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 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
   6 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
   7 ;;;
   8 ;;; This file is part of GNU Guix.
   9 ;;;
  10 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  11 ;;; under the terms of the GNU General Public License as published by
  12 ;;; the Free Software Foundation; either version 3 of the License, or (at
  13 ;;; your option) any later version.
  14 ;;;
  15 ;;; GNU Guix is distributed in the hope that it will be useful, but
  16 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  17 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 ;;; GNU General Public License for more details.
  19 ;;;
  20 ;;; You should have received a copy of the GNU General Public License
  21 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 (define-module (gnu packages graph)
  24   #:use-module (guix download)
  25   #:use-module (guix git-download)
  26   #:use-module (guix packages)
  27   #:use-module (guix utils)
  28   #:use-module (guix build-system cmake)
  29   #:use-module (guix build-system gnu)
  30   #:use-module (guix build-system python)
  31   #:use-module (guix build-system r)
  32   #:use-module ((guix licenses) #:prefix license:)
  33   #:use-module (gnu packages)
  34   #:use-module (gnu packages gcc)
  35   #:use-module (gnu packages autotools)
  36   #:use-module (gnu packages bioconductor)
  37   #:use-module (gnu packages bioinformatics)
  38   #:use-module (gnu packages check)
  39   #:use-module (gnu packages compression)
  40   #:use-module (gnu packages cran)
  41   #:use-module (gnu packages graphviz)
  42   #:use-module (gnu packages maths)
  43   #:use-module (gnu packages multiprecision)
  44   #:use-module (gnu packages pkg-config)
  45   #:use-module (gnu packages python)
  46   #:use-module (gnu packages python-science)
  47   #:use-module (gnu packages python-web)
  48   #:use-module (gnu packages python-xyz)
  49   #:use-module (gnu packages statistics)
  50   #:use-module (gnu packages swig)
  51   #:use-module (gnu packages time)
  52   #:use-module (gnu packages xml))
  53
  54 (define-public igraph
  55   (package
  56     (name "igraph")
  57     (version "0.7.1")
  58     (source
  59      (origin
  60        (method url-fetch)
  61        (uri (string-append "http://igraph.org/nightly/get/c/igraph-"
  62                            version ".tar.gz"))
  63        (sha256
  64         (base32
  65          "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
  66     (build-system gnu-build-system)
  67     (arguments
  68      `(#:configure-flags
  69        (list "--with-external-glpk"
  70              "--with-external-blas"
  71              "--with-external-lapack")))
  72     (inputs
  73      `(("gmp" ,gmp)
  74        ("glpk" ,glpk)
  75        ("libxml2" ,libxml2)
  76        ("lapack" ,lapack)
  77        ("openblas" ,openblas)
  78        ("zlib" ,zlib)))
  79     (home-page "http://igraph.org")
  80     (synopsis "Network analysis and visualization")
  81     (description
  82      "This package provides a library for the analysis of networks and graphs.
  83 It can handle large graphs very well and provides functions for generating
  84 random and regular graphs, graph visualization, centrality methods and much
  85 more.")
