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Merge branch 'master' into core-updates
[jackhill/guix/guix.git] / gnu / packages / machine-learning.scm
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741115b6 1;;; GNU Guix --- Functional package management for GNU
7d4cab74 2;;; Copyright © 2015, 2016, 2017, 2018, 2019 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>
5ed72097 6;;; Copyright © 2018, 2019 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>
564cf93f 11;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
df4c8434 12;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
d60b064d 13;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
6e760872 14;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
741115b6
RW		 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 machine-learning)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix utils)
35 #:use-module (guix download)
23aab4ab 36 #:use-module (guix svn-download)
6e760872 37 #:use-module (guix build-system asdf)
c1670a81 38 #:use-module (guix build-system cmake)
741115b6 39 #:use-module (guix build-system gnu)
0a3063d6 40 #:use-module (guix build-system ocaml)
be6eb2f1 41 #:use-module (guix build-system python)
8406138b 42 #:use-module (guix build-system r)
a9b34762 43 #:use-module (guix git-download)
71f80f54 44 #:use-module (gnu packages)
0dfeb285 45 #:use-module (gnu packages adns)
5a14e81e 46 #:use-module (gnu packages algebra)
b9445d0b 47 #:use-module (gnu packages audio)
23aab4ab 48 #:use-module (gnu packages autotools)
b9445d0b 49 #:use-module (gnu packages base)
99260014 50 #:use-module (gnu packages bash)
0931c609 51 #:use-module (gnu packages boost)
be6eb2f1 52 #:use-module (gnu packages check)
0931c609 53 #:use-module (gnu packages compression)
9e37e537 54 #:use-module (gnu packages cran)
4fa16c9a 55 #:use-module (gnu packages databases)
23aab4ab 56 #:use-module (gnu packages dejagnu)
0931c609 57 #:use-module (gnu packages gcc)
b9445d0b 58 #:use-module (gnu packages glib)
f1765b57 59 #:use-module (gnu packages graphviz)
b9445d0b 60 #:use-module (gnu packages gstreamer)
5f0ff6a9 61 #:use-module (gnu packages image)
b9445d0b 62 #:use-module (gnu packages linux)
88f06fd0 63 #:use-module (gnu packages lisp-xyz)
0931c609 64 #:use-module (gnu packages maths)
112c2c01 65 #:use-module (gnu packages mpi)
0a3063d6 66 #:use-module (gnu packages ocaml)
3929f46c 67 #:use-module (gnu packages onc-rpc)
791c11d6 68 #:use-module (gnu packages perl)
c1670a81 69 #:use-module (gnu packages pkg-config)
0dfeb285 70 #:use-module (gnu packages protobuf)
0931c609 71 #:use-module (gnu packages python)
ec1224a7 72 #:use-module (gnu packages python-science)
10451f6b 73 #:use-module (gnu packages python-web)
44d10b1f 74 #:use-module (gnu packages python-xyz)
4fa16c9a 75 #:use-module (gnu packages serialization)
f1765b57 76 #:use-module (gnu packages sphinx)
c1670a81 77 #:use-module (gnu packages statistics)
4fa16c9a 78 #:use-module (gnu packages sqlite)
c1670a81 79 #:use-module (gnu packages swig)
0dfeb285 80 #:use-module (gnu packages tls)
99260014 81 #:use-module (gnu packages web)
5f0ff6a9 82 #:use-module (gnu packages xml)
39bb4937
RW		 83 #:use-module (gnu packages xorg)
84 #:use-module (ice-9 match))
741115b6 85
a9b34762
MM		 86(define-public fann
87 ;; The last release is >100 commits behind, so we package from git.
88 (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
89 (package
90 (name "fann")
91 (version (string-append "2.2.0-1." (string-take commit 8)))
92 (source (origin
93 (method git-fetch)
94 (uri (git-reference
95 (url "https://github.com/libfann/fann.git")
96 (commit commit)))
97 (file-name (string-append name "-" version "-checkout"))
98 (sha256
99 (base32
100 "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
101 (build-system cmake-build-system)
102 (arguments
103 `(#:phases
104 (modify-phases %standard-phases
105 (replace 'check
106 (lambda* (#:key outputs #:allow-other-keys)
107 (let* ((out (assoc-ref outputs "out")))
108 (with-directory-excursion (string-append (getcwd) "/tests")
109 (invoke "./fann_tests"))))))))
110 (home-page "http://leenissen.dk/fann/wp/")
111 (synopsis "Fast Artificial Neural Network")
112 (description
bd2bd80d
MB		 113 "FANN is a neural network library, which implements multilayer
114artificial neural networks in C with support for both fully connected and
115sparsely connected networks.")
