Commit | Line | Data |
---|---|---|
e57fffad | 1 | ;;; GNU Guix --- Functional package management for GNU |
06b13f51 | 2 | ;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> |
5f3616d6 | 3 | ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> |
8c9dcdea | 4 | ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr> |
3776dc09 | 5 | ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il> |
f455d99d | 6 | ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr> |
56973172 | 7 | ;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru> |
6e31d6f3 | 8 | ;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com> |
e57fffad RW |
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) | |
4e35c429 | 27 | #:use-module (guix git-download) |
e57fffad | 28 | #:use-module (guix packages) |
51a9971c | 29 | #:use-module (guix utils) |
3e403187 | 30 | #:use-module (guix build-system cmake) |
e57fffad | 31 | #:use-module (guix build-system gnu) |
31476df3 | 32 | #:use-module (guix build-system python) |
1738138c | 33 | #:use-module (guix build-system r) |
e57fffad RW |
34 | #:use-module ((guix licenses) #:prefix license:) |
35 | #:use-module (gnu packages) | |
1738138c | 36 | #:use-module (gnu packages gcc) |
f455d99d | 37 | #:use-module (gnu packages autotools) |
d53aeeaf | 38 | #:use-module (gnu packages bioconductor) |
e206de67 | 39 | #:use-module (gnu packages bioinformatics) |
3e403187 | 40 | #:use-module (gnu packages check) |
e57fffad | 41 | #:use-module (gnu packages compression) |
fff9b884 | 42 | #:use-module (gnu packages cran) |
56973172 | 43 | #:use-module (gnu packages gd) |
e206de67 | 44 | #:use-module (gnu packages graphviz) |
e57fffad RW |
45 | #:use-module (gnu packages maths) |
46 | #:use-module (gnu packages multiprecision) | |
31476df3 | 47 | #:use-module (gnu packages pkg-config) |
5f3616d6 | 48 | #:use-module (gnu packages python) |
312ec128 | 49 | #:use-module (gnu packages python-science) |
5f3616d6 | 50 | #:use-module (gnu packages python-web) |
44d10b1f | 51 | #:use-module (gnu packages python-xyz) |
1738138c | 52 | #:use-module (gnu packages statistics) |
51a9971c | 53 | #:use-module (gnu packages swig) |
5f3616d6 | 54 | #:use-module (gnu packages time) |
e57fffad RW |
55 | #:use-module (gnu packages xml)) |
56 | ||
57 | (define-public igraph | |
58 | (package | |
59 | (name "igraph") | |
2b1c4a5c | 60 | (version "0.8.2") |
e57fffad RW |
61 | (source |
62 | (origin | |
63 | (method url-fetch) | |
06b13f51 RW |
64 | (uri (string-append "https://github.com/igraph/igraph/releases/" |
65 | "download/" version "/igraph-" version ".tar.gz")) | |
e57fffad | 66 | (sha256 |
2b1c4a5c | 67 | (base32 "158flvl80qh1l1ikfa04p1dzh8kapsvm6q80x3ih5gwcgcg4g2ki")))) |
e57fffad RW |
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))) | |
00a34333 | 81 | (home-page "https://igraph.org") |
e57fffad RW |
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+))) | |
31476df3 RW |
89 | |
90 | (define-public python-igraph | |
91 | (package (inherit igraph) | |
92 | (name "python-igraph") | |
fe55ff38 | 93 | (version "0.8.2") |
31476df3 RW |
94 | (source |
95 | (origin | |
96 | (method url-fetch) | |
97 | (uri (pypi-uri "python-igraph" version)) | |
98 | (sha256 | |
fe55ff38 | 99 | (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6")))) |
31476df3 | 100 | (build-system python-build-system) |
7daae3c9 RW |
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")))))) | |
31476df3 RW |
114 | (inputs |
115 | `(("igraph" ,igraph))) | |
7daae3c9 RW |
116 | (propagated-inputs |
117 | `(("python-texttable" ,python-texttable))) | |
31476df3 | 118 | (native-inputs |
7daae3c9 RW |
119 | `(("pkg-config" ,pkg-config) |
120 | ("python-pytest" ,python-pytest))) | |
e85af137 | 121 | (home-page "https://pypi.org/project/python-igraph/") |
31476df3 | 122 | (synopsis "Python bindings for the igraph network analysis library"))) |
1738138c RW |
123 | |
124 | (define-public r-igraph | |
125 | (package | |
