237 lines
8.2 KiB
Scheme
237 lines
8.2 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages graph)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix packages)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module (guix build-system r)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (gnu packages)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages bioinformatics)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages time)
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#:use-module (gnu packages xml))
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(define-public igraph
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(package
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(name "igraph")
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(version "0.7.1")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "http://igraph.org/nightly/get/c/igraph-"
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version ".tar.gz"))
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(sha256
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(base32
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"1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
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(build-system gnu-build-system)
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(arguments
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`(#:configure-flags
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(list "--with-external-glpk"
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"--with-external-blas"
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"--with-external-lapack")))
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(inputs
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`(("gmp" ,gmp)
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("glpk" ,glpk)
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("libxml2" ,libxml2)
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("lapack" ,lapack)
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("openblas" ,openblas)
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("zlib" ,zlib)))
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(home-page "http://igraph.org")
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(synopsis "Network analysis and visualization")
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(description
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"This package provides a library for the analysis of networks and graphs.
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It can handle large graphs very well and provides functions for generating
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random and regular graphs, graph visualization, centrality methods and much
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more.")
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(license license:gpl2+)))
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(define-public python-igraph
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(package (inherit igraph)
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(name "python-igraph")
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(version "0.7.1.post6")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "python-igraph" version))
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(sha256
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(base32
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"0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
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(build-system python-build-system)
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(arguments '())
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(inputs
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`(("igraph" ,igraph)))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(home-page "http://pypi.python.org/pypi/python-igraph")
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(synopsis "Python bindings for the igraph network analysis library")))
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(define-public r-igraph
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(package
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(name "r-igraph")
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(version "1.1.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "igraph" version))
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(sha256
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(base32
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"1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9"))))
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(build-system r-build-system)
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(native-inputs
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`(("gfortran" ,gfortran)))
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(inputs
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`(("gmp" ,gmp)
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("libxml2" ,libxml2)))
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(propagated-inputs
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`(("r-irlba" ,r-irlba)
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("r-magrittr" ,r-magrittr)
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("r-matrix" ,r-matrix)
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("r-pkgconfig" ,r-pkgconfig)))
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(home-page "http://igraph.org")
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(synopsis "Network analysis and visualization")
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(description
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"This package provides routines for simple graphs and network analysis.
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It can handle large graphs very well and provides functions for generating
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random and regular graphs, graph visualization, centrality methods and much
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more.")
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(license license:gpl2+)))
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(define-public r-diffusionmap
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(package
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(name "r-diffusionmap")
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(version "1.1-0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "diffusionMap" version))
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(sha256
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(base32
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"1l985q2hfc8ss5afajik4p25dx628yikvhdimz5s0pql800q2yv3"))))
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(properties `((upstream-name . "diffusionMap")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-igraph" ,r-igraph)
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("r-matrix" ,r-matrix)
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("r-scatterplot3d" ,r-scatterplot3d)))
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(home-page "https://www.r-project.org")
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(synopsis "Diffusion map")
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(description "This package implements the diffusion map method of data
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parametrization, including creation and visualization of diffusion maps,
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clustering with diffusion K-means and regression using the adaptive regression
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model.")
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(license license:gpl2)))
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(define-public r-rgraphviz
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(package
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(name "r-rgraphviz")
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(version "2.22.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "Rgraphviz" version))
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(sha256
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(base32
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"1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv"))))
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(properties `((upstream-name . "Rgraphviz")))
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(build-system r-build-system)
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;; FIXME: Rgraphviz bundles the sources of an older variant of
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;; graphviz. It does not build with the latest version of graphviz, so
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;; we do not add graphviz to the inputs.
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(inputs `(("zlib" ,zlib)))
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(propagated-inputs
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`(("r-graph" ,r-graph)))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(home-page "http://bioconductor.org/packages/Rgraphviz")
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(synopsis "Plotting capabilities for R graph objects")
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(description
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"This package interfaces R with the graphviz library for plotting R graph
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objects from the @code{graph} package.")
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(license license:epl1.0)))
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(define-public r-rbiofabric
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(let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
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(revision "1"))
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(package
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(name "r-rbiofabric")
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(version (string-append "0.3-" revision "." (string-take commit 7)))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/wjrl/RBioFabric.git")
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(commit commit)))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-igraph" ,r-igraph)))
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(home-page "http://www.biofabric.org/")
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(synopsis "BioFabric network visualization")
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(description "This package provides an implementation of the function
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@code{bioFabric} for creating scalable network digrams where nodes are
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represented by horizontal lines, and edges are represented by vertical
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lines.")
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(license license:expat))))
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(define-public python-plotly
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(package
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(name "python-plotly")
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(version "2.4.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "plotly" version))
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(sha256
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(base32
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"0n18116jz6bl5n9cq23vabv1gcbh1x3yficdnfq55v0z4cwy0zlf"))))
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(build-system python-build-system)
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(arguments
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'(#:tests? #f)) ; The tests are not distributed in the release
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(propagated-inputs
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`(("python-decorator" ,python-decorator)
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("python-nbformat" ,python-nbformat)
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("python-pytz" ,python-pytz)
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("python-requests" ,python-requests)
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("python-six" ,python-six)))
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(home-page "https://plot.ly/python/")
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(synopsis "Interactive plotting library for Python")
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(description "Plotly's Python graphing library makes interactive,
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publication-quality graphs online. Examples of how to make line plots, scatter
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plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
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subplots, multiple-axes, polar charts, and bubble charts. ")
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(license license:expat)))
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(define-public python2-plotly
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(package-with-python2 python-plotly))
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