a9b34762
MM		 116 (license license:lgpl2.1))))
117
741115b6
RW		 118(define-public libsvm
119 (package
120 (name "libsvm")
2cffa2f2 121 (version "3.23")
741115b6
RW		 122 (source
123 (origin
124 (method url-fetch)
d1308c5e
TGR		 125 (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
126 name "-" version ".tar.gz"))
741115b6 127 (sha256
2cffa2f2 128 (base32 "0jpaq0rr92x38p4nk3gjan79ip67m6p80anb28z1d8601miysyi5"))))
741115b6
RW		 129 (build-system gnu-build-system)
130 (arguments
2cffa2f2 131 `(#:tests? #f ; no "check" target
741115b6
RW		 132 #:phases (modify-phases %standard-phases
133 (delete 'configure)
134 (replace
d1308c5e 135 'install ; no ‘install’ target
741115b6
RW		 136 (lambda* (#:key outputs #:allow-other-keys)
137 (let* ((out (assoc-ref outputs "out"))
138 (bin (string-append out "/bin/")))
139 (mkdir-p bin)
140 (for-each (lambda (file)
141 (copy-file file (string-append bin file)))
142 '("svm-train"
143 "svm-predict"
144 "svm-scale")))
145 #t)))))
146 (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
147 (synopsis "Library for Support Vector Machines")
148 (description
149 "LIBSVM is a machine learning library for support vector
150classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
151distribution estimation (one-class SVM). It supports multi-class
152classification.")
153 (license license:bsd-3)))
71f80f54
RW		 154
155(define-public python-libsvm
156 (package (inherit libsvm)
157 (name "python-libsvm")
158 (build-system gnu-build-system)
159 (arguments
2cffa2f2 160 `(#:tests? #f ; no "check" target
71f80f54
RW		 161 #:make-flags '("-C" "python")
162 #:phases
163 (modify-phases %standard-phases
164 (delete 'configure)
165 (replace
d1308c5e 166 'install ; no ‘install’ target
71f80f54
RW		 167 (lambda* (#:key inputs outputs #:allow-other-keys)
168 (let ((site (string-append (assoc-ref outputs "out")
169 "/lib/python"
170 (string-take
171 (string-take-right
172 (assoc-ref inputs "python") 5) 3)
173 "/site-packages/")))
174 (substitute* "python/svm.py"
175 (("../libsvm.so.2") "libsvm.so.2"))
176 (mkdir-p site)
177 (for-each (lambda (file)
178 (copy-file file (string-append site (basename file))))
179 (find-files "python" "\\.py"))
180 (copy-file "libsvm.so.2"
181 (string-append site "libsvm.so.2")))
182 #t)))))
183 (inputs
184 `(("python" ,python)))
185 (synopsis "Python bindings of libSVM")))
0931c609 186
23aab4ab
RW		 187(define-public ghmm
188 ;; The latest release candidate is several years and a couple of fixes have
189 ;; been published since. This is why we download the sources from the SVN
190 ;; repository.
