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741115b6 1;;; GNU Guix --- Functional package management for GNU
3c441be0 2;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
25e0037a 3;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
be6eb2f1
RW		 4;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
5;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
d1308c5e 6;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
3a354e10 7;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
a9b34762
MM		 8;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
9;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
2dab4188 10;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
741115b6
RW		 11;;;
12;;; This file is part of GNU Guix.
13;;;
14;;; GNU Guix is free software; you can redistribute it and/or modify it
15;;; under the terms of the GNU General Public License as published by
16;;; the Free Software Foundation; either version 3 of the License, or (at
17;;; your option) any later version.
18;;;
19;;; GNU Guix is distributed in the hope that it will be useful, but
20;;; WITHOUT ANY WARRANTY; without even the implied warranty of
21;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22;;; GNU General Public License for more details.
23;;;
24;;; You should have received a copy of the GNU General Public License
25;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
26
27(define-module (gnu packages machine-learning)
28 #:use-module ((guix licenses) #:prefix license:)
29 #:use-module (guix packages)
30 #:use-module (guix utils)
31 #:use-module (guix download)
23aab4ab 32 #:use-module (guix svn-download)
c1670a81 33 #:use-module (guix build-system cmake)
741115b6 34 #:use-module (guix build-system gnu)
0a3063d6 35 #:use-module (guix build-system ocaml)
be6eb2f1 36 #:use-module (guix build-system python)
8406138b 37 #:use-module (guix build-system r)
a9b34762 38 #:use-module (guix git-download)
71f80f54 39 #:use-module (gnu packages)
5a14e81e 40 #:use-module (gnu packages algebra)
23aab4ab 41 #:use-module (gnu packages autotools)
0931c609 42 #:use-module (gnu packages boost)
be6eb2f1 43 #:use-module (gnu packages check)
0931c609 44 #:use-module (gnu packages compression)
9e37e537 45 #:use-module (gnu packages cran)
23aab4ab 46 #:use-module (gnu packages dejagnu)
0931c609 47 #:use-module (gnu packages gcc)
5f0ff6a9 48 #:use-module (gnu packages image)
0931c609 49 #:use-module (gnu packages maths)
112c2c01 50 #:use-module (gnu packages mpi)
0a3063d6 51 #:use-module (gnu packages ocaml)
3929f46c 52 #:use-module (gnu packages onc-rpc)
791c11d6 53 #:use-module (gnu packages perl)
c1670a81 54 #:use-module (gnu packages pkg-config)
0931c609 55 #:use-module (gnu packages python)
c1670a81
RW		 56 #:use-module (gnu packages statistics)
57 #:use-module (gnu packages swig)
5f0ff6a9
MB		 58 #:use-module (gnu packages xml)
59 #:use-module (gnu packages xorg))
741115b6 60
a9b34762
MM		 61(define-public fann
62 ;; The last release is >100 commits behind, so we package from git.
63 (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
64 (package
65 (name "fann")
66 (version (string-append "2.2.0-1." (string-take commit 8)))
67 (source (origin
68 (method git-fetch)
69 (uri (git-reference
70 (url "https://github.com/libfann/fann.git")
71 (commit commit)))
72 (file-name (string-append name "-" version "-checkout"))
73 (sha256
74 (base32
75 "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
76 (build-system cmake-build-system)
77 (arguments
78 `(#:phases
79 (modify-phases %standard-phases
80 (replace 'check
81 (lambda* (#:key outputs #:allow-other-keys)
82 (let* ((out (assoc-ref outputs "out")))
83 (with-directory-excursion (string-append (getcwd) "/tests")
84 (invoke "./fann_tests"))))))))
85 (home-page "http://leenissen.dk/fann/wp/")
86 (synopsis "Fast Artificial Neural Network")
87 (description
88 "FANN is a free open source neural network library, which implements
89multilayer artificial neural networks in C with support for both fully
90connected and sparsely connected networks.")
