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     (arguments
 138      `(#:phases
 139        (modify-phases %standard-phases
 140          (add-after 'unpack 'make-reproducible
 141            (lambda _
 142              ;; The replacement value is taken from src/graphviz/builddate.h
 143              (substitute* "src/graphviz/configure"
 144                (("VERSION_DATE=.*")
 145                 "VERSION_DATE=20200427.2341\n"))
 146              #t)))))
 147     ;; FIXME: Rgraphviz bundles the sources of an older variant of
 148     ;; graphviz.  It does not build with the latest version of graphviz, so
 149     ;; we do not add graphviz to the inputs.
 150     (inputs `(("zlib" ,zlib)))
 151     (propagated-inputs
 152      `(("r-graph" ,r-graph)))
 153     (native-inputs
 154      `(("pkg-config" ,pkg-config)))
 155     (home-page "https://bioconductor.org/packages/Rgraphviz")
 156     (synopsis "Plotting capabilities for R graph objects")
 157     (description
 158      "This package interfaces R with the graphviz library for plotting R graph
 159 objects from the @code{graph} package.")
 160     (license license:epl1.0)))
 161
 162 (define-public r-rbiofabric
 163   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
 164         (revision "1"))
 165     (package
 166       (name "r-rbiofabric")
 167       (version (string-append "0.3-" revision "." (string-take commit 7)))
 168       (source (origin
 169                 (method git-fetch)
 170                 (uri (git-reference
 171                       (url "https://github.com/wjrl/RBioFabric")
 172                       (commit commit)))
 173                 (file-name (string-append name "-" version "-checkout"))
 174                 (sha256
 175                  (base32
 176                   "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
 177       (build-system r-build-system)
 178       (propagated-inputs
 179        `(("r-igraph" ,r-igraph)))
 180       (home-page "http://www.biofabric.org/")
 181       (synopsis "BioFabric network visualization")
 182       (description "This package provides an implementation of the function
 183 @code{bioFabric} for creating scalable network digrams where nodes are
 184 represented by horizontal lines, and edges are represented by vertical
 185 lines.")
 186       (license license:expat))))
 187
 188 (define-public python-plotly
 189   (package
 190     (name "python-plotly")
 191     (version "4.8.1")
 192     (source (origin
 193               (method git-fetch)
 194               (uri (git-reference
 195                     (url "https://github.com/plotly/plotly.py")
 196                     (commit (string-append "v" version))))
 197               (file-name (git-file-name name version))
 198               (sha256
 199                (base32
 200                 "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz"))))
 201     (build-system python-build-system)
 202     (arguments
 203      `(#:phases
 204        (modify-phases %standard-phases
 205          (add-after 'unpack 'chdir
 206            (lambda _
 207              (chdir "packages/python/plotly")
 208              #t))
 209          (replace 'check
 210            (lambda _
 211              (invoke "pytest" "-x" "plotly/tests/test_core")
 212              (invoke "pytest" "-x" "plotly/tests/test_io")
 213              ;; FIXME: Add optional dependencies and enable their tests.
