gnu/packages/graph.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017, 2018, 2019, 2020 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 ;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
   8 ;;;
   9 ;;; This file is part of GNU Guix.
  10 ;;;
  11 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  12 ;;; under the terms of the GNU General Public License as published by
  13 ;;; the Free Software Foundation; either version 3 of the License, or (at
  14 ;;; your option) any later version.
  15 ;;;
  16 ;;; GNU Guix is distributed in the hope that it will be useful, but
  17 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  18 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  19 ;;; GNU General Public License for more details.
  20 ;;;
  21 ;;; You should have received a copy of the GNU General Public License
  22 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  23
  24 (define-module (gnu packages graph)
  25   #:use-module (guix download)
  26   #:use-module (guix git-download)
  27   #:use-module (guix packages)
  28   #:use-module (guix utils)
  29   #:use-module (guix build-system cmake)
  30   #:use-module (guix build-system gnu)
  31   #:use-module (guix build-system python)
  32   #:use-module (guix build-system r)
  33   #:use-module ((guix licenses) #:prefix license:)
  34   #:use-module (gnu packages)
  35   #:use-module (gnu packages gcc)
  36   #:use-module (gnu packages autotools)
  37   #:use-module (gnu packages bioconductor)
  38   #:use-module (gnu packages bioinformatics)
  39   #:use-module (gnu packages check)
  40   #:use-module (gnu packages compression)
  41   #:use-module (gnu packages cran)
  42   #:use-module (gnu packages gd)
  43   #:use-module (gnu packages graphviz)
  44   #:use-module (gnu packages maths)
  45   #:use-module (gnu packages multiprecision)
  46   #:use-module (gnu packages pkg-config)
  47   #:use-module (gnu packages python)
  48   #:use-module (gnu packages python-science)
  49   #:use-module (gnu packages python-web)
  50   #:use-module (gnu packages python-xyz)
  51   #:use-module (gnu packages statistics)
  52   #:use-module (gnu packages swig)
  53   #:use-module (gnu packages time)
  54   #:use-module (gnu packages xml))
  55
  56 (define-public igraph
  57   (package
  58     (name "igraph")
  59     (version "0.8.0")
  60     (source
  61      (origin
  62        (method url-fetch)
  63        (uri (string-append "https://github.com/igraph/igraph/releases/"
  64                            "download/" version "/igraph-" version ".tar.gz"))
  65        (sha256
  66         (base32
  67          "0jcnfvahrlj08y46vnax5y5bb294v4b9n00qsy7pbx0cc0sp6qvj"))))
  68     (build-system gnu-build-system)
  69     (arguments
  70      `(#:configure-flags
  71        (list "--with-external-glpk"
  72              "--with-external-blas"
  73              "--with-external-lapack")))
  74     (inputs
  75      `(("gmp" ,gmp)
  76        ("glpk" ,glpk)
  77        ("libxml2" ,libxml2)
  78        ("lapack" ,lapack)
  79        ("openblas" ,openblas)
  80        ("zlib" ,zlib)))
  81     (home-page "http://igraph.org")
  82     (synopsis "Network analysis and visualization")
  83     (description
  84      "This package provides a library for the analysis of networks and graphs.
  85 It can handle large graphs very well and provides functions for generating
  86 random and regular graphs, graph visualization, centrality methods and much
  87 more.")
