gnu/packages/graphviz.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2013, 2015, 2021 Ludovic Courtès <ludo@gnu.org>
   3 ;;; Copyright © 2015, 2020 Efraim Flashner <efraim@flashner.co.il>
   4 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
   5 ;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   6 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
   7 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
   8 ;;; Copyright © 2018 Mathieu Lirzin <mthl@gnu.org>
   9 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
  10 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  11 ;;; Copyright © 2020 Pjotr Prins <pjotr.guix@thebird.nl>
  12 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
  13 ;;; Copyright © 2021 Giacomo Leidi <goodoldpaul@autistici.org>
  14 ;;; Copyright © 2021 Justin Veilleux <terramorpha@cock.li>
  15 ;;;
  16 ;;; This file is part of GNU Guix.
  17 ;;;
  18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  19 ;;; under the terms of the GNU General Public License as published by
  20 ;;; the Free Software Foundation; either version 3 of the License, or (at
  21 ;;; your option) any later version.
  22 ;;;
  23 ;;; GNU Guix is distributed in the hope that it will be useful, but
  24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  26 ;;; GNU General Public License for more details.
  27 ;;;
  28 ;;; You should have received a copy of the GNU General Public License
  29 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  30
  31 (define-module (gnu packages graphviz)
  32   #:use-module (guix packages)
  33   #:use-module (guix build-system gnu)
  34   #:use-module (guix build-system python)
  35   #:use-module (guix download)
  36   #:use-module (guix git-download)
  37   #:use-module (guix utils)
  38   #:use-module (guix gexp)
  39   #:use-module (gnu packages)
  40   #:use-module (gnu packages autotools)
  41   #:use-module (gnu packages bison)
  42   #:use-module (gnu packages check)
  43   #:use-module (gnu packages compression)
  44   #:use-module (gnu packages flex)
  45   #:use-module (gnu packages fontutils)
  46   #:use-module (gnu packages gd)
  47   #:use-module (gnu packages glib)
  48   #:use-module (gnu packages gnome)
  49   #:use-module (gnu packages gtk)
  50   #:use-module (gnu packages guile)
  51   #:use-module (gnu packages image)
  52   #:use-module (gnu packages perl)
  53   #:use-module (gnu packages pkg-config)
  54   #:use-module (gnu packages python)
  55   #:use-module (gnu packages python-build)
  56   #:use-module (gnu packages python-check)
  57   #:use-module (gnu packages python-xyz)
  58   #:use-module (gnu packages sphinx)
  59   #:use-module (gnu packages swig)
  60   #:use-module (gnu packages tcl)
  61   #:use-module (gnu packages tex)
  62   #:use-module (gnu packages xml)
  63   #:use-module (gnu packages xorg)
  64   #:use-module ((guix licenses) #:prefix license:))
  65
  66 (define-public graphviz
  67   (package
  68     (name "graphviz")
  69     (version "2.49.0")
  70     (source (origin
  71               (method url-fetch)
  72               (uri (string-append "https://gitlab.com/api/v4/projects/4207231"
  73                                   "/packages/generic/graphviz-releases/"
  74                                   version "/graphviz-" version ".tar.xz"))
  75               (sha256
  76                (base32
  77                 "042s6mbi681pwgffqww2ap780230nrsrfpfiz9a41dcjb5a0m524"))))
  78     (build-system gnu-build-system)
  79     (arguments
  80      ;; FIXME: rtest/rtest.sh is a ksh script (!).  Add ksh as an input.
