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>
10 ;;; This file is part of GNU Guix.
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.
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.
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/>.
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))
64 (uri (string-append "https://github.com/igraph/igraph/releases/"
65 "download/" version "/igraph-" version ".tar.gz"))
67 (base32 "158flvl80qh1l1ikfa04p1dzh8kapsvm6q80x3ih5gwcgcg4g2ki"))))
68 (build-system gnu-build-system)
71 (list "--with-external-glpk"
72 "--with-external-blas"
73 "--with-external-lapack")))
79 ("openblas" ,openblas)
81 (home-page "https://igraph.org")
82 (synopsis "Network analysis and visualization")
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
88 (license license:gpl2+)))
90 (define-public python-igraph
91 (package (inherit igraph)
92 (name "python-igraph")
97 (uri (pypi-uri "python-igraph" version))
99 (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6"))))
100 (build-system python-build-system)
103 (list "--use-pkg-config")
105 (modify-phases %standard-phases
108 (invoke "python" "./setup.py" "build" "--use-pkg-config")))
110 (add-after 'install 'check
111 (lambda* (#:key inputs outputs #:allow-other-keys)
112 (add-installed-pythonpath inputs outputs)
113 (invoke "pytest" "-v"))))))
115 `(("igraph" ,igraph)))
117 `(("python-texttable" ,python-texttable)))
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")))
124 (define-public r-rgraphviz
131 (uri (bioconductor-uri "Rgraphviz" version))
134 "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
135 (properties `((upstream-name . "Rgraphviz")))
136 (build-system r-build-system)
139 (modify-phases %standard-phases
140 (add-after 'unpack 'make-reproducible
142 ;; The replacement value is taken from src/graphviz/builddate.h
143 (substitute* "src/graphviz/configure"
145 "VERSION_DATE=20200427.2341\n"))
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)))
152 `(("r-graph" ,r-graph)))
154 `(("pkg-config" ,pkg-config)))
155 (home-page "https://bioconductor.org/packages/Rgraphviz")
156 (synopsis "Plotting capabilities for R graph objects")
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)))
162 (define-public r-rbiofabric
163 (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
166 (name "r-rbiofabric")
167 (version (string-append "0.3-" revision "." (string-take commit 7)))
171 (url "https://github.com/wjrl/RBioFabric")
173 (file-name (string-append name "-" version "-checkout"))
176 "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
177 (build-system r-build-system)
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
186 (license license:expat))))
188 (define-public python-plotly
190 (name "python-plotly")
195 (url "https://github.com/plotly/plotly.py")
196 (commit (string-append "v" version))))
197 (file-name (git-file-name name version))
200 "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz"))))
201 (build-system python-build-system)
204 (modify-phases %standard-phases
205 (add-after 'unpack 'chdir
207 (chdir "packages/python/plotly")
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"))
223 `(("python-pytest" ,python-pytest)))
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)))
241 (define-public python-plotly-2.4.1
242 (package (inherit python-plotly)
247 (uri (pypi-uri "plotly" version))
250 "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
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)))
260 '(#:tests? #f)))) ; The tests are not distributed in the release
262 (define-public python2-plotly
263 (package-with-python2 python-plotly-2.4.1))
265 (define-public python-louvain
267 (name "python-louvain")
269 ;; The tarball on Pypi does not include the tests.
273 (url "https://github.com/vtraag/louvain-igraph")
275 (file-name (git-file-name name version))
278 "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
279 (build-system python-build-system)
281 `(("python-ddt" ,python-ddt)
282 ("python-igraph" ,python-igraph)))
284 `(("igraph" ,igraph)))
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")
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.
295 This package has been superseded by the @code{leidenalg} package and should
296 not be used for new projects.")
297 (license license:gpl3+)))
306 (url "https://github.com/facebookresearch/faiss")
307 (commit (string-append "v" version))))
308 (file-name (git-file-name name version))
311 "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
312 (modules '((guix build utils)))
315 (substitute* "utils.cpp"
316 (("#include <immintrin.h>")
317 "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
319 (build-system cmake-build-system)
322 (list "-DBUILD_WITH_GPU=OFF" ; thanks, but no thanks, CUDA.
323 "-DBUILD_TUTORIAL=OFF") ; we don't need those
325 (modify-phases %standard-phases
326 (add-after 'unpack 'prepare-build
328 (let ((features (list ,@(let ((system (or (%current-target-system)
331 ((string-prefix? "x86_64" system)
332 '("-mavx" "-msse2" "-mpopcnt"))
333 ((string-prefix? "i686" system)
334 '("-msse2" "-mpopcnt"))
337 (substitute* "CMakeLists.txt"
339 (("-mpopcnt") "") ; only some architectures
342 (string-join features)
344 ;; Build also the shared library
345 (("ARCHIVE DESTINATION lib")
346 "LIBRARY DESTINATION lib")
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 ${faiss_lib}_static ARCHIVE DESTINATION lib)
356 ;; See https://github.com/facebookresearch/faiss/issues/520
357 (substitute* "IndexScalarQuantizer.cpp"
358 (("#define USE_AVX") ""))
360 ;; Make header files available for compiling tests.
362 (for-each (lambda (file)
363 (mkdir-p (string-append "faiss/" (dirname file)))
364 (copy-file file (string-append "faiss/" file)))
365 (find-files "." "\\.h$"))
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")
378 `(("openblas" ,openblas)))
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)))
389 (define-public python-faiss
390 (package (inherit faiss)
391 (name "python-faiss")
392 (build-system python-build-system)
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"
402 (let ((python-version ,(version-major+minor (package-version python))))
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
412 (list ,@(let ((system (or (%current-target-system)
415 ((string-prefix? "x86_64" system)
416 '("-mavx" "-msse2" "-mpopcnt"))
417 ((string-prefix? "i686" system)
418 '("-msse2" "-mpopcnt"))
421 (substitute* "Makefile"
422 (("../libfaiss.a") ""))
423 (invoke "make" "cpu"))))))
426 ("openblas" ,openblas)
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
436 (define-public python-leidenalg
438 (name "python-leidenalg")
443 (uri (pypi-uri "leidenalg" version))
446 "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
447 (build-system python-build-system)
448 (arguments '(#:tests? #f)) ; tests are not included
450 `(("pkg-config" ,pkg-config)))
452 `(("igraph" ,igraph)))
454 `(("python-igraph" ,python-igraph)))
455 (home-page "https://github.com/vtraag/leidenalg")
456 (synopsis "Community detection in large networks")
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+)))
467 (define-public edge-addition-planarity-suite
469 (name "edge-addition-planarity-suite")
475 (url (string-append "https://github.com/graph-algorithms/"
477 (commit (string-append "Version_" version))))
478 (file-name (git-file-name name version))
481 "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
482 (build-system gnu-build-system)
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)
493 "https://github.com/graph-algorithms/edge-addition-planarity-suite")))
498 ;; There is a version 0.8, but the tarball is broken with symlinks
503 (uri (string-append "mirror://sourceforge/rankwidth/"
504 "rw-" version ".tar.gz"))
507 "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
508 (build-system gnu-build-system)
510 `(("pkg-config" ,pkg-config)))
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
517 (license license:gpl2+)))
519 (define-public mscgen
526 (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
530 "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
531 (build-system gnu-build-system)
533 `(("pkg-config" ,pkg-config)))
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+)))