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, 2020 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 ;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
   9 ;;;
  10 ;;; This file is part of GNU Guix.
  11 ;;;
  12 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  13 ;;; under the terms of the GNU General Public License as published by
  14 ;;; the Free Software Foundation; either version 3 of the License, or (at
  15 ;;; your option) any later version.
  16 ;;;
  17 ;;; GNU Guix is distributed in the hope that it will be useful, but
  18 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  19 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20 ;;; GNU General Public License for more details.
  21 ;;;
  22 ;;; You should have received a copy of the GNU General Public License
  23 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  24
  25 (define-module (gnu packages graph)
  26   #:use-module (guix download)
  27   #:use-module (guix git-download)
  28   #:use-module (guix packages)
  29   #:use-module (guix utils)
  30   #:use-module (guix build-system cmake)
  31   #:use-module (guix build-system gnu)
  32   #:use-module (guix build-system python)
  33   #:use-module (guix build-system r)
  34   #:use-module ((guix licenses) #:prefix license:)
  35   #:use-module (gnu packages)
  36   #:use-module (gnu packages gcc)
  37   #:use-module (gnu packages autotools)
  38   #:use-module (gnu packages bioconductor)
  39   #:use-module (gnu packages bioinformatics)
  40   #:use-module (gnu packages check)
  41   #:use-module (gnu packages compression)
  42   #:use-module (gnu packages cran)
  43   #:use-module (gnu packages gd)
  44   #:use-module (gnu packages graphviz)
  45   #:use-module (gnu packages maths)
  46   #:use-module (gnu packages multiprecision)
  47   #:use-module (gnu packages pkg-config)
  48   #:use-module (gnu packages python)
  49   #:use-module (gnu packages python-science)
  50   #:use-module (gnu packages python-web)
  51   #:use-module (gnu packages python-xyz)
  52   #:use-module (gnu packages statistics)
  53   #:use-module (gnu packages swig)
  54   #:use-module (gnu packages time)
  55   #:use-module (gnu packages xml))
  56
  57 (define-public igraph
  58   (package
  59     (name "igraph")
  60     (version "0.8.2")
  61     (source
  62      (origin
  63        (method url-fetch)
  64        (uri (string-append "https://github.com/igraph/igraph/releases/"
  65                            "download/" version "/igraph-" version ".tar.gz"))
  66        (sha256
  67         (base32 "158flvl80qh1l1ikfa04p1dzh8kapsvm6q80x3ih5gwcgcg4g2ki"))))
  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 "https://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 "0.8.2")
  94     (source
  95      (origin
  96        (method url-fetch)
  97        (uri (pypi-uri "python-igraph" version))
  98        (sha256
  99         (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6"))))
 100     (build-system python-build-system)
 101     (arguments
 102      '(#:configure-flags
 103        (list "--use-pkg-config")
 104        #:phases
 105        (modify-phases %standard-phases
 106          (replace 'build
 107            (lambda _
 108              (invoke "python" "./setup.py" "build" "--use-pkg-config")))
 109          (delete 'check)
 110          (add-after 'install 'check
 111            (lambda* (#:key inputs outputs #:allow-other-keys)
 112              (add-installed-pythonpath inputs outputs)
 113              (invoke "pytest" "-v"))))))
 114     (inputs
 115      `(("igraph" ,igraph)))
 116     (propagated-inputs
 117      `(("python-texttable" ,python-texttable)))
 118     (native-inputs
 119      `(("pkg-config" ,pkg-config)
 120        ("python-pytest" ,python-pytest)))
 121     (home-page "https://pypi.org/project/python-igraph/")
 122     (synopsis "Python bindings for the igraph network analysis library")))
 123
 124 (define-public r-rgraphviz
 125   (package
 126     (name "r-rgraphviz")
 127     (version "2.32.0")
 128     (source
 129      (origin
 130        (method url-fetch)
 131        (uri (bioconductor-uri "Rgraphviz" version))
 132        (sha256
 133         (base32
 134          "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
 135     (properties `((upstream-name . "Rgraphviz")))
 136     (build-system r-build-system)
 137     ;; FIXME: Rgraphviz bundles the sources of an older variant of
 138     ;; graphviz.  It does not build with the latest version of graphviz, so
 139     ;; we do not add graphviz to the inputs.