  81      (list #:tests? #f
  82            #:phases
  83            #~(modify-phases %standard-phases
  84                (add-after 'install 'move-docs
  85                  (lambda* (#:key outputs #:allow-other-keys)
  86                    (let ((out (assoc-ref outputs "out"))
  87                          (doc (assoc-ref outputs "doc")))
  88                      (mkdir-p (string-append doc "/share/graphviz"))
  89                      (rename-file (string-append out "/share/graphviz/doc")
  90                                   (string-append doc "/share/graphviz/doc")))))
  91                (add-after 'move-docs 'move-guile-bindings
  92                  (lambda* (#:key outputs #:allow-other-keys)
  93                    (let* ((out (assoc-ref outputs "out"))
  94                           (lib (string-append out "/lib"))
  95                           (extdir (string-append lib "/guile/"
  96                                                  #$(version-major+minor
  97                                                     (package-version
  98                                                      (this-package-input "guile")))
  99                                                  "/extensions")))
 100                      (mkdir-p extdir)
 101                      (rename-file (string-append
 102                                    lib "/graphviz/guile/libgv_guile.so")
 103                                   (string-append extdir
 104                                                  "/libgv_guile.so"))))))))
 105     (inputs
 106      `(("libXrender" ,libxrender)
 107        ("libX11" ,libx11)
 108        ("gts" ,gts)
 109        ("gd" ,gd)
 110        ("guile" ,guile-3.0)                       ;Guile bindings
 111        ("pango" ,pango)
 112        ("fontconfig" ,fontconfig)
 113        ("freetype" ,freetype)
 114        ("libltdl" ,libltdl)
 115        ("libXaw" ,libxaw)
 116        ("expat" ,expat)
 117        ("libjpeg" ,libjpeg-turbo)
 118        ("libpng" ,libpng)))
 119     (native-inputs
 120      (list bison swig pkg-config))
 121     (outputs '("out" "doc"))                      ; 5 MiB of html + pdfs
 122     (home-page "https://www.graphviz.org/")
 123     (synopsis "Graph visualization software")
 124     (description
 125      "Graphviz is a graph visualization tool suite.  Graph visualization is a
 126 way of representing structural information as diagrams of abstract graphs and
 127 networks.  It has important applications in networking, bioinformatics,
 128 software engineering, database and web design, machine learning, and in visual
 129 interfaces for other technical domains.")
 130     (license license:epl1.0)))
 131
 132 ;; Older Graphviz needed for pygraphviz.  See
 133 ;; https://github.com/pygraphviz/pygraphviz/issues/175
 134 (define-public graphviz-2.38
 135   ;; This commit corresponds to the changelog change for version 2.38.0.
 136   ;; There are no tags.
 137   (let ((commit "f54ac2c9313ae80ccf76ef4ac6aa9be820a23126")
 138         (revision "1"))
 139     (package (inherit graphviz)
 140       (name "graphviz")
 141       (version (git-version "2.38.0" revision commit))
 142       (source (origin
 143                 (method git-fetch)
 144                 (uri (git-reference
 145                       (url "https://gitlab.com/graphviz/graphviz.git")
 146                       (commit commit)))
 147                 (file-name (git-file-name name version))
 148                 (sha256
 149                  (base32
 150                   "1vjg308gflmi1khgjmcj431cnkrlv12bg4cqah39mwhny92jy92x"))))
 151       (arguments
 152        (substitute-keyword-arguments (package-arguments graphviz)
 153          ((#:phases phases)
 154           #~(modify-phases #$phases
 155               (add-after 'unpack 'prepare-bootstrap
 156                 (lambda _
 157                   (substitute* "autogen.sh"
 158                     (("/bin/sh") (which "sh"))
 159                     (("\\$GRAPHVIZ_VERSION_DATE") "0"))
 160                   (setenv "CONFIG_SHELL" (which "sh"))
 161                   (setenv "SHELL" (which "sh"))
 162
 163                   (map make-file-writable (find-files "." ".*"))
 164                   #t))
 165               (replace 'bootstrap
 166                 (lambda _
 167                   (invoke (which "sh") "autogen.sh" "NOCONFIG") #t))))))
 168       (native-inputs
 169        (modify-inputs (package-native-inputs graphviz)
 170          (prepend autoconf
 171                   automake
 172                   libtool
 173                   flex
 174                   perl
 175                   tcl))))))
 176
 177 (define-public python-graphviz
 178   (package
 179     (name "python-graphviz")
 180     (version "0.13.2")
 181     (source (origin
 182               (method url-fetch)
 183               (uri (pypi-uri "graphviz" version ".zip"))
 184               (sha256
 185                (base32
 186                 "009alrilzx0v7kl41khbq7k6k8b8pxyvbsi1b1ai933f6kpbxb30"))))
 187     (build-system python-build-system)
 188     (arguments
 189      '(#:phases (modify-phases %standard-phases
 190                   (replace 'check
 191                     (lambda* (#:key tests #:allow-other-keys)
 192                       (if tests
 193                           (invoke "pytest" "-vv")
 194                           (format #t "test suite not run~%"))
 195                       #t)))))
 196     (native-inputs
 197      (list unzip
 198            ;; For tests.
