gnu/packages/graph.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
   4 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
   5 ;;;
   6 ;;; This file is part of GNU Guix.
   7 ;;;
   8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   9 ;;; under the terms of the GNU General Public License as published by
  10 ;;; the Free Software Foundation; either version 3 of the License, or (at
  11 ;;; your option) any later version.
  12 ;;;
  13 ;;; GNU Guix is distributed in the hope that it will be useful, but
  14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16 ;;; GNU General Public License for more details.
  17 ;;;
  18 ;;; You should have received a copy of the GNU General Public License
  19 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  20
  21 (define-module (gnu packages graph)
  22   #:use-module (guix download)
  23   #:use-module (guix git-download)
  24   #:use-module (guix packages)
  25   #:use-module (guix build-system gnu)
  26   #:use-module (guix build-system python)
  27   #:use-module (guix build-system r)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (gnu packages)
  30   #:use-module (gnu packages gcc)
  31   #:use-module (gnu packages bioconductor)
  32   #:use-module (gnu packages bioinformatics)
  33   #:use-module (gnu packages compression)
  34   #:use-module (gnu packages cran)
  35   #:use-module (gnu packages graphviz)
  36   #:use-module (gnu packages maths)
  37   #:use-module (gnu packages multiprecision)
  38   #:use-module (gnu packages pkg-config)
  39   #:use-module (gnu packages python)
  40   #:use-module (gnu packages python-web)
  41   #:use-module (gnu packages python-xyz)
  42   #:use-module (gnu packages statistics)
  43   #:use-module (gnu packages time)
  44   #:use-module (gnu packages xml))
  45
  46 (define-public igraph
  47   (package
  48     (name "igraph")
  49     (version "0.7.1")
  50     (source
  51      (origin
  52        (method url-fetch)
  53        (uri (string-append "http://igraph.org/nightly/get/c/igraph-"
  54                            version ".tar.gz"))
  55        (sha256
  56         (base32
  57          "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
  58     (build-system gnu-build-system)
  59     (arguments
  60      `(#:configure-flags
  61        (list "--with-external-glpk"
  62              "--with-external-blas"
  63              "--with-external-lapack")))
  64     (inputs
  65      `(("gmp" ,gmp)
  66        ("glpk" ,glpk)
  67        ("libxml2" ,libxml2)
  68        ("lapack" ,lapack)
  69        ("openblas" ,openblas)
  70        ("zlib" ,zlib)))
  71     (home-page "http://igraph.org")
  72     (synopsis "Network analysis and visualization")
  73     (description
  74      "This package provides a library for the analysis of networks and graphs.
  75 It can handle large graphs very well and provides functions for generating
  76 random and regular graphs, graph visualization, centrality methods and much
  77 more.")
  78     (license license:gpl2+)))
  79
  80 (define-public python-igraph
  81   (package (inherit igraph)
  82     (name "python-igraph")
  83     (version "0.7.1.post6")
  84     (source
  85      (origin
  86        (method url-fetch)
  87        (uri (pypi-uri "python-igraph" version))
  88        (sha256
  89         (base32
  90          "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
  91     (build-system python-build-system)
  92     (arguments '())
  93     (inputs
  94      `(("igraph" ,igraph)))
  95     (native-inputs
  96      `(("pkg-config" ,pkg-config)))
  97     (home-page "http://pypi.python.org/pypi/python-igraph")
  98     (synopsis "Python bindings for the igraph network analysis library")))
  99
 100 (define-public r-igraph
 101   (package
 102     (name "r-igraph")
 103     (version "1.2.4")
 104     (source
 105      (origin
 106        (method url-fetch)
 107        (uri (cran-uri "igraph" version))
 108        (sha256
 109         (base32
 110          "1jwjjl0l4054w05bik17p2d6rj3lx68iv716phajhnbbmckfnj0h"))))
 111     (build-system r-build-system)
 112     (native-inputs
 113      `(("gfortran" ,gfortran)))
 114     (inputs
 115      `(("gmp" ,gmp)
 116        ("glpk" ,glpk)
 117        ("libxml2" ,libxml2)
 118        ("zlib" ,zlib)))
 119     (propagated-inputs
 120      `(("r-magrittr" ,r-magrittr)
 121        ("r-matrix" ,r-matrix)
 122        ("r-pkgconfig" ,r-pkgconfig)))
 123     (home-page "http://igraph.org")
 124     (synopsis "Network analysis and visualization")
 125     (description
 126      "This package provides routines for simple graphs and network analysis.
