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 ;;;
   7 ;;; This file is part of GNU Guix.
   8 ;;;
   9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  10 ;;; under the terms of the GNU General Public License as published by
  11 ;;; the Free Software Foundation; either version 3 of the License, or (at
  12 ;;; your option) any later version.
  13 ;;;
  14 ;;; GNU Guix is distributed in the hope that it will be useful, but
  15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  17 ;;; GNU General Public License for more details.
  18 ;;;
  19 ;;; You should have received a copy of the GNU General Public License
  20 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  21
  22 (define-module (gnu packages graph)
  23   #:use-module (guix download)
  24   #:use-module (guix git-download)
  25   #:use-module (guix packages)
  26   #:use-module (guix utils)
  27   #:use-module (guix build-system cmake)
  28   #:use-module (guix build-system gnu)
  29   #:use-module (guix build-system python)
  30   #:use-module (guix build-system r)
  31   #:use-module ((guix licenses) #:prefix license:)
  32   #:use-module (gnu packages)
  33   #:use-module (gnu packages gcc)
  34   #:use-module (gnu packages bioconductor)
  35   #:use-module (gnu packages bioinformatics)
  36   #:use-module (gnu packages check)
  37   #:use-module (gnu packages compression)
  38   #:use-module (gnu packages cran)
  39   #:use-module (gnu packages graphviz)
  40   #:use-module (gnu packages maths)
  41   #:use-module (gnu packages multiprecision)
  42   #:use-module (gnu packages pkg-config)
  43   #:use-module (gnu packages python)
  44   #:use-module (gnu packages python-web)
  45   #:use-module (gnu packages python-xyz)
  46   #:use-module (gnu packages statistics)
  47   #:use-module (gnu packages swig)
  48   #:use-module (gnu packages time)
  49   #:use-module (gnu packages xml))
  50
  51 (define-public igraph
  52   (package
  53     (name "igraph")
  54     (version "0.7.1")
  55     (source
  56      (origin
  57        (method url-fetch)
  58        (uri (string-append "http://igraph.org/nightly/get/c/igraph-"
  59                            version ".tar.gz"))
  60        (sha256
  61         (base32
  62          "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
  63     (build-system gnu-build-system)
  64     (arguments
  65      `(#:configure-flags
  66        (list "--with-external-glpk"
  67              "--with-external-blas"
  68              "--with-external-lapack")))
  69     (inputs
  70      `(("gmp" ,gmp)
  71        ("glpk" ,glpk)
  72        ("libxml2" ,libxml2)
  73        ("lapack" ,lapack)
  74        ("openblas" ,openblas)
  75        ("zlib" ,zlib)))
  76     (home-page "http://igraph.org")
  77     (synopsis "Network analysis and visualization")
  78     (description
  79      "This package provides a library for the analysis of networks and graphs.
  80 It can handle large graphs very well and provides functions for generating
  81 random and regular graphs, graph visualization, centrality methods and much
  82 more.")
  83     (license license:gpl2+)))
  84
  85 (define-public python-igraph
  86   (package (inherit igraph)
  87     (name "python-igraph")
  88     (version "0.7.1.post6")
  89     (source
  90      (origin
  91        (method url-fetch)
  92        (uri (pypi-uri "python-igraph" version))
  93        (sha256
  94         (base32
  95          "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
  96     (build-system python-build-system)
  97     (arguments '())
  98     (inputs
  99      `(("igraph" ,igraph)))
 100     (native-inputs
 101      `(("pkg-config" ,pkg-config)))
 102     (home-page "http://pypi.python.org/pypi/python-igraph")
 103     (synopsis "Python bindings for the igraph network analysis library")))
 104
 105 (define-public r-igraph
 106   (package
 107     (name "r-igraph")
 108     (version "1.2.4.1")
 109     (source
 110      (origin
 111        (method url-fetch)
 112        (uri (cran-uri "igraph" version))
 113        (sha256
 114         (base32
 115          "1074y8mvprrqlkb4vwa2qc9l03r8d7p5vaaqacj4ljjs7dvcq6l9"))))
 116     (build-system r-build-system)
 117     (native-inputs
 118      `(("gfortran" ,gfortran)))
 119     (inputs
 120      `(("gmp" ,gmp)
 121        ("glpk" ,glpk)
 122        ("libxml2" ,libxml2)
 123        ("zlib" ,zlib)))
 124     (propagated-inputs
 125      `(("r-magrittr" ,r-magrittr)
 126        ("r-matrix" ,r-matrix)
 127        ("r-pkgconfig" ,r-pkgconfig)))
 128     (home-page "http://igraph.org")
 129     (synopsis "Network analysis and visualization")
 130     (description
 131      "This package provides routines for simple graphs and network analysis.