 199            graphviz
 200            python-mock
 201            python-pytest
 202            python-pytest-cov
 203            python-pytest-mock))
 204     (home-page "https://github.com/xflr6/graphviz")
 205     (synopsis "Simple Python interface for Graphviz")
 206     (description
 207      "This package provides a simple Python interface for the Graphviz graph
 208 visualization tool suite.")
 209     (license license:expat)))
 210
 211 (define-public python-pygraphviz
 212   (package
 213     (name "python-pygraphviz")
 214     (version "1.7")
 215     (source
 216      (origin
 217        (method git-fetch)
 218        (uri (git-reference
 219              (url "https://github.com/pygraphviz/pygraphviz")
 220              (commit (string-append "pygraphviz-" version))))
 221        (file-name (string-append "pygraphviz-" version "-checkout"))
 222        (sha256
 223         (base32
 224          "0jqc3dzy9n0hn3b99zq8jp53901zpjzvvi5ns5mbaxg8kdrb1lfx"))))
 225     (build-system python-build-system)
 226     (inputs
 227      (list graphviz))
 228     (native-inputs
 229      (list python-nose python-mock python-pytest
 230            python-doctest-ignore-unicode))
 231     (home-page "https://pygraphviz.github.io")
 232     (synopsis "Python interface to Graphviz")
 233     (description "PyGraphviz is a Python interface to the Graphviz graph
 234 layout and visualization package.  With PyGraphviz you can create, edit, read,
 235 write, and draw graphs using Python to access the Graphviz graph data
 236 structure and layout algorithms.")
 237     (license license:bsd-3)))
 238
 239 (define-public python-uqbar
 240   (package
 241     (name "python-uqbar")
 242     (version "0.5.6")
 243     (source
 244      (origin
 245        (method git-fetch)
 246        (uri (git-reference
 247              (url "https://github.com/josiah-wolf-oberholtzer/uqbar")
 248              (commit (string-append "v" version))))
 249        (file-name (git-file-name name version))
 250        (sha256
 251         (base32
 252          "1ml3x2mf7nlnvrh9lari5yk0sz2mmg39jwsbjxnpzhnw4kcwpdrs"))))
 253     (build-system python-build-system)
 254     (arguments
 255      `(#:phases
 256        (modify-phases %standard-phases
 257          (add-after 'unpack 'patch
 258            (lambda _
 259              (substitute* "setup.py"
 260                ;; Latest versions of sphink-rtd-theme require npm to build.
 261                (("sphinx-rtd-theme >= 0.5.0") "sphinx-rtd-theme >= 0.2.4")
 262                (("black") "black >= 19.10b0"))
 263              #t))
 264          (replace 'check
 265            (lambda* (#:key tests? #:allow-other-keys)
 266              (when tests?
 267                (invoke "python" "-m" "pytest" "tests"))
 268              #t)))))
 269     (native-inputs
 270      (list graphviz
 271            python-flake8
 272            python-isort
 273            python-mypy
 274            python-pytest
 275            python-pytest-cov))
 276     (propagated-inputs
 277      (list python-black python-sphinx python-sphinx-rtd-theme
 278            python-unidecode))
 279     (home-page "https://github.com/josiah-wolf-oberholtzer/uqbar")
 280     (synopsis "Tools for building documentation with Sphinx, Graphviz and LaTeX")
 281     (description
 282      "This package contains tools for building documentation with Sphinx,
 283 Graphviz and LaTeX.")
 284     (license license:expat)))
 285
 286 (define-public gts
 287   (package
 288     (name "gts")
 289     (version "0.7.6")
 290     (source (origin
 291              (method url-fetch)
 292              (uri (string-append "mirror://sourceforge/gts/gts/" version
 293                                  "/gts-" version ".tar.gz"))
 294              (sha256
 295               (base32
 296                "07mqx09jxh8cv9753y2d2jsv7wp8vjmrd7zcfpbrddz3wc9kx705"))))
 297     (build-system gnu-build-system)
 298     (arguments
 299      '(#:phases
 300        (modify-phases %standard-phases
 301          (add-before 'check 'pre-check
 302            (lambda _
 303              (chmod "test/boolean/test.sh" #o777)
 304              #t)))
 305
 306        ;; Some data files used by the test suite are missing.