 127 It can handle large graphs very well and provides functions for generating
 128 random and regular graphs, graph visualization, centrality methods and much
 129 more.")
 130     (license license:gpl2+)))
 131
 132 (define-public r-diffusionmap
 133   (package
 134     (name "r-diffusionmap")
 135     (version "1.1-0.1")
 136     (source
 137      (origin
 138        (method url-fetch)
 139        (uri (cran-uri "diffusionMap" version))
 140        (sha256
 141         (base32
 142          "11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j"))))
 143     (properties `((upstream-name . "diffusionMap")))
 144     (build-system r-build-system)
 145     (propagated-inputs
 146      `(("r-igraph" ,r-igraph)
 147        ("r-matrix" ,r-matrix)
 148        ("r-scatterplot3d" ,r-scatterplot3d)))
 149     (home-page "https://www.r-project.org")
 150     (synopsis "Diffusion map")
 151     (description "This package implements the diffusion map method of data
 152 parametrization, including creation and visualization of diffusion maps,
 153 clustering with diffusion K-means and regression using the adaptive regression
 154 model.")
 155     (license license:gpl2)))
 156
 157 (define-public r-rgraphviz
 158   (package
 159     (name "r-rgraphviz")
 160     (version "2.26.0")
 161     (source
 162      (origin
 163        (method url-fetch)
 164        (uri (bioconductor-uri "Rgraphviz" version))
 165        (sha256
 166         (base32
 167          "0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"))))
 168     (properties `((upstream-name . "Rgraphviz")))
 169     (build-system r-build-system)
 170     ;; FIXME: Rgraphviz bundles the sources of an older variant of
 171     ;; graphviz.  It does not build with the latest version of graphviz, so
 172     ;; we do not add graphviz to the inputs.
 173     (inputs `(("zlib" ,zlib)))
 174     (propagated-inputs
 175      `(("r-graph" ,r-graph)))
 176     (native-inputs
 177      `(("pkg-config" ,pkg-config)))
 178     (home-page "http://bioconductor.org/packages/Rgraphviz")
 179     (synopsis "Plotting capabilities for R graph objects")
 180     (description
 181      "This package interfaces R with the graphviz library for plotting R graph
 182 objects from the @code{graph} package.")
 183     (license license:epl1.0)))
 184
 185 (define-public r-rbiofabric
 186   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
 187         (revision "1"))
 188     (package
 189       (name "r-rbiofabric")
 190       (version (string-append "0.3-" revision "." (string-take commit 7)))
 191       (source (origin
 192                 (method git-fetch)
 193                 (uri (git-reference
 194                       (url "https://github.com/wjrl/RBioFabric.git")
 195                       (commit commit)))
 196                 (file-name (string-append name "-" version "-checkout"))
 197                 (sha256
 198                  (base32
 199                   "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
 200       (build-system r-build-system)
 201       (propagated-inputs
 202        `(("r-igraph" ,r-igraph)))
 203       (home-page "http://www.biofabric.org/")
 204       (synopsis "BioFabric network visualization")
 205       (description "This package provides an implementation of the function
 206 @code{bioFabric} for creating scalable network digrams where nodes are
 207 represented by horizontal lines, and edges are represented by vertical
 208 lines.")
 209       (license license:expat))))
 210
 211 (define-public python-plotly
 212   (package
 213     (name "python-plotly")
 214     (version "2.4.1")
 215     (source
 216       (origin
 217         (method url-fetch)
 218         (uri (pypi-uri "plotly" version))
 219         (sha256
 220          (base32
 221           "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
 222     (build-system python-build-system)
 223     (arguments
 224      '(#:tests? #f)) ; The tests are not distributed in the release
 225     (propagated-inputs
 226      `(("python-decorator" ,python-decorator)
 227        ("python-nbformat" ,python-nbformat)
 228        ("python-pandas" ,python-pandas)
 229        ("python-pytz" ,python-pytz)
 230        ("python-requests" ,python-requests)
 231        ("python-six" ,python-six)))
 232     (home-page "https://plot.ly/python/")
 233     (synopsis "Interactive plotting library for Python")
 234     (description "Plotly's Python graphing library makes interactive,
 235 publication-quality graphs online.  Examples of how to make line plots, scatter
 236 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
 237 subplots, multiple-axes, polar charts, and bubble charts. ")
 238     (license license:expat)))
 239
 240 (define-public python2-plotly
 241   (package-with-python2 python-plotly))