191 (let ((svn-revision 2341))
192 (package
193 (name "ghmm")
194 (version (string-append "0.9-rc3-0." (number->string svn-revision)))
195 (source (origin
196 (method svn-fetch)
197 (uri (svn-reference
198 (url "http://svn.code.sf.net/p/ghmm/code/trunk")
199 (revision svn-revision)))
e3a69938 200 (file-name (string-append name "-" version "-checkout"))
23aab4ab
RW		 201 (sha256
202 (base32
203 "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
204 (build-system gnu-build-system)
205 (arguments
ced12a7b
RW		 206 `(#:imported-modules (,@%gnu-build-system-modules
207 (guix build python-build-system))
208 #:phases
23aab4ab
RW		 209 (modify-phases %standard-phases
210 (add-after 'unpack 'enter-dir
211 (lambda _ (chdir "ghmm") #t))
ced12a7b
RW		 212 (delete 'check)
213 (add-after 'install 'check
214 (assoc-ref %standard-phases 'check))
215 (add-before 'check 'fix-PYTHONPATH
216 (lambda* (#:key inputs outputs #:allow-other-keys)
9c2563a8 217 (let ((python-version (python-version
ced12a7b
RW		 218 (assoc-ref inputs "python"))))
219 (setenv "PYTHONPATH"
220 (string-append (getenv "PYTHONPATH")
221 ":" (assoc-ref outputs "out")
222 "/lib/python" python-version
223 "/site-packages")))
23aab4ab
RW		 224 #t))
225 (add-after 'enter-dir 'fix-runpath
226 (lambda* (#:key outputs #:allow-other-keys)
227 (substitute* "ghmmwrapper/setup.py"
228 (("^(.*)extra_compile_args = \\[" line indent)
229 (string-append indent
230 "extra_link_args = [\"-Wl,-rpath="
231 (assoc-ref outputs "out") "/lib\"],\n"
232 line
233 "\"-Wl,-rpath="
234 (assoc-ref outputs "out")
235 "/lib\", ")))
236 #t))
237 (add-after 'enter-dir 'disable-broken-tests
238 (lambda _
239 (substitute* "tests/Makefile.am"
240 ;; GHMM_SILENT_TESTS is assumed to be a command.
241 (("TESTS_ENVIRONMENT.*") "")
242 ;; Do not build broken tests.
243 (("chmm .*") "")
244 (("read_fa .*") "")
245 (("mcmc .*") "")
246 (("label_higher_order_test.*$")
247 "label_higher_order_test\n"))
248
249 ;; These Python unittests are broken as there is no gato.
250 ;; See https://sourceforge.net/p/ghmm/support-requests/3/
251 (substitute* "ghmmwrapper/ghmmunittests.py"
252 (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
253 line indent)
254 (string-append indent
255 "@unittest.skip(\"Disabled by Guix\")\n"
256 line)))
a491856f 257 #t)))))
23aab4ab
RW		 258 (inputs
259 `(("python" ,python-2) ; only Python 2 is supported
260 ("libxml2" ,libxml2)))
261 (native-inputs
262 `(("pkg-config" ,pkg-config)
263 ("dejagnu" ,dejagnu)
264 ("swig" ,swig)
265 ("autoconf" ,autoconf)
266 ("automake" ,automake)
267 ("libtool" ,libtool)))
268 (home-page "http://ghmm.org")
269 (synopsis "Hidden Markov Model library")
270 (description
271 "The General Hidden Markov Model library (GHMM) is a C library with
272additional Python bindings implementing a wide range of types of @dfn{Hidden
d1e4ad1b 273Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
23aab4ab
RW		 274training, HMM clustering, HMM mixtures.")
275 (license license:lgpl2.0+))))
276
791c11d6
BW		 277(define-public mcl
278 (package
279 (name "mcl")
280 (version "14.137")
281 (source (origin
282 (method url-fetch)
283 (uri (string-append
284 "http://micans.org/mcl/src/mcl-"
285 (string-replace-substring version "." "-")
286 ".tar.gz"))
287 (sha256
288 (base32
289 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
290 (build-system gnu-build-system)
291 (arguments
292 `(#:configure-flags (list "--enable-blast")))
293 (inputs
294 `(("perl" ,perl)))
295 (home-page "http://micans.org/mcl/")
296 (synopsis "Clustering algorithm for graphs")
297 (description
298 "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
299fast and scalable unsupervised cluster algorithm for graphs (also known as
300networks) based on simulation of (stochastic) flow in graphs.")
301 ;; In the LICENCE file and web page it says "The software is licensed
302 ;; under the GNU General Public License, version 3.", but in several of
303 ;; the source code files it suggests GPL3 or later.
