index 62cfe230bb..2828d8913f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1610,7 +1610,6 @@ dist_patch_DATA = \ %D%/packages/patches/id3lib-CVE-2007-4460.patch \ %D%/packages/patches/id3lib-UTF16-writing-bug.patch \ %D%/packages/patches/idris-test-ffi008.patch \ - %D%/packages/patches/igraph-fix-varargs-integer-size.patch \ %D%/packages/patches/ilmbase-fix-tests.patch \ %D%/packages/patches/indent-CVE-2024-0911.patch \ %D%/packages/patches/inferno-fix-crash.patch \ diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 467a7f661b..af4943c281 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -106,7 +106,7 @@ (define-public plfit (define-public igraph (package (name "igraph") - (version "0.10.7") + (version "0.10.15") (source (origin (method git-fetch) @@ -114,7 +114,6 @@ (define-public igraph (url "https://github.com/igraph/igraph") (commit version))) (file-name (git-file-name name version)) - (patches (search-patches "igraph-fix-varargs-integer-size.patch")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26))) @@ -136,7 +135,7 @@ (define-public igraph (("add_sub.*vendor.*") "")))) (sha256 (base32 - "025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn")))) + "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))) (build-system cmake-build-system) (arguments (list @@ -201,7 +200,7 @@ (define-public igraph ;lapack openblas plfit - suitesparse-cxsparse)) + suitesparse)) ;; libxml2 is in the 'Requires.private' of igraph.pc. (propagated-inputs (list libxml2)) (home-page "https://igraph.org") diff --git a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch b/gnu/packages/patches/igraph-fix-varargs-integer-size.patch deleted file mode 100644 index 2d7ffd7e68..0000000000 --- a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch +++ /dev/null @@ -1,39 +0,0 @@ -If the size of int is different from IGRAPH_INTEGER_SIZE, the integer size -passed to these vararg arguments is different from the assumed one, -leading to undefined behavior. -Submitted upstream: https://github.com/igraph/igraph/pull/2423 - - -diff -ur a/examples/simple/igraph_union.c b/examples/simple/igraph_union.c ---- a/examples/simple/igraph_union.c -+++ b/examples/simple/igraph_union.c -@@ -103,7 +103,7 @@ - igraph_vector_ptr_init(&glist, 10); - for (i = 0; i < igraph_vector_ptr_size(&glist); i++) { - VECTOR(glist)[i] = calloc(1, sizeof(igraph_t)); -- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1); -+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1); - igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_DIRECTED); - igraph_vector_int_destroy(&v); - } -@@ -123,7 +123,7 @@ - igraph_vector_ptr_init(&glist, 10); - for (i = 0; i < igraph_vector_ptr_size(&glist); i++) { - VECTOR(glist)[i] = calloc(1, sizeof(igraph_t)); -- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1); -+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1); - igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_UNDIRECTED); - igraph_vector_int_destroy(&v); - } -diff -ur a/src/core/matrix.pmt b/src/core/matrix.pmt ---- a/src/core/matrix.pmt -+++ b/src/core/matrix.pmt -@@ -1863,7 +1863,7 @@ - #ifdef FPRINTFUNC_ALIGNED - FPRINTFUNC_ALIGNED(file, VECTOR(column_width)[j], MATRIX(*m, i, j)); - #else -- fprintf(file, format, VECTOR(column_width)[j], MATRIX(*m, i, j)); -+ fprintf(file, format, (int) VECTOR(column_width)[j], MATRIX(*m, i, j)); - #endif - } - fprintf(file, "\n"); -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 18 11:15:24 2025 Received: (at 77902) by debbugs.gnu.org; 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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f2c2b0f80asm11563896d6.45.2025.04.18.08.14.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 18 Apr 2025 08:14:42 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH science-team 1/2] gnu: Add %suitesparse-package-versions. Date: Fri, 18 Apr 2025 15:14:09 +0000 Message-ID: <0199e4a26c0ac3f0c07c9e80963f4562f49544e3.1744988258.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: "X-Debbugs-Cc: Andreas Enge" , Sharlatan Hellseher , Greg Hogan , Eric Bavier 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 (-) * gnu/packages/maths.scm (%suitesparse-package-versions): New variable. (suitesparse-version): Update to 7.10.2. (suitesparse-source)[origin]: Update deletion list. (suitesparse-amd, suitesparse-btf, suitesparse-camd, suitesparse-colamd, suitesparse-ccolamd, suitesparse-cholmod, suitesparse-cxsparse, suitesparse-klu, suitesparse-ldl, suitesparse-rbio, suitesparse-monUse goose, suitesparse-spex, suitesparse-spqr, suitesparse-umfpack) [version]: Use %suitesparse-package-versions. (suitesparse-cholmod)[arguments]<#:phases>('install-license-files): Update paths. (suitesparse-klu)[arguments]<#:phases>('build-doc): Update paths. (suitesparse-spex)[native-inputs]: Add texlive-fncychap. (suitesparse-spqr)[native-inputs]: Add texlive-etoolbox. * gnu/packages/patches/gklib-suitesparse.patch: Update version and path. Change-Id: I14a9bfeddb37330c88a2e94b0992c2f1afbc5310 --- gnu/packages/maths.scm | 64 ++++++++++++-------- gnu/packages/patches/gklib-suitesparse.patch | 6 +- 2 files changed, 42 insertions(+), 28 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4be9e71320..4cfcd5ba9e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6060,9 +6060,25 @@ (define-public openspecfun ;; public domain software. (license (list license:expat license:public-domain)))) +(define %suitesparse-package-versions + '(("AMD" . "3.3.3") + ("BTF" . "2.3.2") + ("CAMD" . "3.3.3") + ("CCOLAMD" . "3.3.4") + ("CHOLMOD" . "5.3.2") + ("COLAMD" . "3.3.4") + ("CXSparse" . "4.4.1") + ("KLU" . "2.3.5") + ("LDL" . "3.3.2") + ("SuiteSparse_Mongoose" . "3.3.4") + ("RBio" . "4.3.4") + ("SPEX" . "3.2.3") + ("SPQR" . "4.3.4") + ("UMFPACK" . "6.3.5"))) + ;; Source for the modular SuiteSparse packages. When updating, also update the ;; (different) versions of the subpackages. -(define suitesparse-version "7.2.0") +(define suitesparse-version "7.10.2") (define suitesparse-source (origin (method git-fetch) @@ -6072,10 +6088,12 @@ (define suitesparse-source (file-name (git-file-name "suitesparse" suitesparse-version)) (sha256 (base32 - "1draljn8i46862drc6008cnb2zjpklf74j8c34jirjazzpf53kaa")) + "1ndwx2cp5zxrikq4xdrzjrxk1b5ps7lyi6qw34m8jpfpa0ba01ln")) (modules '((guix build utils))) (snippet #~(begin + ;; Empty except for a .gitignore. + (delete-file-recursively "build") ;; Delete autogenerated and bundled files (for-each delete-file (find-files "." "\\.pdf$")) ;; ssget @@ -6086,19 +6104,13 @@ (define suitesparse-source (delete-file-recursively "CHOLMOD/SuiteSparse_metis") ; GraphBLAS (delete-file "GraphBLAS/README.md") - (delete-file "GraphBLAS/Config/GB_config.h") (delete-file "GraphBLAS/Config/GB_prejit.c") (delete-file-recursively "GraphBLAS/cpu_features") - (delete-file "GraphBLAS/CUDA/GB_cuda_common_jitFactory.hpp") - (delete-file "GraphBLAS/JITpackage/GB_JITpackage.c") (delete-file-recursively "GraphBLAS/lz4/lz4.c") (delete-file-recursively "GraphBLAS/lz4/lz4.h") (delete-file-recursively "GraphBLAS/lz4/lz4hc.c") (delete-file-recursively "GraphBLAS/lz4/lz4hc.h") - (delete-file "GraphBLAS/GraphBLAS/Config/GB_config.h") (delete-file "GraphBLAS/Tcov/PreJIT/GB_prejit.c") - (delete-file-recursively "GraphBLAS/Source/FactoryKernels") - (delete-file "GraphBLAS/Source/GB_AxB__include1.h") (delete-file "GraphBLAS/xxHash/xxhash.h") (delete-file-recursively "GraphBLAS/zstd/zstd_subset") ;; KLU @@ -6144,7 +6156,7 @@ (define-public suitesparse-config (define-public suitesparse-amd (package (name "suitesparse-amd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "AMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6192,7 +6204,7 @@ (define-public suitesparse-amd (define-public suitesparse-btf (package (name "suitesparse-btf") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "BTF")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6225,7 +6237,7 @@ (define-public suitesparse-btf (define-public suitesparse-camd (package (name "suitesparse-camd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "CAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6270,7 +6282,7 @@ (define-public suitesparse-camd (define-public suitesparse-colamd (package (name "suitesparse-colamd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "COLAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6303,7 +6315,7 @@ (define-public suitesparse-colamd (define-public suitesparse-ccolamd (package (name "suitesparse-ccolamd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "CCOLAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6386,7 +6398,7 @@ (define-public metis-suitesparse (define-public suitesparse-cholmod (package (name "suitesparse-cholmod") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "CHOLMOD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6448,7 +6460,7 @@ (define-public suitesparse-cholmod (let ((out (string-append #$output "/share/doc/" #$name "-" #$version))) (install-file "../CHOLMOD/Doc/License.txt" out) - (install-file "../CHOLMOD/Core/lesser.txt" out) + (install-file "../CHOLMOD/Check/lesser.txt" out) (install-file "../CHOLMOD/MatrixOps/gpl.txt" out))))))) (inputs (list gklib-suitesparse @@ -6471,7 +6483,7 @@ (define-public suitesparse-cholmod (define-public suitesparse-cxsparse (package (name "suitesparse-cxsparse") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "CXSparse")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6505,7 +6517,7 @@ (define-public suitesparse-cxsparse (define-public suitesparse-klu (package (name "suitesparse-klu") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "KLU")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6537,7 +6549,7 @@ (define-public suitesparse-klu (lambda _ (substitute* "../KLU/Doc/Makefile" (("\\.\\./\\.\\./BTF/Include/btf.h") - (string-append #$suitesparse-btf "/include/btf.h"))) + (string-append #$suitesparse-btf "/include/suitesparse/btf.h"))) (with-directory-excursion "../KLU/Doc" (invoke "make")))) (add-after 'install 'install-doc @@ -6569,7 +6581,7 @@ (define-public suitesparse-klu (define-public suitesparse-ldl (package (name "suitesparse-ldl") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "LDL")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6622,7 +6634,7 @@ (define-public suitesparse-ldl (define-public suitesparse-rbio (package (name "suitesparse-rbio") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "RBio")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6660,7 +6672,7 @@ (define-public suitesparse-rbio (define-public suitesparse-mongoose (package (name "suitesparse-mongoose") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "SuiteSparse_Mongoose")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6735,7 +6747,7 @@ (define-public suitesparse-mongoose (define-public suitesparse-spex (package (name "suitesparse-spex") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "SPEX")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6778,6 +6790,7 @@ (define-public suitesparse-spex texlive-soul texlive-multirow texlive-algorithms + texlive-fncychap texlive-float texlive-algorithmicx texlive-cprotect @@ -6801,7 +6814,7 @@ (define-public suitesparse-spex (define-public suitesparse-spqr (package (name "suitesparse-spqr") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "SPQR")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6851,7 +6864,8 @@ (define-public suitesparse-spqr (propagated-inputs (list suitesparse-cholmod)) (native-inputs (list (texlive-updmap.cfg - (list texlive-epsf)))) + (list texlive-epsf + texlive-etoolbox)))) (home-page "https://people.engr.tamu.edu/davis/suitesparse.html") (synopsis "Sparse QR factorization method") (description "The SPQR (SuiteSparseQR) package provides sparse QR @@ -6862,7 +6876,7 @@ (define-public suitesparse-spqr (define-public suitesparse-umfpack (package (name "suitesparse-umfpack") - (version "6.2.0") + (version (assoc-ref %suitesparse-package-versions "UMFPACK")) (source suitesparse-source) (build-system cmake-build-system) (arguments diff --git a/gnu/packages/patches/gklib-suitesparse.patch b/gnu/packages/patches/gklib-suitesparse.patch index 8b6c708b6a..d207f080b1 100644 --- a/gnu/packages/patches/gklib-suitesparse.patch +++ b/gnu/packages/patches/gklib-suitesparse.patch @@ -1,5 +1,5 @@ This patch contains the relevant changes to GKlib made in SuiteSparse -(CHOLMOD) for the version 7.2.0 +(CHOLMOD) for the version 7.10.2 (https://github.com/DrTimothyAldenDavis/SuiteSparse/commit/8a7641cdb4809533c681417e94f98058c07c5da2). The disabling of signal handling when MATLAB_MEX_FILE is defined is omitted. @@ -10,7 +10,7 @@ diff -ur a/CMakeLists.txt b/CMakeLists.txt option(BUILD_SHARED_LIBS "Build shared libraries (.dll/.so) instead of static ones (.lib/.a)" OFF) -+find_package ( SuiteSparse_config 7.1.0 REQUIRED ) ++find_package ( SuiteSparse_config 7.10.2 REQUIRED ) + get_filename_component(abs "." 