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, 2021 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 "0.8.4")
  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 "127q6q40kbmvd62yhbz6dlfk370qiq98s1iscyagpgbpjwb4xvyf"))))
  68     (build-system gnu-build-system)
  69     (arguments
  70      `(#:configure-flags
  71        (list "--disable-static"
  72              "--with-external-glpk"
  73              "--with-external-blas"
  74              "--with-external-lapack")))
  75     (inputs
  76      `(("gmp" ,gmp)
  77        ("glpk" ,glpk)
  78        ("libxml2" ,libxml2)
  79        ("lapack" ,lapack)
  80        ("openblas" ,openblas)
  81        ("zlib" ,zlib)))
  82     (home-page "https://igraph.org")
  83     (synopsis "Network analysis and visualization")
  84     (description
  85      "This package provides a library for the analysis of networks and graphs.
  86 It can handle large graphs very well and provides functions for generating
  87 random and regular graphs, graph visualization, centrality methods and much
  88 more.")
  89     (license license:gpl2+)))
  90
  91 (define-public python-igraph
  92   (package (inherit igraph)
  93     (name "python-igraph")
  94     (version "0.8.2")
  95     (source
  96      (origin
  97        (method url-fetch)
  98        (uri (pypi-uri "python-igraph" version))
  99        (sha256
 100         (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6"))))
 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-rbiofabric
 126   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
 127         (revision "1"))
 128     (package
 129       (name "r-rbiofabric")
 130       (version (string-append "0.3-" revision "." (string-take commit 7)))
 131       (source (origin
 132                 (method git-fetch)
 133                 (uri (git-reference
 134                       (url "https://github.com/wjrl/RBioFabric")
 135                       (commit commit)))
 136                 (file-name (string-append name "-" version "-checkout"))
 137                 (sha256
 138                  (base32
 139                   "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
 140       (build-system r-build-system)
 141       (propagated-inputs
 142        `(("r-igraph" ,r-igraph)))
 143       (home-page "http://www.biofabric.org/")
 144       (synopsis "BioFabric network visualization")
 145       (description "This package provides an implementation of the function
 146 @code{bioFabric} for creating scalable network digrams where nodes are
 147 represented by horizontal lines, and edges are represented by vertical
 148 lines.")
 149       (license license:expat))))
 150
 151 (define-public python-plotly
 152   (package
 153     (name "python-plotly")
 154     (version "4.14.3")
 155     (source (origin
 156               (method git-fetch)
 157               (uri (git-reference
 158                     (url "https://github.com/plotly/plotly.py")
 159                     (commit (string-append "v" version))))
 160               (file-name (git-file-name name version))
 161               (sha256
 162                (base32
 163                 "02wlgy7gf3v5ckiq9ab3prm53cckxkavlghqgkk9xw2sfmmrn61q"))))
 164     (build-system python-build-system)
 165     (arguments
 166      `(#:phases
 167        (modify-phases %standard-phases
 168          (add-after 'unpack 'chdir
 169            (lambda _
 170              (chdir "packages/python/plotly")
 171              #t))
 172          (replace 'check
 173            (lambda* (#:key tests? #:allow-other-keys)
 174              (when tests?
 175                (invoke "pytest" "-x" "plotly/tests/test_core")
 176                (invoke "pytest" "-x" "plotly/tests/test_io")
 177                ;; FIXME: Add optional dependencies and enable their tests.