91 (license license:lgpl2.1))))
92
741115b6
RW		 93(define-public libsvm
94 (package
95 (name "libsvm")
d1308c5e 96 (version "3.22")
741115b6
RW		 97 (source
98 (origin
99 (method url-fetch)
d1308c5e
TGR		 100 (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
101 name "-" version ".tar.gz"))
741115b6
RW		 102 (sha256
103 (base32
d1308c5e 104 "0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
741115b6
RW		 105 (build-system gnu-build-system)
106 (arguments
107 `(#:tests? #f ;no "check" target
108 #:phases (modify-phases %standard-phases
109 (delete 'configure)
110 (replace
d1308c5e 111 'install ; no ‘install’ target
741115b6
RW		 112 (lambda* (#:key outputs #:allow-other-keys)
113 (let* ((out (assoc-ref outputs "out"))
114 (bin (string-append out "/bin/")))
115 (mkdir-p bin)
116 (for-each (lambda (file)
117 (copy-file file (string-append bin file)))
118 '("svm-train"
119 "svm-predict"
120 "svm-scale")))
121 #t)))))
122 (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
123 (synopsis "Library for Support Vector Machines")
124 (description
125 "LIBSVM is a machine learning library for support vector
126classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
127distribution estimation (one-class SVM). It supports multi-class
128classification.")
129 (license license:bsd-3)))
71f80f54
RW		 130
131(define-public python-libsvm
132 (package (inherit libsvm)
133 (name "python-libsvm")
134 (build-system gnu-build-system)
135 (arguments
136 `(#:tests? #f ;no "check" target
137 #:make-flags '("-C" "python")
138 #:phases
139 (modify-phases %standard-phases
140 (delete 'configure)
141 (replace
d1308c5e 142 'install ; no ‘install’ target
71f80f54
RW		 143 (lambda* (#:key inputs outputs #:allow-other-keys)
144 (let ((site (string-append (assoc-ref outputs "out")
145 "/lib/python"
146 (string-take
147 (string-take-right
148 (assoc-ref inputs "python") 5) 3)
149 "/site-packages/")))
150 (substitute* "python/svm.py"
151 (("../libsvm.so.2") "libsvm.so.2"))
152 (mkdir-p site)
153 (for-each (lambda (file)
154 (copy-file file (string-append site (basename file))))
155 (find-files "python" "\\.py"))
156 (copy-file "libsvm.so.2"
157 (string-append site "libsvm.so.2")))
158 #t)))))
159 (inputs
160 `(("python" ,python)))
161 (synopsis "Python bindings of libSVM")))
0931c609 162
23aab4ab
RW		 163(define-public ghmm
164 ;; The latest release candidate is several years and a couple of fixes have
165 ;; been published since. This is why we download the sources from the SVN
166 ;; repository.
167 (let ((svn-revision 2341))
168 (package
169 (name "ghmm")
170 (version (string-append "0.9-rc3-0." (number->string svn-revision)))
171 (source (origin
172 (method svn-fetch)
173 (uri (svn-reference
174 (url "http://svn.code.sf.net/p/ghmm/code/trunk")
175 (revision svn-revision)))
176 (file-name (string-append name "-" version))
177 (sha256
178 (base32
179 "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
180 (build-system gnu-build-system)
181 (arguments
ced12a7b
RW		 182 `(#:imported-modules (,@%gnu-build-system-modules
183 (guix build python-build-system))
184 #:phases
23aab4ab
RW		 185 (modify-phases %standard-phases
186 (add-after 'unpack 'enter-dir
187 (lambda _ (chdir "ghmm") #t))
ced12a7b
RW		 188 (delete 'check)
189 (add-after 'install 'check
190 (assoc-ref %standard-phases 'check))
191 (add-before 'check 'fix-PYTHONPATH
192 (lambda* (#:key inputs outputs #:allow-other-keys)
193 (let ((python-version ((@@ (guix build python-build-system)
194 get-python-version)
195 (assoc-ref inputs "python"))))
196 (setenv "PYTHONPATH"
197 (string-append (getenv "PYTHONPATH")
198 ":" (assoc-ref outputs "out")
199 "/lib/python" python-version
200 "/site-packages")))
23aab4ab
RW		 201 #t))
202 (add-after 'enter-dir 'fix-runpath
203 (lambda* (#:key outputs #:allow-other-keys)
204 (substitute* "ghmmwrapper/setup.py"
205 (("^(.*)extra_compile_args = \\[" line indent)
206 (string-append indent
207 "extra_link_args = [\"-Wl,-rpath="
208 (assoc-ref outputs "out") "/lib\"],\n"
209 line
210 "\"-Wl,-rpath="
211 (assoc-ref outputs "out")
212 "/lib\", ")))
213 #t))
214 (add-after 'enter-dir 'disable-broken-tests
215 (lambda _
216 (substitute* "tests/Makefile.am"
217 ;; GHMM_SILENT_TESTS is assumed to be a command.