304 ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
305 (license license:gpl3)))
306
0a3063d6
BW		 307(define-public ocaml-mcl
308 (package
309 (name "ocaml-mcl")
310 (version "12-068oasis4")
311 (source
312 (origin
fb168a31
RW		 313 (method git-fetch)
314 (uri (git-reference
315 (url "https://github.com/fhcrc/mcl.git")
316 (commit version)))
317 (file-name (git-file-name name version))
0a3063d6
BW		 318 (sha256
319 (base32
fb168a31 320 "0009dc3h2jp3qg5val452wngpqnbfyhbcxylghq0mrjqxx0jdq5p"))))
0a3063d6
BW		 321 (build-system ocaml-build-system)
322 (arguments
b24aaeec 323 `(#:phases
0a3063d6
BW		 324 (modify-phases %standard-phases
325 (add-before 'configure 'patch-paths
326 (lambda _
327 (substitute* "configure"
b24aaeec 328 (("/bin/sh") (which "sh")))
0a3063d6
BW		 329 (substitute* "setup.ml"
330 (("LDFLAGS=-fPIC")
b24aaeec
RW		 331 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))
332 (("-std=c89") "-std=gnu99")
333
334 ;; This is a mutable string, which is no longer supported. Use
335 ;; a byte buffer instead.
336 (("String.make \\(String.length s\\)")
337 "Bytes.make (String.length s)")
338
339 ;; These two belong together.
340 (("OASISString.replace_chars")
341 "Bytes.to_string (OASISString.replace_chars")
342 ((" s;")
343 " s);"))
344 (substitute* "myocamlbuild.ml"
345 (("std=c89") "std=gnu99"))
346 ;; Since we build with a more recent OCaml, we have to use C99 or
347 ;; later. This causes problems with the old C code.
348 (substitute* "src/impala/matrix.c"
349 (("restrict") "restrict_"))
0a3063d6 350 #t)))))
b24aaeec
RW		 351 (native-inputs
352 `(("ocamlbuild" ,ocamlbuild)))
0a3063d6
BW		 353 (home-page "https://github.com/fhcrc/mcl")
354 (synopsis "OCaml wrappers around MCL")
355 (description
356 "This package provides OCaml bindings for the MCL graph clustering
357algorithm.")
358 (license license:gpl3)))
359
0931c609
RW		 360(define-public randomjungle
361 (package
362 (name "randomjungle")
363 (version "2.1.0")
364 (source
365 (origin
366 (method url-fetch)
367 (uri (string-append
df4c8434
BH		 368 "https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
369 "/randomjungle/randomjungle-" version ".tar_.gz"))
1e92d311 370 (patches (search-patches "randomjungle-disable-static-build.patch"))
0931c609
RW		 371 (sha256
372 (base32
373 "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
374 (build-system gnu-build-system)
375 (arguments
376 `(#:configure-flags
1e92d311
MB		 377 (list "--disable-static"
378 (string-append "--with-boost="
0931c609
RW		 379 (assoc-ref %build-inputs "boost")))
380 #:phases
381 (modify-phases %standard-phases
382 (add-before
383 'configure 'set-CXXFLAGS
384 (lambda _
385 (setenv "CXXFLAGS" "-fpermissive ")
386 #t)))))
387 (inputs
388 `(("boost" ,boost)
389 ("gsl" ,gsl)
390 ("libxml2" ,libxml2)
391 ("zlib" ,zlib)))
392 (native-inputs
25e0037a
EF		 393 `(("gfortran" ,gfortran)
394 ("gfortran:lib" ,gfortran "lib")))
47818201
RW		 395 ;; Non-portable assembly instructions are used so building fails on
396 ;; platforms other than x86_64 or i686.
397 (supported-systems '("x86_64-linux" "i686-linux"))
df4c8434 398 (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
0931c609
RW		 399 (synopsis "Implementation of the Random Forests machine learning method")
400 (description
401 "Random Jungle is an implementation of Random Forests. It is supposed to
402analyse high dimensional data. In genetics, it can be used for analysing big
403Genome Wide Association (GWA) data. Random Forests is a powerful machine
404learning method. Most interesting features are variable selection, missing
405value imputation, classifier creation, generalization error estimation and
406sample proximities between pairs of cases.")
407 (license license:gpl3+)))
c1670a81 408
7d4cab74
RW		 409(define-public openfst
410 (package
411 (name "openfst")
5ed72097 412 (version "1.7.2")
7d4cab74
RW		 413 (source (origin
414 (method url-fetch)
415 (uri (string-append "http://www.openfst.org/twiki/pub/FST/"
416 "FstDownload/openfst-" version ".tar.gz"))
417 (sha256
418 (base32
5ed72097 419 "0fqgk8195kz21is09gwzwnrg7fr9526bi9mh4apyskapz27pbhr1"))))
7d4cab74
RW		 420 (build-system gnu-build-system)
421 (home-page "http://www.openfst.org")
422 (synopsis "Library for weighted finite-state transducers")
423 (description "OpenFst is a library for constructing, combining,
424optimizing, and searching weighted finite-state transducers (FSTs).")
