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e57fffad | 1 | ;;; GNU Guix --- Functional package management for GNU |
4e35c429 | 2 | ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net> |
5f3616d6 | 3 | ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> |
ef803aa5 | 4 | ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> |
e57fffad RW |
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) | |
4e35c429 | 23 | #:use-module (guix git-download) |
e57fffad RW |
24 | #:use-module (guix packages) |
25 | #:use-module (guix build-system gnu) | |
31476df3 | 26 | #:use-module (guix build-system python) |
1738138c | 27 | #:use-module (guix build-system r) |
e57fffad RW |
28 | #:use-module ((guix licenses) #:prefix license:) |
29 | #:use-module (gnu packages) | |
1738138c | 30 | #:use-module (gnu packages gcc) |
d53aeeaf | 31 | #:use-module (gnu packages bioconductor) |
e206de67 | 32 | #:use-module (gnu packages bioinformatics) |
e57fffad | 33 | #:use-module (gnu packages compression) |
fff9b884 | 34 | #:use-module (gnu packages cran) |
e206de67 | 35 | #:use-module (gnu packages graphviz) |
e57fffad RW |
36 | #:use-module (gnu packages maths) |
37 | #:use-module (gnu packages multiprecision) | |
31476df3 | 38 | #:use-module (gnu packages pkg-config) |
5f3616d6 LF |
39 | #:use-module (gnu packages python) |
40 | #:use-module (gnu packages python-web) | |
1738138c | 41 | #:use-module (gnu packages statistics) |
5f3616d6 | 42 | #:use-module (gnu packages time) |
e57fffad RW |
43 | #:use-module (gnu packages xml)) |
44 | ||
45 | (define-public igraph | |
46 | (package | |
47 | (name "igraph") | |
48 | (version "0.7.1") | |
49 | (source | |
50 | (origin | |
51 | (method url-fetch) | |
52 | (uri (string-append "http://igraph.org/nightly/get/c/igraph-" | |
53 | version ".tar.gz")) | |
54 | (sha256 | |
55 | (base32 | |
56 | "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r")))) | |
57 | (build-system gnu-build-system) | |
58 | (arguments | |
59 | `(#:configure-flags | |
60 | (list "--with-external-glpk" | |
61 | "--with-external-blas" | |
62 | "--with-external-lapack"))) | |
63 | (inputs | |
64 | `(("gmp" ,gmp) | |
65 | ("glpk" ,glpk) | |
66 | ("libxml2" ,libxml2) | |
67 | ("lapack" ,lapack) | |
68 | ("openblas" ,openblas) | |
69 | ("zlib" ,zlib))) | |
70 | (home-page "http://igraph.org") | |
71 | (synopsis "Network analysis and visualization") | |
72 | (description | |
73 | "This package provides a library for the analysis of networks and graphs. | |
74 | It can handle large graphs very well and provides functions for generating | |
75 | random and regular graphs, graph visualization, centrality methods and much | |
76 | more.") | |
77 | (license license:gpl2+))) | |
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78 | |
79 | (define-public python-igraph | |
80 | (package (inherit igraph) | |
81 | (name "python-igraph") | |
82 | (version "0.7.1.post6") | |
83 | (source | |
84 | (origin | |
85 | (method url-fetch) | |
86 | (uri (pypi-uri "python-igraph" version)) | |
87 | (sha256 | |
88 | (base32 | |
89 | "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5")))) | |
90 | (build-system python-build-system) | |
91 | (arguments '()) | |
92 | (inputs | |
93 | `(("igraph" ,igraph))) | |
94 | (native-inputs | |
95 | `(("pkg-config" ,pkg-config))) | |
96 | (home-page "http://pypi.python.org/pypi/python-igraph") | |
97 | (synopsis "Python bindings for the igraph network analysis library"))) | |
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98 | |
99 | (define-public r-igraph | |
100 | (package | |
101 | (name "r-igraph") | |
eb251fe5 | 102 | (version "1.2.2") |
1738138c RW |
103 | (source |
104 | (origin | |
105 | (method url-fetch) | |
106 | (uri (cran-uri "igraph" version)) | |
107 | (sha256 | |
108 | (base32 | |
eb251fe5 | 109 | "1bggm7b8v3bh7q2589w26qvd7sgs69m4qiij7d0rbm0ykkgxm8lx")))) |
1738138c RW |
110 | (build-system r-build-system) |
111 | (native-inputs | |
112 | `(("gfortran" ,gfortran))) | |
113 | (inputs | |
114 | `(("gmp" ,gmp) | |
8cf7b28f RW |
115 | ("glpk" ,glpk) |
116 | ("libxml2" ,libxml2) | |
117 | ("zlib" ,zlib))) | |
1738138c | 118 | (propagated-inputs |
8cf7b28f | 119 | `(("r-magrittr" ,r-magrittr) |
1738138c RW |
120 | ("r-matrix" ,r-matrix) |
121 | ("r-pkgconfig" ,r-pkgconfig))) | |
122 | (home-page "http://igraph.org") | |
123 | (synopsis "Network analysis and visualization") | |
124 | (description | |
125 | "This package provides routines for simple graphs and network analysis. | |
126 | It can handle large graphs very well and provides functions for generating | |
127 | random and regular graphs, graph visualization, centrality methods and much | |
128 | more.") | |
129 | (license license:gpl2+))) | |
e206de67 | 130 | |
fff9b884 RW |