 140     (inputs `(("zlib" ,zlib)))
 141     (propagated-inputs
 142      `(("r-graph" ,r-graph)))
 143     (native-inputs
 144      `(("pkg-config" ,pkg-config)))
 145     (home-page "https://bioconductor.org/packages/Rgraphviz")
 146     (synopsis "Plotting capabilities for R graph objects")
 147     (description
 148      "This package interfaces R with the graphviz library for plotting R graph
 149 objects from the @code{graph} package.")
 150     (license license:epl1.0)))
 151
 152 (define-public r-rbiofabric
 153   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
 154         (revision "1"))
 155     (package
 156       (name "r-rbiofabric")
 157       (version (string-append "0.3-" revision "." (string-take commit 7)))
 158       (source (origin
 159                 (method git-fetch)
 160                 (uri (git-reference
 161                       (url "https://github.com/wjrl/RBioFabric")
 162                       (commit commit)))
 163                 (file-name (string-append name "-" version "-checkout"))
 164                 (sha256
 165                  (base32
 166                   "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
 167       (build-system r-build-system)
 168       (propagated-inputs
 169        `(("r-igraph" ,r-igraph)))
 170       (home-page "http://www.biofabric.org/")
 171       (synopsis "BioFabric network visualization")
 172       (description "This package provides an implementation of the function
 173 @code{bioFabric} for creating scalable network digrams where nodes are
 174 represented by horizontal lines, and edges are represented by vertical
 175 lines.")
 176       (license license:expat))))
 177
 178 (define-public python-plotly
 179   (package
 180     (name "python-plotly")
 181     (version "4.8.1")
 182     (source (origin
 183               (method git-fetch)
 184               (uri (git-reference
 185                     (url "https://github.com/plotly/plotly.py")
 186                     (commit (string-append "v" version))))
 187               (file-name (git-file-name name version))
 188               (sha256
 189                (base32
 190                 "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz"))))
 191     (build-system python-build-system)
 192     (arguments
 193      `(#:phases
 194        (modify-phases %standard-phases
 195          (add-after 'unpack 'chdir
 196            (lambda _
 197              (chdir "packages/python/plotly")
 198              #t))
 199          (replace 'check
 200            (lambda _
 201              (invoke "pytest" "-x" "plotly/tests/test_core")
 202              (invoke "pytest" "-x" "plotly/tests/test_io")
 203              ;; FIXME: Add optional dependencies and enable their tests.
 204              ;; (invoke "pytest" "-x" "plotly/tests/test_optional")
 205              (invoke "pytest" "_plotly_utils/tests")))
 206          (add-before 'reset-gzip-timestamps 'make-files-writable
 207            (lambda* (#:key outputs #:allow-other-keys)
 208              (let ((out (assoc-ref outputs "out")))
 209                (for-each (lambda (file) (chmod file #o644))
 210                  (find-files out "\\.gz"))
 211                #t))))))
 212     (native-inputs
 213      `(("python-pytest" ,python-pytest)))
 214     (propagated-inputs
 215      `(("python-decorator" ,python-decorator)
 216        ("python-ipywidgets" ,python-ipywidgets)
 217        ("python-pandas" ,python-pandas)
 218        ("python-requests" ,python-requests)
 219        ("python-retrying" ,python-retrying)
 220        ("python-six" ,python-six)
 221        ("python-statsmodels" ,python-statsmodels)
 222        ("python-xarray" ,python-xarray)))
 223     (home-page "https://plotly.com/python/")
 224     (synopsis "Interactive plotting library for Python")
 225     (description "Plotly's Python graphing library makes interactive,
 226 publication-quality graphs online.  Examples of how to make line plots, scatter
 227 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
 228 subplots, multiple-axes, polar charts, and bubble charts. ")
 229     (license license:expat)))
 230
 231 (define-public python-plotly-2.4.1
 232   (package (inherit python-plotly)
 233     (version "2.4.1")
 234     (source
 235       (origin
 236         (method url-fetch)
 237         (uri (pypi-uri "plotly" version))
 238         (sha256
 239          (base32
 240           "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
 241    (native-inputs '())
 242    (propagated-inputs
 243     `(("python-decorator" ,python-decorator)
 244       ("python-nbformat" ,python-nbformat)
 245       ("python-pandas" ,python-pandas)
 246       ("python-pytz" ,python-pytz)
 247       ("python-requests" ,python-requests)
 248       ("python-six" ,python-six)))
 249     (arguments
 250      '(#:tests? #f)))) ; The tests are not distributed in the release
 251
 252 (define-public python2-plotly
 253   (package-with-python2 python-plotly-2.4.1))
 254
 255 (define-public python-louvain
 256   (package
 257     (name "python-louvain")
 258     (version "0.6.1")
 259     ;; The tarball on Pypi does not include the tests.