  86     (license license:gpl2+)))
  87
  88 (define-public python-igraph
  89   (package (inherit igraph)
  90     (name "python-igraph")
  91     (version "0.7.1.post6")
  92     (source
  93      (origin
  94        (method url-fetch)
  95        (uri (pypi-uri "python-igraph" version))
  96        (sha256
  97         (base32
  98          "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
  99     (build-system python-build-system)
 100     (arguments '())
 101     (inputs
 102      `(("igraph" ,igraph)))
 103     (native-inputs
 104      `(("pkg-config" ,pkg-config)))
 105     (home-page "http://pypi.python.org/pypi/python-igraph")
 106     (synopsis "Python bindings for the igraph network analysis library")))
 107
 108 (define-public r-igraph
 109   (package
 110     (name "r-igraph")
 111     (version "1.2.4.2")
 112     (source
 113      (origin
 114        (method url-fetch)
 115        (uri (cran-uri "igraph" version))
 116        (sha256
 117         (base32
 118          "0scrbqb26pam8akblb4g9rkz888s0xffw3gcly78s4ijj67barxd"))))
 119     (build-system r-build-system)
 120     (native-inputs
 121      `(("gfortran" ,gfortran)))
 122     (inputs
 123      `(("gmp" ,gmp)
 124        ("glpk" ,glpk)
 125        ("libxml2" ,libxml2)
 126        ("zlib" ,zlib)))
 127     (propagated-inputs
 128      `(("r-magrittr" ,r-magrittr)
 129        ("r-matrix" ,r-matrix)
 130        ("r-pkgconfig" ,r-pkgconfig)))
 131     (home-page "http://igraph.org")
 132     (synopsis "Network analysis and visualization")
 133     (description
 134      "This package provides routines for simple graphs and network analysis.
 135 It can handle large graphs very well and provides functions for generating
 136 random and regular graphs, graph visualization, centrality methods and much
 137 more.")
 138     (license license:gpl2+)))
 139
 140 (define-public r-diffusionmap
 141   (package
 142     (name "r-diffusionmap")
 143     (version "1.2.0")
 144     (source
 145      (origin
 146        (method url-fetch)
 147        (uri (cran-uri "diffusionMap" version))
 148        (sha256
 149         (base32
 150          "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
 151     (properties `((upstream-name . "diffusionMap")))
 152     (build-system r-build-system)
 153     (propagated-inputs
 154      `(("r-igraph" ,r-igraph)
 155        ("r-matrix" ,r-matrix)
 156        ("r-scatterplot3d" ,r-scatterplot3d)))
 157     (home-page "https://www.r-project.org")
 158     (synopsis "Diffusion map")
 159     (description "This package implements the diffusion map method of data
 160 parametrization, including creation and visualization of diffusion maps,
 161 clustering with diffusion K-means and regression using the adaptive regression
 162 model.")
 163     (license license:gpl2)))
 164
 165 (define-public r-rgraphviz
 166   (package
 167     (name "r-rgraphviz")
 168     (version "2.30.0")
 169     (source
 170      (origin
 171        (method url-fetch)
 172        (uri (bioconductor-uri "Rgraphviz" version))
 173        (sha256
 174         (base32
 175          "00lrkbgbb4payybckcmazsv8skysgdlglyqbl7yjb37vv3gnfc6c"))))
 176     (properties `((upstream-name . "Rgraphviz")))
 177     (build-system r-build-system)
 178     ;; FIXME: Rgraphviz bundles the sources of an older variant of
 179     ;; graphviz.  It does not build with the latest version of graphviz, so
 180     ;; we do not add graphviz to the inputs.
 181     (inputs `(("zlib" ,zlib)))
 182     (propagated-inputs
 183      `(("r-graph" ,r-graph)))
 184     (native-inputs
 185      `(("pkg-config" ,pkg-config)))
 186     (home-page "http://bioconductor.org/packages/Rgraphviz")
 187     (synopsis "Plotting capabilities for R graph objects")
 188     (description
 189      "This package interfaces R with the graphviz library for plotting R graph
 190 objects from the @code{graph} package.")
 191     (license license:epl1.0)))
 192
 193 (define-public r-rbiofabric
 194   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
 195         (revision "1"))
 196     (package
 197       (name "r-rbiofabric")
 198       (version (string-append "0.3-" revision "." (string-take commit 7)))
 199       (source (origin
 200                 (method git-fetch)
 201                 (uri (git-reference
 202                       (url "https://github.com/wjrl/RBioFabric.git")
 203                       (commit commit)))
 204                 (file-name (string-append name "-" version "-checkout"))
 205                 (sha256
 206                  (base32
 207                   "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
 208       (build-system r-build-system)
 209       (propagated-inputs
 210        `(("r-igraph" ,r-igraph)))
 211       (home-page "http://www.biofabric.org/")
 212       (synopsis "BioFabric network visualization")
 213       (description "This package provides an implementation of the function
 214 @code{bioFabric} for creating scalable network digrams where nodes are
 215 represented by horizontal lines, and edges are represented by vertical
 216 lines.")