218 (("TESTS_ENVIRONMENT.*") "")
219 ;; Do not build broken tests.
220 (("chmm .*") "")
221 (("read_fa .*") "")
222 (("mcmc .*") "")
223 (("label_higher_order_test.*$")
224 "label_higher_order_test\n"))
225
226 ;; These Python unittests are broken as there is no gato.
227 ;; See https://sourceforge.net/p/ghmm/support-requests/3/
228 (substitute* "ghmmwrapper/ghmmunittests.py"
229 (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
230 line indent)
231 (string-append indent
232 "@unittest.skip(\"Disabled by Guix\")\n"
233 line)))
234 #t))
d10092b8 235 (add-after 'disable-broken-tests 'autogen
23aab4ab 236 (lambda _
3107259f 237 (invoke "bash" "autogen.sh"))))))
23aab4ab
RW		 238 (inputs
239 `(("python" ,python-2) ; only Python 2 is supported
240 ("libxml2" ,libxml2)))
241 (native-inputs
242 `(("pkg-config" ,pkg-config)
243 ("dejagnu" ,dejagnu)
244 ("swig" ,swig)
245 ("autoconf" ,autoconf)
246 ("automake" ,automake)
247 ("libtool" ,libtool)))
248 (home-page "http://ghmm.org")
249 (synopsis "Hidden Markov Model library")
250 (description
251 "The General Hidden Markov Model library (GHMM) is a C library with
252additional Python bindings implementing a wide range of types of @dfn{Hidden
d1e4ad1b 253Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
23aab4ab
RW		 254training, HMM clustering, HMM mixtures.")
255 (license license:lgpl2.0+))))
256
791c11d6
BW		 257(define-public mcl
258 (package
259 (name "mcl")
260 (version "14.137")
261 (source (origin
262 (method url-fetch)
263 (uri (string-append
264 "http://micans.org/mcl/src/mcl-"
265 (string-replace-substring version "." "-")
266 ".tar.gz"))
267 (sha256
268 (base32
269 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
270 (build-system gnu-build-system)
271 (arguments
272 `(#:configure-flags (list "--enable-blast")))
273 (inputs
274 `(("perl" ,perl)))
275 (home-page "http://micans.org/mcl/")
276 (synopsis "Clustering algorithm for graphs")
277 (description
278 "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
279fast and scalable unsupervised cluster algorithm for graphs (also known as
280networks) based on simulation of (stochastic) flow in graphs.")
281 ;; In the LICENCE file and web page it says "The software is licensed
282 ;; under the GNU General Public License, version 3.", but in several of
283 ;; the source code files it suggests GPL3 or later.
284 ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
285 (license license:gpl3)))
286
0a3063d6
BW		 287(define-public ocaml-mcl
288 (package
289 (name "ocaml-mcl")
290 (version "12-068oasis4")
291 (source
292 (origin
293 (method url-fetch)
294 (uri (string-append
295 "https://github.com/fhcrc/mcl/archive/"
296 version ".tar.gz"))
297 (file-name (string-append name "-" version ".tar.gz"))
298 (sha256
299 (base32
300 "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
301 (build-system ocaml-build-system)
302 (arguments
303 `(#:phases
304 (modify-phases %standard-phases
305 (add-before 'configure 'patch-paths
306 (lambda _
307 (substitute* "configure"
308 (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
309 (substitute* "setup.ml"
310 (("LDFLAGS=-fPIC")
311 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
312 #t)))))
313 (home-page "https://github.com/fhcrc/mcl")
314 (synopsis "OCaml wrappers around MCL")
315 (description
316 "This package provides OCaml bindings for the MCL graph clustering
317algorithm.")