  88     (license license:gpl2+)))
  89
  90 (define-public python-igraph
  91   (package (inherit igraph)
  92     (name "python-igraph")
  93     (version "0.8.0")
  94     (source
  95      (origin
  96        (method url-fetch)
  97        (uri (pypi-uri "python-igraph" version))
  98        (sha256
  99         (base32
 100          "13mbrlmnbgbzw6y8ws7wj0a3ly3in8j4l1ngi6yxvgvxxi4bprj7"))))
 101     (build-system python-build-system)
 102     (arguments
 103      '(#:configure-flags
 104        (list "--use-pkg-config")
 105        #:phases
 106        (modify-phases %standard-phases
 107          (replace 'build
 108            (lambda _
 109              (invoke "python" "./setup.py" "build" "--use-pkg-config")))
 110          (delete 'check)
 111          (add-after 'install 'check
 112            (lambda* (#:key inputs outputs #:allow-other-keys)
 113              (add-installed-pythonpath inputs outputs)
 114              (invoke "pytest" "-v"))))))
 115     (inputs
 116      `(("igraph" ,igraph)))
 117     (propagated-inputs
 118      `(("python-texttable" ,python-texttable)))
 119     (native-inputs
 120      `(("pkg-config" ,pkg-config)
 121        ("python-pytest" ,python-pytest)))
 122     (home-page "https://pypi.org/project/python-igraph/")
 123     (synopsis "Python bindings for the igraph network analysis library")))
 124
 125 (define-public r-igraph
 126   (package
 127     (name "r-igraph")
 128     (version "1.2.4.2")
 129     (source
 130      (origin
 131        (method url-fetch)
 132        (uri (cran-uri "igraph" version))
 133        (sha256
 134         (base32
 135          "0scrbqb26pam8akblb4g9rkz888s0xffw3gcly78s4ijj67barxd"))))
 136     (build-system r-build-system)
 137     (native-inputs
 138      `(("gfortran" ,gfortran)))
 139     (inputs
 140      `(("gmp" ,gmp)
 141        ("glpk" ,glpk)
 142        ("libxml2" ,libxml2)
 143        ("zlib" ,zlib)))
 144     (propagated-inputs
 145      `(("r-magrittr" ,r-magrittr)
 146        ("r-matrix" ,r-matrix)
 147        ("r-pkgconfig" ,r-pkgconfig)))
 148     (home-page "http://igraph.org")
 149     (synopsis "Network analysis and visualization")
 150     (description
 151      "This package provides routines for simple graphs and network analysis.
 152 It can handle large graphs very well and provides functions for generating
 153 random and regular graphs, graph visualization, centrality methods and much
 154 more.")
 155     (license license:gpl2+)))
 156
 157 (define-public r-diffusionmap
 158   (package
 159     (name "r-diffusionmap")
 160     (version "1.2.0")
 161     (source
 162      (origin
 163        (method url-fetch)
 164        (uri (cran-uri "diffusionMap" version))
 165        (sha256
 166         (base32
 167          "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
 168     (properties `((upstream-name . "diffusionMap")))
 169     (build-system r-build-system)
 170     (propagated-inputs
 171      `(("r-igraph" ,r-igraph)
 172        ("r-matrix" ,r-matrix)
 173        ("r-scatterplot3d" ,r-scatterplot3d)))
 174     (home-page "https://www.r-project.org")
 175     (synopsis "Diffusion map")
 176     (description "This package implements the diffusion map method of data
 177 parametrization, including creation and visualization of diffusion maps,
 178 clustering with diffusion K-means and regression using the adaptive regression
 179 model.")
 180     (license license:gpl2)))
 181
 182 (define-public r-rgraphviz
 183   (package
 184     (name "r-rgraphviz")
 185     (version "2.30.0")
 186     (source
 187      (origin
 188        (method url-fetch)
 189        (uri (bioconductor-uri "Rgraphviz" version))
 190        (sha256
 191         (base32
 192          "00lrkbgbb4payybckcmazsv8skysgdlglyqbl7yjb37vv3gnfc6c"))))
 193     (properties `((upstream-name . "Rgraphviz")))
 194     (build-system r-build-system)
 195     ;; FIXME: Rgraphviz bundles the sources of an older variant of
 196     ;; graphviz.  It does not build with the latest version of graphviz, so
 197     ;; we do not add graphviz to the inputs.
 198     (inputs `(("zlib" ,zlib)))
 199     (propagated-inputs
 200      `(("r-graph" ,r-graph)))
 201     (native-inputs
 202      `(("pkg-config" ,pkg-config)))
 203     (home-page "https://bioconductor.org/packages/Rgraphviz")
 204     (synopsis "Plotting capabilities for R graph objects")
 205     (description
 206      "This package interfaces R with the graphviz library for plotting R graph
 207 objects from the @code{graph} package.")
