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-rw-r--r--gnu/packages/graph.scm145
1 files changed, 102 insertions, 43 deletions
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 084fdf8c90..de68ff78b1 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -8,6 +8,8 @@
;;; 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 © 2022 Marius Bakke <marius@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -26,6 +28,7 @@
(define-module (gnu packages graph)
#:use-module (guix download)
+ #:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix utils)
@@ -60,31 +63,72 @@
#:use-module (gnu packages time)
#:use-module (gnu packages xml))
+(define-public plfit
+ (package
+ (name "plfit")
+ (version "0.9.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ntamas/plfit")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "03x5jbvg8vwr92682swy58ljxrhqwmga1xzd0cpfbfmda41gm2fb"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON")))
+ (home-page "https://github.com/ntamas/plfit")
+ (synopsis "Tool for fitting power-law distributions to empirical data")
+ (description "The @command{plfit} command fits power-law distributions to
+empirical (discrete or continuous) data, according to the method of Clauset,
+Shalizi and Newman (@cite{Clauset A, Shalizi CR and Newman MEJ: Power-law
+distributions in empirical data. SIAM Review 51, 661-703 (2009)}).")
+ (license license:gpl2+)))
+
(define-public igraph
(package
(name "igraph")
- (version "0.8.4")
+ (version "0.9.6")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/igraph/igraph/releases/"
"download/" version "/igraph-" version ".tar.gz"))
+ (modules '((guix build utils)))
+ (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")))
+ (substitute* '("src/CMakeLists.txt"
+ "etc/cmake/benchmark_helpers.cmake")
+ ;; Remove bundling related variables.
+ ((".*_IS_VENDORED.*")
+ ""))))
(sha256
- (base32 "127q6q40kbmvd62yhbz6dlfk370qiq98s1iscyagpgbpjwb4xvyf"))))
- (build-system gnu-build-system)
+ (base32 "11zkj9bpqcadb0rc4ahvjp9047dp9hna8cn3b0vl3zpc9v2rwabw"))))
+ (build-system cmake-build-system)
(arguments
- `(#:configure-flags
- (list "--disable-static"
- "--with-external-glpk"
- "--with-external-blas"
- "--with-external-lapack")))
+ '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON")))
+ (native-inputs (list pkg-config))
(inputs
- (list gmp
+ (list arpack-ng
+ gmp
glpk
libxml2
lapack
openblas
- zlib))
+ plfit
+ suitesparse))
(home-page "https://igraph.org")
(synopsis "Network analysis and visualization")
(description
@@ -95,36 +139,47 @@ more.")
(license license:gpl2+)))
(define-public python-igraph
- (package (inherit igraph)
+ (package
+ (inherit igraph)
(name "python-igraph")
- (version "0.8.2")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "python-igraph" version))
- (sha256
- (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6"))))
+ (version "0.9.9")
+ (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
+ "0ravcww2jcr8fgi97gdxv00s5nkx59ljxy928nnniyd0231bqwlc"))))
(build-system python-build-system)
(arguments
- '(#:configure-flags
- (list "--use-pkg-config")
- #:phases
- (modify-phases %standard-phases
- (replace 'build
- (lambda _
- (invoke "python" "./setup.py" "build" "--use-pkg-config")))
- (delete 'check)
- (add-after 'install 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "-v"))))))
+ (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 pkg-config python-pytest))
- (home-page "https://pypi.org/project/python-igraph/")
+ (list python-pytest))
+ (home-page "https://igraph.org/python/")
(synopsis "Python bindings for the igraph network analysis library")))
(define-public r-rbiofabric
@@ -181,14 +236,7 @@ lines.")
(invoke "pytest" "-x" "plotly/tests/test_io")
;; FIXME: Add optional dependencies and enable their tests.
;; (invoke "pytest" "-x" "plotly/tests/test_optional")
- (invoke "pytest" "_plotly_utils/tests"))
- #t))
- (add-before 'reset-gzip-timestamps 'make-files-writable
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (for-each (lambda (file) (chmod file #o644))
- (find-files out "\\.gz"))
- #t))))))
+ (invoke "pytest" "_plotly_utils/tests")))))))
(native-inputs
(list python-ipywidgets python-pytest python-xarray))
(propagated-inputs
@@ -204,7 +252,7 @@ lines.")
(description "Plotly's Python graphing library makes interactive,
publication-quality graphs online. Examples of how to make line plots, scatter
plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
-subplots, multiple-axes, polar charts, and bubble charts. ")
+subplots, multiple-axes, polar charts, and bubble charts.")
(license license:expat)))
(define-public python-plotly-2.4.1
@@ -239,6 +287,8 @@ subplots, multiple-axes, polar charts, and bubble charts. ")
(sha256
(base32 "1sqp97fwh4asx0jr72x8hil8z8fcg2xq92jklmh2m599pvgnx19a"))))
(build-system python-build-system)
+ (native-inputs
+ (list python-setuptools)) ;for use_2to3 support
(propagated-inputs
(list python-networkx python-numpy))
(home-page "https://github.com/taynaud/python-louvain")
@@ -428,9 +478,18 @@ Faiss library.")))
(base32
"15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
(build-system python-build-system)
- (arguments '(#:tests? #f)) ; tests are not included
+ (arguments
+ '(#:tests? #f ;tests are not included
+ #:phases (modify-phases %standard-phases
+ (add-after 'unpack 'fix-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("python-igraph >=")
+ "igraph >=")))))))
(native-inputs
- (list pkg-config))
+ ;; XXX: setuptools >= 58 as shipped with Python 3.9+ removes support
+ ;; for lib2to3, so use this older variant.
+ (list pkg-config python-setuptools))
(inputs
(list igraph))
(propagated-inputs
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-19 20:35:37 +0000