318 (license license:gpl3)))
319
b32208e7
BW		 320(define-public ocaml4.01-mcl
321 (package-with-ocaml4.01 ocaml-mcl))
322
0931c609
RW		 323(define-public randomjungle
324 (package
325 (name "randomjungle")
326 (version "2.1.0")
327 (source
328 (origin
329 (method url-fetch)
330 (uri (string-append
331 "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
332 "randomjungle-" version ".tar_.gz"))
333 (sha256
334 (base32
335 "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
336 (build-system gnu-build-system)
337 (arguments
338 `(#:configure-flags
339 (list (string-append "--with-boost="
340 (assoc-ref %build-inputs "boost")))
341 #:phases
342 (modify-phases %standard-phases
343 (add-before
344 'configure 'set-CXXFLAGS
345 (lambda _
346 (setenv "CXXFLAGS" "-fpermissive ")
347 #t)))))
348 (inputs
349 `(("boost" ,boost)
350 ("gsl" ,gsl)
351 ("libxml2" ,libxml2)
352 ("zlib" ,zlib)))
353 (native-inputs
25e0037a
EF		 354 `(("gfortran" ,gfortran)
355 ("gfortran:lib" ,gfortran "lib")))
47818201
RW		 356 ;; Non-portable assembly instructions are used so building fails on
357 ;; platforms other than x86_64 or i686.
358 (supported-systems '("x86_64-linux" "i686-linux"))
0931c609
RW		 359 (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
360 (synopsis "Implementation of the Random Forests machine learning method")
361 (description
362 "Random Jungle is an implementation of Random Forests. It is supposed to
363analyse high dimensional data. In genetics, it can be used for analysing big
364Genome Wide Association (GWA) data. Random Forests is a powerful machine
365learning method. Most interesting features are variable selection, missing
366value imputation, classifier creation, generalization error estimation and
367sample proximities between pairs of cases.")
368 (license license:gpl3+)))
c1670a81
RW		 369
370(define-public shogun
371 (package
372 (name "shogun")
5a14e81e 373 (version "6.1.3")
c1670a81
RW		 374 (source
375 (origin
376 (method url-fetch)
377 (uri (string-append
378 "ftp://shogun-toolbox.org/shogun/releases/"
379 (version-major+minor version)
380 "/sources/shogun-" version ".tar.bz2"))
381 (sha256
382 (base32
5a14e81e 383 "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
c1670a81
RW		 384 (modules '((guix build utils)
385 (ice-9 rdelim)))
386 (snippet
387 '(begin
388 ;; Remove non-free sources and files referencing them
389 (for-each delete-file
390 (find-files "src/shogun/classifier/svm/"
391 "SVMLight\\.(cpp|h)"))
392 (for-each delete-file
393 (find-files "examples/undocumented/libshogun/"
394 (string-append
395 "(classifier_.*svmlight.*|"
396 "evaluation_cross_validation_locked_comparison).cpp")))
397 ;; Remove non-free functions.
398 (define (delete-ifdefs file)
399 (with-atomic-file-replacement file
400 (lambda (in out)
401 (let loop ((line (read-line in 'concat))
402 (skipping? #f))
403 (if (eof-object? line)
404 #t
405 (let ((skip-next?
406 (or (and skipping?
407 (not (string-prefix?
408 "#endif //USE_SVMLIGHT" line)))
409 (string-prefix?
410 "#ifdef USE_SVMLIGHT" line))))
411 (when (or (not skipping?)
412 (and skipping? (not skip-next?)))
413 (display line out))
414 (loop (read-line in 'concat) skip-next?)))))))