 208     (license license:epl1.0)))
 209
 210 (define-public r-rbiofabric
 211   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
 212         (revision "1"))
 213     (package
 214       (name "r-rbiofabric")
 215       (version (string-append "0.3-" revision "." (string-take commit 7)))
 216       (source (origin
 217                 (method git-fetch)
 218                 (uri (git-reference
 219                       (url "https://github.com/wjrl/RBioFabric.git")
 220                       (commit commit)))
 221                 (file-name (string-append name "-" version "-checkout"))
 222                 (sha256
 223                  (base32
 224                   "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
 225       (build-system r-build-system)
 226       (propagated-inputs
 227        `(("r-igraph" ,r-igraph)))
 228       (home-page "http://www.biofabric.org/")
 229       (synopsis "BioFabric network visualization")
 230       (description "This package provides an implementation of the function
 231 @code{bioFabric} for creating scalable network digrams where nodes are
 232 represented by horizontal lines, and edges are represented by vertical
 233 lines.")
 234       (license license:expat))))
 235
 236 (define-public python-plotly
 237   (package
 238     (name "python-plotly")
 239     (version "2.4.1")
 240     (source
 241       (origin
 242         (method url-fetch)
 243         (uri (pypi-uri "plotly" version))
 244         (sha256
 245          (base32
 246           "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
 247     (build-system python-build-system)
 248     (arguments
 249      '(#:tests? #f)) ; The tests are not distributed in the release
 250     (propagated-inputs
 251      `(("python-decorator" ,python-decorator)
 252        ("python-nbformat" ,python-nbformat)
 253        ("python-pandas" ,python-pandas)
 254        ("python-pytz" ,python-pytz)
 255        ("python-requests" ,python-requests)
 256        ("python-six" ,python-six)))
 257     (home-page "https://plot.ly/python/")
 258     (synopsis "Interactive plotting library for Python")
 259     (description "Plotly's Python graphing library makes interactive,
 260 publication-quality graphs online.  Examples of how to make line plots, scatter
 261 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
 262 subplots, multiple-axes, polar charts, and bubble charts. ")
 263     (license license:expat)))
 264
 265 (define-public python2-plotly
 266   (package-with-python2 python-plotly))
 267
 268 (define-public python-louvain
 269   (package
 270     (name "python-louvain")
 271     (version "0.6.1")
 272     ;; The tarball on Pypi does not include the tests.
 273     (source (origin
 274               (method git-fetch)
 275               (uri (git-reference
 276                     (url "https://github.com/vtraag/louvain-igraph.git")
 277                     (commit version)))
 278               (file-name (git-file-name name version))
 279               (sha256
 280                (base32
 281                 "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
 282     (build-system python-build-system)
 283     (propagated-inputs
 284      `(("python-ddt" ,python-ddt)
 285        ("python-igraph" ,python-igraph)))
 286     (inputs
 287      `(("igraph" ,igraph)))
 288     (native-inputs
 289      `(("pkg-config" ,pkg-config)
 290        ("python-pytest" ,python-pytest)))
 291     (home-page "https://github.com/vtraag/louvain-igraph")
 292     (synopsis "Algorithm for methods of community detection in large networks")
 293     (description
 294      "This package provides an implementation of the Louvain algorithm for use
 295 with igraph.  Louvain is a general algorithm for methods of community
 296 detection in large networks.
 297
 298 This package has been superseded by the @code{leidenalg} package and should
 299 not be used for new projects.")
 300     (license license:gpl3+)))
 301
 302 (define-public faiss
 303   (package
 304     (name "faiss")
 305     (version "1.5.0")
 306     (source (origin
 307               (method git-fetch)
 308               (uri (git-reference
 309                     (url "https://github.com/facebookresearch/faiss.git")
 310                     (commit (string-append "v" version))))
 311               (file-name (git-file-name name version))
 312               (sha256
 313                (base32
 314                 "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
 315               (modules '((guix build utils)))
 316               (snippet
 317                '(begin
 318                   (substitute* "utils.cpp"
 319                     (("#include <immintrin.h>")
 320                      "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
 321                   #t))))
 322     (build-system cmake-build-system)
 323     (arguments
 324      `(#:configure-flags
 325        (list "-DBUILD_WITH_GPU=OFF"  ; thanks, but no thanks, CUDA.
