;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018, 2019, 2020, 2022 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2021 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
;;; 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.
;;;
(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)
#:use-module (guix build-system r)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
- #:use-module (gnu packages gcc)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#: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 "0.9.8")
(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 "15v3ydq95gahnas37cip637hvc2nwrmk76xp0nv3gq53rrrk9a7r"))))
+ (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
(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 "0.9.10")
+ (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
+ "06qvwmiw2klk3bg8g5af0ppjwrm9kzy4595w5d06qh2v3gq0svbk"))))
(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
(define-public python-plotly
(package
(name "python-plotly")
- (version "4.14.3")
+ (version "5.6.0")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "02wlgy7gf3v5ckiq9ab3prm53cckxkavlghqgkk9xw2sfmmrn61q"))))
+ "0kc9v5ampq2paw6sls6zdchvqvis7b1z8xhdvlhz5xxdr1vj5xnn"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-before 'build 'skip-npm
+ ;; npm is not packaged so build without it
+ (lambda _
+ (setenv "SKIP_NPM" "T")))
(add-after 'unpack 'chdir
(lambda _
(chdir "packages/python/plotly")
(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
python-requests
python-retrying
python-six
+ python-tenacity
python-statsmodels))
(home-page "https://plotly.com/python/")
(synopsis "Interactive plotting library for Python")
(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
(define-public python-louvain
(package
(name "python-louvain")
- (version "0.15")
+ (version "0.16")
(source
(origin
(method url-fetch)
(uri (pypi-uri "python-louvain" version))
(sha256
- (base32 "1sqp97fwh4asx0jr72x8hil8z8fcg2xq92jklmh2m599pvgnx19a"))))
+ (base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
(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")
algorithm for community detection in large networks.")
(license license:bsd-3)))
-(define-public python-louvain-0.6
+(define-public python-louvain-0.7
(package
(name "python-louvain")
- (version "0.6.1")
+ (version "0.7.1")
;; The tarball on Pypi does not include the tests.
(source (origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
+ "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))
+ (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
(define-public python-leidenalg
(package
(name "python-leidenalg")
- (version "0.7.0")
+ (version "0.8.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "leidenalg" version))
(sha256
(base32
- "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
+ "1hbvagp1yyazvl7cid7mii5263qi48lpkq543n5w71qysgz1f0v7"))))
(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"
+ (("self.external = False")
+ "self.external = True")
+ (("self.use_pkgconfig = False")
+ "self.use_pkgconfig = True")
+ (("python-igraph >=")
+ "igraph >=")))))))
(native-inputs
- (list pkg-config))
+ (list pkg-config python-setuptools-scm))
(inputs
(list igraph))
(propagated-inputs
"0v58in4rwk9fhjarjw6xfxpx5zz2z13sy3yvd14b5kr0884yw6sz"))))
(build-system gnu-build-system)
(arguments
- `(#:configure-flags
+ `(#:imported-modules (,@%gnu-build-system-modules
+ (guix build python-build-system))
+ #:modules (,@%gnu-build-system-modules
+ ((guix build python-build-system) #:select (site-packages)))
+ #:configure-flags
(list (string-append "--with-boost="
(assoc-ref %build-inputs "boost"))
(string-append "--with-python-module-path="
- (assoc-ref %outputs "out")
- "/lib/python"
- ,(version-major+minor
- (package-version
- (car (assoc-ref
- (package-inputs this-package)
- "python"))))
- "/site-packages/"))))
+ (site-packages %build-inputs %outputs)))))
(native-inputs
- `(("gcc-10" ,gcc-10)
- ("ncurses" ,ncurses)
- ("pkg-config" ,pkg-config)))
+ (list ncurses pkg-config))
(inputs
- `(("boost" ,boost)
- ("cairomm" ,cairomm)
- ("cgal" ,cgal)
- ("expat" ,expat)
- ("gmp" ,gmp)
- ("gtk+" ,gtk+)
- ("python" ,python-wrapper)
- ("sparsehash" ,sparsehash)))
+ (list boost
+ cairomm-1.14
+ cgal
+ expat
+ gmp
+ gtk+
+ python-wrapper
+ sparsehash))
(propagated-inputs
(list python-matplotlib python-numpy python-pycairo python-scipy))
(synopsis "Manipulate and analyze graphs with Python efficiently")
HCoop / jackhill / guix / guix.git / blobdiff