126 | (name "r-igraph") | |
d8dc2a7c | 127 | (version "1.2.5") |
1738138c RW |
128 | (source |
129 | (origin | |
130 | (method url-fetch) | |
131 | (uri (cran-uri "igraph" version)) | |
132 | (sha256 | |
133 | (base32 | |
d8dc2a7c | 134 | "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c")))) |
1738138c RW |
135 | (build-system r-build-system) |
136 | (native-inputs | |
137 | `(("gfortran" ,gfortran))) | |
138 | (inputs | |
139 | `(("gmp" ,gmp) | |
8cf7b28f RW |
140 | ("glpk" ,glpk) |
141 | ("libxml2" ,libxml2) | |
142 | ("zlib" ,zlib))) | |
1738138c | 143 | (propagated-inputs |
8cf7b28f | 144 | `(("r-magrittr" ,r-magrittr) |
1738138c RW |
145 | ("r-matrix" ,r-matrix) |
146 | ("r-pkgconfig" ,r-pkgconfig))) | |
00a34333 | 147 | (home-page "https://igraph.org") |
1738138c RW |
148 | (synopsis "Network analysis and visualization") |
149 | (description | |
150 | "This package provides routines for simple graphs and network analysis. | |
151 | It can handle large graphs very well and provides functions for generating | |
152 | random and regular graphs, graph visualization, centrality methods and much | |
153 | more.") | |
154 | (license license:gpl2+))) | |
e206de67 | 155 | |
fff9b884 RW |
156 | (define-public r-diffusionmap |
157 | (package | |
158 | (name "r-diffusionmap") | |
17f3960f | 159 | (version "1.2.0") |
fff9b884 RW |
160 | (source |
161 | (origin | |
162 | (method url-fetch) | |
163 | (uri (cran-uri "diffusionMap" version)) | |
164 | (sha256 | |
165 | (base32 | |
17f3960f | 166 | "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j")))) |
fff9b884 RW |
167 | (properties `((upstream-name . "diffusionMap"))) |
168 | (build-system r-build-system) | |
169 | (propagated-inputs | |
170 | `(("r-igraph" ,r-igraph) | |
171 | ("r-matrix" ,r-matrix) | |
172 | ("r-scatterplot3d" ,r-scatterplot3d))) | |
d062957a | 173 | (home-page "https://www.r-project.org") |
fff9b884 RW |
174 | (synopsis "Diffusion map") |
175 | (description "This package implements the diffusion map method of data | |
176 | parametrization, including creation and visualization of diffusion maps, | |
177 | clustering with diffusion K-means and regression using the adaptive regression | |
178 | model.") | |
179 | (license license:gpl2))) | |
180 | ||
e206de67 RW |
181 | (define-public r-rgraphviz |
182 | (package | |
183 | (name "r-rgraphviz") | |
c85e5ac0 | 184 | (version "2.32.0") |
e206de67 RW |
185 | (source |
186 | (origin | |
187 | (method url-fetch) | |
188 | (uri (bioconductor-uri "Rgraphviz" version)) | |
189 | (sha256 | |
190 | (base32 | |
c85e5ac0 | 191 | "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y")))) |
e206de67 RW |
192 | (properties `((upstream-name . "Rgraphviz"))) |
193 | (build-system r-build-system) | |
194 | ;; FIXME: Rgraphviz bundles the sources of an older variant of | |
195 | ;; graphviz. It does not build with the latest version of graphviz, so | |
196 | ;; we do not add graphviz to the inputs. | |
197 | (inputs `(("zlib" ,zlib))) | |
198 | (propagated-inputs | |
199 | `(("r-graph" ,r-graph))) | |
200 | (native-inputs | |
201 | `(("pkg-config" ,pkg-config))) | |
99db6db7 | 202 | (home-page "https://bioconductor.org/packages/Rgraphviz") |
e206de67 RW |
203 | (synopsis "Plotting capabilities for R graph objects") |
204 | (description | |
205 | "This package interfaces R with the graphviz library for plotting R graph | |
206 | objects from the @code{graph} package.") | |
207 | (license license:epl1.0))) | |
4e35c429 RW |
208 | |
209 | (define-public r-rbiofabric | |
210 | (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") | |
211 | (revision "1")) | |
212 | (package | |
213 | (name "r-rbiofabric") | |
214 | (version (string-append "0.3-" revision "." (string-take commit 7))) | |
215 | (source (origin | |
216 | (method git-fetch) | |
217 | (uri (git-reference | |
b0e7b699 | 218 | (url "https://github.com/wjrl/RBioFabric") |
4e35c429 RW |
219 | (commit commit))) |