 326              "-DBUILD_TUTORIAL=OFF") ; we don't need those
 327        #:phases
 328        (modify-phases %standard-phases
 329          (add-after 'unpack 'prepare-build
 330            (lambda _
 331              (let ((features (list ,@(let ((system (or (%current-target-system)
 332                                                        (%current-system))))
 333                                        (cond
 334                                         ((string-prefix? "x86_64" system)
 335                                          '("-mavx" "-msse2" "-mpopcnt"))
 336                                         ((string-prefix? "i686" system)
 337                                          '("-msse2" "-mpopcnt"))
 338                                         (else
 339                                          '()))))))
 340                (substitute* "CMakeLists.txt"
 341                  (("-m64") "")
 342                  (("-mpopcnt") "") ; only some architectures
 343                  (("-msse4")
 344                   (string-append
 345                    (string-join features)
 346                    " -I" (getcwd)))
 347                  ;; Build also the shared library
 348                  (("ARCHIVE DESTINATION lib")
 349                   "LIBRARY DESTINATION lib")
 350                  (("add_library.*" m)
 351                   "\
 352 add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
 353 set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
 354 add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
 355 add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
 356 install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
 357 \n")))
 358
 359              ;; See https://github.com/facebookresearch/faiss/issues/520
 360              (substitute* "IndexScalarQuantizer.cpp"
 361                (("#define USE_AVX") ""))
 362
 363              ;; Make header files available for compiling tests.
 364              (mkdir-p "faiss")
 365              (for-each (lambda (file)
 366                          (mkdir-p (string-append "faiss/" (dirname file)))
 367                          (copy-file file (string-append "faiss/" file)))
 368                        (find-files "." "\\.h$"))
 369              #t))
 370          (replace 'check
 371            (lambda _
 372              (invoke "make" "-C" "tests"
 373                      (format #f "-j~a" (parallel-job-count)))))
 374          (add-after 'install 'remove-tests
 375            (lambda* (#:key outputs #:allow-other-keys)
 376              (delete-file-recursively
 377               (string-append (assoc-ref outputs "out")
 378                              "/test"))
 379              #t)))))
 380     (inputs
 381      `(("openblas" ,openblas)))
 382     (native-inputs
 383      `(("googletest" ,googletest)))
 384     (home-page "https://github.com/facebookresearch/faiss")
 385     (synopsis "Efficient similarity search and clustering of dense vectors")
 386     (description "Faiss is a library for efficient similarity search and
 387 clustering of dense vectors.  It contains algorithms that search in sets of
 388 vectors of any size, up to ones that possibly do not fit in RAM.  It also
 389 contains supporting code for evaluation and parameter tuning.")
 390     (license license:bsd-3)))
 391
 392 (define-public python-faiss
 393   (package (inherit faiss)
 394     (name "python-faiss")
 395     (build-system python-build-system)
 396     (arguments
 397      `(#:phases
 398        (modify-phases %standard-phases
 399          (add-after 'unpack 'chdir
 400            (lambda _ (chdir "python") #t))
 401          (add-after 'chdir 'build-swig
 402            (lambda* (#:key inputs #:allow-other-keys)
 403              (with-output-to-file "../makefile.inc"
 404                (lambda ()
 405                  (let ((python-version ,(version-major+minor (package-version python))))
 406                    (format #t "\
 407 PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
 408 LIBS = -lpython~am -lfaiss
 409 SHAREDFLAGS = -shared -fopenmp
 410 CXXFLAGS = -fpermissive -fopenmp -fPIC
 411 CPUFLAGS = ~{~a ~}~%"
 412                            (assoc-ref inputs "python*") python-version
 413                            (assoc-ref inputs "python-numpy") python-version
 414                            python-version
 415                            (list ,@(let ((system (or (%current-target-system)
 416                                                      (%current-system))))
 417                                      (cond
 418                                        ((string-prefix? "x86_64" system)
 419                                         '("-mavx" "-msse2" "-mpopcnt"))
 420                                        ((string-prefix? "i686" system)
 421                                         '("-msse2" "-mpopcnt"))
 422                                        (else
 423                                          '()))))))))
 424              (substitute* "Makefile"
 425                (("../libfaiss.a") ""))
 426              (invoke "make" "cpu"))))))
 427     (inputs
 428      `(("faiss" ,faiss)
 429        ("openblas" ,openblas)
 430        ("python*" ,python)
 431        ("swig" ,swig)))
 432     (propagated-inputs
 433      `(("python-matplotlib" ,python-matplotlib)
 434        ("python-numpy" ,python-numpy)))