5a14e81e
KK		 415 (for-each delete-ifdefs
416 (append
417 (find-files "src/shogun/classifier/mkl"
418 "^MKLClassification\\.cpp")
419 (find-files "src/shogun/classifier/svm"
420 "^SVMLightOneClass\\.(cpp|h)")
421 (find-files "src/shogun/multiclass"
422 "^ScatterSVM\\.(cpp|h)")
423 (find-files "src/shogun/kernel/"
424 "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
425 (find-files "src/shogun/regression/svr"
426 "^(MKLRegression|SVRLight)\\.(cpp|h)")
427 (find-files "src/shogun/transfer/domain_adaptation"
c0d7c124 428 "^DomainAdaptationSVM\\.(cpp|h)")))
6cbee49d 429 #t))))
c1670a81
RW		 430 (build-system cmake-build-system)
431 (arguments
432 '(#:tests? #f ;no check target
433 #:phases
dc1d3cde
KK		 434 (modify-phases %standard-phases
435 (add-after 'unpack 'delete-broken-symlinks
436 (lambda _
437 (for-each delete-file '("applications/arts/data"
438 "applications/asp/data"
439 "applications/easysvm/data"
440 "applications/msplicer/data"
441 "applications/ocr/data"
5a14e81e
KK		 442 "examples/meta/data"
443 "examples/undocumented/data"))
dc1d3cde
KK		 444 #t))
445 (add-after 'unpack 'change-R-target-path
446 (lambda* (#:key outputs #:allow-other-keys)
5a14e81e
KK		 447 (substitute* '("src/interfaces/r/CMakeLists.txt"
448 "examples/meta/r/CMakeLists.txt")
dc1d3cde
KK		 449 (("\\$\\{R_COMPONENT_LIB_PATH\\}")
450 (string-append (assoc-ref outputs "out")
451 "/lib/R/library/")))
452 #t))
453 (add-after 'unpack 'fix-octave-modules
454 (lambda* (#:key outputs #:allow-other-keys)
5a14e81e 455 (substitute* "src/interfaces/octave/CMakeLists.txt"
dc1d3cde 456 (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
5a14e81e
KK		 457 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
458 ;; change target directory
dc1d3cde
KK		 459 (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
460 (string-append (assoc-ref outputs "out")
461 "/share/octave/packages")))
5a14e81e
KK		 462 (substitute* '("src/interfaces/octave/swig_typemaps.i"
463 "src/interfaces/octave/sg_print_functions.cpp")
464 ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
465 (("octave/config\\.h") "octave/octave-config.h")
466 (("octave/oct-obj.h") "octave/ovl.h"))
dc1d3cde 467 #t))
5a14e81e
KK		 468 (add-after 'unpack 'move-rxcpp
469 (lambda* (#:key inputs #:allow-other-keys)
470 (let ((rxcpp-dir "shogun/third-party/rxcpp"))
471 (mkdir-p rxcpp-dir)
472 (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
473 #t)))
dc1d3cde 474 (add-before 'build 'set-HOME
c1670a81 475 ;; $HOME needs to be set at some point during the build phase
dc1d3cde 476 (lambda _ (setenv "HOME" "/tmp") #t)))
c1670a81
RW		 477 #:configure-flags
478 (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
479 "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
5a14e81e
KK		 480 "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
481 ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
482 ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
483 ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
484 ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
485 "-DINTERFACE_OCTAVE=ON"
486 "-DINTERFACE_PYTHON=ON"
487 "-DINTERFACE_R=ON")))
c1670a81
RW		 488 (inputs
489 `(("python" ,python)
490 ("numpy" ,python-numpy)
2d7c4ae3 491 ("r-minimal" ,r-minimal)
c1670a81
RW		 492 ("octave" ,octave)
493 ("swig" ,swig)
5a14e81e 494 ("eigen" ,eigen)
c1670a81
RW		 495 ("hdf5" ,hdf5)
496 ("atlas" ,atlas)
497 ("arpack" ,arpack-ng)
498 ("lapack" ,lapack)
499 ("glpk" ,glpk)
500 ("libxml2" ,libxml2)
501 ("lzo" ,lzo)
502 ("zlib" ,zlib)))
503 (native-inputs
5a14e81e
KK		 504 `(("pkg-config" ,pkg-config)
505 ("rxcpp" ,rxcpp)))
6b5b656f
RW		 506 ;; Non-portable SSE instructions are used so building fails on platforms
507 ;; other than x86_64.
508 (supported-systems '("x86_64-linux"))
c1670a81
RW		 509 (home-page "http://shogun-toolbox.org/")
510 (synopsis "Machine learning toolbox")
511 (description
512 "The Shogun Machine learning toolbox provides a wide range of unified and
513efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
514combine multiple data representations, algorithm classes, and general purpose
515tools. This enables both rapid prototyping of data pipelines and extensibility
516in terms of new algorithms.")
517 (license license:gpl3+)))
8406138b 518
3a354e10
KK		 519(define-public rxcpp
520 (package
521 (name "rxcpp")
522 (version "4.0.0")
523 (source
524 (origin
525 (method url-fetch)
526 (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
527 version ".tar.gz"))
528 (sha256
529 (base32
530 "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
531 (file-name (string-append name "-" version ".tar.gz"))))
532 (build-system cmake-build-system)
533 (arguments
534 `(#:phases
535 (modify-phases %standard-phases
536 (add-after 'unpack 'remove-werror
537 (lambda _
538 (substitute* (find-files ".")