 217       (license license:expat))))
 218
 219 (define-public python-plotly
 220   (package
 221     (name "python-plotly")
 222     (version "2.4.1")
 223     (source
 224       (origin
 225         (method url-fetch)
 226         (uri (pypi-uri "plotly" version))
 227         (sha256
 228          (base32
 229           "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
 230     (build-system python-build-system)
 231     (arguments
 232      '(#:tests? #f)) ; The tests are not distributed in the release
 233     (propagated-inputs
 234      `(("python-decorator" ,python-decorator)
 235        ("python-nbformat" ,python-nbformat)
 236        ("python-pandas" ,python-pandas)
 237        ("python-pytz" ,python-pytz)
 238        ("python-requests" ,python-requests)
 239        ("python-six" ,python-six)))
 240     (home-page "https://plot.ly/python/")
 241     (synopsis "Interactive plotting library for Python")
 242     (description "Plotly's Python graphing library makes interactive,
 243 publication-quality graphs online.  Examples of how to make line plots, scatter
 244 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
 245 subplots, multiple-axes, polar charts, and bubble charts. ")
 246     (license license:expat)))
 247
 248 (define-public python2-plotly
 249   (package-with-python2 python-plotly))
 250
 251 (define-public python-louvain
 252   (package
 253     (name "python-louvain")
 254     (version "0.6.1")
 255     ;; The tarball on Pypi does not include the tests.
 256     (source (origin
 257               (method git-fetch)
 258               (uri (git-reference
 259                     (url "https://github.com/vtraag/louvain-igraph.git")
 260                     (commit version)))
 261               (file-name (git-file-name name version))
 262               (sha256
 263                (base32
 264                 "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
 265     (build-system python-build-system)
 266     (propagated-inputs
 267      `(("python-ddt" ,python-ddt)
 268        ("python-igraph" ,python-igraph)))
 269     (inputs
 270      `(("igraph" ,igraph)))
 271     (native-inputs
 272      `(("pkg-config" ,pkg-config)
 273        ("python-pytest" ,python-pytest)))
 274     (home-page "https://github.com/vtraag/louvain-igraph")
 275     (synopsis "Algorithm for methods of community detection in large networks")
 276     (description
 277      "This package provides an implementation of the Louvain algorithm for use
 278 with igraph.  Louvain is a general algorithm for methods of community
 279 detection in large networks.
 280
 281 This package has been superseded by the @code{leidenalg} package and should
 282 not be used for new projects.")
 283     (license license:gpl3+)))
 284
 285 (define-public faiss
 286   (package
 287     (name "faiss")
 288     (version "1.5.0")
 289     (source (origin
 290               (method git-fetch)
 291               (uri (git-reference
 292                     (url "https://github.com/facebookresearch/faiss.git")
 293                     (commit (string-append "v" version))))
 294               (file-name (git-file-name name version))
 295               (sha256
 296                (base32
 297                 "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
 298               (modules '((guix build utils)))
 299               (snippet
 300                '(begin
 301                   (substitute* "utils.cpp"
 302                     (("#include <immintrin.h>")
 303                      "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
 304                   #t))))
 305     (build-system cmake-build-system)
 306     (arguments
 307      `(#:configure-flags
 308        (list "-DBUILD_WITH_GPU=OFF"  ; thanks, but no thanks, CUDA.
