;;; 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 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 boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
+ #:use-module (gnu packages datastructures)
#:use-module (gnu packages gd)
+ #:use-module (gnu packages graphics)
#:use-module (gnu packages graphviz)
+ #:use-module (gnu packages gtk)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
+ #: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 "0.8.2")
+ (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 "158flvl80qh1l1ikfa04p1dzh8kapsvm6q80x3ih5gwcgcg4g2ki"))))
- (build-system gnu-build-system)
+ (base32 "15v3ydq95gahnas37cip637hvc2nwrmk76xp0nv3gq53rrrk9a7r"))))
+ (build-system cmake-build-system)
(arguments
- `(#:configure-flags
- (list "--with-external-glpk"
- "--with-external-blas"
- "--with-external-lapack")))
+ '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON")))
+ (native-inputs (list pkg-config))
(inputs
- `(("gmp" ,gmp)
- ("glpk" ,glpk)
- ("libxml2" ,libxml2)
- ("lapack" ,lapack)
- ("openblas" ,openblas)
- ("zlib" ,zlib)))
+ (list arpack-ng
+ gmp
+ glpk
+ libxml2
+ lapack
+ openblas
+ 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
- `(("igraph" ,igraph)))
+ (list igraph))
(propagated-inputs
- `(("python-texttable" ,python-texttable)))
+ (list python-texttable))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("python-pytest" ,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
"1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-igraph" ,r-igraph)))
+ (list r-igraph))
(home-page "http://www.biofabric.org/")
(synopsis "BioFabric network visualization")
(description "This package provides an implementation of the function
(define-public python-plotly
(package
(name "python-plotly")
- (version "4.8.1")
+ (version "5.6.0")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz"))))
+ "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")
#t))
(replace 'check
- (lambda _
- (invoke "pytest" "-x" "plotly/tests/test_core")
- (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")))
- (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))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-x" "plotly/tests/test_core")
+ (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")))))))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-ipywidgets python-pytest python-xarray))
(propagated-inputs
- `(("python-decorator" ,python-decorator)
- ("python-ipywidgets" ,python-ipywidgets)
- ("python-pandas" ,python-pandas)
- ("python-requests" ,python-requests)
- ("python-retrying" ,python-retrying)
- ("python-six" ,python-six)
- ("python-statsmodels" ,python-statsmodels)
- ("python-xarray" ,python-xarray)))
+ (list python-ipython
+ python-pandas
+ python-pillow
+ 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
"0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
(native-inputs '())
(propagated-inputs
- `(("python-decorator" ,python-decorator)
- ("python-nbformat" ,python-nbformat)
- ("python-pandas" ,python-pandas)
- ("python-pytz" ,python-pytz)
- ("python-requests" ,python-requests)
- ("python-six" ,python-six)))
+ (list python-decorator
+ python-nbformat
+ python-pandas
+ python-pytz
+ python-requests
+ python-six))
(arguments
'(#:tests? #f)))) ; The tests are not distributed in the release
-(define-public python2-plotly
- (package-with-python2 python-plotly-2.4.1))
-
(define-public python-louvain
(package
(name "python-louvain")
- (version "0.6.1")
+ (version "0.16")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "python-louvain" version))
+ (sha256
+ (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")
+ (synopsis "Louvain algorithm for community detection")
+ (description
+ "This package provides a pure Python implementation of the Louvain
+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)
(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
- `(("python-ddt" ,python-ddt)
- ("python-igraph" ,python-igraph)))
+ (list python-ddt python-igraph))
(inputs
- `(("igraph" ,igraph)))
+ (list igraph))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("python-pytest" ,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
"/test"))
#t)))))
(inputs
- `(("openblas" ,openblas)))
+ (list openblas))
(native-inputs
- `(("googletest" ,googletest)))
+ (list googletest))
(home-page "https://github.com/facebookresearch/faiss")
(synopsis "Efficient similarity search and clustering of dense vectors")
(description "Faiss is a library for efficient similarity search and
("python*" ,python)
("swig" ,swig)))
(propagated-inputs
- `(("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)))
+ (list python-matplotlib python-numpy))
(description "Faiss is a library for efficient similarity search and
clustering of dense vectors. This package provides Python bindings to the
Faiss library.")))
(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
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config python-setuptools-scm))
(inputs
- `(("igraph" ,igraph)))
+ (list igraph))
(propagated-inputs
- `(("python-igraph" ,python-igraph)))
+ (list python-igraph))
(home-page "https://github.com/vtraag/leidenalg")
(synopsis "Community detection in large networks")
(description
"01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
(build-system gnu-build-system)
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("libtool" ,libtool)))
+ (list autoconf automake libtool))
(synopsis "Embedding of planar graphs")
(description "The package provides a reference implementation of the
linear time edge addition algorithm for embedding planar graphs and
"1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
(build-system gnu-build-system)
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(inputs
- `(("igraph" ,igraph)))
+ (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
"08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
(build-system gnu-build-system)
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(inputs
- `(("gd" ,gd)))
+ (list gd))
(home-page "http://www.mcternan.me.uk/mscgen/")
(synopsis "Message Sequence Chart Generator")
(description "Mscgen is a small program that parses Message Sequence Chart
text language that is clear to create, edit and understand, which can also be
transformed into common image formats for display or printing.")
(license license:gpl2+)))
+
+(define-public python-graph-tool
+ (package
+ (name "python-graph-tool")
+ (version "2.43")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://downloads.skewed.de/graph-tool/graph-tool-"
+ version ".tar.bz2"))
+ (sha256
+ (base32
+ "0v58in4rwk9fhjarjw6xfxpx5zz2z13sy3yvd14b5kr0884yw6sz"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#: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="
+ (site-packages %build-inputs %outputs)))))
+ (native-inputs
+ (list ncurses pkg-config))
+ (inputs
+ (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")
+ (description "Graph-tool is an efficient Python module for manipulation
+and statistical analysis of graphs (a.k.a. networks). Contrary to most other
+Python modules with similar functionality, the core data structures and
+algorithms are implemented in C++, making extensive use of template
+metaprogramming, based heavily on the Boost Graph Library. This confers it a
+level of performance that is comparable (both in memory usage and computation
+time) to that of a pure C/C++ library.")
+ (home-page "https://graph-tool.skewed.de/")
+ (license license:lgpl3+)))
HCoop / jackhill / guix / guix.git / blobdiff