 307        ;; See <http://sourceforge.net/p/gts/bugs/41/>.
 308        #:tests? #f))
 309     (native-inputs
 310      (list pkg-config))
 311     (propagated-inputs
 312      ;; The gts.pc file has glib-2.0 as required.
 313      (list glib))
 314     (home-page "http://gts.sourceforge.net/")
 315
 316     ;; Note: Despite the name, this is not official GNU software.
 317     (synopsis "Triangulated Surface Library")
 318     (description
 319      "Library intended to provide a set of useful functions to deal with
 320 3D surfaces meshed with interconnected triangles.")
 321     (license license:lgpl2.0+)))
 322
 323 (define-public xdot
 324   (package
 325     (name "xdot")
 326     (version "1.1")
 327     (source
 328      (origin
 329       (method url-fetch)
 330       (uri (pypi-uri "xdot" version))
 331       (sha256
 332        (base32
 333         "0cr4rh7dz4dfzyxrk5pzhm0d15gkrgkfp3i5lw178xy81pc56p71"))))
 334     (build-system python-build-system)
 335     (arguments
 336      `(#:phases
 337        (modify-phases %standard-phases
 338          ;; We wrap xdot, so that we don't propagate gtk+ and graphviz
 339          (add-after 'install 'wrap
 340            (lambda* (#:key inputs outputs #:allow-other-keys)
 341              (wrap-program (string-append (assoc-ref outputs "out") "/bin/xdot")
 342                `("GI_TYPELIB_PATH" ":" prefix
 343                  (,(string-append
 344                     (assoc-ref inputs "gtk+") "/lib/girepository-1.0"
 345                     ":" (assoc-ref inputs "pango") "/lib/girepository-1.0"
 346                     ":" (assoc-ref inputs "gdk-pixbuf") "/lib/girepository-1.0"
 347                     ":" (assoc-ref inputs "atk") "/lib/girepository-1.0"
 348                     ":" (assoc-ref inputs "harfbuzz") "/lib/girepository-1.0")))
 349                `("PATH" ":" prefix
 350                  (,(dirname (search-input-file inputs "bin/dot"))))))))))
 351     (inputs
 352      (list atk
 353            librsvg
 354            harfbuzz
 355            graphviz
 356            gtk+
 357            python-pycairo
 358            python-pygobject))
 359     (home-page "https://pypi.org/project/xdot/")
 360     (synopsis "Interactive viewer for graphviz dot files")
 361     (description "Xdot is an interactive viewer for graphs written in
 362 @code{graphviz}’s dot language.  Internally, it uses the xdot output format as
 363 an intermediate format, and @code{gtk} and @code{cairo} for rendering.  Xdot
 364 can be used either as a standalone application, or as a Python library.")
 365     (license license:lgpl3+)))
 366
 367 (define-public python-pydot
 368   (package
 369     (name "python-pydot")
 370     (version "1.4.2")
 371     (source
 372      (origin
 373        (method url-fetch)
 374        (uri (pypi-uri "pydot" version))
 375        (sha256
 376         (base32
 377          "0z80zwldf7ffkwrpm28hixsiqp3053j7g281xd6phmnbkfiq3014"))))
 378     (build-system python-build-system)
 379     (arguments
 380      '(#:phases
 381        (modify-phases %standard-phases
 382          (replace 'check
 383            ;; Taken from .travis.yaml
 384            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
 385              (when tests?
 386                (add-installed-pythonpath inputs outputs)
 387                (with-directory-excursion "test"
 388                  (invoke "python" "pydot_unittest.py"))))))))
 389     (native-inputs
 390      ;; For tests.