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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:43 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 0/7] Update SuiteSparse. Date: Mon, 5 May 2025 16:43:20 +0000 Message-ID: X-Mailer: git-send-email 2.49.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) v2 restores the installation directory of the suitesparse header files by overriding the new default subdirectory "suitesparse". Also includes updates and fixes for dependent packages. Greg Hogan (7): gnu: Add %suitesparse-package-versions. gnu: igraph: Update to 0.10.15. gnu: python-igraph: Update to 0.11.8. gnu: python-vtraag-louvain: Deprecate. gnu: python-louvain-igraph: Update to 0.8.2. gnu: Add libleidenalg. gnu: python-leidenalg: Update to 0.10.2. gnu/local.mk | 1 - gnu/packages/graph.scm | 183 ++++++++---------- gnu/packages/maths.scm | 77 +++++--- gnu/packages/patches/gklib-suitesparse.patch | 4 +- .../igraph-fix-varargs-integer-size.patch | 39 ---- 5 files changed, 141 insertions(+), 163 deletions(-) delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch base-commit: 90f0f8713da9cf0dc0bb5c93446a4eba11075352 -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Mon May 05 12:47:55 2025 Received: (at 77902) by debbugs.gnu.org; 5 May 2025 16:47:56 +0000 Received: from localhost ([127.0.0.1]:42282 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uByyx-0004SU-5Z for submit@debbugs.gnu.org; Mon, 05 May 2025 12:47:55 -0400 Received: from mail-qv1-xf30.google.com ([2607:f8b0:4864:20::f30]:53711) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.84_2) (envelope-from ) id 1uByyu-0004Re-0K for 77902@debbugs.gnu.org; Mon, 05 May 2025 12:47:52 -0400 Received: by mail-qv1-xf30.google.com with SMTP id 6a1803df08f44-6e8f8657f29so46672116d6.3 for <77902@debbugs.gnu.org>; Mon, 05 May 2025 09:47:51 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=greghogan-com.20230601.gappssmtp.com; s=20230601; t=1746463666; x=1747068466; darn=debbugs.gnu.org; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:from:to:cc:subject:date :message-id:reply-to; bh=K1r1TCfz2aqOQvMo4ynB94nkhgRkvVoGRVZfO1Yw8vg=; b=vvZvMeQc7RDLxz07MoM2oZkf6B3OqRxkjD4TP7qGkIApB30RvwaKfP1C2cHF6MngfH Q7FbVEyv4spgn+agyuXfQEMPckCEa4+48ty/kPziaaTTi7dQPmGVkFIP9IrBQaX9W8E4 WYz24ISx0jx+RpnmF1Bxz5ATYMmbeanI2QZ8IiyNr5osl1AyN0U+Hm18OFRUnbpEM+Qh 2WfYPKaLgmUbQguZNNifZApqGnTEFInPsRZj+c1kF4Vj5+sR/Jm29wzy8hlh/MIJHTTu +SZ8OrngAo252aUzv3WqvVmG5tUtz3q8+OSewEfghJzYEBgLN6ceYYL9OzLlo0IjvEZa 6prQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1746463666; x=1747068466; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=K1r1TCfz2aqOQvMo4ynB94nkhgRkvVoGRVZfO1Yw8vg=; b=EXW229XSMXOSsN4Oi1BllapBmR9V8yc4noTalu55ehCK0r2B+iHO0XOKzYlz92a3q2 CHEeH9B7kC8NHNr3pP4VfNHLKkzjEZ9rNu9XWYG7OMnqLOz+ChT8RpiulfG4hRYzdDfM n9tt/snqLjmkrgaUqo7OCgFRKnq1iBSnalZXJ8XQtVuDx0HMu+hERASQD3uZi6TO8Xef qxVTnWDIx1RUXBtsNQxJ1Ahq6CLIYtB9vPSUF6f/YsNlVu5T7Azyu5pQ4tPiPp+w+fms cF6HpM6QZoDj8cSZ+7xuvp66+vt20ucGXlY1AoP7DH550Ko6SM06MaNA6hzKiN85wyLq h9TQ== X-Gm-Message-State: AOJu0YztQctLdjbcd415Wbm8z06KdYr4hfK/grmT+CXr+jR53ylchhC0 YykiG3b2/mj3+KkeoGEXi+hiBoyWO1SkIKwozYTznFAUr+zNpV5hIm6ZBIGRSnKrojeObTw9QvI z X-Gm-Gg: ASbGnctIIfr2nzKZ/B+uPRk8ybW1S178h5DLD0QqTwVAjppFvHakQA5FSsoihBV8AjD 1t9rtrUqy5zd7//oyXlJpvVP8uS17B78TCROXgv5xCUowO2OtcV/3m0zTPo6uLCdC5c2i/ZynOr PT/wJW66TlYA8rOu1j5SGNSpRH7c7AftJNXB3ZBubRt3ibZltpjuvPn02J9U2Fb22sJAVjlQ2hY 7e61jED/fCJJCdjtJjB9g+90Sl7nFBlto/5d56GdvaC33XVzhDrSdf5C/lVUwk36ngcgbGUEpXs KesElf8gT4coN/JjEuR+0TNnE1qli556mlKy5NY4aP9TNt27fGd+HwqJUDGYEjB/YMDtX3wiEVe LZ0RFtFPxeY7S9Rn8OuADkgZ1J88qukh8jyuvA1x+ X-Google-Smtp-Source: AGHT+IFgNYso7QTCEcljQQxziEIRHy4LsNB9ljIitKpTJctOc4vdNlL4IUn0nrJ0WWhEBWnvHSVorQ== X-Received: by 2002:a05:6214:e67:b0:6e8:f464:c9a9 with SMTP id 6a1803df08f44-6f5353cf6d6mr1837906d6.2.1746463665948; Mon, 05 May 2025 09:47:45 -0700 (PDT) Received: from ip-10-117-149-49.evoforge.org (ec2-52-70-167-183.compute-1.amazonaws.com. [52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:45 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 2/7] gnu: igraph: Update to 0.10.15. Date: Mon, 5 May 2025 16:43:22 +0000 Message-ID: <655499c1d007f27fa6d2c81fc9d58ddda945f019.1746463068.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/graph.scm (igraph): Update to 0.10.15. [source]: Remove patches. * gnu/packages/patches/igraph-fix-varargs-integer-size.patch: Delete. * gnu/local.mk (dist_patch_DATA): Update accordingly. Change-Id: Iffbfdc83b347f9abf82891f5b97954903d3df3dd --- gnu/local.mk | 1 - gnu/packages/graph.scm | 5 +-- .../igraph-fix-varargs-integer-size.patch | 39 ------------------- 3 files changed, 2 insertions(+), 43 deletions(-) delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch diff --git a/gnu/local.mk b/gnu/local.mk index e25fcc115b..d351005ae3 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1614,7 +1614,6 @@ dist_patch_DATA = \ %D%/packages/patches/id3lib-CVE-2007-4460.patch \ %D%/packages/patches/id3lib-UTF16-writing-bug.patch \ %D%/packages/patches/idris-test-ffi008.patch \ - %D%/packages/patches/igraph-fix-varargs-integer-size.patch \ %D%/packages/patches/ilmbase-fix-tests.patch \ %D%/packages/patches/indent-CVE-2024-0911.patch \ %D%/packages/patches/inferno-fix-crash.patch \ diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 9cca8520ba..0d65558a60 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -106,7 +106,7 @@ (define-public plfit (define-public igraph (package (name "igraph") - (version "0.10.7") + (version "0.10.15") (source (origin (method git-fetch) @@ -114,7 +114,6 @@ (define-public igraph (url "https://github.com/igraph/igraph") (commit version))) (file-name (git-file-name name version)) - (patches (search-patches "igraph-fix-varargs-integer-size.patch")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26))) @@ -136,7 +135,7 @@ (define-public igraph (("add_sub.*vendor.