diff options
Diffstat (limited to 'gnu/packages/graph.scm')
| -rw-r--r-- | gnu/packages/graph.scm | 168 |
1 files changed, 135 insertions, 33 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 45a591b9f3..9dfe2efbc9 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017, 2018, 2019, 2020, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017-2024 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> @@ -10,6 +10,7 @@ ;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org> ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2022 Marius Bakke <marius@gnu.org> +;;; Copyright © 2023 David Elsing <david.elsing@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -40,13 +41,18 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages autotools) + #:use-module (gnu packages base) #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages bison) #:use-module (gnu packages boost) + #:use-module (gnu packages c) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages datastructures) + #:use-module (gnu packages docbook) + #:use-module (gnu packages flex) #:use-module (gnu packages gd) #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) @@ -55,6 +61,7 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-compression) @@ -93,49 +100,102 @@ distributions in empirical data. SIAM Review 51, 661-703 (2009)}).") (define-public igraph (package (name "igraph") - (version "0.10.4") + (version "0.10.7") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/igraph/igraph/releases/" - "download/" version "/igraph-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (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))) (snippet '(begin - ;; igraph insists on building its own copy of CxSparse - ;; (see: https://github.com/igraph/igraph/commit/\ - ;; 334318b7dfe46501236272ca336580f4748114b0) and the build - ;; has no support to use a system provided 'pcg'. - (define keep-libraries '("cs" "pcg")) - (define keep (append '("." ".." "CMakeLists.txt") - keep-libraries)) - (define keep? (cut member <> keep)) - (with-directory-excursion "vendor" - (for-each delete-file-recursively - (scandir "." (negate keep?)))) - (call-with-output-file "vendor/CMakeLists.txt" - (cut format <> "~{add_subdirectory(~a)~%~}" - keep-libraries)) + + (delete-file-recursively "vendor") + (delete-file-recursively "src/isomorphism/bliss") (substitute* '("src/CMakeLists.txt" "etc/cmake/benchmark_helpers.cmake") ;; Remove extraneous bundling related variables. - ((".*_IS_VENDORED.*") - "")))) + ((".*_IS_VENDORED.*") "") + ((".*add_sub.*isomorphism/bliss.*") "") + (("(.*TARGETS.*)bliss(.*)cxsparse_vendored(.*)pcg(.*)" + _ part1 part2 part3 part4) + (string-append part1 part2 part3 part4)) + (("cxsparse_vendored") "cxsparse") + ((" pcg ") " pcg_random ")) + (substitute* "CMakeLists.txt" + (("add_sub.*vendor.*") "")))) (sha256 - (base32 "1z1ay3l1h64jc2igbl2ibvi20sswy56v2yk3ykhis7jzijsh0mxa")))) + (base32 + "025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn")))) (build-system cmake-build-system) - (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON") - #:test-target "check")) - (native-inputs (list pkg-config)) + (arguments + (list + #:configure-flags + #~(list "-DBUILD_SHARED_LIBS=ON" + ;; Use the same integer width as suitesparse-cxsparse, which + ;; uses int64_t in SuiteSparse v6.0.0 and later. + "-DIGRAPH_INTEGER_SIZE=64") + #:test-target "check" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'version-file + (lambda _ + (let ((port (open-file "IGRAPH_VERSION" "w"))) + (display #$version port) + (close port)))) + (add-after 'unpack 'patch-suitesparse + (lambda _ + (substitute* '("src/core/sparsemat.c" + "include/igraph_sparsemat.h") + (("<cs/cs\\.h>") "<cs.h>") + (("cs_igraph") "cs_dl") + (("__BEGIN_DECLS.*" all) + (string-append all "\n#define CS_LONG\n"))))) + (add-after 'unpack 'patch-pcg + (lambda _ + (substitute* '("src/random/rng_pcg32.c" + "src/random/rng_pcg64.c") + (("#include \"pcg/(.*)\"" _ name) + (string-append "#include <" name ">"))))) + (add-after 'unpack 'patch-bliss + (lambda _ + (substitute* "src/isomorphism/bliss.cc" + (("#include \"bliss.*") + (string-append + "#include <bliss/graph.hh>\n" + "#include <bliss/digraph.hh>\n"))))) + (add-after 'build 'build-doc + (lambda _ + (invoke "cmake" "--build" "." "--target" "html"))) + (add-after 'install 'install-doc + (lambda _ + (copy-recursively + "doc/html" + (string-append #$output "/share/doc/" + #$name "-" #$version "/html"))))))) + (native-inputs + (list bison + docbook-xml-4.3 + docbook-xsl + flex + pcg-c + pkg-config + ;; For the HTML documentation. + python + source-highlight + xmlto)) (inputs (list arpack-ng - gmp + bliss glpk - libxml2 lapack openblas - plfit)) + plfit + suitesparse-cxsparse)) ;; libxml2 is in the 'Requires.private' of igraph.pc. (propagated-inputs (list libxml2)) (home-page "https://igraph.org") @@ -366,6 +426,48 @@ algorithm for community detection in large networks.") large networks.") (license license:gpl3+))) +(define-public python-louvain-igraph + (package + (name "python-louvain-igraph") + (version "0.8.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vtraag/louvain-igraph") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1j2ybihvvzggwjb9zvm829aqb5b94q10h8bw6v0h42xd9w75z9sv")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'find-igraph + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + (substitute* "setup.py" + (("/usr/include/igraph") + (string-append #$(this-package-input "igraph") + "/include/igraph")))))))) + (propagated-inputs (list python-igraph)) + (inputs (list igraph)) + (native-inputs + (list python-ddt + python-setuptools-scm + pkg-config)) + (home-page "https://github.com/vtraag/louvain-igraph") + (synopsis "Implementation of the Louvain algorithm") + (description "This package implements the Louvain algorithm for community +detection 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 louvain +algorithm for a number of different methods.") + (license license:gpl3+))) + (define-public faiss (package (name "faiss") @@ -389,8 +491,8 @@ large networks.") (build-system cmake-build-system) (arguments `(#:configure-flags - (list "-DBUILD_WITH_GPU=OFF" ; thanks, but no thanks, CUDA. - "-DBUILD_TUTORIAL=OFF") ; we don't need those + (list "-DBUILD_WITH_GPU=OFF" ; thanks, but no thanks, CUDA. + "-DBUILD_TUTORIAL=OFF") ; we don't need those #:phases (modify-phases %standard-phases (add-after 'unpack 'prepare-build @@ -406,7 +508,7 @@ large networks.") '())))))) (substitute* "CMakeLists.txt" (("-m64") "") - (("-mpopcnt") "") ; only some architectures + (("-mpopcnt") "") ; only some architectures (("-msse4") (string-append (string-join features) @@ -625,7 +727,7 @@ transformed into common image formats for display or printing.") (define-public python-graph-tool (package (name "python-graph-tool") - (version "2.57") + (version "2.59") (source (origin (method url-fetch) (uri (string-append @@ -633,7 +735,7 @@ transformed into common image formats for display or printing.") version ".tar.bz2")) (sha256 (base32 - "0wmvzx509lvigja6cfxh45r4b7wns64vmik0x4rz4y4fnxrhw2m2")))) + "1bmck5fcihj9lr5kd8x624bdi9xhfc13pl4mwzv74jr5lz07kr6d")))) (build-system gnu-build-system) (arguments `(#:imported-modules (,@%gnu-build-system-modules |