539 (("-Werror") ""))
540 #t))
541 (replace 'check
542 (lambda _
543 (invoke "ctest"))))))
544 (native-inputs
545 `(("catch" ,catch-framework)))
546 (home-page "http://reactivex.io/")
547 (synopsis "Reactive Extensions for C++")
548 (description
549 "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
550values-distributed-in-time. ReactiveX is a library for composing asynchronous
551and event-based programs by using observable sequences.
552
553It extends the observer pattern to support sequences of data and/or events and
554adds operators that allow you to compose sequences together declaratively while
555abstracting away concerns about things like low-level threading,
556synchronization, thread-safety, concurrent data structures, and non-blocking
557I/O.")
558 (license license:asl2.0)))
559
8406138b
RW		 560(define-public r-adaptivesparsity
561 (package
562 (name "r-adaptivesparsity")
c0608f81 563 (version "1.6")
8406138b
RW		 564 (source (origin
565 (method url-fetch)
566 (uri (cran-uri "AdaptiveSparsity" version))
567 (sha256
568 (base32
c0608f81 569 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
8406138b
RW		 570 (properties
571 `((upstream-name . "AdaptiveSparsity")))
572 (build-system r-build-system)
573 (arguments
574 `(#:phases
575 (modify-phases %standard-phases
576 (add-after 'unpack 'link-against-armadillo
577 (lambda _
578 (substitute* "src/Makevars"
579 (("PKG_LIBS=" prefix)
580 (string-append prefix "-larmadillo"))))))))
581 (propagated-inputs
c0608f81
RW		 582 `(("r-mass" ,r-mass)
583 ("r-matrix" ,r-matrix)
584 ("r-rcpp" ,r-rcpp)
8406138b 585 ("r-rcpparmadillo" ,r-rcpparmadillo)))
60e36bff
LC		 586 (inputs
587 `(("armadillo" ,armadillo)))
e9960d8c 588 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
8406138b
RW		 589 (synopsis "Adaptive sparsity models")
590 (description
591 "This package implements the Figueiredo machine learning algorithm for
592adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
593geometric models.")
594 (license license:lgpl3+)))
e4785eb8 595
f05c7eb4
RW		 596(define-public r-kernlab
597 (package
598 (name "r-kernlab")
c28d8d8d 599 (version "0.9-27")
f05c7eb4
RW		 600 (source
601 (origin
602 (method url-fetch)
603 (uri (cran-uri "kernlab" version))
604 (sha256
605 (base32
c28d8d8d 606 "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
f05c7eb4 607 (build-system r-build-system)
e9960d8c 608 (home-page "https://cran.r-project.org/web/packages/kernlab")
f05c7eb4
RW		 609 (synopsis "Kernel-based machine learning tools")
610 (description
611 "This package provides kernel-based machine learning methods for
612classification, regression, clustering, novelty detection, quantile regression
613and dimensionality reduction. Among other methods @code{kernlab} includes
614Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
615and a QP solver.")
616 (license license:gpl2)))
617
5f0ff6a9
MB		 618(define-public dlib
619 (package
620 (name "dlib")
abe97a58 621 (version "19.7")
5f0ff6a9
MB		 622 (source (origin
623 (method url-fetch)
624 (uri (string-append
625 "http://dlib.net/files/dlib-" version ".tar.bz2"))
626 (sha256
627 (base32
abe97a58 628 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
5f0ff6a9
MB		 629 (modules '((guix build utils)))
630 (snippet
631 '(begin
632 ;; Delete ~13MB of bundled dependencies.
633 (delete-file-recursively "dlib/external")
0ef7ea66
MB		 634 (delete-file-recursively "docs/dlib/external")
635 #t))))
5f0ff6a9
MB		 636 (build-system cmake-build-system)
637 (arguments
677bc34d 638 `(#:phases
5f0ff6a9
MB		 639 (modify-phases %standard-phases
640 (add-after 'unpack 'disable-asserts
641 (lambda _
642 ;; config.h recommends explicitly enabling or disabling asserts
643 ;; when building as a shared library. By default neither is set.
644 (substitute* "dlib/config.h"
645 (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
646 #t))
4fba38db
MB		 647 (add-after 'disable-asserts 'disable-failing-tests
648 (lambda _
649 ;; One test times out on MIPS, so we need to disable it.
0ef7ea66 650 ;; Others are flaky on some platforms.