*") "")))) (sha256 (base32 - "025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn")))) + "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))) (build-system cmake-build-system) (arguments (list diff --git a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch b/gnu/packages/patches/igraph-fix-varargs-integer-size.patch deleted file mode 100644 index 2d7ffd7e68..0000000000 --- a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch +++ /dev/null @@ -1,39 +0,0 @@ -If the size of int is different from IGRAPH_INTEGER_SIZE, the integer size -passed to these vararg arguments is different from the assumed one, -leading to undefined behavior. -Submitted upstream: https://github.com/igraph/igraph/pull/2423 - - -diff -ur a/examples/simple/igraph_union.c b/examples/simple/igraph_union.c ---- a/examples/simple/igraph_union.c -+++ b/examples/simple/igraph_union.c -@@ -103,7 +103,7 @@ - igraph_vector_ptr_init(&glist, 10); - for (i = 0; i < igraph_vector_ptr_size(&glist); i++) { - VECTOR(glist)[i] = calloc(1, sizeof(igraph_t)); -- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1); -+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1); - igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_DIRECTED); - igraph_vector_int_destroy(&v); - } -@@ -123,7 +123,7 @@ - igraph_vector_ptr_init(&glist, 10); - for (i = 0; i < igraph_vector_ptr_size(&glist); i++) { - VECTOR(glist)[i] = calloc(1, sizeof(igraph_t)); -- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1); -+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1); - igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_UNDIRECTED); - igraph_vector_int_destroy(&v); - } -diff -ur a/src/core/matrix.pmt b/src/core/matrix.pmt ---- a/src/core/matrix.pmt -+++ b/src/core/matrix.pmt -@@ -1863,7 +1863,7 @@ - #ifdef FPRINTFUNC_ALIGNED - FPRINTFUNC_ALIGNED(file, VECTOR(column_width)[j], MATRIX(*m, i, j)); - #else -- fprintf(file, format, VECTOR(column_width)[j], MATRIX(*m, i, j)); 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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.44 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:44 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 1/7] gnu: Add %suitesparse-package-versions. Date: Mon, 5 May 2025 16:43:21 +0000 Message-ID: <2f8f06e8816ede1d5f1785661db92ef727aeb577.1746463068.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/maths.scm (%suitesparse-package-versions): New variable. (suitesparse-version): Update to 7.10.2. (suitesparse-source)[origin]: Update deletion list. (suitesparse-amd, suitesparse-btf, suitesparse-camd, suitesparse-colamd, suitesparse-ccolamd, suitesparse-cholmod, suitesparse-cxsparse, suitesparse-klu, suitesparse-ldl, suitesparse-rbio, suitesparse-mongoose, suitesparse-spex, suitesparse-spqr, suitesparse-umfpack)[version]: Use %suitesparse-package-versions. [arguments]<#:configure-flags>: Preserve include path. (suitesparse-cholmod)[arguments]<#:phases>('install-license-files): Update paths. (suitesparse-cholmod)[arguments]<#:phases>('build-doc): Update paths. (suitesparse-spex)[native-inputs]: Add texlive-fncychap. (suitesparse-spqr)[native-inputs]: Add texlive-etoolbox. * gnu/packages/patches/gklib-suitesparse.patch: Update version. Change-Id: I14a9bfeddb37330c88a2e94b0992c2f1afbc5310 --- gnu/packages/maths.scm | 77 ++++++++++++++------ gnu/packages/patches/gklib-suitesparse.patch | 4 +- 2 files changed, 55 insertions(+), 26 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index eb23a375b4..b1ff9c36bd 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6179,9 +6179,25 @@ (define-public openspecfun ;; public domain software. (license (list license:expat license:public-domain)))) +(define %suitesparse-package-versions + '(("AMD" . "3.3.3") + ("BTF" . "2.3.2") + ("CAMD" . "3.3.3") + ("CCOLAMD" . "3.3.4") + ("CHOLMOD" . "5.3.2") + ("COLAMD" . "3.3.4") + ("CXSparse" . "4.4.1") + ("KLU" . "2.3.5") + ("LDL" . "3.3.2") + ("SuiteSparse_Mongoose" . "3.3.4") + ("RBio" . "4.3.4") + ("SPEX" . "3.2.3") + ("SPQR" . "4.3.4") + ("UMFPACK" . "6.3.5"))) + ;; Source for the modular SuiteSparse packages. When updating, also update the ;; (different) versions of the subpackages. -(define suitesparse-version "7.2.0") +(define suitesparse-version "7.10.2") (define suitesparse-source (origin (method git-fetch) @@ -6191,10 +6207,12 @@ (define suitesparse-source (file-name (git-file-name "suitesparse" suitesparse-version)) (sha256 (base32 - "1draljn8i46862drc6008cnb2zjpklf74j8c34jirjazzpf53kaa")) + "1ndwx2cp5zxrikq4xdrzjrxk1b5ps7lyi6qw34m8jpfpa0ba01ln")) (modules '((guix build utils))) (snippet #~(begin + ;; Empty except for a .gitignore. + (delete-file-recursively "build") ;; Delete autogenerated and bundled files (for-each delete-file (find-files "." "\\.pdf$")) ;; ssget @@ -6205,19 +6223,13 @@ (define suitesparse-source (delete-file-recursively "CHOLMOD/SuiteSparse_metis") ; GraphBLAS (delete-file "GraphBLAS/README.md") - (delete-file "GraphBLAS/Config/GB_config.h") (delete-file "GraphBLAS/Config/GB_prejit.c") (delete-file-recursively "GraphBLAS/cpu_features") - (delete-file "GraphBLAS/CUDA/GB_cuda_common_jitFactory.hpp") - (delete-file "GraphBLAS/JITpackage/GB_JITpackage.c") (delete-file-recursively "GraphBLAS/lz4/lz4.c") (delete-file-recursively "GraphBLAS/lz4/lz4.h") (delete-file-recursively "GraphBLAS/lz4/lz4hc.c") (delete-file-recursively "GraphBLAS/lz4/lz4hc.h") - (delete-file "GraphBLAS/GraphBLAS/Config/GB_config.h") (delete-file "GraphBLAS/Tcov/PreJIT/GB_prejit.c") - (delete-file-recursively "GraphBLAS/Source/FactoryKernels") - (delete-file "GraphBLAS/Source/GB_AxB__include1.h") (delete-file "GraphBLAS/xxHash/xxhash.h") (delete-file-recursively "GraphBLAS/zstd/zstd_subset") ;; KLU @@ -6247,6 +6259,7 @@ (define-public suitesparse-config (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6263,12 +6276,13 @@ (define-public suitesparse-config (define-public suitesparse-amd (package (name "suitesparse-amd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "AMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6311,12 +6325,13 @@ (define-public suitesparse-amd (define-public suitesparse-btf (package (name "suitesparse-btf") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "BTF")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6344,12 +6359,13 @@ (define-public suitesparse-btf (define-public suitesparse-camd (package (name "suitesparse-camd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "CAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6389,12 +6405,13 @@ (define-public suitesparse-camd (define-public suitesparse-colamd (package (name "suitesparse-colamd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "COLAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6422,12 +6439,13 @@ (define-public suitesparse-colamd (define-public suitesparse-ccolamd (package (name "suitesparse-ccolamd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "CCOLAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6505,12 +6523,13 @@ (define-public metis-suitesparse (define-public suitesparse-cholmod (package (name "suitesparse-cholmod") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "CHOLMOD")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6567,7 +6586,7 @@ (define-public suitesparse-cholmod (let ((out (string-append #$output "/share/doc/" #$name "-" #$version))) (install-file "../CHOLMOD/Doc/License.txt" out) - (install-file "../CHOLMOD/Core/lesser.txt" out) + (install-file "../CHOLMOD/Check/lesser.txt" out) (install-file "../CHOLMOD/MatrixOps/gpl.txt" out))))))) (inputs (list gklib-suitesparse @@ -6590,12 +6609,13 @@ (define-public suitesparse-cholmod (define-public suitesparse-cxsparse (package (name "suitesparse-cxsparse") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "CXSparse")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6624,12 +6644,13 @@ (define-public suitesparse-cxsparse (define-public suitesparse-klu (package (name "suitesparse-klu") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "KLU")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6688,12 +6709,13 @@ (define-public suitesparse-klu (define-public suitesparse-ldl (package (name "suitesparse-ldl") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "LDL")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6741,12 +6763,13 @@ (define-public suitesparse-ldl (define-public suitesparse-rbio (package (name "suitesparse-rbio") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "RBio")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6779,12 +6802,13 @@ (define-public suitesparse-rbio (define-public suitesparse-mongoose (package (name "suitesparse-mongoose") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "SuiteSparse_Mongoose")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6854,12 +6878,13 @@ (define-public suitesparse-mongoose (define-public suitesparse-spex (package (name "suitesparse-spex") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "SPEX")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6897,6 +6922,7 @@ (define-public suitesparse-spex texlive-soul texlive-multirow texlive-algorithms + texlive-fncychap texlive-float texlive-algorithmicx texlive-cprotect @@ -6920,12 +6946,13 @@ (define-public suitesparse-spex (define-public suitesparse-spqr (package (name "suitesparse-spqr") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "SPQR")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -6970,7 +6997,8 @@ (define-public suitesparse-spqr (propagated-inputs (list suitesparse-cholmod)) (native-inputs (list (texlive-updmap.cfg - (list texlive-epsf)))) + (list texlive-epsf + texlive-etoolbox)))) (home-page "https://people.engr.tamu.edu/davis/suitesparse.html") (synopsis "Sparse QR factorization method") (description "The SPQR (SuiteSparseQR) package provides sparse QR @@ -6981,12 +7009,13 @@ (define-public suitesparse-spqr (define-public suitesparse-umfpack (package (name "suitesparse-umfpack") - (version "6.2.0") + (version (assoc-ref %suitesparse-package-versions "UMFPACK")) (source suitesparse-source) (build-system cmake-build-system) (arguments (list #:tests? #f + #:configure-flags #~(list "-DSUITESPARSE_INCLUDEDIR_POSTFIX=") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir diff --git a/gnu/packages/patches/gklib-suitesparse.patch b/gnu/packages/patches/gklib-suitesparse.patch index 8b6c708b6a..757354f9ba 100644 --- a/gnu/packages/patches/gklib-suitesparse.patch +++ b/gnu/packages/patches/gklib-suitesparse.patch @@ -1,5 +1,5 @@ This patch contains the relevant changes to GKlib made in SuiteSparse -(CHOLMOD) for the version 7.2.0 +(CHOLMOD) for the version 7.10.2 (https://github.com/DrTimothyAldenDavis/SuiteSparse/commit/8a7641cdb4809533c681417e94f98058c07c5da2). The disabling of signal handling when MATLAB_MEX_FILE is defined is omitted. @@ -10,7 +10,7 @@ diff -ur a/CMakeLists.txt b/CMakeLists.txt option(BUILD_SHARED_LIBS "Build shared libraries (.dll/.so) instead of static ones (.lib/.a)" OFF) -+find_package ( SuiteSparse_config 7.1.0 REQUIRED ) ++find_package ( SuiteSparse_config 7.10.2 REQUIRED ) + get_filename_component(abs "." 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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.46 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:46 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 3/7] gnu: python-igraph: Update to 0.11.8. Date: Mon, 5 May 2025 16:43:23 +0000 Message-ID: <4cad788f1da07ddc6076011ad8a2ac6a310a31ec.1746463068.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/graph.scm (python-igraph): Update to 0.11.8. Change-Id: I6493392a700ea64bb0bf3c300a39a323e9eebf36 --- gnu/packages/graph.scm | 85 ++++++++++++++++++++---------------------- 1 file changed, 40 insertions(+), 45 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 0d65558a60..6a0b16d79a 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -213,51 +213,46 @@ (define-public igraph (license license:gpl2+))) (define-public python-igraph - ;; Temporarily use a precise commit, as there was a mistake in the last - ;; release that was fixed by it (see: - ;; https://github.com/igraph/python-igraph/issues/632). - (let ((revision "0") - (commit "b6ebd8eb277fc1d0e33340a6624629a10c638992")) - (package - (inherit igraph) - (name "python-igraph") - (version (git-version "0.10.4" revision commit)) - (source (origin - (method git-fetch) - ;; The PyPI archive lacks tests. - (uri (git-reference - (url "https://github.com/igraph/python-igraph") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0dhrz5a6pi6vs94fm8q4nmkh6v1nmpw1sk482xls213zcbbh67hd")))) - (build-system