 309              "-DBUILD_TUTORIAL=OFF") ; we don't need those
 310        #:phases
 311        (modify-phases %standard-phases
 312          (add-after 'unpack 'prepare-build
 313            (lambda _
 314              (let ((features (list ,@(let ((system (or (%current-target-system)
 315                                                        (%current-system))))
 316                                        (cond
 317                                         ((string-prefix? "x86_64" system)
 318                                          '("-mavx" "-msse2" "-mpopcnt"))
 319                                         ((string-prefix? "i686" system)
 320                                          '("-msse2" "-mpopcnt"))
 321                                         (else
 322                                          '()))))))
 323                (substitute* "CMakeLists.txt"
 324                  (("-m64") "")
 325                  (("-mpopcnt") "") ; only some architectures
 326                  (("-msse4")
 327                   (string-append
 328                    (string-join features)
 329                    " -I" (getcwd)))
 330                  ;; Build also the shared library
 331                  (("ARCHIVE DESTINATION lib")
 332                   "LIBRARY DESTINATION lib")
 333                  (("add_library.*" m)
 334                   "\
 335 add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
 336 set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
 337 add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
 338 add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
 339 install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
 340 \n")))
 341
 342              ;; See https://github.com/facebookresearch/faiss/issues/520
 343              (substitute* "IndexScalarQuantizer.cpp"
 344                (("#define USE_AVX") ""))
 345
 346              ;; Make header files available for compiling tests.
 347              (mkdir-p "faiss")
 348              (for-each (lambda (file)
 349                          (mkdir-p (string-append "faiss/" (dirname file)))
 350                          (copy-file file (string-append "faiss/" file)))
 351                        (find-files "." "\\.h$"))
 352              #t))
 353          (replace 'check
 354            (lambda _
 355              (invoke "make" "-C" "tests"
 356                      (format #f "-j~a" (parallel-job-count)))))
 357          (add-after 'install 'remove-tests
 358            (lambda* (#:key outputs #:allow-other-keys)
 359              (delete-file-recursively
 360               (string-append (assoc-ref outputs "out")
 361                              "/test"))
 362              #t)))))
 363     (inputs
 364      `(("openblas" ,openblas)))
 365     (native-inputs
 366      `(("googletest" ,googletest)))
 367     (home-page "https://github.com/facebookresearch/faiss")
 368     (synopsis "Efficient similarity search and clustering of dense vectors")
 369     (description "Faiss is a library for efficient similarity search and
 370 clustering of dense vectors.  It contains algorithms that search in sets of
 371 vectors of any size, up to ones that possibly do not fit in RAM.  It also
 372 contains supporting code for evaluation and parameter tuning.")
 373     (license license:bsd-3)))
 374
 375 (define-public python-faiss
 376   (package (inherit faiss)
 377     (name "python-faiss")
 378     (build-system python-build-system)
 379     (arguments
 380      `(#:phases
 381        (modify-phases %standard-phases
 382          (add-after 'unpack 'chdir
 383            (lambda _ (chdir "python") #t))
 384          (add-after 'chdir 'build-swig
 385            (lambda* (#:key inputs #:allow-other-keys)
 386              (with-output-to-file "../makefile.inc"
 387                (lambda ()
 388                  (let ((python-version ,(version-major+minor (package-version python))))
 389                    (format #t "\
 390 PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
 391 LIBS = -lpython~am -lfaiss
 392 SHAREDFLAGS = -shared -fopenmp
 393 CXXFLAGS = -fpermissive -fopenmp -fPIC
 394 CPUFLAGS = ~{~a ~}~%"
 395                            (assoc-ref inputs "python*") python-version
 396                            (assoc-ref inputs "python-numpy") python-version
 397                            python-version
 398                            (list ,@(let ((system (or (%current-target-system)
 399                                                      (%current-system))))
 400                                      (cond
 401                                        ((string-prefix? "x86_64" system)
 402                                         '("-mavx" "-msse2" "-mpopcnt"))
 403                                        ((string-prefix? "i686" system)
 404                                         '("-msse2" "-mpopcnt"))
 405                                        (else
 406                                          '()))))))))
 407              (substitute* "Makefile"
 408                (("../libfaiss.a") ""))
 409              (invoke "make" "cpu"))))))
 410     (inputs
 411      `(("faiss" ,faiss)
 412        ("openblas" ,openblas)
 413        ("python*" ,python)
 414        ("swig" ,swig)))
 415     (propagated-inputs
 416      `(("python-matplotlib" ,python-matplotlib)
 417        ("python-numpy" ,python-numpy)))
