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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 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-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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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 6a1803df08f44-6f50f3c32b5sm57738656d6.30.2025.05.05.09.47.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 May 2025 09:47:45 -0700 (PDT) From: Greg Hogan 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 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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)); -+ fprintf(file, format, (int) VECTOR(column_width)[j], MATRIX(*m, i, j)); - #endif - } - fprintf(file, "\n"); From patchwork Mon May 5 16:43:23 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Greg Hogan X-Patchwork-Id: 42329 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8619027BC4B; Mon, 5 May 2025 17:48:25 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B486B27BC49 for ; Mon, 5 May 2025 17:48:24 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uByz9-0004kQ-89; 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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 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 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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") From patchwork Mon May 5 16:43:24 2025 Content-Type: text/plain; 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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 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 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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.") (license license:gpl3+))) +(define-public python-vtraag-louvain + (deprecated-package "python-vtraag-louvain" python-louvain-igraph)) + (define-public python-pygsp (package (name "python-pygsp") From patchwork Mon May 5 16:43:25 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Greg Hogan X-Patchwork-Id: 42335 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8370F27BC4A; Mon, 5 May 2025 17:49:06 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 1582727BC49 for ; Mon, 5 May 2025 17:49:05 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uByzv-0005HO-AD; Mon, 05 May 2025 12:48:55 -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 1uByz7-0004iM-5R for guix-patches@gnu.org; Mon, 05 May 2025 12:48:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1uByz6-0001ls-Q3 for guix-patches@gnu.org; Mon, 05 May 2025 12:48:04 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=vFVfqtRSU9UJYpEq/wegttb4GhD6QDjRSoLn7sM/jzM=; b=e/MH/rpe1Y3fJ/mhIaUIyCMlLkMUARWEFIDwYQdqrDdhbZ7WP5egpXwjKFK7bZ9IVXsTcEnuGlaYnyg1HlRHC1hECAQIg9OfbSFyEVrtczc5Rxogoq42Vw+dA+nEGbw1VA5oPyeLxxwbkObASZNvJ420C3CTMCCEklbFDSSLX3NPaxyj4o8p2VN9R77125VxTy1f7o4zrxdpJOQSaVlJGbYb2wg8Nx32O+oD4qo1MIJzo+vwSVIiOezicAebbMuBibhnOPTNUzcoxVLqXGtHRr9WN9QCq1ZBNmKGl3HodDdOtyMRGRLSoDnXAlbThLBo+6QbLafRmic6u8ymr8CLew==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uByz6-0004Uc-KW for guix-patches@gnu.org; Mon, 05 May 2025 12:48:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77902] [PATCH v2 science-team 5/7] gnu: python-louvain-igraph: Update to 0.8.2. 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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 From patchwork Mon May 5 16:43:26 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Greg Hogan X-Patchwork-Id: 42334 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 7B74327BC4B; Mon, 5 May 2025 17:48:59 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 0746327BC49 for ; Mon, 5 May 2025 17:48:59 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uByzu-0005Gh-As; Mon, 05 May 2025 12:48:55 -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 1uByz7-0004iw-M5 for guix-patches@gnu.org; Mon, 05 May 2025 12:48:06 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1uByz7-0001m2-BH for guix-patches@gnu.org; Mon, 05 May 2025 12:48:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=UuZ3TTkxB8EltDLjKYll11mw0zpCqF9ZgKThVHWUfDY=; b=mmq3s3TPVQzOCOtz7qdd+j2Pi1/A8IlMpF/GACjLnRauaGLR86TPyTTiK5mV4pBw44ZaERLx07r9Tv7EXh/cMXxH1+DSug14vkiaz1hX+6kgDfKsH4Xf7vv6ftbsPtCBDEIRsDCcbAB9WDMjeE7FyjXNl+tN6MQg255lQonRsfGYCiAavhT/FDKnXWnMZU5TrGDmCh4/R9sAne2AGSaWExys5s2f8GYc7Lsy+1z6VjBMvApq5mRrX8x6Qs/8JjGe6NaOFJ/50gkwXLGPieThlweDAohUbsF3G1St15K2I+ruetpCu8WPQkrK6XxmAOGHlsPrEvGvmF280CkTINn5XQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uByz7-0004Ul-5o for guix-patches@gnu.org; Mon, 05 May 2025 12:48:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77902] [PATCH v2 science-team 6/7] gnu: Add libleidenalg. 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[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 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 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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") From patchwork Mon May 5 16:43:27 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Greg Hogan X-Patchwork-Id: 42330 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 6319727BC4B; Mon, 5 May 2025 17:48:35 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C54D227BC49 for ; Mon, 5 May 2025 17:48:34 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uByz9-0004kd-Dx; Mon, 05 May 2025 12:48:08 -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 1uByz8-0004j8-B0 for guix-patches@gnu.org; Mon, 05 May 2025 12:48:06 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1uByz7-0001mB-RI for guix-patches@gnu.org; Mon, 05 May 2025 12:48:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=XLmNyjfzq2XqGaXLdVTaN/daJ/SXLTkJhrF/y6iFGTc=; b=ZqFr1gSdb77r3+0K3vQD1H3aJoMW/RztDaCNtLSAJHxRjP9p6iAYIlMsSz6ipmncdVu5GF/h2rmlIkLCaL3g7C0qADBDJv/qg6udPAdLXuV2WAUKe8S6+nRYpoPoOdb98kJ4SJw0GBXuIAoV1lOIj/DncCIDNbCUKZ3m361TEOcZx6gYNjz6G6z+zycqUg6QT+/3NNdrLQa7iUAJz+0wynLsHfGKsJkU3FXzjpwIjO5yQ7myvgK5mvS62WOrC6LmHQpVhfIpZVlb6RRYp3aJCf48enq4xZZiqUj4p+0F2W6eyJ+gIh6J252G50Yxfk2GMxVKErk/EGJ5nHlvb9S13w==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uByz7-0004Ut-Mc for guix-patches@gnu.org; Mon, 05 May 2025 12:48:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77902] [PATCH v2 science-team 7/7] gnu: python-leidenalg: Update to 0.10.2. 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[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 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 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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