pyproject-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'specify-libigraph-location - (lambda _ - (let ((igraph #$(this-package-input "igraph"))) - (substitute* "setup.py" - (("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var) - (string-append - var (format #f "[~s]~%" - (string-append igraph "/include/igraph")))) - (("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var) - (string-append - var (format #f "[~s]~%" - (string-append igraph "/lib"))))))))))) - (inputs (list igraph)) - (propagated-inputs - (list python-texttable)) - (native-inputs - (list python-pytest - python-setuptools - python-wheel)) - (home-page "https://igraph.org/python/") - (synopsis "Python bindings for the igraph network analysis library")))) + (package + (inherit igraph) + (name "python-igraph") + (version "0.11.8") + (source (origin + (method git-fetch) + ;; The PyPI archive lacks tests. + (uri (git-reference + (url "https://github.com/igraph/python-igraph") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c73nypzm2apqqwzqxxhbh692h4ri2x8q4i8f7q2kwczz156v19k")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'specify-libigraph-location + (lambda _ + (let ((igraph #$(this-package-input "igraph"))) + (substitute* "setup.py" + (("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var) + (string-append + var (format #f "[~s]~%" + (string-append igraph "/include/igraph")))) + (("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var) + (string-append + var (format #f "[~s]~%" + (string-append igraph "/lib"))))))))))) + (inputs (list igraph)) + (propagated-inputs + (list python-texttable)) + (native-inputs + (list python-pytest + python-setuptools + python-wheel)) + (home-page "https://igraph.org/python/") + (synopsis "Python bindings for the igraph network analysis library"))) (define-public r-rbiofabric (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Mon May 05 12:47:59 2025 Received: (at 77902) by debbugs.gnu.org; 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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:47 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 4/7] gnu: python-vtraag-louvain: Deprecate. Date: Mon, 5 May 2025 16:43:24 +0000 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/graph.scm (python-vtraag-louvain): Deprecate with replacement python-louvain-igraph. Change-Id: I4e8b938a0a7ffb1932209bfff97a84b075aabb0e --- gnu/packages/graph.scm | 39 +++------------------------------------ 1 file changed, 3 insertions(+), 36 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 6a0b16d79a..65aeb79830 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -395,42 +395,6 @@ (define-public python-louvain algorithm for community detection in large networks.") (license license:bsd-3))) -(define-public python-vtraag-louvain - (package - (name "python-vtraag-louvain") - (version "0.8.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "louvain" version)) - (sha256 - (base32 - "16l2zi4jwc3vpvpnz32jv7xy0g5087dp9y57wxplj1xa9r312x0i")))) - (build-system pyproject-build-system) - (arguments - (list - #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'do-not-use-bundled-igraph - (lambda _ - (substitute* "setup.py" - (("self.external = False") - "self.external = True") - (("self.use_pkgconfig = False") - "self.use_pkgconfig = True"))))))) - (inputs (list igraph)) - (propagated-inputs (list python-igraph python-setuptools)) - (native-inputs - (list pkg-config - python-ddt - python-setuptools-scm - python-wheel)) - (home-page "https://github.com/vtraag/louvain") - (synopsis "Community detection in large networks") - (description - "Louvain is a general algorithm for methods of community detection in -large networks.") - (license license:gpl3+))) - (define-public python-graphtools (package (name "python-graphtools") @@ -535,6 +499,9 @@ (define-public python-louvain-igraph algorithm for a number of different methods.") 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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:48 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 5/7] gnu: python-louvain-igraph: Update to 0.8.2. Date: Mon, 5 May 2025 16:43:25 +0000 Message-ID: <5194a0371a40cfd3d7196e81298e29d7552d19b0.1746463068.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/graph.scm (python-louvain-igraph): Update to 0.8.2. Change-Id: Ifa755464fb88e0af6829d6f2569b900a80949e76 --- gnu/packages/graph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 65aeb79830..6bbcd30724 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -458,7 +458,7 @@ (define-public python-graphtools (define-public python-louvain-igraph (package (name "python-louvain-igraph") - (version "0.8.1") + (version "0.8.2") (source (origin (method git-fetch) @@ -468,7 +468,7 @@ (define-public python-louvain-igraph (file-name (git-file-name name version)) (sha256 (base32 - "1j2ybihvvzggwjb9zvm829aqb5b94q10h8bw6v0h42xd9w75z9sv")))) + "1aab6rnsnssi6wib939zy4vdzz3s2gcwwingn2dfjrijk05zjapv")))) (build-system pyproject-build-system) (arguments (list -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Mon May 05 12:47:59 2025 Received: (at 77902) by debbugs.gnu.org; 5 May 2025 16:48:00 +0000 Received: from localhost ([127.0.0.1]:42294 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uByz1-0004TW-JG for submit@debbugs.gnu.org; Mon, 05 May 2025 12:47:59 -0400 Received: from mail-qv1-xf29.google.com ([2607:f8b0:4864:20::f29]:55351) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.84_2) (envelope-from ) id 1uByyx-0004Rn-It for 77902@debbugs.gnu.org; Mon, 05 May 2025 12:47:56 -0400 Received: by mail-qv1-xf29.google.com with SMTP id 6a1803df08f44-6e8f05acc13so65396566d6.2 for <77902@debbugs.gnu.org>; Mon, 05 May 2025 09:47:55 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=greghogan-com.20230601.gappssmtp.com; s=20230601; t=1746463669; x=1747068469; darn=debbugs.gnu.org; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:from:to:cc:subject:date :message-id:reply-to; bh=UuZ3TTkxB8EltDLjKYll11mw0zpCqF9ZgKThVHWUfDY=; b=TahWLefYGK5lAIPBXRrND4WgcHQ8K1dMeEQmsq7/WVxAC+c+qPN5Z0eB4JVXLfapSS kgmh/47Qq3nRk455H5dqf0E1LiYyl9iBoc7IHb/Dwb5s4eQU9IvmOvx4UFMKZbfpAlOK w0cC28VqpyJYz3QJRfvAx7++K9oDn1famRJC/ZCzWsZXafVQPFS5halJnif/w7lvCG8b EeJVv2bqaIsT+o0e/ir79DGqQemT+EaG8dPndr7e/pSMVK6bkFLo8TjQKbKNeaFHK7rj