4fba38db
MB		 651 (let* ((system ,(or (%current-target-system)
652 (%current-system)))
653 (disabled-tests (cond
654 ((string-prefix? "mips64" system)
655 '("object_detector" ; timeout
656 "data_io"))
657 ((string-prefix? "armhf" system)
a343c461 658 '("learning_to_track"))
4fba38db 659 ((string-prefix? "i686" system)
0ef7ea66 660 '("optimization"))
4fba38db 661 (else '()))))
4fba38db
MB		 662 (for-each
663 (lambda (test)
664 (substitute* "dlib/test/makefile"
0ef7ea66
MB		 665 (((string-append "SRC \\+= " test "\\.cpp")) "")))
666 disabled-tests)
667 #t)))
5f0ff6a9
MB		 668 (replace 'check
669 (lambda _
670 ;; No test target, so we build and run the unit tests here.
8eaf53e3 671 (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
5f0ff6a9 672 (with-directory-excursion test-dir
8448e6bf
TGR		 673 (invoke "make" "-j" (number->string (parallel-job-count)))
674 (invoke "./dtest" "--runall"))
675 #t)))
5f0ff6a9
MB		 676 (add-after 'install 'delete-static-library
677 (lambda* (#:key outputs #:allow-other-keys)
0ef7ea66
MB		 678 (delete-file (string-append (assoc-ref outputs "out")
679 "/lib/libdlib.a"))
680 #t)))))
5f0ff6a9 681 (native-inputs
3929f46c
TGR		 682 `(("pkg-config" ,pkg-config)
683 ;; For tests.
684 ("libnsl" ,libnsl)))
5f0ff6a9 685 (inputs
f40841e9 686 `(("giflib" ,giflib)
4fba38db 687 ("lapack" ,lapack)
5f0ff6a9
MB		 688 ("libjpeg" ,libjpeg)
689 ("libpng" ,libpng)
690 ("libx11" ,libx11)
691 ("openblas" ,openblas)
692 ("zlib" ,zlib)))
693 (synopsis
694 "Toolkit for making machine learning and data analysis applications in C++")
695 (description
696 "Dlib is a modern C++ toolkit containing machine learning algorithms and
697tools. It is used in both industry and academia in a wide range of domains
698including robotics, embedded devices, mobile phones, and large high performance
699computing environments.")
700 (home-page "http://dlib.net")
701 (license license:boost1.0)))
be6eb2f1
RW		 702
703(define-public python-scikit-learn
704 (package
705 (name "python-scikit-learn")
d3cdb25d 706 (version "0.19.1")
be6eb2f1
RW		 707 (source
708 (origin
709 (method url-fetch)
710 (uri (string-append
711 "https://github.com/scikit-learn/scikit-learn/archive/"
712 version ".tar.gz"))
713 (file-name (string-append name "-" version ".tar.gz"))
714 (sha256
715 (base32
8a6cd65a
BW		 716 "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))
717 (patches (search-patches
718 "python-scikit-learn-fix-test-non-determinism.patch"))))
be6eb2f1
RW		 719 (build-system python-build-system)
720 (arguments
721 `(#:phases
722 (modify-phases %standard-phases
723 (delete 'check)
724 (add-after 'install 'check
725 ;; Running tests from the source directory requires
726 ;; an "inplace" build with paths relative to CWD.
727 ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing
728 ;; Use the installed version instead.
729 (lambda* (#:key inputs outputs #:allow-other-keys)
730 (add-installed-pythonpath inputs outputs)
731 ;; some tests require access to "$HOME"
732 (setenv "HOME" "/tmp")
733 ;; Step out of the source directory just to be sure.
734 (chdir "..")
e96ba83f 735 (invoke "nosetests" "-v" "sklearn"))))))
be6eb2f1
RW		 736 (inputs
737 `(("openblas" ,openblas)))
738 (native-inputs
739 `(("python-nose" ,python-nose)
740 ("python-cython" ,python-cython)))
741 (propagated-inputs
742 `(("python-numpy" ,python-numpy)
743 ("python-scipy" ,python-scipy)))
744 (home-page "http://scikit-learn.org/")
745 (synopsis "Machine Learning in Python")
746 (description
747 "Scikit-learn provides simple and efficient tools for data
748mining and data analysis.")