425 (license license:asl2.0)))
426
c1670a81
RW		 427(define-public shogun
428 (package
429 (name "shogun")
5a14e81e 430 (version "6.1.3")
c1670a81
RW		 431 (source
432 (origin
433 (method url-fetch)
434 (uri (string-append
435 "ftp://shogun-toolbox.org/shogun/releases/"
436 (version-major+minor version)
437 "/sources/shogun-" version ".tar.bz2"))
438 (sha256
439 (base32
5a14e81e 440 "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
c1670a81
RW		 441 (modules '((guix build utils)
442 (ice-9 rdelim)))
443 (snippet
444 '(begin
445 ;; Remove non-free sources and files referencing them
446 (for-each delete-file
447 (find-files "src/shogun/classifier/svm/"
448 "SVMLight\\.(cpp|h)"))
449 (for-each delete-file
450 (find-files "examples/undocumented/libshogun/"
451 (string-append
452 "(classifier_.*svmlight.*|"
453 "evaluation_cross_validation_locked_comparison).cpp")))
454 ;; Remove non-free functions.
455 (define (delete-ifdefs file)
456 (with-atomic-file-replacement file
457 (lambda (in out)
458 (let loop ((line (read-line in 'concat))
459 (skipping? #f))
460 (if (eof-object? line)
461 #t
462 (let ((skip-next?
463 (or (and skipping?
464 (not (string-prefix?
465 "#endif //USE_SVMLIGHT" line)))
466 (string-prefix?
467 "#ifdef USE_SVMLIGHT" line))))
468 (when (or (not skipping?)
469 (and skipping? (not skip-next?)))
470 (display line out))
471 (loop (read-line in 'concat) skip-next?)))))))
5a14e81e
KK		 472 (for-each delete-ifdefs
473 (append
474 (find-files "src/shogun/classifier/mkl"
475 "^MKLClassification\\.cpp")
476 (find-files "src/shogun/classifier/svm"
477 "^SVMLightOneClass\\.(cpp|h)")
478 (find-files "src/shogun/multiclass"
479 "^ScatterSVM\\.(cpp|h)")
480 (find-files "src/shogun/kernel/"
481 "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
482 (find-files "src/shogun/regression/svr"
483 "^(MKLRegression|SVRLight)\\.(cpp|h)")
484 (find-files "src/shogun/transfer/domain_adaptation"
c0d7c124 485 "^DomainAdaptationSVM\\.(cpp|h)")))
6cbee49d 486 #t))))
c1670a81
RW		 487 (build-system cmake-build-system)
488 (arguments
489 '(#:tests? #f ;no check target
490 #:phases
dc1d3cde
KK		 491 (modify-phases %standard-phases
492 (add-after 'unpack 'delete-broken-symlinks
493 (lambda _
494 (for-each delete-file '("applications/arts/data"
495 "applications/asp/data"
496 "applications/easysvm/data"
497 "applications/msplicer/data"
498 "applications/ocr/data"
5a14e81e
KK		 499 "examples/meta/data"
500 "examples/undocumented/data"))
dc1d3cde
KK		 501 #t))
502 (add-after 'unpack 'change-R-target-path
503 (lambda* (#:key outputs #:allow-other-keys)
5a14e81e
KK		 504 (substitute* '("src/interfaces/r/CMakeLists.txt"
505 "examples/meta/r/CMakeLists.txt")
dc1d3cde
KK		 506 (("\\$\\{R_COMPONENT_LIB_PATH\\}")
507 (string-append (assoc-ref outputs "out")
508 "/lib/R/library/")))
509 #t))
510 (add-after 'unpack 'fix-octave-modules
511 (lambda* (#:key outputs #:allow-other-keys)
5a14e81e 512 (substitute* "src/interfaces/octave/CMakeLists.txt"
dc1d3cde 513 (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
5a14e81e
KK		 514 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
515 ;; change target directory
dc1d3cde
KK		 516 (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
517 (string-append (assoc-ref outputs "out")
518 "/share/octave/packages")))
5a14e81e
KK		 519 (substitute* '("src/interfaces/octave/swig_typemaps.i"
520 "src/interfaces/octave/sg_print_functions.cpp")
521 ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
522 (("octave/config\\.h") "octave/octave-config.h")