220 | (file-name (string-append name "-" version "-checkout")) | |
221 | (sha256 | |
222 | (base32 | |
223 | "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z")))) | |
224 | (build-system r-build-system) | |
225 | (propagated-inputs | |
226 | `(("r-igraph" ,r-igraph))) | |
227 | (home-page "http://www.biofabric.org/") | |
228 | (synopsis "BioFabric network visualization") | |
229 | (description "This package provides an implementation of the function | |
230 | @code{bioFabric} for creating scalable network digrams where nodes are | |
231 | represented by horizontal lines, and edges are represented by vertical | |
232 | lines.") | |
233 | (license license:expat)))) | |
5f3616d6 LF |
234 | |
235 | (define-public python-plotly | |
236 | (package | |
237 | (name "python-plotly") | |
6e31d6f3 PL |
238 | (version "4.8.1") |
239 | (source (origin | |
240 | (method git-fetch) | |
241 | (uri (git-reference | |
b0e7b699 | 242 | (url "https://github.com/plotly/plotly.py") |
6e31d6f3 PL |
243 | (commit (string-append "v" version)))) |
244 | (file-name (git-file-name name version)) | |
245 | (sha256 | |
246 | (base32 | |
247 | "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz")))) | |
5f3616d6 LF |
248 | (build-system python-build-system) |
249 | (arguments | |
6e31d6f3 PL |
250 | `(#:phases |
251 | (modify-phases %standard-phases | |
252 | (add-after 'unpack 'chdir | |
253 | (lambda _ | |
254 | (chdir "packages/python/plotly") | |
255 | #t)) | |
256 | (replace 'check | |
257 | (lambda _ | |
258 | (invoke "pytest" "-x" "plotly/tests/test_core") | |
259 | (invoke "pytest" "-x" "plotly/tests/test_io") | |
260 | ;; FIXME: Add optional dependencies and enable their tests. | |
261 | ;; (invoke "pytest" "-x" "plotly/tests/test_optional") | |
262 | (invoke "pytest" "_plotly_utils/tests"))) | |
263 | (add-before 'reset-gzip-timestamps 'make-files-writable | |
264 | (lambda* (#:key outputs #:allow-other-keys) | |
265 | (let ((out (assoc-ref outputs "out"))) | |
266 | (for-each (lambda (file) (chmod file #o644)) | |
267 | (find-files out "\\.gz")) | |
268 | #t)))))) | |
269 | (native-inputs | |
270 | `(("python-pytest" ,python-pytest))) | |
5f3616d6 LF |
271 | (propagated-inputs |
272 | `(("python-decorator" ,python-decorator) | |
6e31d6f3 | 273 | ("python-ipywidgets" ,python-ipywidgets) |
1a28b9ab | 274 | ("python-pandas" ,python-pandas) |
5f3616d6 | 275 | ("python-requests" ,python-requests) |
6e31d6f3 PL |
276 | ("python-retrying" ,python-retrying) |
277 | ("python-six" ,python-six) | |
278 | ("python-statsmodels" ,python-statsmodels) | |
279 | ("python-xarray" ,python-xarray))) | |
280 | (home-page "https://plotly.com/python/") | |
5f3616d6 LF |
281 | (synopsis "Interactive plotting library for Python") |
282 | (description "Plotly's Python graphing library makes interactive, | |
283 | publication-quality graphs online. Examples of how to make line plots, scatter | |
284 | plots, area charts, bar charts, error bars, box plots, histograms, heatmaps, | |
285 | subplots, multiple-axes, polar charts, and bubble charts. ") | |
286 | (license license:expat))) | |
287 | ||
6e31d6f3 PL |
288 | (define-public python-plotly-2.4.1 |
289 | (package (inherit python-plotly) | |
290 | (version "2.4.1") | |
291 | (source | |
292 | (origin | |
293 | (method url-fetch) | |
294 | (uri (pypi-uri "plotly" version)) | |
295 | (sha256 | |
296 | (base32 | |
297 | "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m")))) | |
298 | (native-inputs '()) | |
299 | (propagated-inputs | |
300 | `(("python-decorator" ,python-decorator) | |
301 | ("python-nbformat" ,python-nbformat) | |
302 | ("python-pandas" ,python-pandas) | |
303 | ("python-pytz" ,python-pytz) | |
304 | ("python-requests" ,python-requests) | |
305 | ("python-six" ,python-six))) | |
306 | (arguments | |
307 | '(#:tests? #f)))) ; The tests are not distributed in the release | |
308 | ||
5f3616d6 | 309 | (define-public python2-plotly |
6e31d6f3 | 310 | (package-with-python2 python-plotly-2.4.1)) |