paK+K3YUGec6MkZNn24Dlim4T/I/6wVXlWhkUxwh6HG3s3i0eYsYZVi1O9qWNWkaY2v9 3Cqg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1746463669; x=1747068469; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=UuZ3TTkxB8EltDLjKYll11mw0zpCqF9ZgKThVHWUfDY=; b=pL7OjqFncxoVEA5uXqwzo6lA+8AQ/9VRJjhlbFesd9SxV0ImUBvXcw4Eix2kENbAym doH/uTVTfT3w0qvrDv/kRcf4BfNF0T/xptVyQKD43BuBSHcrs/2JDyzP3aMB2vvPNBfX ACyHlZGXKGMdnbi39YEIiKSaIy4l8b+7yNKiJ5V47Rg8UrueJ/8PHm1N/s+PHNZ27SBl PSdyShwnbJ/zO84yIHHum/XMgYpxYn59dNL2fuXJNo+F60JbTUewOmscZsXWRO0GVCrA vhBdKmgVrb4u68ZaHv/G+2hYhzll2maX0MONounWBPXUxCeta59jXRTmPJ7knxXhxaUC Btjg== X-Gm-Message-State: AOJu0Yxeetrk8Jd7YrVvdAOdPetw6PqRZgyIaaw98uKTXdsQAT25hzOG FbIIk0GWvTCsJ/34V5JwpbCxbI8mHxb2BEnLOPNAyNdoE3n/+HbQ//o+QvE+WFspU4+DPUTcdvk Q X-Gm-Gg: ASbGncspD6noEsrYNvVgeRfSBIGpf1bY3WUHH5AZQqdhVMSFgSmJY/UYc2goNQImbRY VuQdPybLHqBZTG4UzvpSZ0PDxyj86a2KfP4zU0lvQPpPBNTs5Q8JszhYwUwoZ/YlpuOlBlwu270 kBdMf1sisCOaqQ1x6TGgaD7d3T9NPz0yfTapntIn+FMlP/r8r8+KDqHudtxKBOD3nbaH8wcYD81 GISahvCgUqov4fHXzWxFm30IIJoexRB2rUW8g/WkQPvLCGbduCseSEA2eSWjoLcY52LfhuLXiRE BeZbLof8t/KnqtWyBqWTZiMiuHL3Yl2IyFUpzqnLcJ+d8anaxjKQQAQU8kXhs6DeGZQS14DYtHe 3SGPEQ/pfODGOPQOmB1egwjfBL3ngUb3fbcwGanAj X-Google-Smtp-Source: AGHT+IEFmG+WYv1mI7edQKba6EVWFi9zlCyiT+jjW9Zf9GCo3FR5DmLBKjj0b7dmua9qUh2DYIReXg== X-Received: by 2002:a05:6214:d43:b0:6e8:fee2:aadf with SMTP id 6a1803df08f44-6f5354174d6mr1417516d6.31.1746463669628; Mon, 05 May 2025 09:47:49 -0700 (PDT) Received: from ip-10-117-149-49.evoforge.org (ec2-52-70-167-183.compute-1.amazonaws.com. [52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:49 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 6/7] gnu: Add libleidenalg. Date: Mon, 5 May 2025 16:43:26 +0000 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/graph.scm (libleidenalg): New variable. Change-Id: I73b21fcbca63ec26f521e8a17d45537dbcf82ffe --- gnu/packages/graph.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 6bbcd30724..49d2bd72a1 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -658,6 +658,39 @@ (define-public python-faiss clustering of dense vectors. This package provides Python bindings to the Faiss library."))) +(define-public libleidenalg + (package + (name "libleidenalg") + (version "0.11.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vtraag/libleidenalg") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0fqy79yrgnrifhyc2lys5jv84siq01ph6038qyz7qagl1yq5gdw8")))) + (build-system cmake-build-system) + (arguments + (list + #:tests? #f ;tests are not included + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'version-file + (lambda _ + (let ((port (open-file "VERSION" "w"))) + (display #$version port) + (close port))))))) + (inputs (list igraph)) + (home-page "https://github.com/vtraag/libleidenalg") + (synopsis "Community detection in large networks") + (description "Leiden is a general algorithm for methods of community +detection in large networks and is an extension of the Louvain algorithm. +This package implements the Leiden algorithm in C++ and can be run on graphs +of millions of nodes (as long as they can fit in memory).") + (license license:gpl3+))) + (define-public python-leidenalg (package (name "python-leidenalg") -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Mon May 05 12:48:00 2025 Received: (at 77902) by debbugs.gnu.org; 5 May 2025 16:48:00 +0000 Received: from localhost ([127.0.0.1]:42296 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uByz1-0004TZ-Tx for submit@debbugs.gnu.org; Mon, 05 May 2025 12:48:00 -0400 Received: from mail-qv1-xf34.google.com ([2607:f8b0:4864:20::f34]:56457) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.84_2) (envelope-from ) id 1uByyy-0004Rr-FA for 77902@debbugs.gnu.org; Mon, 05 May 2025 12:47:57 -0400 Received: by mail-qv1-xf34.google.com with SMTP id 6a1803df08f44-6f521957182so27893506d6.0 for <77902@debbugs.gnu.org>; Mon, 05 May 2025 09:47:56 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=greghogan-com.20230601.gappssmtp.com; s=20230601; t=1746463670; x=1747068470; darn=debbugs.gnu.org; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:from:to:cc:subject:date :message-id:reply-to; bh=XLmNyjfzq2XqGaXLdVTaN/daJ/SXLTkJhrF/y6iFGTc=; b=JFpJXaZhkrJ6iEuUA4P546an43Ro5bKOe2rQXeCCyEbntHhaFTq/CfEq/TmU4LuW7W 5FlSYspHs82lJxieM7qi3Lj62U2ZqEGaPa2CdzPBS9veQ6R1lrU+5CdO4rUYDHoCiYjc 5uM8D8xV/eCdOOu09Xal3gwYnMTC2BmbiyJkcD2KrV1DePQyiDkkAWBxf+fGtZv8Vcdb jnXEE1OQIqGHUaVN5bzKoaMwR/s1d8QfphNCbCQajj6NNDyQ9S/rKrHBMavCOmjz41ck LUG5uYsglPGsAZi7OklDH8BtDpaw/ZJDWC3/XibvgpQmI33ZGoFXA/WAA5OayPrEuo4N rRXQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1746463670; x=1747068470; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=XLmNyjfzq2XqGaXLdVTaN/daJ/SXLTkJhrF/y6iFGTc=; b=Mo3rpj3QRNLYRQBXkt7vAQeYY03CZym/JNEizxUqyAxmikafiJfo9qmm9+nRoy7Zfd j+qVLZgIrTcERLyjVaCWXFHEe8o2fgWxYkltYOlUFB8negCuC5IASay0ZtzZWpK88feO SbfghYeRB/pw4m98WZ6Xa1ssFuK57rJnFfx9bs+mvzfxaqA/vmuZzOJvEaATm4gWSryr rKlBe9W9/Iov38N87i8g413GGPYJwsxH/AXmsLxEy0UhzieFBwv6+xAPDsnAlN8J8zAc bd5q8pMTKbs+Dtcc9uRhmcDisKif/eh6DBnLyQWs9/7RpkJTRmjAjJIOE77eAhQ57HKQ CUzQ== X-Gm-Message-State: AOJu0YxLcicJvZkUn3PKrDhCjbmVkkQ3qVtpsaoLYbn5RqAPcbTWP+WO S03hE74LS88tI78uqwm/VFWQgQMV2vXmxTZSJnIVAcbjJecXHOdbTH87U/Qn2IV1jcdTSGCgY5w d X-Gm-Gg: ASbGncuMRq515mx1YaWWpfkCnynVIZ8kXwiDW4ncj8EFEFY4n2KSHC8xsKxmI8KHS5g GA4ktUlyy/GvXg7CVlwzVLP4AUTbzy6a02TWZ9pHvvExBjh5kIWQR09KZJ6HTJ9G7ta59r6BI+P iiDSG4xLpUG03xASF4xGYLRQLxSvXs09W61usY58UkGgF6HygQWj3H0csux1kWCMU0wagBItJpB oWUsAe2C5904UEX3TbTS+LyMelTYNOGMYt3SVqzTKtECvWoTFzQTCSoTJ1Pc5Yb9lvpM/BwxKg0 6txHdevphxSS/Jl8OSLB17aD//CoWM/GifSy1Ym2ZEf5mBCZqbUXjKErDLJG3Ykt1AkFOmaCI0X 7pKSkUu8W1CHsWm8n0cQw1Aw/BkDX+bux3qDBuiQZ X-Google-Smtp-Source: AGHT+IE5HZxpdD9iQtt3Tp4JQ38u0smLaWwUEYR6aH/MXIekqLduzCoJof5b8atNx3DZsQh/UUhJfw== X-Received: by 2002:a05:6214:c22:b0:6e6:9ce0:da9d with SMTP id 6a1803df08f44-6f528c96fd9mr117099276d6.27.1746463670458; Mon, 05 May 2025 09:47:50 -0700 (PDT) Received: from ip-10-117-149-49.evoforge.org (ec2-52-70-167-183.compute-1.amazonaws.com. [52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:50 -0700 (PDT) From: Greg Hogan To: 77902@debbugs.gnu.org Subject: [PATCH v2 science-team 7/7] gnu: python-leidenalg: Update to 0.10.2. Date: Mon, 5 May 2025 16:43:27 +0000 Message-ID: <3fafb273744601c085787d8aec370fdb4e2a5074.1746463068.