523 (("octave/oct-obj.h") "octave/ovl.h"))
dc1d3cde 524 #t))
5a14e81e
KK		 525 (add-after 'unpack 'move-rxcpp
526 (lambda* (#:key inputs #:allow-other-keys)
527 (let ((rxcpp-dir "shogun/third-party/rxcpp"))
528 (mkdir-p rxcpp-dir)
529 (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
530 #t)))
dc1d3cde 531 (add-before 'build 'set-HOME
c1670a81 532 ;; $HOME needs to be set at some point during the build phase
dc1d3cde 533 (lambda _ (setenv "HOME" "/tmp") #t)))
c1670a81
RW		 534 #:configure-flags
535 (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
536 "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
5a14e81e
KK		 537 "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
538 ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
539 ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
540 ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
541 ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
542 "-DINTERFACE_OCTAVE=ON"
543 "-DINTERFACE_PYTHON=ON"
544 "-DINTERFACE_R=ON")))
c1670a81
RW		 545 (inputs
546 `(("python" ,python)
547 ("numpy" ,python-numpy)
2d7c4ae3 548 ("r-minimal" ,r-minimal)
5537603f 549 ("octave" ,octave-cli)
c1670a81 550 ("swig" ,swig)
5a14e81e 551 ("eigen" ,eigen)
c1670a81
RW		 552 ("hdf5" ,hdf5)
553 ("atlas" ,atlas)
554 ("arpack" ,arpack-ng)
555 ("lapack" ,lapack)
556 ("glpk" ,glpk)
557 ("libxml2" ,libxml2)
558 ("lzo" ,lzo)
559 ("zlib" ,zlib)))
560 (native-inputs
5a14e81e
KK		 561 `(("pkg-config" ,pkg-config)
562 ("rxcpp" ,rxcpp)))
6b5b656f
RW		 563 ;; Non-portable SSE instructions are used so building fails on platforms
564 ;; other than x86_64.
565 (supported-systems '("x86_64-linux"))
c1670a81
RW		 566 (home-page "http://shogun-toolbox.org/")
567 (synopsis "Machine learning toolbox")
568 (description
569 "The Shogun Machine learning toolbox provides a wide range of unified and
570efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
571combine multiple data representations, algorithm classes, and general purpose
572tools. This enables both rapid prototyping of data pipelines and extensibility
573in terms of new algorithms.")
574 (license license:gpl3+)))
8406138b 575
3a354e10
KK		 576(define-public rxcpp
577 (package
578 (name "rxcpp")
e91a0bff 579 (version "4.1.0")
3a354e10
KK		 580 (source
581 (origin
5daafe0b
TGR		 582 (method git-fetch)
583 (uri (git-reference
584 (url "https://github.com/ReactiveX/RxCpp.git")
585 (commit (string-append "v" version))))
3a354e10 586 (sha256
5daafe0b
TGR		 587 (base32 "1rdpa3jlc181jd08nk437aar085h28i45s6nzrv65apb3xyyz0ij"))
588 (file-name (git-file-name name version))))
3a354e10
KK		 589 (build-system cmake-build-system)
590 (arguments
591 `(#:phases
592 (modify-phases %standard-phases
593 (add-after 'unpack 'remove-werror
594 (lambda _
595 (substitute* (find-files ".")
596 (("-Werror") ""))
597 #t))
598 (replace 'check
599 (lambda _
600 (invoke "ctest"))))))
601 (native-inputs
602 `(("catch" ,catch-framework)))
603 (home-page "http://reactivex.io/")
604 (synopsis "Reactive Extensions for C++")
605 (description
606 "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
607values-distributed-in-time. ReactiveX is a library for composing asynchronous
608and event-based programs by using observable sequences.
609
610It extends the observer pattern to support sequences of data and/or events and
611adds operators that allow you to compose sequences together declaratively while
612abstracting away concerns about things like low-level threading,
613synchronization, thread-safety, concurrent data structures, and non-blocking
614I/O.")
