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-rw-r--r--gnu/packages/graph.scm208
1 files changed, 81 insertions, 127 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 109ba68675..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:)
@@ -67,7 +68,7 @@
(define-public plfit
(package
(name "plfit")
- (version "0.9.3")
+ (version "0.9.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -76,7 +77,7 @@
(file-name (git-file-name name version))
(sha256
(base32
- "03x5jbvg8vwr92682swy58ljxrhqwmga1xzd0cpfbfmda41gm2fb"))))
+ "042b60cnsz5wy27sz026xs0mnn9p58j46crgs78skncgkvzqyyc6"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON")))
@@ -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")
@@ -290,11 +296,12 @@ subplots, multiple-axes, polar charts, and bubble charts.")
(origin
(method url-fetch)
(uri (pypi-uri "python-louvain" version))
+ (patches (search-patches "python-louvain-fix-test.patch"))
(sha256
(base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
(build-system python-build-system)
(native-inputs
- (list python-setuptools)) ;for use_2to3 support
+ (list python-setuptools-57)) ;for use_2to3 support
(propagated-inputs
(list python-networkx python-numpy))
(home-page "https://github.com/taynaud/python-louvain")
@@ -304,58 +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")
@@ -495,14 +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
@@ -565,19 +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
generated by cgit v1.2.3 (git 2.46.2) at 2024-11-10 13:40:36 +0000