diff options
Diffstat (limited to 'gnu/packages/graph.scm')
| -rw-r--r-- | gnu/packages/graph.scm | 201 |
1 files changed, 77 insertions, 124 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index a2f771799f..560764bb33 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com> ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org> -;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2022 Marius Bakke <marius@gnu.org> ;;; ;;; This file is part of GNU Guix. @@ -34,6 +34,7 @@ #:use-module (guix utils) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system r) #:use-module ((guix licenses) #:prefix license:) @@ -91,35 +92,40 @@ distributions in empirical data. SIAM Review 51, 661-703 (2009)}).") (define-public igraph (package (name "igraph") - (version "0.9.8") + (version "0.10.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/igraph/igraph/releases/" "download/" version "/igraph-" version ".tar.gz")) - (modules '((guix build utils))) + (modules '((guix build utils) + (ice-9 ftw) + (srfi srfi-26))) (snippet '(begin - ;; Fully unbundle igraph (see: - ;; https://github.com/igraph/igraph/issues/1897). - (delete-file-recursively "vendor") - (substitute* "CMakeLists.txt" - (("add_subdirectory\\(vendor\\).*") - "")) - ;; Help CMake to find our plfit headers. - (substitute* "etc/cmake/FindPLFIT.cmake" - (("^ NAMES plfit.h.*" all) - (string-append all - " PATH_SUFFIXES plfit"))) + ;; 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)) (substitute* '("src/CMakeLists.txt" "etc/cmake/benchmark_helpers.cmake") - ;; Remove bundling related variables. + ;; Remove extraneous bundling related variables. ((".*_IS_VENDORED.*") "")))) (sha256 - (base32 "15v3ydq95gahnas37cip637hvc2nwrmk76xp0nv3gq53rrrk9a7r")))) + (base32 "1z1ay3l1h64jc2igbl2ibvi20sswy56v2yk3ykhis7jzijsh0mxa")))) (build-system cmake-build-system) - (arguments - '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON"))) + (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON") + #:test-target "check")) (native-inputs (list pkg-config)) (inputs (list arpack-ng @@ -128,8 +134,9 @@ distributions in empirical data. SIAM Review 51, 661-703 (2009)}).") libxml2 lapack openblas - plfit - suitesparse)) + plfit)) + ;; libxml2 is in the 'Requires.private' of igraph.pc. + (propagated-inputs (list libxml2)) (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description @@ -140,48 +147,47 @@ more.") (license license:gpl2+))) (define-public python-igraph - (package - (inherit igraph) - (name "python-igraph") - (version "0.9.11") - (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 - "1xlr0cnf3a1vs9n2psvgrmjhld4n1xr79kkjqzby4pxxyzk1bydn")))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'specify-libigraph-location - (lambda _ - (let ((igraph #$(this-package-input "igraph"))) - (substitute* "setup.py" - (("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var) - (string-append - var (format #f "[~s]~%" (string-append igraph - "/include/igraph")))) - (("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var) - (string-append - var (format #f "[~s]~%" (string-append igraph "/lib")))))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-v"))))))) - (inputs - (list igraph)) - (propagated-inputs - (list python-texttable)) - (native-inputs - (list python-pytest)) - (home-page "https://igraph.org/python/") - (synopsis "Python bindings for the igraph network analysis library"))) + ;; Temporarily use a precise commit, as there was a mistake in the last + ;; release that was fixed by it (see: + ;; https://github.com/igraph/python-igraph/issues/632). + (let ((revision "0") + (commit "b6ebd8eb277fc1d0e33340a6624629a10c638992")) + (package + (inherit igraph) + (name "python-igraph") + (version (git-version "0.10.4" revision commit)) + (source (origin + (method git-fetch) + ;; The PyPI archive lacks tests. + (uri (git-reference + (url "https://github.com/igraph/python-igraph") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0dhrz5a6pi6vs94fm8q4nmkh6v1nmpw1sk482xls213zcbbh67hd")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'specify-libigraph-location + (lambda _ + (let ((igraph #$(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)) + (home-page "https://igraph.org/python/") + (synopsis "Python bindings for the igraph network analysis library")))) (define-public r-rbiofabric (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") @@ -305,58 +311,6 @@ subplots, multiple-axes, polar charts, and bubble charts.") algorithm for community detection in large networks.") (license license:bsd-3))) -(define-public python-louvain-0.7 - (package - (name "python-louvain") - (version "0.7.1") - ;; The tarball on Pypi does not include the tests. - (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 - "1g6b5c2jgwagnhnqh859g61h7x6a81d8hm3g6mkin6kzwafww3g2")))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-before 'build 'pretend-version - ;; The version string is usually derived via setuptools-scm, but - ;; without the git metadata available this fails. - (lambda _ - (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) - (add-before 'build 'find-igraph - (lambda* (#:key inputs #:allow-other-keys) - (setenv "IGRAPH_EXTRA_INCLUDE_PATH" - (string-append (assoc-ref inputs "igraph") - "/include/igraph:" - (getenv "C_INCLUDE_PATH"))) - (setenv "IGRAPH_EXTRA_LIBRARY_PATH" - (getenv "LIBRARY_PATH"))))))) - (propagated-inputs - (list python-ddt python-igraph)) - (inputs - (list igraph)) - (native-inputs - (list pkg-config - python-pytest - python-setuptools-scm - python-wheel)) - (home-page "https://github.com/vtraag/louvain-igraph") - (synopsis "Algorithm for methods of community detection in large networks") - (description - "This package provides an implementation of the Louvain algorithm for use -with igraph. Louvain is a general algorithm for methods of community -detection in large networks. - -This package has been superseded by the @code{leidenalg} package and should -not be used for new projects.") - (license license:gpl3+))) - (define-public faiss (package (name "faiss") @@ -496,14 +450,14 @@ Faiss library."))) (define-public python-leidenalg (package (name "python-leidenalg") - (version "0.8.10") + (version "0.9.1") (source (origin (method url-fetch) (uri (pypi-uri "leidenalg" version)) (sha256 (base32 - "1hbvagp1yyazvl7cid7mii5263qi48lpkq543n5w71qysgz1f0v7")))) + "1wvmi6ca9kf8pbxg6b18n64h82wr9a6wcdazyn82pww0dwxzwp3y")))) (build-system python-build-system) (arguments '(#:tests? #f ;tests are not included @@ -566,19 +520,18 @@ isolating planarity obstructions.") (name "rw") ;; There is a version 0.8, but the tarball is broken with symlinks ;; to /usr/share. - (version "0.7") + (version "0.9") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/rankwidth/" "rw-" version ".tar.gz")) - (sha256 - (base32 - "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0")))) + (sha256 + (base32 + "0hdlxxmlccb6fp7g58zv0rdzpbyjn9bgqlf052sgrk95zq33bq61")) + (patches (search-patches "rw-igraph-0.10.patch")))) (build-system gnu-build-system) - (native-inputs - (list pkg-config)) - (inputs - (list igraph)) + (native-inputs (list pkg-config)) + (inputs (list igraph)) (home-page "https://sourceforge.net/projects/rankwidth/") (synopsis "Rank-width and rank-decomposition of graphs") (description "rw computes rank-width and rank-decompositions |