 132 It can handle large graphs very well and provides functions for generating
 133 random and regular graphs, graph visualization, centrality methods and much
 134 more.")
 135     (license license:gpl2+)))
 136
 137 (define-public r-diffusionmap
 138   (package
 139     (name "r-diffusionmap")
 140     (version "1.1-0.1")
 141     (source
 142      (origin
 143        (method url-fetch)
 144        (uri (cran-uri "diffusionMap" version))
 145        (sha256
 146         (base32
 147          "11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j"))))
 148     (properties `((upstream-name . "diffusionMap")))
 149     (build-system r-build-system)
 150     (propagated-inputs
 151      `(("r-igraph" ,r-igraph)
 152        ("r-matrix" ,r-matrix)
 153        ("r-scatterplot3d" ,r-scatterplot3d)))
 154     (home-page "https://www.r-project.org")
 155     (synopsis "Diffusion map")
 156     (description "This package implements the diffusion map method of data
 157 parametrization, including creation and visualization of diffusion maps,
 158 clustering with diffusion K-means and regression using the adaptive regression
 159 model.")
 160     (license license:gpl2)))
 161
 162 (define-public r-rgraphviz
 163   (package
 164     (name "r-rgraphviz")
 165     (version "2.28.0")
 166     (source
 167      (origin
 168        (method url-fetch)
 169        (uri (bioconductor-uri "Rgraphviz" version))
 170        (sha256
 171         (base32
 172          "0nivz8fshaqig6ynjqbya2gmxsy4hm7jnd8fhb853z5g0ydp7g0c"))))
 173     (properties `((upstream-name . "Rgraphviz")))
 174     (build-system r-build-system)
 175     ;; FIXME: Rgraphviz bundles the sources of an older variant of
 176     ;; graphviz.  It does not build with the latest version of graphviz, so
 177     ;; we do not add graphviz to the inputs.
 178     (inputs `(("zlib" ,zlib)))
 179     (propagated-inputs
 180      `(("r-graph" ,r-graph)))
 181     (native-inputs
 182      `(("pkg-config" ,pkg-config)))
 183     (home-page "http://bioconductor.org/packages/Rgraphviz")
 184     (synopsis "Plotting capabilities for R graph objects")
 185     (description
 186      "This package interfaces R with the graphviz library for plotting R graph
 187 objects from the @code{graph} package.")
 188     (license license:epl1.0)))
 189
 190 (define-public r-rbiofabric
 191   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
 192         (revision "1"))
 193     (package
 194       (name "r-rbiofabric")
 195       (version (string-append "0.3-" revision "." (string-take commit 7)))
 196       (source (origin
 197                 (method git-fetch)
 198                 (uri (git-reference
 199                       (url "https://github.com/wjrl/RBioFabric.git")
 200                       (commit commit)))
 201                 (file-name (string-append name "-" version "-checkout"))
 202                 (sha256
 203                  (base32
 204                   "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
 205       (build-system r-build-system)
 206       (propagated-inputs
 207        `(("r-igraph" ,r-igraph)))
 208       (home-page "http://www.biofabric.org/")
 209       (synopsis "BioFabric network visualization")
 210       (description "This package provides an implementation of the function
 211 @code{bioFabric} for creating scalable network digrams where nodes are
 212 represented by horizontal lines, and edges are represented by vertical
 213 lines.")