 391      (list graphviz python-chardet))
 392     (propagated-inputs
 393      ;; XXX: Two test failures with 3.0+:
 394      ;; https://github.com/pydot/pydot/issues/277
 395      (list python-pyparsing-2.4.7))
 396     (home-page "https://github.com/pydot/pydot")
 397     (synopsis "Python interface to Graphviz's DOT language")
 398     (description
 399      "Pydot provides an interface to create, handle, modify and process
 400 graphs in Graphviz's DOT language, written in pure Python.")
 401     (license license:expat)))
 402
 403 (define-public dot2tex
 404   (package
 405     (name "dot2tex")
 406     (version "2.11.3")
 407     (source (origin
 408               (method url-fetch)
 409               (uri (pypi-uri "dot2tex" version))
 410               (sha256
 411                (base32
 412                 "1kp77wiv7b5qib82i3y3sn9r49rym43aaqm5aw1bwnzfbbq2m6i9"))))
 413     (build-system python-build-system)
 414     (arguments
 415      (list
 416       #:phases
 417       #~(modify-phases %standard-phases
 418           (replace 'check
 419             (lambda* (#:key tests? #:allow-other-keys)
 420               (when tests?
 421                 (invoke "pytest" "-vv" "tests"
 422                         ;; The test_semicolon test fails for unknown reason
 423                         ;; (see:
 424                         ;; https://github.com/kjellmf/dot2tex/issues/94).
 425                         "-k" "not test_semicolon")))))))
 426     (native-inputs (list python-pytest))
 427     (inputs (list graphviz))
 428     (propagated-inputs
 429      (list python-pyparsing
 430            ;; These TeX dependencies are propagated to make it easier to build
 431            ;; the resulting generated TeX files, which \usepackage them.
 432            texlive-bin
 433            texlive-amsmath
 434            texlive-latex-geometry
 435            texlive-latex-graphics
 436            texlive-latex-base
 437            texlive-latex-preview
 438            texlive-latex-xkeyval
 439            texlive-pgf
 440            texlive-pstricks
 441            texlive-xcolor))
 442     (home-page "https://github.com/kjellmf/dot2tex")
 443     (synopsis "Graphviz to LaTeX converter")
 444     (description
 445      "The purpose of @code{dot2tex} is to give graphs generated by Graphviz a
 446 more LaTeX friendly look and feel.  This is accomplished by converting
 447 @code{xdot} output from Graphviz to a series of PSTricks or PGF/TikZ commands.
 448 This approach allows:
 449
 450 @itemize @bullet
 451 @item Typesetting labels with LaTeX, allowing mathematical notation
 452 @item Using native PSTricks and PGF/TikZ commands for drawing arrows
 453 @item Using backend specific styles to customize the output
 454 @end itemize")
 455     (license license:expat)))
 456
 457 (define-public gprof2dot
 458   (package
 459     (name "gprof2dot")
 460     (version "2021.02.21")
 461     (source
 462      (origin
 463        (method git-fetch)
 464        (uri (git-reference
 465              (url "https://github.com/jrfonseca/gprof2dot")
 466              (commit version)))
 467        (file-name (git-file-name name version))
 468        (sha256
 469         (base32
 470          "1jjhsjf5fdi1fkn7mvhnzkh6cynl8gcjrygd3cya5mmda3akhzic"))))
 471     (build-system python-build-system)
 472     (arguments
 473      `(#:phases
 474        (modify-phases %standard-phases
 475          (replace 'check
 476            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
 477              (when tests?
 478                (add-installed-pythonpath inputs outputs)
 479                (invoke "python" "tests/test.py")))))))
 480     (native-inputs
 481      (list graphviz))
 482     (home-page "https://github.com/jrfonseca/gprof2dot")
 483     (synopsis "Generate a dot graph from the output of several profilers")
 484     (description "This package provides a Python script to convert the output
 485 from many profilers into a dot graph.
 486
 487 It can:
 488
 489 @itemize
 490
 491 @item prune nodes and edges below a certain threshold;
 492 @item use an heuristic to propagate time inside mutually recursive functions;
 493 @item use color efficiently to draw attention to hot-spots;
 494 @item work on any platform where Python and Graphviz is available.
 495
 496 @end itemize")
 497     (license license:lgpl3+)))