 418     (description "Faiss is a library for efficient similarity search and
 419 clustering of dense vectors.  This package provides Python bindings to the
 420 Faiss library.")))
 421
 422 (define-public python-leidenalg
 423   (package
 424     (name "python-leidenalg")
 425     (version "0.7.0")
 426     (source
 427      (origin
 428        (method url-fetch)
 429        (uri (pypi-uri "leidenalg" version))
 430        (sha256
 431         (base32
 432          "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
 433     (build-system python-build-system)
 434     (arguments '(#:tests? #f)) ; tests are not included
 435     (native-inputs
 436      `(("pkg-config" ,pkg-config)))
 437     (inputs
 438      `(("igraph" ,igraph)))
 439     (propagated-inputs
 440      `(("python-igraph" ,python-igraph)))
 441     (home-page "https://github.com/vtraag/leidenalg")
 442     (synopsis "Community detection in large networks")
 443     (description
 444      "Leiden is a general algorithm for methods of community detection in
 445 large networks.  This package implements the Leiden algorithm in C++ and
 446 exposes it to Python.  Besides the relative flexibility of the implementation,
 447 it also scales well, and can be run on graphs of millions of nodes (as long as
 448 they can fit in memory).  The core function is @code{find_partition} which
 449 finds the optimal partition using the Leiden algorithm, which is an extension
 450 of the Louvain algorithm, for a number of different methods.")
 451     (license license:gpl3+)))
 452
 453 (define-public edge-addition-planarity-suite
 454   (package
 455     (name "edge-addition-planarity-suite")
 456     (version "3.0.0.5")
 457     (source
 458      (origin
 459        (method git-fetch)
 460        (uri (git-reference
 461               (url (string-append "https://github.com/graph-algorithms/"
 462                                   name))
 463               (commit (string-append "Version_" version))))
 464        (file-name (git-file-name name version))
 465        (sha256
 466         (base32
 467          "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
 468     (build-system gnu-build-system)
 469     (native-inputs
 470      `(("autoconf" ,autoconf)
 471        ("automake" ,automake)
 472        ("libtool" ,libtool)))
 473     (synopsis "Embedding of planar graphs")
 474     (description "The package provides a reference implementation of the
 475 linear time edge addition algorithm for embedding planar graphs and
 476 isolating planarity obstructions.")
 477     (license license:bsd-3)
 478     (home-page
 479       "https://github.com/graph-algorithms/edge-addition-planarity-suite")))
 480
 481 (define-public rw
 482   (package
 483     (name "rw")
 484     ;; There is a version 0.8, but the tarball is broken with symlinks
 485     ;; to /usr/share.
 486     (version "0.7")
 487     (source (origin
 488               (method url-fetch)
 489               (uri (string-append "mirror://sourceforge/rankwidth/"
 490                                   "rw-" version ".tar.gz"))
 491        (sha256
 492         (base32
 493          "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
 494     (build-system gnu-build-system)
 495     (native-inputs
 496      `(("pkg-config" ,pkg-config)))
 497     (inputs
 498      `(("igraph" ,igraph)))
 499     (home-page "https://sourceforge.net/projects/rankwidth/")
 500     (synopsis "Rank-width and rank-decomposition of graphs")
 501     (description "rw computes rank-width and rank-decompositions
 502 of graphs.")
 503     (license license:gpl2+)))