 214              ;; (invoke "pytest" "-x" "plotly/tests/test_optional")
 215              (invoke "pytest" "_plotly_utils/tests")))
 216          (add-before 'reset-gzip-timestamps 'make-files-writable
 217            (lambda* (#:key outputs #:allow-other-keys)
 218              (let ((out (assoc-ref outputs "out")))
 219                (for-each (lambda (file) (chmod file #o644))
 220                  (find-files out "\\.gz"))
 221                #t))))))
 222     (native-inputs
 223      `(("python-pytest" ,python-pytest)))
 224     (propagated-inputs
 225      `(("python-decorator" ,python-decorator)
 226        ("python-ipywidgets" ,python-ipywidgets)
 227        ("python-pandas" ,python-pandas)
 228        ("python-requests" ,python-requests)
 229        ("python-retrying" ,python-retrying)
 230        ("python-six" ,python-six)
 231        ("python-statsmodels" ,python-statsmodels)
 232        ("python-xarray" ,python-xarray)))
 233     (home-page "https://plotly.com/python/")
 234     (synopsis "Interactive plotting library for Python")
 235     (description "Plotly's Python graphing library makes interactive,
 236 publication-quality graphs online.  Examples of how to make line plots, scatter
 237 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
 238 subplots, multiple-axes, polar charts, and bubble charts. ")
 239     (license license:expat)))
 240
 241 (define-public python-plotly-2.4.1
 242   (package (inherit python-plotly)
 243     (version "2.4.1")
 244     (source
 245       (origin
 246         (method url-fetch)
 247         (uri (pypi-uri "plotly" version))
 248         (sha256
 249          (base32
 250           "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
 251    (native-inputs '())
 252    (propagated-inputs
 253     `(("python-decorator" ,python-decorator)
 254       ("python-nbformat" ,python-nbformat)
 255       ("python-pandas" ,python-pandas)
 256       ("python-pytz" ,python-pytz)
 257       ("python-requests" ,python-requests)
 258       ("python-six" ,python-six)))
 259     (arguments
 260      '(#:tests? #f)))) ; The tests are not distributed in the release
 261
 262 (define-public python2-plotly
 263   (package-with-python2 python-plotly-2.4.1))
 264
 265 (define-public python-louvain
 266   (package
 267     (name "python-louvain")
 268     (version "0.6.1")
 269     ;; The tarball on Pypi does not include the tests.
 270     (source (origin
 271               (method git-fetch)
 272               (uri (git-reference
 273                     (url "https://github.com/vtraag/louvain-igraph")
 274                     (commit version)))
 275               (file-name (git-file-name name version))
 276               (sha256
 277                (base32
 278                 "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
 279     (build-system python-build-system)
 280     (propagated-inputs
 281      `(("python-ddt" ,python-ddt)
 282        ("python-igraph" ,python-igraph)))
 283     (inputs
 284      `(("igraph" ,igraph)))
 285     (native-inputs
 286      `(("pkg-config" ,pkg-config)
 287        ("python-pytest" ,python-pytest)))
 288     (home-page "https://github.com/vtraag/louvain-igraph")
 289     (synopsis "Algorithm for methods of community detection in large networks")
 290     (description
 291      "This package provides an implementation of the Louvain algorithm for use
 292 with igraph.  Louvain is a general algorithm for methods of community
 293 detection in large networks.
 294
 295 This package has been superseded by the @code{leidenalg} package and should
 296 not be used for new projects.")
 297     (license license:gpl3+)))
 298
 299 (define-public faiss
 300   (package
 301     (name "faiss")
 302     (version "1.5.0")
 303     (source (origin
 304               (method git-fetch)
 305               (uri (git-reference
 306                     (url "https://github.com/facebookresearch/faiss")
 307                     (commit (string-append "v" version))))
 308               (file-name (git-file-name name version))
 309               (sha256
 310                (base32
 311                 "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
 312               (modules '((guix build utils)))
 313               (snippet
 314                '(begin
 315                   (substitute* "utils.cpp"
 316                     (("#include <immintrin.h>")
 317                      "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
 318                   #t))))
 319     (build-system cmake-build-system)
 320     (arguments
 321      `(#:configure-flags
 322        (list "-DBUILD_WITH_GPU=OFF"  ; thanks, but no thanks, CUDA.
 323              "-DBUILD_TUTORIAL=OFF") ; we don't need those
 324        #:phases
 325        (modify-phases %standard-phases
 326          (add-after 'unpack 'prepare-build
 327            (lambda _
 328              (let ((features (list ,@(let ((system (or (%current-target-system)
 329                                                        (%current-system))))
 330                                        (cond
 331                                         ((string-prefix? "x86_64" system)
 332                                          '("-mavx" "-msse2" "-mpopcnt"))
 333                                         ((string-prefix? "i686" system)
 334                                          '("-msse2" "-mpopcnt"))
 335                                         (else
 336                                          '()))))))
 337                (substitute* "CMakeLists.txt"
 338                  (("-m64") "")
 339                  (("-mpopcnt") "") ; only some architectures
 340                  (("-msse4")
 341                   (string-append
 342                    (string-join features)
 343                    " -I" (getcwd)))
 344                  ;; Build also the shared library
 345                  (("ARCHIVE DESTINATION lib")
 346                   "LIBRARY DESTINATION lib")
 347                  (("add_library.*" m)
 348                   "\
 349 add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
 350 set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
 351 add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
 352 add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
 353 install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
 354 \n")))
 355
 356              ;; See https://github.com/facebookresearch/faiss/issues/520
 357              (substitute* "IndexScalarQuantizer.cpp"
 358                (("#define USE_AVX") ""))
 359
 360              ;; Make header files available for compiling tests.