615 (license license:asl2.0)))
616
8406138b
RW		 617(define-public r-adaptivesparsity
618 (package
619 (name "r-adaptivesparsity")
c0608f81 620 (version "1.6")
8406138b
RW		 621 (source (origin
622 (method url-fetch)
623 (uri (cran-uri "AdaptiveSparsity" version))
624 (sha256
625 (base32
c0608f81 626 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
8406138b
RW		 627 (properties
628 `((upstream-name . "AdaptiveSparsity")))
629 (build-system r-build-system)
630 (arguments
631 `(#:phases
632 (modify-phases %standard-phases
633 (add-after 'unpack 'link-against-armadillo
634 (lambda _
635 (substitute* "src/Makevars"
636 (("PKG_LIBS=" prefix)
637 (string-append prefix "-larmadillo"))))))))
638 (propagated-inputs
c0608f81
RW		 639 `(("r-mass" ,r-mass)
640 ("r-matrix" ,r-matrix)
641 ("r-rcpp" ,r-rcpp)
8406138b 642 ("r-rcpparmadillo" ,r-rcpparmadillo)))
60e36bff
LC		 643 (inputs
644 `(("armadillo" ,armadillo)))
e9960d8c 645 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
8406138b
RW		 646 (synopsis "Adaptive sparsity models")
647 (description
648 "This package implements the Figueiredo machine learning algorithm for
649adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
650geometric models.")
651 (license license:lgpl3+)))
e4785eb8 652
39bb4937
RW		 653(define-public gemmlowp-for-tensorflow
654 ;; The commit hash is taken from "tensorflow/workspace.bzl".
655 (let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
656 (revision "2"))
657 (package
658 (name "gemmlowp")
659 (version (git-version "0" revision commit))
660 (source (origin
661 (method url-fetch)
662 (uri (string-append "https://mirror.bazel.build/"
663 "github.com/google/gemmlowp/archive/"
664 commit ".zip"))
665 (file-name (string-append "gemmlowp-" version ".zip"))
666 (sha256
667 (base32
668 "0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
669 (build-system cmake-build-system)
670 (arguments
671 `(#:configure-flags
672 (list ,@(match (%current-system)
673 ((or "x86_64-linux" "i686-linux")
a32e3b90 674 '("-DCMAKE_CXX_FLAGS=-msse2"))
39bb4937
RW		 675 (_ '())))
676 #:phases
677 (modify-phases %standard-phases
678 ;; This directory contains the CMakeLists.txt.
679 (add-after 'unpack 'chdir
680 (lambda _ (chdir "contrib") #t))
681 ;; There is no install target
682 (replace 'install
683 (lambda* (#:key outputs #:allow-other-keys)
684 (let* ((out (assoc-ref outputs "out"))
685 (lib (string-append out "/lib/"))
686 (inc (string-append out "/include/")))
687 (install-file "../build/libeight_bit_int_gemm.so" lib)
688 (for-each (lambda (dir)
689 (let ((target (string-append inc "/" dir)))
690 (mkdir-p target)
691 (for-each (lambda (h)
692 (install-file h target))
693 (find-files (string-append "../" dir)
694 "\\.h$"))))
695 '("meta" "profiling" "public" "fixedpoint"
696 "eight_bit_int_gemm" "internal"))
697 #t))))))
698 (native-inputs
699 `(("unzip" ,unzip)))
700 (home-page "https://github.com/google/gemmlowp")
701 (synopsis "Small self-contained low-precision GEMM library")
702 (description
703 "This is a small self-contained low-precision @dfn{general matrix
704multiplication} (GEMM) library. It is not a full linear algebra library.
705Low-precision means that the input and output matrix entries are integers on
706at most 8 bits. To avoid overflow, results are internally accumulated on more
707than 8 bits, and at the end only some significant 8 bits are kept.")
708 (license license:asl2.0))))
f05c7eb4 709
5f0ff6a9
MB		 710(define-public dlib
711 (package
712 (name "dlib")
abe97a58 713 (version "19.7")
5f0ff6a9
MB		 714 (source (origin
715 (method url-fetch)
716 (uri (string-append
717 "http://dlib.net/files/dlib-" version ".tar.bz2"))
718 (sha256
719 (base32
abe97a58 720 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
5f0ff6a9
MB		 721 (modules '((guix build utils)))
722 (snippet
723 '(begin
724 ;; Delete ~13MB of bundled dependencies.