3e403187 | 311 | |
6ee48091 RW |
312 | (define-public python-louvain |
313 | (package | |
314 | (name "python-louvain") | |
315 | (version "0.6.1") | |
316 | ;; The tarball on Pypi does not include the tests. | |
317 | (source (origin | |
318 | (method git-fetch) | |
319 | (uri (git-reference | |
b0e7b699 | 320 | (url "https://github.com/vtraag/louvain-igraph") |
6ee48091 RW |
321 | (commit version))) |
322 | (file-name (git-file-name name version)) | |
323 | (sha256 | |
324 | (base32 | |
325 | "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k")))) | |
326 | (build-system python-build-system) | |
327 | (propagated-inputs | |
328 | `(("python-ddt" ,python-ddt) | |
329 | ("python-igraph" ,python-igraph))) | |
330 | (inputs | |
331 | `(("igraph" ,igraph))) | |
332 | (native-inputs | |
333 | `(("pkg-config" ,pkg-config) | |
334 | ("python-pytest" ,python-pytest))) | |
335 | (home-page "https://github.com/vtraag/louvain-igraph") | |
336 | (synopsis "Algorithm for methods of community detection in large networks") | |
337 | (description | |
338 | "This package provides an implementation of the Louvain algorithm for use | |
339 | with igraph. Louvain is a general algorithm for methods of community | |
340 | detection in large networks. | |
341 | ||
342 | This package has been superseded by the @code{leidenalg} package and should | |
343 | not be used for new projects.") | |
344 | (license license:gpl3+))) | |
345 | ||
3e403187 RW |
346 | (define-public faiss |
347 | (package | |
348 | (name "faiss") | |
349 | (version "1.5.0") | |
350 | (source (origin | |
351 | (method git-fetch) | |
352 | (uri (git-reference | |
b0e7b699 | 353 | (url "https://github.com/facebookresearch/faiss") |
3e403187 RW |
354 | (commit (string-append "v" version)))) |
355 | (file-name (git-file-name name version)) | |
356 | (sha256 | |
357 | (base32 | |
3776dc09 EF |
358 | "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w")) |
359 | (modules '((guix build utils))) | |
360 | (snippet | |
361 | '(begin | |
362 | (substitute* "utils.cpp" | |
363 | (("#include <immintrin.h>") | |
364 | "#ifdef __SSE__\n#include <immintrin.h>\n#endif")) | |
365 | #t)))) | |
3e403187 RW |
366 | (build-system cmake-build-system) |
367 | (arguments | |
368 | `(#:configure-flags | |
369 | (list "-DBUILD_WITH_GPU=OFF" ; thanks, but no thanks, CUDA. | |
370 | "-DBUILD_TUTORIAL=OFF") ; we don't need those | |
371 | #:phases | |
372 | (modify-phases %standard-phases | |
373 | (add-after 'unpack 'prepare-build | |
374 | (lambda _ | |
375 | (let ((features (list ,@(let ((system (or (%current-target-system) | |
376 | (%current-system)))) | |
377 | (cond | |
378 | ((string-prefix? "x86_64" system) | |
3776dc09 | 379 | '("-mavx" "-msse2" "-mpopcnt")) |
3e403187 | 380 | ((string-prefix? "i686" system) |
3776dc09 | 381 | '("-msse2" "-mpopcnt")) |
3e403187 RW |
382 | (else |
383 | '())))))) | |
384 | (substitute* "CMakeLists.txt" | |
3776dc09 EF |
385 | (("-m64") "") |
386 | (("-mpopcnt") "") ; only some architectures | |
3e403187 RW |
387 | (("-msse4") |
388 | (string-append | |
389 | (string-join features) | |
390 | " -I" (getcwd))) | |
391 | ;; Build also the shared library | |
392 | (("ARCHIVE DESTINATION lib") | |
393 | "LIBRARY DESTINATION lib") | |
394 | (("add_library.*" m) | |
395 | "\ | |
396 | add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp}) | |
397 | set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1) | |
398 | add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>) | |
399 | add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>) | |
400 | install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib) | |
401 | \n"))) | |
402 | ||
403 | ;; See https://github.com/facebookresearch/faiss/issues/520 | |
404 | (substitute* "IndexScalarQuantizer.cpp" | |
405 | (("#define USE_AVX") "")) | |
406 | ||
407 | ;; Make header files available for compiling tests. | |
408 | (mkdir-p "faiss") | |