 214       (license license:expat))))
 215
 216 (define-public python-plotly
 217   (package
 218     (name "python-plotly")
 219     (version "2.4.1")
 220     (source
 221       (origin
 222         (method url-fetch)
 223         (uri (pypi-uri "plotly" version))
 224         (sha256
 225          (base32
 226           "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
 227     (build-system python-build-system)
 228     (arguments
 229      '(#:tests? #f)) ; The tests are not distributed in the release
 230     (propagated-inputs
 231      `(("python-decorator" ,python-decorator)
 232        ("python-nbformat" ,python-nbformat)
 233        ("python-pandas" ,python-pandas)
 234        ("python-pytz" ,python-pytz)
 235        ("python-requests" ,python-requests)
 236        ("python-six" ,python-six)))
 237     (home-page "https://plot.ly/python/")
 238     (synopsis "Interactive plotting library for Python")
 239     (description "Plotly's Python graphing library makes interactive,
 240 publication-quality graphs online.  Examples of how to make line plots, scatter
 241 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
 242 subplots, multiple-axes, polar charts, and bubble charts. ")
 243     (license license:expat)))
 244
 245 (define-public python2-plotly
 246   (package-with-python2 python-plotly))
 247
 248 (define-public python-louvain
 249   (package
 250     (name "python-louvain")
 251     (version "0.6.1")
 252     ;; The tarball on Pypi does not include the tests.
 253     (source (origin
 254               (method git-fetch)
 255               (uri (git-reference
 256                     (url "https://github.com/vtraag/louvain-igraph.git")
 257                     (commit version)))
 258               (file-name (git-file-name name version))
 259               (sha256
 260                (base32
 261                 "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
 262     (build-system python-build-system)
 263     (propagated-inputs
 264      `(("python-ddt" ,python-ddt)
 265        ("python-igraph" ,python-igraph)))
 266     (inputs
 267      `(("igraph" ,igraph)))
 268     (native-inputs
 269      `(("pkg-config" ,pkg-config)
 270        ("python-pytest" ,python-pytest)))
 271     (home-page "https://github.com/vtraag/louvain-igraph")
 272     (synopsis "Algorithm for methods of community detection in large networks")
 273     (description
 274      "This package provides an implementation of the Louvain algorithm for use
 275 with igraph.  Louvain is a general algorithm for methods of community
 276 detection in large networks.
 277
 278 This package has been superseded by the @code{leidenalg} package and should
 279 not be used for new projects.")
 280     (license license:gpl3+)))
 281
 282 (define-public faiss
 283   (package
 284     (name "faiss")
 285     (version "1.5.0")
 286     (source (origin
 287               (method git-fetch)
 288               (uri (git-reference
 289                     (url "https://github.com/facebookresearch/faiss.git")
 290                     (commit (string-append "v" version))))
 291               (file-name (git-file-name name version))
 292               (sha256
 293                (base32
 294                 "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
 295               (modules '((guix build utils)))
 296               (snippet
 297                '(begin
 298                   (substitute* "utils.cpp"
 299                     (("#include <immintrin.h>")
 300                      "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
 301                   #t))))
 302     (build-system cmake-build-system)
 303     (arguments
 304      `(#:configure-flags
 305        (list "-DBUILD_WITH_GPU=OFF"  ; thanks, but no thanks, CUDA.
 306              "-DBUILD_TUTORIAL=OFF") ; we don't need those
 307        #:phases
 308        (modify-phases %standard-phases
 309          (add-after 'unpack 'prepare-build
 310            (lambda _
 311              (let ((features (list ,@(let ((system (or (%current-target-system)
 312                                                        (%current-system))))
 313                                        (cond
 314                                         ((string-prefix? "x86_64" system)
 315                                          '("-mavx" "-msse2" "-mpopcnt"))
 316                                         ((string-prefix? "i686" system)
 317                                          '("-msse2" "-mpopcnt"))
 318                                         (else
 319                                          '()))))))
 320                (substitute* "CMakeLists.txt"
 321                  (("-m64") "")
 322                  (("-mpopcnt") "") ; only some architectures
 323                  (("-msse4")
 324                   (string-append
 325                    (string-join features)
 326                    " -I" (getcwd)))
 327                  ;; Build also the shared library
 328                  (("ARCHIVE DESTINATION lib")
 329                   "LIBRARY DESTINATION lib")
 330                  (("add_library.*" m)
 331                   "\
 332 add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
 333 set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
 334 add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
 335 add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
 336 install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
 337 \n")))
 338
 339              ;; See https://github.com/facebookresearch/faiss/issues/520
 340              (substitute* "IndexScalarQuantizer.cpp"
 341                (("#define USE_AVX") ""))
 342
 343              ;; Make header files available for compiling tests.