 260     (source (origin
 261               (method git-fetch)
 262               (uri (git-reference
 263                     (url "https://github.com/vtraag/louvain-igraph")
 264                     (commit version)))
 265               (file-name (git-file-name name version))
 266               (sha256
 267                (base32
 268                 "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
 269     (build-system python-build-system)
 270     (propagated-inputs
 271      `(("python-ddt" ,python-ddt)
 272        ("python-igraph" ,python-igraph)))
 273     (inputs
 274      `(("igraph" ,igraph)))
 275     (native-inputs
 276      `(("pkg-config" ,pkg-config)
 277        ("python-pytest" ,python-pytest)))
 278     (home-page "https://github.com/vtraag/louvain-igraph")
 279     (synopsis "Algorithm for methods of community detection in large networks")
 280     (description
 281      "This package provides an implementation of the Louvain algorithm for use
 282 with igraph.  Louvain is a general algorithm for methods of community
 283 detection in large networks.
 284
 285 This package has been superseded by the @code{leidenalg} package and should
 286 not be used for new projects.")
 287     (license license:gpl3+)))
 288
 289 (define-public faiss
 290   (package
 291     (name "faiss")
 292     (version "1.5.0")
 293     (source (origin
 294               (method git-fetch)
 295               (uri (git-reference
 296                     (url "https://github.com/facebookresearch/faiss")
 297                     (commit (string-append "v" version))))
 298               (file-name (git-file-name name version))
 299               (sha256
 300                (base32
 301                 "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
 302               (modules '((guix build utils)))
 303               (snippet
 304                '(begin
 305                   (substitute* "utils.cpp"
 306                     (("#include <immintrin.h>")
 307                      "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
 308                   #t))))
 309     (build-system cmake-build-system)
 310     (arguments
 311      `(#:configure-flags
 312        (list "-DBUILD_WITH_GPU=OFF"  ; thanks, but no thanks, CUDA.
 313              "-DBUILD_TUTORIAL=OFF") ; we don't need those
 314        #:phases
 315        (modify-phases %standard-phases
 316          (add-after 'unpack 'prepare-build
 317            (lambda _
 318              (let ((features (list ,@(let ((system (or (%current-target-system)
 319                                                        (%current-system))))
 320                                        (cond
 321                                         ((string-prefix? "x86_64" system)
 322                                          '("-mavx" "-msse2" "-mpopcnt"))
 323                                         ((string-prefix? "i686" system)
 324                                          '("-msse2" "-mpopcnt"))
 325                                         (else
 326                                          '()))))))
 327                (substitute* "CMakeLists.txt"
 328                  (("-m64") "")
 329                  (("-mpopcnt") "") ; only some architectures
 330                  (("-msse4")
 331                   (string-append
 332                    (string-join features)
 333                    " -I" (getcwd)))
 334                  ;; Build also the shared library
 335                  (("ARCHIVE DESTINATION lib")
 336                   "LIBRARY DESTINATION lib")
 337                  (("add_library.*" m)
 338                   "\
 339 add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
 340 set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
 341 add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
 342 add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
 343 install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
 344 \n")))
 345
 346              ;; See https://github.com/facebookresearch/faiss/issues/520
 347              (substitute* "IndexScalarQuantizer.cpp"
 348                (("#define USE_AVX") ""))
 349
 350              ;; Make header files available for compiling tests.