 361              (mkdir-p "faiss")
 362              (for-each (lambda (file)
 363                          (mkdir-p (string-append "faiss/" (dirname file)))
 364                          (copy-file file (string-append "faiss/" file)))
 365                        (find-files "." "\\.h$"))
 366              #t))
 367          (replace 'check
 368            (lambda _
 369              (invoke "make" "-C" "tests"
 370                      (format #f "-j~a" (parallel-job-count)))))
 371          (add-after 'install 'remove-tests
 372            (lambda* (#:key outputs #:allow-other-keys)
 373              (delete-file-recursively
 374               (string-append (assoc-ref outputs "out")
 375                              "/test"))
 376              #t)))))
 377     (inputs
 378      `(("openblas" ,openblas)))
 379     (native-inputs
 380      `(("googletest" ,googletest)))
 381     (home-page "https://github.com/facebookresearch/faiss")
 382     (synopsis "Efficient similarity search and clustering of dense vectors")
 383     (description "Faiss is a library for efficient similarity search and
 384 clustering of dense vectors.  It contains algorithms that search in sets of
 385 vectors of any size, up to ones that possibly do not fit in RAM.  It also
 386 contains supporting code for evaluation and parameter tuning.")
 387     (license license:bsd-3)))
 388
 389 (define-public python-faiss
 390   (package (inherit faiss)
 391     (name "python-faiss")
 392     (build-system python-build-system)
 393     (arguments
 394      `(#:phases
 395        (modify-phases %standard-phases
 396          (add-after 'unpack 'chdir
 397            (lambda _ (chdir "python") #t))
 398          (add-after 'chdir 'build-swig
 399            (lambda* (#:key inputs #:allow-other-keys)
 400              (with-output-to-file "../makefile.inc"
 401                (lambda ()
 402                  (let ((python-version ,(version-major+minor (package-version python))))
 403                    (format #t "\
 404 PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
 405 LIBS = -lpython~am -lfaiss
 406 SHAREDFLAGS = -shared -fopenmp
 407 CXXFLAGS = -fpermissive -fopenmp -fPIC
 408 CPUFLAGS = ~{~a ~}~%"
 409                            (assoc-ref inputs "python*") python-version
 410                            (assoc-ref inputs "python-numpy") python-version
 411                            python-version
 412                            (list ,@(let ((system (or (%current-target-system)
 413                                                      (%current-system))))
 414                                      (cond
 415                                        ((string-prefix? "x86_64" system)
 416                                         '("-mavx" "-msse2" "-mpopcnt"))
 417                                        ((string-prefix? "i686" system)
 418                                         '("-msse2" "-mpopcnt"))
 419                                        (else
 420                                          '()))))))))
 421              (substitute* "Makefile"
 422                (("../libfaiss.a") ""))
 423              (invoke "make" "cpu"))))))
 424     (inputs
 425      `(("faiss" ,faiss)
 426        ("openblas" ,openblas)
 427        ("python*" ,python)
 428        ("swig" ,swig)))
 429     (propagated-inputs
 430      `(("python-matplotlib" ,python-matplotlib)
 431        ("python-numpy" ,python-numpy)))