 435     (description "Faiss is a library for efficient similarity search and
 436 clustering of dense vectors.  This package provides Python bindings to the
 437 Faiss library.")))
 438
 439 (define-public python-leidenalg
 440   (package
 441     (name "python-leidenalg")
 442     (version "0.7.0")
 443     (source
 444      (origin
 445        (method url-fetch)
 446        (uri (pypi-uri "leidenalg" version))
 447        (sha256
 448         (base32
 449          "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
 450     (build-system python-build-system)
 451     (arguments '(#:tests? #f)) ; tests are not included
 452     (native-inputs
 453      `(("pkg-config" ,pkg-config)))
 454     (inputs
 455      `(("igraph" ,igraph)))
 456     (propagated-inputs
 457      `(("python-igraph" ,python-igraph)))
 458     (home-page "https://github.com/vtraag/leidenalg")
 459     (synopsis "Community detection in large networks")
 460     (description
 461      "Leiden is a general algorithm for methods of community detection in
 462 large networks.  This package implements the Leiden algorithm in C++ and
 463 exposes it to Python.  Besides the relative flexibility of the implementation,
 464 it also scales well, and can be run on graphs of millions of nodes (as long as
 465 they can fit in memory).  The core function is @code{find_partition} which
 466 finds the optimal partition using the Leiden algorithm, which is an extension
 467 of the Louvain algorithm, for a number of different methods.")
 468     (license license:gpl3+)))
 469
 470 (define-public edge-addition-planarity-suite
 471   (package
 472     (name "edge-addition-planarity-suite")
 473     (version "3.0.0.5")
 474     (source
 475      (origin
 476        (method git-fetch)
 477        (uri (git-reference
 478               (url (string-append "https://github.com/graph-algorithms/"
 479                                   name))
 480               (commit (string-append "Version_" version))))
 481        (file-name (git-file-name name version))
 482        (sha256
 483         (base32
 484          "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
 485     (build-system gnu-build-system)
 486     (native-inputs
 487      `(("autoconf" ,autoconf)
 488        ("automake" ,automake)
 489        ("libtool" ,libtool)))
 490     (synopsis "Embedding of planar graphs")
 491     (description "The package provides a reference implementation of the
 492 linear time edge addition algorithm for embedding planar graphs and
 493 isolating planarity obstructions.")
 494     (license license:bsd-3)
 495     (home-page
 496       "https://github.com/graph-algorithms/edge-addition-planarity-suite")))
 497
 498 (define-public rw
 499   (package
 500     (name "rw")
 501     ;; There is a version 0.8, but the tarball is broken with symlinks
 502     ;; to /usr/share.
 503     (version "0.7")
 504     (source (origin
 505               (method url-fetch)
 506               (uri (string-append "mirror://sourceforge/rankwidth/"
 507                                   "rw-" version ".tar.gz"))
 508        (sha256
 509         (base32
 510          "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
 511     (build-system gnu-build-system)
 512     (native-inputs
 513      `(("pkg-config" ,pkg-config)))
 514     (inputs
 515      `(("igraph" ,igraph)))
 516     (home-page "https://sourceforge.net/projects/rankwidth/")
 517     (synopsis "Rank-width and rank-decomposition of graphs")
 518     (description "rw computes rank-width and rank-decompositions
 519 of graphs.")
 520     (license license:gpl2+)))
 521
 522 (define-public mscgen
 523   (package
 524     (name "mscgen")
 525     (version "0.20")
 526     (source
 527      (origin
 528        (method url-fetch)
 529        (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
 530                            version ".tar.gz"))
 531        (sha256
 532         (base32
 533          "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
 534     (build-system gnu-build-system)
 535     (inputs
 536      `(("gd" ,gd)))
 537     (home-page "http://www.mcternan.me.uk/mscgen/")
 538     (synopsis "Message Sequence Chart Generator")
 539     (description "Mscgen is a small program that parses Message Sequence Chart
 540 descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as
 541 the output.  Message Sequence Charts (MSCs) are a way of representing entities
 542 and interactions over some time period and are often used in combination with
 543 SDL.  MSCs are popular in Telecoms to specify how protocols operate although
 544 MSCs need not be complicated to create or use.  Mscgen aims to provide a simple
 545 text language that is clear to create, edit and understand, which can also be
 546 transformed into common image formats for display or printing.")
 547     (license license:gpl2+)))