409 | (for-each (lambda (file) | |
410 | (mkdir-p (string-append "faiss/" (dirname file))) | |
411 | (copy-file file (string-append "faiss/" file))) | |
412 | (find-files "." "\\.h$")) | |
413 | #t)) | |
414 | (replace 'check | |
415 | (lambda _ | |
416 | (invoke "make" "-C" "tests" | |
417 | (format #f "-j~a" (parallel-job-count))))) | |
418 | (add-after 'install 'remove-tests | |
419 | (lambda* (#:key outputs #:allow-other-keys) | |
420 | (delete-file-recursively | |
421 | (string-append (assoc-ref outputs "out") | |
422 | "/test")) | |
423 | #t))))) | |
424 | (inputs | |
425 | `(("openblas" ,openblas))) | |
426 | (native-inputs | |
427 | `(("googletest" ,googletest))) | |
428 | (home-page "https://github.com/facebookresearch/faiss") | |
429 | (synopsis "Efficient similarity search and clustering of dense vectors") | |
430 | (description "Faiss is a library for efficient similarity search and | |
431 | clustering of dense vectors. It contains algorithms that search in sets of | |
432 | vectors of any size, up to ones that possibly do not fit in RAM. It also | |
433 | contains supporting code for evaluation and parameter tuning.") | |
434 | (license license:bsd-3))) | |
51a9971c RW |
435 | |
436 | (define-public python-faiss | |
437 | (package (inherit faiss) | |
438 | (name "python-faiss") | |
439 | (build-system python-build-system) | |
440 | (arguments | |
441 | `(#:phases | |
442 | (modify-phases %standard-phases | |
443 | (add-after 'unpack 'chdir | |
444 | (lambda _ (chdir "python") #t)) | |
445 | (add-after 'chdir 'build-swig | |
446 | (lambda* (#:key inputs #:allow-other-keys) | |
447 | (with-output-to-file "../makefile.inc" | |
448 | (lambda () | |
449 | (let ((python-version ,(version-major+minor (package-version python)))) | |
450 | (format #t "\ | |
451 | PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include | |
452 | LIBS = -lpython~am -lfaiss | |
453 | SHAREDFLAGS = -shared -fopenmp | |
0fe041bd | 454 | CXXFLAGS = -fpermissive -fopenmp -fPIC |
51a9971c RW |
455 | CPUFLAGS = ~{~a ~}~%" |
456 | (assoc-ref inputs "python*") python-version | |
457 | (assoc-ref inputs "python-numpy") python-version | |
458 | python-version | |
8339ccac EF |
459 | (list ,@(let ((system (or (%current-target-system) |
460 | (%current-system)))) | |
461 | (cond | |
462 | ((string-prefix? "x86_64" system) | |
463 | '("-mavx" "-msse2" "-mpopcnt")) | |
464 | ((string-prefix? "i686" system) | |
465 | '("-msse2" "-mpopcnt")) | |
466 | (else | |
467 | '())))))))) | |
51a9971c RW |
468 | (substitute* "Makefile" |
469 | (("../libfaiss.a") "")) | |
470 | (invoke "make" "cpu")))))) | |
471 | (inputs | |
472 | `(("faiss" ,faiss) | |
473 | ("openblas" ,openblas) | |
474 | ("python*" ,python) | |
475 | ("swig" ,swig))) | |
476 | (propagated-inputs | |
477 | `(("python-matplotlib" ,python-matplotlib) | |
478 | ("python-numpy" ,python-numpy))) | |
479 | (description "Faiss is a library for efficient similarity search and | |
480 | clustering of dense vectors. This package provides Python bindings to the | |
481 | Faiss library."))) | |
e865e0b9 RW |
482 | |
483 | (define-public python-leidenalg | |
484 | (package | |
485 | (name "python-leidenalg") | |
486 | (version "0.7.0") | |
487 | (source | |
488 | (origin | |
489 | (method url-fetch) | |
490 | (uri (pypi-uri "leidenalg" version)) | |
491 | (sha256 | |
492 | (base32 | |
493 | "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1")))) | |
494 | (build-system python-build-system) | |
495 | (arguments '(#:tests? #f)) ; tests are not included | |
496 | (native-inputs | |
497 | `(("pkg-config" ,pkg-config))) | |
498 | (inputs | |
499 | `(("igraph" ,igraph))) | |
500 | (propagated-inputs | |
501 | `(("python-igraph" ,python-igraph))) | |
502 | (home-page "https://github.com/vtraag/leidenalg") | |
503 | (synopsis "Community detection in large networks") | |
504 | (description | |
505 | "Leiden is a general algorithm for methods of community detection in | |