 432     (description "Faiss is a library for efficient similarity search and
 433 clustering of dense vectors.  This package provides Python bindings to the
 434 Faiss library.")))
 435
 436 (define-public python-leidenalg
 437   (package
 438     (name "python-leidenalg")
 439     (version "0.7.0")
 440     (source
 441      (origin
 442        (method url-fetch)
 443        (uri (pypi-uri "leidenalg" version))
 444        (sha256
 445         (base32
 446          "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
 447     (build-system python-build-system)
 448     (arguments '(#:tests? #f)) ; tests are not included
 449     (native-inputs
 450      `(("pkg-config" ,pkg-config)))
 451     (inputs
 452      `(("igraph" ,igraph)))
 453     (propagated-inputs
 454      `(("python-igraph" ,python-igraph)))
 455     (home-page "https://github.com/vtraag/leidenalg")
 456     (synopsis "Community detection in large networks")
 457     (description
 458      "Leiden is a general algorithm for methods of community detection in
 459 large networks.  This package implements the Leiden algorithm in C++ and
 460 exposes it to Python.  Besides the relative flexibility of the implementation,
 461 it also scales well, and can be run on graphs of millions of nodes (as long as
 462 they can fit in memory).  The core function is @code{find_partition} which
 463 finds the optimal partition using the Leiden algorithm, which is an extension
 464 of the Louvain algorithm, for a number of different methods.")
 465     (license license:gpl3+)))
 466
 467 (define-public edge-addition-planarity-suite
 468   (package
 469     (name "edge-addition-planarity-suite")
 470     (version "3.0.0.5")
 471     (source
 472      (origin
 473        (method git-fetch)
 474        (uri (git-reference
 475               (url (string-append "https://github.com/graph-algorithms/"
 476                                   name))
 477               (commit (string-append "Version_" version))))
 478        (file-name (git-file-name name version))
 479        (sha256
 480         (base32
 481          "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
 482     (build-system gnu-build-system)
 483     (native-inputs
 484      `(("autoconf" ,autoconf)
 485        ("automake" ,automake)
 486        ("libtool" ,libtool)))
 487     (synopsis "Embedding of planar graphs")
 488     (description "The package provides a reference implementation of the
 489 linear time edge addition algorithm for embedding planar graphs and
 490 isolating planarity obstructions.")
 491     (license license:bsd-3)
 492     (home-page
 493       "https://github.com/graph-algorithms/edge-addition-planarity-suite")))
 494
 495 (define-public rw
 496   (package
 497     (name "rw")
 498     ;; There is a version 0.8, but the tarball is broken with symlinks
 499     ;; to /usr/share.
 500     (version "0.7")
 501     (source (origin
 502               (method url-fetch)
 503               (uri (string-append "mirror://sourceforge/rankwidth/"
 504                                   "rw-" version ".tar.gz"))
 505        (sha256
 506         (base32
 507          "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
 508     (build-system gnu-build-system)
 509     (native-inputs
 510      `(("pkg-config" ,pkg-config)))
 511     (inputs
 512      `(("igraph" ,igraph)))
 513     (home-page "https://sourceforge.net/projects/rankwidth/")
 514     (synopsis "Rank-width and rank-decomposition of graphs")
 515     (description "rw computes rank-width and rank-decompositions
 516 of graphs.")
 517     (license license:gpl2+)))
 518
 519 (define-public mscgen
 520   (package
 521     (name "mscgen")
 522     (version "0.20")
 523     (source
 524      (origin
 525        (method url-fetch)
 526        (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
 527                            version ".tar.gz"))
 528        (sha256
 529         (base32
 530          "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
 531     (build-system gnu-build-system)
 532     (native-inputs
 533      `(("pkg-config" ,pkg-config)))
 534     (inputs
 535      `(("gd" ,gd)))
 536     (home-page "http://www.mcternan.me.uk/mscgen/")
 537     (synopsis "Message Sequence Chart Generator")
 538     (description "Mscgen is a small program that parses Message Sequence Chart
 539 descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as
 540 the output.  Message Sequence Charts (MSCs) are a way of representing entities
 541 and interactions over some time period and are often used in combination with
 542 SDL.  MSCs are popular in Telecoms to specify how protocols operate although
 543 MSCs need not be complicated to create or use.  Mscgen aims to provide a simple
 544 text language that is clear to create, edit and understand, which can also be
 545 transformed into common image formats for display or printing.")
 546     (license license:gpl2+)))