 178                ;; (invoke "pytest" "-x" "plotly/tests/test_optional")
 179                (invoke "pytest" "_plotly_utils/tests"))
 180              #t))
 181          (add-before 'reset-gzip-timestamps 'make-files-writable
 182            (lambda* (#:key outputs #:allow-other-keys)
 183              (let ((out (assoc-ref outputs "out")))
 184                (for-each (lambda (file) (chmod file #o644))
 185                  (find-files out "\\.gz"))
 186                #t))))))
 187     (native-inputs
 188      `(("python-ipywidgets" ,python-ipywidgets)
 189        ("python-pytest" ,python-pytest)
 190        ("python-xarray" ,python-xarray)))
 191     (propagated-inputs
 192      `(("python-ipython" ,python-ipython)
 193        ("python-pandas" ,python-pandas)
 194        ("python-pillow" ,python-pillow)
 195        ("python-requests" ,python-requests)
 196        ("python-retrying" ,python-retrying)
 197        ("python-six" ,python-six)
 198        ("python-statsmodels" ,python-statsmodels)))
 199     (home-page "https://plotly.com/python/")
 200     (synopsis "Interactive plotting library for Python")
 201     (description "Plotly's Python graphing library makes interactive,
 202 publication-quality graphs online.  Examples of how to make line plots, scatter
 203 plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
 204 subplots, multiple-axes, polar charts, and bubble charts. ")
 205     (license license:expat)))
 206
 207 (define-public python-plotly-2.4.1
 208   (package (inherit python-plotly)
 209     (version "2.4.1")
 210     (source
 211       (origin
 212         (method url-fetch)
 213         (uri (pypi-uri "plotly" version))
 214         (sha256
 215          (base32
 216           "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
 217    (native-inputs '())
 218    (propagated-inputs
 219     `(("python-decorator" ,python-decorator)
 220       ("python-nbformat" ,python-nbformat)
 221       ("python-pandas" ,python-pandas)
 222       ("python-pytz" ,python-pytz)
 223       ("python-requests" ,python-requests)
 224       ("python-six" ,python-six)))
 225     (arguments
 226      '(#:tests? #f)))) ; The tests are not distributed in the release
 227
 228 (define-public python2-plotly
 229   (package-with-python2 python-plotly-2.4.1))
 230
 231 (define-public python-louvain
 232   (package
 233     (name "python-louvain")
 234     (version "0.6.1")
 235     ;; The tarball on Pypi does not include the tests.
 236     (source (origin
 237               (method git-fetch)
 238               (uri (git-reference
 239                     (url "https://github.com/vtraag/louvain-igraph")
 240                     (commit version)))
 241               (file-name (git-file-name name version))
 242               (sha256
 243                (base32
 244                 "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
 245     (build-system python-build-system)
 246     (propagated-inputs
 247      `(("python-ddt" ,python-ddt)
 248        ("python-igraph" ,python-igraph)))
 249     (inputs
 250      `(("igraph" ,igraph)))
 251     (native-inputs
 252      `(("pkg-config" ,pkg-config)
 253        ("python-pytest" ,python-pytest)))
 254     (home-page "https://github.com/vtraag/louvain-igraph")
 255     (synopsis "Algorithm for methods of community detection in large networks")
 256     (description
 257      "This package provides an implementation of the Louvain algorithm for use
 258 with igraph.  Louvain is a general algorithm for methods of community
 259 detection in large networks.
 260
 261 This package has been superseded by the @code{leidenalg} package and should
 262 not be used for new projects.")
 263     (license license:gpl3+)))
 264
 265 (define-public faiss
 266   (package
 267     (name "faiss")
 268     (version "1.5.0")
 269     (source (origin
 270               (method git-fetch)
 271               (uri (git-reference
 272                     (url "https://github.com/facebookresearch/faiss")
 273                     (commit (string-append "v" version))))
 274               (file-name (git-file-name name version))
 275               (sha256
 276                (base32
 277                 "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
 278               (modules '((guix build utils)))
 279               (snippet
 280                '(begin
 281                   (substitute* "utils.cpp"
 282                     (("#include <immintrin.h>")
 283                      "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
 284                   #t))))
 285     (build-system cmake-build-system)
 286     (arguments
 287      `(#:configure-flags
 288        (list "-DBUILD_WITH_GPU=OFF"  ; thanks, but no thanks, CUDA.