 344              (mkdir-p "faiss")
 345              (for-each (lambda (file)
 346                          (mkdir-p (string-append "faiss/" (dirname file)))
 347                          (copy-file file (string-append "faiss/" file)))
 348                        (find-files "." "\\.h$"))
 349              #t))
 350          (replace 'check
 351            (lambda _
 352              (invoke "make" "-C" "tests"
 353                      (format #f "-j~a" (parallel-job-count)))))
 354          (add-after 'install 'remove-tests
 355            (lambda* (#:key outputs #:allow-other-keys)
 356              (delete-file-recursively
 357               (string-append (assoc-ref outputs "out")
 358                              "/test"))
 359              #t)))))
 360     (inputs
 361      `(("openblas" ,openblas)))
 362     (native-inputs
 363      `(("googletest" ,googletest)))
 364     (home-page "https://github.com/facebookresearch/faiss")
 365     (synopsis "Efficient similarity search and clustering of dense vectors")
 366     (description "Faiss is a library for efficient similarity search and
 367 clustering of dense vectors.  It contains algorithms that search in sets of
 368 vectors of any size, up to ones that possibly do not fit in RAM.  It also
 369 contains supporting code for evaluation and parameter tuning.")
 370     (license license:bsd-3)))
 371
 372 (define-public python-faiss
 373   (package (inherit faiss)
 374     (name "python-faiss")
 375     (build-system python-build-system)
 376     (arguments
 377      `(#:phases
 378        (modify-phases %standard-phases
 379          (add-after 'unpack 'chdir
 380            (lambda _ (chdir "python") #t))
 381          (add-after 'chdir 'build-swig
 382            (lambda* (#:key inputs #:allow-other-keys)
 383              (with-output-to-file "../makefile.inc"
 384                (lambda ()
 385                  (let ((python-version ,(version-major+minor (package-version python))))
 386                    (format #t "\
 387 PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
 388 LIBS = -lpython~am -lfaiss
 389 SHAREDFLAGS = -shared -fopenmp
 390 CXXFLAGS = -fpermissive -std=c++11 -fopenmp -fPIC
 391 CPUFLAGS = ~{~a ~}~%"
 392                            (assoc-ref inputs "python*") python-version
 393                            (assoc-ref inputs "python-numpy") python-version
 394                            python-version
 395                            (list ,@(let ((system (or (%current-target-system)
 396                                                      (%current-system))))
 397                                      (cond
 398                                        ((string-prefix? "x86_64" system)
 399                                         '("-mavx" "-msse2" "-mpopcnt"))
 400                                        ((string-prefix? "i686" system)
 401                                         '("-msse2" "-mpopcnt"))
 402                                        (else
 403                                          '()))))))))
 404              (substitute* "Makefile"
 405                (("../libfaiss.a") ""))
 406              (invoke "make" "cpu"))))))
 407     (inputs
 408      `(("faiss" ,faiss)
 409        ("openblas" ,openblas)
 410        ("python*" ,python)
 411        ("swig" ,swig)))
 412     (propagated-inputs
 413      `(("python-matplotlib" ,python-matplotlib)
 414        ("python-numpy" ,python-numpy)))
 415     (description "Faiss is a library for efficient similarity search and
 416 clustering of dense vectors.  This package provides Python bindings to the
 417 Faiss library.")))
 418
 419 (define-public python-leidenalg
 420   (package
 421     (name "python-leidenalg")
 422     (version "0.7.0")
 423     (source
 424      (origin
 425        (method url-fetch)
 426        (uri (pypi-uri "leidenalg" version))
 427        (sha256
 428         (base32
 429          "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
 430     (build-system python-build-system)
 431     (arguments '(#:tests? #f)) ; tests are not included
 432     (native-inputs
 433      `(("pkg-config" ,pkg-config)))
 434     (inputs
 435      `(("igraph" ,igraph)))
 436     (propagated-inputs
 437      `(("python-igraph" ,python-igraph)))
 438     (home-page "https://github.com/vtraag/leidenalg")
 439     (synopsis "Community detection in large networks")
 440     (description
 441      "Leiden is a general algorithm for methods of community detection in
 442 large networks.  This package implements the Leiden algorithm in C++ and
 443 exposes it to Python.  Besides the relative flexibility of the implementation,
 444 it also scales well, and can be run on graphs of millions of nodes (as long as
 445 they can fit in memory).  The core function is @code{find_partition} which
 446 finds the optimal partition using the Leiden algorithm, which is an extension
 447 of the Louvain algorithm, for a number of different methods.")
 448     (license license:gpl3+)))