506 | large networks. This package implements the Leiden algorithm in C++ and | |
507 | exposes it to Python. Besides the relative flexibility of the implementation, | |
508 | it also scales well, and can be run on graphs of millions of nodes (as long as | |
509 | they can fit in memory). The core function is @code{find_partition} which | |
510 | finds the optimal partition using the Leiden algorithm, which is an extension | |
511 | of the Louvain algorithm, for a number of different methods.") | |
512 | (license license:gpl3+))) | |
f455d99d AE |
513 | |
514 | (define-public edge-addition-planarity-suite | |
515 | (package | |
516 | (name "edge-addition-planarity-suite") | |
517 | (version "3.0.0.5") | |
518 | (source | |
519 | (origin | |
520 | (method git-fetch) | |
521 | (uri (git-reference | |
522 | (url (string-append "https://github.com/graph-algorithms/" | |
523 | name)) | |
524 | (commit (string-append "Version_" version)))) | |
525 | (file-name (git-file-name name version)) | |
526 | (sha256 | |
527 | (base32 | |
528 | "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8")))) | |
529 | (build-system gnu-build-system) | |
530 | (native-inputs | |
531 | `(("autoconf" ,autoconf) | |
532 | ("automake" ,automake) | |
533 | ("libtool" ,libtool))) | |
534 | (synopsis "Embedding of planar graphs") | |
535 | (description "The package provides a reference implementation of the | |
536 | linear time edge addition algorithm for embedding planar graphs and | |
537 | isolating planarity obstructions.") | |
538 | (license license:bsd-3) | |
539 | (home-page | |
540 | "https://github.com/graph-algorithms/edge-addition-planarity-suite"))) | |
bf473f0c AE |
541 | |
542 | (define-public rw | |
543 | (package | |
544 | (name "rw") | |
545 | ;; There is a version 0.8, but the tarball is broken with symlinks | |
546 | ;; to /usr/share. | |
547 | (version "0.7") | |
548 | (source (origin | |
549 | (method url-fetch) | |
550 | (uri (string-append "mirror://sourceforge/rankwidth/" | |
551 | "rw-" version ".tar.gz")) | |
552 | (sha256 | |
553 | (base32 | |
554 | "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0")))) | |
555 | (build-system gnu-build-system) | |
556 | (native-inputs | |
557 | `(("pkg-config" ,pkg-config))) | |
558 | (inputs | |
559 | `(("igraph" ,igraph))) | |
560 | (home-page "https://sourceforge.net/projects/rankwidth/") | |
561 | (synopsis "Rank-width and rank-decomposition of graphs") | |
562 | (description "rw computes rank-width and rank-decompositions | |
563 | of graphs.") | |
564 | (license license:gpl2+))) | |
56973172 AK |
565 | |
566 | (define-public mscgen | |
567 | (package | |
568 | (name "mscgen") | |
569 | (version "0.20") | |
570 | (source | |
571 | (origin | |
572 | (method url-fetch) | |
573 | (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-" | |
574 | version ".tar.gz")) | |
575 | (sha256 | |
576 | (base32 | |
577 | "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w")))) | |
578 | (build-system gnu-build-system) | |
cfa66669 MB |
579 | (native-inputs |
580 | `(("pkg-config" ,pkg-config))) | |
56973172 AK |
581 | (inputs |
582 | `(("gd" ,gd))) | |
583 | (home-page "http://www.mcternan.me.uk/mscgen/") | |
584 | (synopsis "Message Sequence Chart Generator") | |
585 | (description "Mscgen is a small program that parses Message Sequence Chart | |
586 | descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as | |
587 | the output. Message Sequence Charts (MSCs) are a way of representing entities | |
588 | and interactions over some time period and are often used in combination with | |
589 | SDL. MSCs are popular in Telecoms to specify how protocols operate although | |
590 | MSCs need not be complicated to create or use. Mscgen aims to provide a simple | |
591 | text language that is clear to create, edit and understand, which can also be | |
592 | transformed into common image formats for display or printing.") | |
593 | (license license:gpl2+))) |