 289              "-DBUILD_TUTORIAL=OFF") ; we don't need those
 290        #:phases
 291        (modify-phases %standard-phases
 292          (add-after 'unpack 'prepare-build
 293            (lambda _
 294              (let ((features (list ,@(let ((system (or (%current-target-system)
 295                                                        (%current-system))))
 296                                        (cond
 297                                         ((string-prefix? "x86_64" system)
 298                                          '("-mavx" "-msse2" "-mpopcnt"))
 299                                         ((string-prefix? "i686" system)
 300                                          '("-msse2" "-mpopcnt"))
 301                                         (else
 302                                          '()))))))
 303                (substitute* "CMakeLists.txt"
 304                  (("-m64") "")
 305                  (("-mpopcnt") "") ; only some architectures
 306                  (("-msse4")
 307                   (string-append
 308                    (string-join features)
 309                    " -I" (getcwd)))
 310                  ;; Build also the shared library
 311                  (("ARCHIVE DESTINATION lib")
 312                   "LIBRARY DESTINATION lib")
 313                  (("add_library.*" m)
 314                   "\
 315 add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
 316 set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
 317 add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
 318 add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
 319 install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
 320 \n")))
 321
 322              ;; See https://github.com/facebookresearch/faiss/issues/520
 323              (substitute* "IndexScalarQuantizer.cpp"
 324                (("#define USE_AVX") ""))
 325
 326              ;; Make header files available for compiling tests.
 327              (mkdir-p "faiss")
 328              (for-each (lambda (file)
 329                          (mkdir-p (string-append "faiss/" (dirname file)))
 330                          (copy-file file (string-append "faiss/" file)))
 331                        (find-files "." "\\.h$"))
 332              #t))
 333          (replace 'check
 334            (lambda _
 335              (invoke "make" "-C" "tests"
 336                      (format #f "-j~a" (parallel-job-count)))))
 337          (add-after 'install 'remove-tests
 338            (lambda* (#:key outputs #:allow-other-keys)
 339              (delete-file-recursively
 340               (string-append (assoc-ref outputs "out")
 341                              "/test"))
 342              #t)))))
 343     (inputs
 344      `(("openblas" ,openblas)))
 345     (native-inputs
 346      `(("googletest" ,googletest)))
 347     (home-page "https://github.com/facebookresearch/faiss")
 348     (synopsis "Efficient similarity search and clustering of dense vectors")
 349     (description "Faiss is a library for efficient similarity search and
 350 clustering of dense vectors.  It contains algorithms that search in sets of
 351 vectors of any size, up to ones that possibly do not fit in RAM.  It also
 352 contains supporting code for evaluation and parameter tuning.")
 353     (license license:bsd-3)))
 354
 355 (define-public python-faiss
 356   (package (inherit faiss)
 357     (name "python-faiss")
 358     (build-system python-build-system)
 359     (arguments
 360      `(#:phases
 361        (modify-phases %standard-phases
 362          (add-after 'unpack 'chdir
 363            (lambda _ (chdir "python") #t))
 364          (add-after 'chdir 'build-swig
 365            (lambda* (#:key inputs #:allow-other-keys)
 366              (with-output-to-file "../makefile.inc"
 367                (lambda ()
 368                  (let ((python-version ,(version-major+minor (package-version python))))
 369                    (format #t "\
 370 PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
 371 LIBS = -lpython~am -lfaiss
 372 SHAREDFLAGS = -shared -fopenmp
 373 CXXFLAGS = -fpermissive -fopenmp -fPIC
 374 CPUFLAGS = ~{~a ~}~%"
 375                            (assoc-ref inputs "python*") python-version
 376                            (assoc-ref inputs "python-numpy") python-version
 377                            python-version
 378                            (list ,@(let ((system (or (%current-target-system)
 379                                                      (%current-system))))
 380                                      (cond
 381                                        ((string-prefix? "x86_64" system)
 382                                         '("-mavx" "-msse2" "-mpopcnt"))
 383                                        ((string-prefix? "i686" system)
 384                                         '("-msse2" "-mpopcnt"))
 385                                        (else
 386                                          '()))))))))
 387              (substitute* "Makefile"
 388                (("../libfaiss.a") ""))
 389              (invoke "make" "cpu"))))))
 390     (inputs
 391      `(("faiss" ,faiss)
 392        ("openblas" ,openblas)
 393        ("python*" ,python)
 394        ("swig" ,swig)))
 395     (propagated-inputs
 396      `(("python-matplotlib" ,python-matplotlib)
 397        ("python-numpy" ,python-numpy)))
