;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 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>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
+ #:use-module (gnu packages gd)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages statistics)
(define-public igraph
(package
(name "igraph")
- (version "0.7.1")
+ (version "0.8.1")
(source
(origin
(method url-fetch)
- (uri (string-append "http://igraph.org/nightly/get/c/igraph-"
- version ".tar.gz"))
+ (uri (string-append "https://github.com/igraph/igraph/releases/"
+ "download/" version "/igraph-" version ".tar.gz"))
(sha256
- (base32
- "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
+ (base32 "0wbvrac3ip3lqmbkckhnxa2swlbc86l1h8mazdlb618kx3winvi6"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
("lapack" ,lapack)
("openblas" ,openblas)
("zlib" ,zlib)))
- (home-page "http://igraph.org")
+ (home-page "https://igraph.org")
(synopsis "Network analysis and visualization")
(description
"This package provides a library for the analysis of networks and graphs.
(define-public python-igraph
(package (inherit igraph)
(name "python-igraph")
- (version "0.7.1.post6")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "python-igraph" version))
(sha256
(base32
- "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
+ "13mbrlmnbgbzw6y8ws7wj0a3ly3in8j4l1ngi6yxvgvxxi4bprj7"))))
(build-system python-build-system)
- (arguments '())
+ (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"))))))
(inputs
`(("igraph" ,igraph)))
+ (propagated-inputs
+ `(("python-texttable" ,python-texttable)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
- (home-page "http://pypi.python.org/pypi/python-igraph")
+ `(("pkg-config" ,pkg-config)
+ ("python-pytest" ,python-pytest)))
+ (home-page "https://pypi.org/project/python-igraph/")
(synopsis "Python bindings for the igraph network analysis library")))
(define-public r-igraph
(package
(name "r-igraph")
- (version "1.2.4.2")
+ (version "1.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "igraph" version))
(sha256
(base32
- "0scrbqb26pam8akblb4g9rkz888s0xffw3gcly78s4ijj67barxd"))))
+ "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
`(("r-magrittr" ,r-magrittr)
("r-matrix" ,r-matrix)
("r-pkgconfig" ,r-pkgconfig)))
- (home-page "http://igraph.org")
+ (home-page "https://igraph.org")
(synopsis "Network analysis and visualization")
(description
"This package provides routines for simple graphs and network analysis.
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
- (version "2.28.0")
+ (version "2.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
- "0nivz8fshaqig6ynjqbya2gmxsy4hm7jnd8fhb853z5g0ydp7g0c"))))
+ "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
;; FIXME: Rgraphviz bundles the sources of an older variant of
`(("r-graph" ,r-graph)))
(native-inputs
`(("pkg-config" ,pkg-config)))
- (home-page "http://bioconductor.org/packages/Rgraphviz")
+ (home-page "https://bioconductor.org/packages/Rgraphviz")
(synopsis "Plotting capabilities for R graph objects")
(description
"This package interfaces R with the graphviz library for plotting R graph
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/wjrl/RBioFabric.git")
+ (url "https://github.com/wjrl/RBioFabric")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(define-public python-plotly
(package
(name "python-plotly")
- (version "2.4.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "plotly" version))
- (sha256
- (base32
- "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
+ (version "4.8.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/plotly/plotly.py")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz"))))
(build-system python-build-system)
(arguments
- '(#:tests? #f)) ; The tests are not distributed in the release
+ `(#:phases
+ (modify-phases %standard-phases
+ (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))))))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(propagated-inputs
`(("python-decorator" ,python-decorator)
- ("python-nbformat" ,python-nbformat)
+ ("python-ipywidgets" ,python-ipywidgets)
("python-pandas" ,python-pandas)
- ("python-pytz" ,python-pytz)
("python-requests" ,python-requests)
- ("python-six" ,python-six)))
- (home-page "https://plot.ly/python/")
+ ("python-retrying" ,python-retrying)
+ ("python-six" ,python-six)
+ ("python-statsmodels" ,python-statsmodels)
+ ("python-xarray" ,python-xarray)))
+ (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
subplots, multiple-axes, polar charts, and bubble charts. ")
(license license:expat)))
+(define-public python-plotly-2.4.1
+ (package (inherit python-plotly)
+ (version "2.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "plotly" version))
+ (sha256
+ (base32
+ "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)))
+ (arguments
+ '(#:tests? #f)))) ; The tests are not distributed in the release
+
(define-public python2-plotly
- (package-with-python2 python-plotly))
+ (package-with-python2 python-plotly-2.4.1))
(define-public python-louvain
(package
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/vtraag/louvain-igraph.git")
+ (url "https://github.com/vtraag/louvain-igraph")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/facebookresearch/faiss.git")
+ (url "https://github.com/facebookresearch/faiss")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(description "rw computes rank-width and rank-decompositions
of graphs.")
(license license:gpl2+)))
+
+(define-public mscgen
+ (package
+ (name "mscgen")
+ (version "0.20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("gd" ,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
+descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as
+the output. Message Sequence Charts (MSCs) are a way of representing entities
+and interactions over some time period and are often used in combination with
+SDL. MSCs are popular in Telecoms to specify how protocols operate although
+MSCs need not be complicated to create or use. Mscgen aims to provide a simple
+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+)))
HCoop / jackhill / guix / guix.git / blobdiff