 351              (mkdir-p "faiss")
 352              (for-each (lambda (file)
 353                          (mkdir-p (string-append "faiss/" (dirname file)))
 354                          (copy-file file (string-append "faiss/" file)))
 355                        (find-files "." "\\.h$"))
 356              #t))
 357          (replace 'check
 358            (lambda _
 359              (invoke "make" "-C" "tests"
 360                      (format #f "-j~a" (parallel-job-count)))))
 361          (add-after 'install 'remove-tests
 362            (lambda* (#:key outputs #:allow-other-keys)
 363              (delete-file-recursively
 364               (string-append (assoc-ref outputs "out")
 365                              "/test"))
 366              #t)))))
 367     (inputs
 368      `(("openblas" ,openblas)))
 369     (native-inputs
 370      `(("googletest" ,googletest)))
 371     (home-page "https://github.com/facebookresearch/faiss")
 372     (synopsis "Efficient similarity search and clustering of dense vectors")
 373     (description "Faiss is a library for efficient similarity search and
 374 clustering of dense vectors.  It contains algorithms that search in sets of
 375 vectors of any size, up to ones that possibly do not fit in RAM.  It also
 376 contains supporting code for evaluation and parameter tuning.")
 377     (license license:bsd-3)))
 378
 379 (define-public python-faiss
 380   (package (inherit faiss)
 381     (name "python-faiss")
 382     (build-system python-build-system)
 383     (arguments
 384      `(#:phases
 385        (modify-phases %standard-phases
 386          (add-after 'unpack 'chdir
 387            (lambda _ (chdir "python") #t))
 388          (add-after 'chdir 'build-swig
 389            (lambda* (#:key inputs #:allow-other-keys)
 390              (with-output-to-file "../makefile.inc"
 391                (lambda ()
 392                  (let ((python-version ,(version-major+minor (package-version python))))
 393                    (format #t "\
 394 PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
 395 LIBS = -lpython~am -lfaiss
 396 SHAREDFLAGS = -shared -fopenmp
 397 CXXFLAGS = -fpermissive -fopenmp -fPIC
 398 CPUFLAGS = ~{~a ~}~%"
 399                            (assoc-ref inputs "python*") python-version
 400                            (assoc-ref inputs "python-numpy") python-version
 401                            python-version
 402                            (list ,@(let ((system (or (%current-target-system)
 403                                                      (%current-system))))
 404                                      (cond
 405                                        ((string-prefix? "x86_64" system)
 406                                         '("-mavx" "-msse2" "-mpopcnt"))
 407                                        ((string-prefix? "i686" system)
 408                                         '("-msse2" "-mpopcnt"))
 409                                        (else
 410                                          '()))))))))
 411              (substitute* "Makefile"
 412                (("../libfaiss.a") ""))
 413              (invoke "make" "cpu"))))))
 414     (inputs
 415      `(("faiss" ,faiss)
 416        ("openblas" ,openblas)
 417        ("python*" ,python)
 418        ("swig" ,swig)))
 419     (propagated-inputs
 420      `(("python-matplotlib" ,python-matplotlib)
 421        ("python-numpy" ,python-numpy)))