 398     (description "Faiss is a library for efficient similarity search and
 399 clustering of dense vectors.  This package provides Python bindings to the
 400 Faiss library.")))
 401
 402 (define-public python-leidenalg
 403   (package
 404     (name "python-leidenalg")
 405     (version "0.7.0")
 406     (source
 407      (origin
 408        (method url-fetch)
 409        (uri (pypi-uri "leidenalg" version))
 410        (sha256
 411         (base32
 412          "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
 413     (build-system python-build-system)
 414     (arguments '(#:tests? #f)) ; tests are not included
 415     (native-inputs
 416      `(("pkg-config" ,pkg-config)))
 417     (inputs
 418      `(("igraph" ,igraph)))
 419     (propagated-inputs
 420      `(("python-igraph" ,python-igraph)))
 421     (home-page "https://github.com/vtraag/leidenalg")
 422     (synopsis "Community detection in large networks")
 423     (description
 424      "Leiden is a general algorithm for methods of community detection in
 425 large networks.  This package implements the Leiden algorithm in C++ and
 426 exposes it to Python.  Besides the relative flexibility of the implementation,
 427 it also scales well, and can be run on graphs of millions of nodes (as long as
 428 they can fit in memory).  The core function is @code{find_partition} which
 429 finds the optimal partition using the Leiden algorithm, which is an extension
 430 of the Louvain algorithm, for a number of different methods.")
 431     (license license:gpl3+)))
 432
 433 (define-public edge-addition-planarity-suite
 434   (package
 435     (name "edge-addition-planarity-suite")
 436     (version "3.0.0.5")
 437     (source
 438      (origin
 439        (method git-fetch)
 440        (uri (git-reference
 441               (url (string-append "https://github.com/graph-algorithms/"
 442                                   name))
 443               (commit (string-append "Version_" version))))
 444        (file-name (git-file-name name version))
 445        (sha256
 446         (base32
 447          "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
 448     (build-system gnu-build-system)
 449     (native-inputs
 450      `(("autoconf" ,autoconf)
 451        ("automake" ,automake)
 452        ("libtool" ,libtool)))
 453     (synopsis "Embedding of planar graphs")
 454     (description "The package provides a reference implementation of the
 455 linear time edge addition algorithm for embedding planar graphs and
 456 isolating planarity obstructions.")
 457     (license license:bsd-3)
 458     (home-page
 459       "https://github.com/graph-algorithms/edge-addition-planarity-suite")))
 460
 461 (define-public rw
 462   (package
 463     (name "rw")
 464     ;; There is a version 0.8, but the tarball is broken with symlinks
 465     ;; to /usr/share.
 466     (version "0.7")
 467     (source (origin
 468               (method url-fetch)
 469               (uri (string-append "mirror://sourceforge/rankwidth/"
 470                                   "rw-" version ".tar.gz"))
 471        (sha256
 472         (base32
 473          "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
 474     (build-system gnu-build-system)
 475     (native-inputs
 476      `(("pkg-config" ,pkg-config)))
 477     (inputs
 478      `(("igraph" ,igraph)))
 479     (home-page "https://sourceforge.net/projects/rankwidth/")
 480     (synopsis "Rank-width and rank-decomposition of graphs")
 481     (description "rw computes rank-width and rank-decompositions
 482 of graphs.")
 483     (license license:gpl2+)))
 484
 485 (define-public mscgen
 486   (package
 487     (name "mscgen")
 488     (version "0.20")
 489     (source
 490      (origin
 491        (method url-fetch)
 492        (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
 493                            version ".tar.gz"))
 494        (sha256
 495         (base32
 496          "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
 497     (build-system gnu-build-system)
 498     (native-inputs
 499      `(("pkg-config" ,pkg-config)))
 500     (inputs
 501      `(("gd" ,gd)))
 502     (home-page "http://www.mcternan.me.uk/mscgen/")
 503     (synopsis "Message Sequence Chart Generator")
 504     (description "Mscgen is a small program that parses Message Sequence Chart
 505 descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as
 506 the output.  Message Sequence Charts (MSCs) are a way of representing entities
 507 and interactions over some time period and are often used in combination with
 508 SDL.  MSCs are popular in Telecoms to specify how protocols operate although
 509 MSCs need not be complicated to create or use.  Mscgen aims to provide a simple
 510 text language that is clear to create, edit and understand, which can also be
 511 transformed into common image formats for display or printing.")
 512     (license license:gpl2+)))