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902 Cc: Greg Hogan 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 (-) * gnu/packages/graph.scm (python-leidenalg): Update to 0.10.2. [inputs]: Add libleidenalg. [description]: Update to account for removal of C++ implementation. Change-Id: Ia00e819eda4c03f25e54dc72483c7bcaf2ab396f --- gnu/packages/graph.scm | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 49d2bd72a1..e2ef93b464 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -694,14 +694,14 @@ (define-public libleidenalg (define-public python-leidenalg (package (name "python-leidenalg") - (version "0.9.1") + (version "0.10.2") (source (origin (method url-fetch) (uri (pypi-uri "leidenalg" version)) (sha256 (base32 - "1wvmi6ca9kf8pbxg6b18n64h82wr9a6wcdazyn82pww0dwxzwp3y")))) + "0k1f35bmgff8vc5fcyqa2dqfa1x17rb0vqzwkdqlm0sr5fllfh8g")))) (build-system python-build-system) (arguments '(#:tests? #f ;tests are not included @@ -718,19 +718,14 @@ (define-public python-leidenalg (native-inputs (list pkg-config python-setuptools-scm)) (inputs - (list igraph)) + (list igraph libleidenalg)) (propagated-inputs (list python-igraph)) (home-page "https://github.com/vtraag/leidenalg") (synopsis "Community detection in large networks") - (description - "Leiden is a general algorithm for methods of community detection in -large networks. This package implements the Leiden algorithm in C++ and -exposes it to Python. Besides the relative flexibility of the implementation, -it also scales well, and can be run on graphs of millions of nodes (as long as -they can fit in memory). The core function is @code{find_partition} which -finds the optimal partition using the Leiden algorithm, which is an extension -of the Louvain algorithm, for a number of different methods.") + (description "Leiden is a general algorithm for methods of community +detection in large networks and is an extension of the Louvain algorithm. This +packages provides a Python wrapper to the C++ implementation.") (license license:gpl3+))) (define-public edge-addition-planarity-suite -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Tue May 13 13:31:53 2025 Received: (at 77902-done) by debbugs.gnu.org; 13 May 2025 17:31:53 +0000 Received: from localhost ([127.0.0.1]:33065 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uEtTs-0005BQ-SX for submit@debbugs.gnu.org; Tue, 13 May 2025 13:31:53 -0400 Received: from mail-oa1-x2c.google.com ([2001:4860:4864:20::2c]:54371) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.84_2) (envelope-from ) id 1uEtTn-00059d-RN for 77902-done@debbugs.gnu.org; Tue, 13 May 2025 13:31:49 -0400 Received: by mail-oa1-x2c.google.com with SMTP id 586e51a60fabf-2c2504fa876so2414615fac.0 for <77902-done@debbugs.gnu.org>; Tue, 13 May 2025 10:31:47 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=greghogan-com.20230601.gappssmtp.com; s=20230601; t=1747157501; x=1747762301; darn=debbugs.gnu.org; h=content-transfer-encoding:to:subject:message-id:date:from :in-reply-to:references:mime-version:from:to:cc:subject:date :message-id:reply-to; bh=66R6ZqYIjQsdf6ZmwPXRV+RyGI53nNaQaw/AaHm4PqM=; b=lRbJOnZ52A6To8/i6DiHorcSWiwG3lqD6gk7FN/5y0xg98sfXTlM3dHOe/36DlFe5j E5JgxAcSNGi3RFAMIOV4ELI5pIhf91D5z3r+XoRtEICOr1B0CoIJSQLYpJl1TEGbuS05 cDPEBDK/2FvVdy/PbH6nNSBsOMOhl9XeMf+CsA6GQcP350RI3yvn7LAAfMZhZ7n2bTUD hFJdmsn9oF/HTa4mQwkJDooYZrwhkXqsyH2GFnyN+1e4y5iilWjTzo77G9flrdc6l2jF VM9u94aZ5HY1Jm1vbdeTfAatWQlrSZROT9H4C9p/6ma/Yt+2p+Ww+6/SedsKocwoeHx5 5m6Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1747157501; x=1747762301; h=content-transfer-encoding:to:subject:message-id:date:from :in-reply-to:references:mime-version:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=66R6ZqYIjQsdf6ZmwPXRV+RyGI53nNaQaw/AaHm4PqM=; b=a6s/+4ackW+19513qAOIKIPO9gYi0Onun1WpiSYdfdrplRuXb1O7wnxBf6Ckltr6Qz 1Fba9SnxO/WiY06m9gAnsog1d/37t9OgfhLdlk2hEt8p+uSs44tvJJmnhASM+w+uhv7W CksiEL3CpU74YYjPuDoEbb5LLot313q9tmTD718IOVUT2BMw/L2BClnXvzvb4FX0LfwM FkE/SmZlMdcwll9g1MewNfPuIqnTlrfEGIFdfvdsc5oRKlbZYbD/xHfqZUormyW31LGx CYD0Z/i8nVsk2L6U8a7FupmWKZyOeM3MphHGRKD6fXYDAaYq9vOMj2Phmur4lTkhlh01 /zww== X-Gm-Message-State: AOJu0YxidfOOaFr8DMtcMgvgTLiToWxRuPJoskr7nLdlxPiDgyT3koJT m50X1Uzxvcbn5odrVADVSxczjb4OIkK5LdlN9eGSncBZ67QYQj99d4OCgVrULumO10nfJUlYK1b e2BP7FfwodvERC9JcXhOVY70febAezH46v92K149IScNHaVqIKLHSnQ== X-Gm-Gg: ASbGncsHGoDk/xGj7oisy6DcZXHpqbMHG6g6sb55eJNhP9VMX1IoC8dLcSgeVU/fpqc 7tf8BQTZXgZJfaK57drfbFJdpSDk7DzyHgBPfN5wkq9reMkAuis/mpryXsTORhPP0QbeDECk13y a6YgRvr6LL35+4w9ILAnnJWNtmf78tevz7vYfdicTxgHA= X-Google-Smtp-Source: AGHT+IHPkZHaYTuUVuPg8iCd6RWlE6l0VcC5IcrYtKQBz49cQzsG9+fUxnu0FtSJM4fkmdKAuwFMXuAaE8LgNIyFisk= X-Received: by 2002:a05:6870:889f:b0:2c2:5270:f182 with SMTP id 586e51a60fabf-2e34889e537mr41523fac.39.1747157501429; Tue, 13 May 2025 10:31:41 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Greg Hogan Date: Tue, 13 May 2025 13:31:30 -0400 X-Gm-Features: AX0GCFs2LErNal28TSU0Qrh33IZ0gmeiHHeyyAxfTUJN1Tnf7-NM4jPfA7hyoaw Message-ID: Subject: Re: [PATCH v2 science-team 0/7] Update SuiteSparse. To: 77902-done@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77902-done 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 (-) On Mon, May 5, 2025 at 12:47=E2=80=AFPM Greg Hogan wro= te: > > v2 restores the installation directory of the suitesparse header files > by overriding the new default subdirectory "suitesparse". > > Also includes updates and fixes for dependent packages. > > Greg Hogan (7): > gnu: Add %suitesparse-package-versions. > gnu: igraph: Update to 0.10.15. > gnu: python-igraph: Update to 0.11.8. > gnu: python-vtraag-louvain: Deprecate. > gnu: python-louvain-igraph: Update to 0.8.2. > gnu: Add libleidenalg. > gnu: python-leidenalg: Update to 0.10.2. > > gnu/local.mk | 1 - > gnu/packages/graph.scm | 183 ++++++++---------- > gnu/packages/maths.scm | 77 +++++--- > gnu/packages/patches/gklib-suitesparse.patch | 4 +- > .../igraph-fix-varargs-integer-size.patch | 39 ---- > 5 files changed, 141 insertions(+), 163 deletions(-) > delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.= patch > > > base-commit: 90f0f8713da9cf0dc0bb5c93446a4eba11075352 > -- > 2.49.0 Pushed as c6aaffba1c766d67cac28c47682952fb3ec095e5^..c0fc7d2a0a8ac1b39f8fe9= a9cbc43bda405d008e. 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