749 (license license:bsd-3)))
750
751(define-public python2-scikit-learn
752 (package-with-python2 python-scikit-learn))
2dab4188
FT		 753
754(define-public python-autograd
755 (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
756 (revision "0")
757 (version (git-version "0.0.0" revision commit)))
758 (package
759 (name "python-autograd")
760 (home-page "https://github.com/HIPS/autograd")
761 (source (origin
762 (method git-fetch)
763 (uri (git-reference
764 (url home-page)
765 (commit commit)))
766 (sha256
767 (base32
768 "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
769 (file-name (git-file-name name version))))
770 (version version)
771 (build-system python-build-system)
772 (native-inputs
773 `(("python-nose" ,python-nose)
774 ("python-pytest" ,python-pytest)))
775 (propagated-inputs
776 `(("python-future" ,python-future)
777 ("python-numpy" ,python-numpy)))
778 (arguments
779 `(#:phases (modify-phases %standard-phases
780 (replace 'check
781 (lambda _
782 (invoke "py.test" "-v"))))))
783 (synopsis "Efficiently computes derivatives of NumPy code")
784 (description "Autograd can automatically differentiate native Python and
785NumPy code. It can handle a large subset of Python's features, including loops,
786ifs, recursion and closures, and it can even take derivatives of derivatives
787of derivatives. It supports reverse-mode differentiation
788(a.k.a. backpropagation), which means it can efficiently take gradients of
789scalar-valued functions with respect to array-valued arguments, as well as
790forward-mode differentiation, and the two can be composed arbitrarily. The
791main intended application of Autograd is gradient-based optimization.")
792 (license license:expat))))
793
794(define-public python2-autograd
795 (package-with-python2 python-autograd))
112c2c01
FT		 796
797(define-public lightgbm
798 (package
799 (name "lightgbm")
800 (version "2.0.12")
801 (source (origin
802 (method url-fetch)
803 (uri (string-append
804 "https://github.com/Microsoft/LightGBM/archive/v"
805 version ".tar.gz"))
806 (sha256
807 (base32
808 "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
809 (file-name (string-append name "-" version ".tar.gz"))))
810 (native-inputs
811 `(("python-pytest" ,python-pytest)
812 ("python-nose" ,python-nose)))
813 (inputs
814 `(("openmpi" ,openmpi)))
815 (propagated-inputs
816 `(("python-numpy" ,python-numpy)
817 ("python-scipy" ,python-scipy)))
818 (arguments
819 `(#:configure-flags
820 '("-DUSE_MPI=ON")
821 #:phases
822 (modify-phases %standard-phases
823 (replace 'check
824 (lambda* (#:key outputs #:allow-other-keys)
825 (with-directory-excursion ,(string-append "../LightGBM-" version)
826 (invoke "pytest" "tests/c_api_test/test_.py")))))))
827 (build-system cmake-build-system)
828 (home-page "https://github.com/Microsoft/LightGBM")
829 (synopsis "Gradient boosting framework based on decision tree algorithms")
830 (description "LightGBM is a gradient boosting framework that uses tree
831based learning algorithms. It is designed to be distributed and efficient with
832the following advantages:
833
834@itemize
835@item Faster training speed and higher efficiency
836@item Lower memory usage
837@item Better accuracy
838@item Parallel and GPU learning supported (not enabled in this package)
839@item Capable of handling large-scale data
840@end itemize\n")
841 (license license:expat)))
a8fb82a8
FT		 842
843(define-public vowpal-wabbit
844 ;; Language bindings not included.
845 (package
846 (name "vowpal-wabbit")
847 (version "8.5.0")
848 (source (origin
849 (method url-fetch)
850 (uri (string-append
851 "https://github.com/JohnLangford/vowpal_wabbit/archive/"
852 version ".tar.gz"))
853 (sha256
854 (base32
855 "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
856 (file-name (string-append name "-" version ".tar.gz"))))
857 (inputs
858 `(("boost" ,boost)
859 ("zlib" ,zlib)))
860 (arguments
861 `(#:configure-flags
862 (list (string-append "--with-boost="
863 (assoc-ref %build-inputs "boost")))))
864 (build-system gnu-build-system)
865 (home-page "https://github.com/JohnLangford/vowpal_wabbit")
866 (synopsis "Fast machine learning library for online learning")
867 (description "Vowpal Wabbit is a machine learning system with techniques
868such as online, hashing, allreduce, reductions, learning2search, active, and
869interactive learning.")
870 (license license:bsd-3)))
jackhill's copy of GNU Guix: https://guix.gnu.org/