131 | (define-public r-diffusionmap |
132 | (package | |
133 | (name "r-diffusionmap") | |
c273bcdf | 134 | (version "1.1-0.1") |
fff9b884 RW |
135 | (source |
136 | (origin | |
137 | (method url-fetch) | |
138 | (uri (cran-uri "diffusionMap" version)) | |
139 | (sha256 | |
140 | (base32 | |
c273bcdf | 141 | "11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j")))) |
fff9b884 RW |
142 | (properties `((upstream-name . "diffusionMap"))) |
143 | (build-system r-build-system) | |
144 | (propagated-inputs | |
145 | `(("r-igraph" ,r-igraph) | |
146 | ("r-matrix" ,r-matrix) | |
147 | ("r-scatterplot3d" ,r-scatterplot3d))) | |
d062957a | 148 | (home-page "https://www.r-project.org") |
fff9b884 RW |
149 | (synopsis "Diffusion map") |
150 | (description "This package implements the diffusion map method of data | |
151 | parametrization, including creation and visualization of diffusion maps, | |
152 | clustering with diffusion K-means and regression using the adaptive regression | |
153 | model.") | |
154 | (license license:gpl2))) | |
155 | ||
e206de67 RW |
156 | (define-public r-rgraphviz |
157 | (package | |
158 | (name "r-rgraphviz") | |
7799a01e | 159 | (version "2.24.0") |
e206de67 RW |
160 | (source |
161 | (origin | |
162 | (method url-fetch) | |
163 | (uri (bioconductor-uri "Rgraphviz" version)) | |
164 | (sha256 | |
165 | (base32 | |
7799a01e | 166 | "1037hzfxxcn46w6y88wm3kk2nixj0s8bk0hkmnshpxih3kmnvqby")))) |
e206de67 RW |
167 | (properties `((upstream-name . "Rgraphviz"))) |
168 | (build-system r-build-system) | |
169 | ;; FIXME: Rgraphviz bundles the sources of an older variant of | |
170 | ;; graphviz. It does not build with the latest version of graphviz, so | |
171 | ;; we do not add graphviz to the inputs. | |
172 | (inputs `(("zlib" ,zlib))) | |
173 | (propagated-inputs | |
174 | `(("r-graph" ,r-graph))) | |
175 | (native-inputs | |
176 | `(("pkg-config" ,pkg-config))) | |
177 | (home-page "http://bioconductor.org/packages/Rgraphviz") | |
178 | (synopsis "Plotting capabilities for R graph objects") | |
179 | (description | |
180 | "This package interfaces R with the graphviz library for plotting R graph | |
181 | objects from the @code{graph} package.") | |
182 | (license license:epl1.0))) | |
4e35c429 RW |
183 | |
184 | (define-public r-rbiofabric | |
185 | (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") | |
186 | (revision "1")) | |
187 | (package | |
188 | (name "r-rbiofabric") | |
189 | (version (string-append "0.3-" revision "." (string-take commit 7))) | |
190 | (source (origin | |
191 | (method git-fetch) | |
192 | (uri (git-reference | |
193 | (url "https://github.com/wjrl/RBioFabric.git") | |
194 | (commit commit))) | |
195 | (file-name (string-append name "-" version "-checkout")) | |
196 | (sha256 | |
197 | (base32 | |
198 | "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z")))) | |
199 | (build-system r-build-system) | |
200 | (propagated-inputs | |
201 | `(("r-igraph" ,r-igraph))) | |
202 | (home-page "http://www.biofabric.org/") | |
203 | (synopsis "BioFabric network visualization") | |
204 | (description "This package provides an implementation of the function | |
205 | @code{bioFabric} for creating scalable network digrams where nodes are | |
206 | represented by horizontal lines, and edges are represented by vertical | |
207 | lines.") | |
208 | (license license:expat)))) | |
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209 | |
210 | (define-public python-plotly | |
211 | (package | |
212 | (name "python-plotly") | |
ef803aa5 | 213 | (version "2.4.1") |
5f3616d6 LF |
214 | (source |
215 | (origin | |
216 | (method url-fetch) | |
217 | (uri (pypi-uri "plotly" version)) | |
218 | (sha256 | |
219 | (base32 | |
ef803aa5 | 220 | "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m")))) |
5f3616d6 LF |
221 | (build-system python-build-system) |
222 | (arguments | |
223 | '(#:tests? #f)) ; The tests are not distributed in the release | |
224 | (propagated-inputs | |
225 | `(("python-decorator" ,python-decorator) | |
226 | ("python-nbformat" ,python-nbformat) | |
227 | ("python-pytz" ,python-pytz) | |
228 | ("python-requests" ,python-requests) | |
229 | ("python-six" ,python-six))) | |
230 | (home-page "https://plot.ly/python/") | |
231 | (synopsis "Interactive plotting library for Python") | |
232 | (description "Plotly's Python graphing library makes interactive, | |
233 | publication-quality graphs online. Examples of how to make line plots, scatter | |
234 | plots, area charts, bar charts, error bars, box plots, histograms, heatmaps, | |
235 | subplots, multiple-axes, polar charts, and bubble charts. ") | |
236 | (license license:expat))) | |
237 | ||
238 | (define-public python2-plotly | |
239 | (package-with-python2 python-plotly)) |