 422     (description "Faiss is a library for efficient similarity search and
 423 clustering of dense vectors.  This package provides Python bindings to the
 424 Faiss library.")))
 425
 426 (define-public python-leidenalg
 427   (package
 428     (name "python-leidenalg")
 429     (version "0.7.0")
 430     (source
 431      (origin
 432        (method url-fetch)
 433        (uri (pypi-uri "leidenalg" version))
 434        (sha256
 435         (base32
 436          "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
 437     (build-system python-build-system)
 438     (arguments '(#:tests? #f)) ; tests are not included
 439     (native-inputs
 440      `(("pkg-config" ,pkg-config)))
 441     (inputs
 442      `(("igraph" ,igraph)))
 443     (propagated-inputs
 444      `(("python-igraph" ,python-igraph)))
 445     (home-page "https://github.com/vtraag/leidenalg")
 446     (synopsis "Community detection in large networks")
 447     (description
 448      "Leiden is a general algorithm for methods of community detection in
 449 large networks.  This package implements the Leiden algorithm in C++ and
 450 exposes it to Python.  Besides the relative flexibility of the implementation,
 451 it also scales well, and can be run on graphs of millions of nodes (as long as
 452 they can fit in memory).  The core function is @code{find_partition} which
 453 finds the optimal partition using the Leiden algorithm, which is an extension
 454 of the Louvain algorithm, for a number of different methods.")
 455     (license license:gpl3+)))
 456
 457 (define-public edge-addition-planarity-suite
 458   (package
 459     (name "edge-addition-planarity-suite")
 460     (version "3.0.0.5")
 461     (source
 462      (origin
 463        (method git-fetch)
 464        (uri (git-reference
 465               (url (string-append "https://github.com/graph-algorithms/"
 466                                   name))
 467               (commit (string-append "Version_" version))))
 468        (file-name (git-file-name name version))
 469        (sha256
 470         (base32
 471          "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
 472     (build-system gnu-build-system)
 473     (native-inputs
 474      `(("autoconf" ,autoconf)
 475        ("automake" ,automake)
 476        ("libtool" ,libtool)))
 477     (synopsis "Embedding of planar graphs")
 478     (description "The package provides a reference implementation of the
 479 linear time edge addition algorithm for embedding planar graphs and
 480 isolating planarity obstructions.")
 481     (license license:bsd-3)
 482     (home-page
 483       "https://github.com/graph-algorithms/edge-addition-planarity-suite")))
 484
 485 (define-public rw
 486   (package
 487     (name "rw")
 488     ;; There is a version 0.8, but the tarball is broken with symlinks
 489     ;; to /usr/share.
 490     (version "0.7")
 491     (source (origin
 492               (method url-fetch)
 493               (uri (string-append "mirror://sourceforge/rankwidth/"
 494                                   "rw-" version ".tar.gz"))
 495        (sha256
 496         (base32
 497          "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
 498     (build-system gnu-build-system)
 499     (native-inputs
 500      `(("pkg-config" ,pkg-config)))
 501     (inputs
 502      `(("igraph" ,igraph)))
 503     (home-page "https://sourceforge.net/projects/rankwidth/")
 504     (synopsis "Rank-width and rank-decomposition of graphs")
 505     (description "rw computes rank-width and rank-decompositions
 506 of graphs.")
 507     (license license:gpl2+)))
 508
 509 (define-public mscgen
 510   (package
 511     (name "mscgen")
 512     (version "0.20")
 513     (source
 514      (origin
 515        (method url-fetch)
 516        (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
 517                            version ".tar.gz"))
 518        (sha256
 519         (base32
 520          "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
 521     (build-system gnu-build-system)
 522     (native-inputs
 523      `(("pkg-config" ,pkg-config)))
 524     (inputs
 525      `(("gd" ,gd)))
 526     (home-page "http://www.mcternan.me.uk/mscgen/")
 527     (synopsis "Message Sequence Chart Generator")
 528     (description "Mscgen is a small program that parses Message Sequence Chart
 529 descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as
 530 the output.  Message Sequence Charts (MSCs) are a way of representing entities
 531 and interactions over some time period and are often used in combination with
 532 SDL.  MSCs are popular in Telecoms to specify how protocols operate although
 533 MSCs need not be complicated to create or use.  Mscgen aims to provide a simple
 534 text language that is clear to create, edit and understand, which can also be
 535 transformed into common image formats for display or printing.")
 536     (license license:gpl2+)))