725 (delete-file-recursively "dlib/external")
0ef7ea66
MB		 726 (delete-file-recursively "docs/dlib/external")
727 #t))))
5f0ff6a9
MB		 728 (build-system cmake-build-system)
729 (arguments
677bc34d 730 `(#:phases
5f0ff6a9
MB		 731 (modify-phases %standard-phases
732 (add-after 'unpack 'disable-asserts
733 (lambda _
734 ;; config.h recommends explicitly enabling or disabling asserts
735 ;; when building as a shared library. By default neither is set.
736 (substitute* "dlib/config.h"
737 (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
738 #t))
4fba38db
MB		 739 (add-after 'disable-asserts 'disable-failing-tests
740 (lambda _
741 ;; One test times out on MIPS, so we need to disable it.
0ef7ea66 742 ;; Others are flaky on some platforms.
4fba38db
MB		 743 (let* ((system ,(or (%current-target-system)
744 (%current-system)))
745 (disabled-tests (cond
746 ((string-prefix? "mips64" system)
747 '("object_detector" ; timeout
748 "data_io"))
749 ((string-prefix? "armhf" system)
a343c461 750 '("learning_to_track"))
4fba38db 751 ((string-prefix? "i686" system)
0ef7ea66 752 '("optimization"))
4fba38db 753 (else '()))))
4fba38db
MB		 754 (for-each
755 (lambda (test)
756 (substitute* "dlib/test/makefile"
0ef7ea66
MB		 757 (((string-append "SRC \\+= " test "\\.cpp")) "")))
758 disabled-tests)
759 #t)))
5f0ff6a9
MB		 760 (replace 'check
761 (lambda _
762 ;; No test target, so we build and run the unit tests here.
8eaf53e3 763 (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
5f0ff6a9 764 (with-directory-excursion test-dir
8448e6bf
TGR		 765 (invoke "make" "-j" (number->string (parallel-job-count)))
766 (invoke "./dtest" "--runall"))
767 #t)))
5f0ff6a9
MB		 768 (add-after 'install 'delete-static-library
769 (lambda* (#:key outputs #:allow-other-keys)
0ef7ea66
MB		 770 (delete-file (string-append (assoc-ref outputs "out")
771 "/lib/libdlib.a"))
772 #t)))))
5f0ff6a9 773 (native-inputs
3929f46c
TGR		 774 `(("pkg-config" ,pkg-config)
775 ;; For tests.
776 ("libnsl" ,libnsl)))
5f0ff6a9 777 (inputs
f40841e9 778 `(("giflib" ,giflib)
4fba38db 779 ("lapack" ,lapack)
5f0ff6a9
MB		 780 ("libjpeg" ,libjpeg)
781 ("libpng" ,libpng)
782 ("libx11" ,libx11)
783 ("openblas" ,openblas)
784 ("zlib" ,zlib)))
785 (synopsis
786 "Toolkit for making machine learning and data analysis applications in C++")
787 (description
788 "Dlib is a modern C++ toolkit containing machine learning algorithms and
789tools. It is used in both industry and academia in a wide range of domains
790including robotics, embedded devices, mobile phones, and large high performance
791computing environments.")
792 (home-page "http://dlib.net")
793 (license license:boost1.0)))
be6eb2f1
RW		 794
795(define-public python-scikit-learn
796 (package
797 (name "python-scikit-learn")
d7e29a2b 798 (version "0.20.4")
be6eb2f1
RW		 799 (source
800 (origin
4a89bdd1
RW		 801 (method git-fetch)
802 (uri (git-reference
803 (url "https://github.com/scikit-learn/scikit-learn.git")
804 (commit version)))
805 (file-name (git-file-name name version))
be6eb2f1
RW		 806 (sha256
807 (base32
d7e29a2b 808 "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))
be6eb2f1
RW		 809 (build-system python-build-system)
810 (arguments
811 `(#:phases
812 (modify-phases %standard-phases
4a89bdd1
RW		 813 (add-after 'build 'build-ext
814 (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
815 (replace 'check
816 (lambda _
817 ;; Restrict OpenBLAS threads to prevent segfaults while testing!
818 (setenv "OPENBLAS_NUM_THREADS" "1")
7ff3f3d2
MB		 819
820 ;; Some tests require write access to $HOME.
821 (setenv "HOME" "/tmp")
822
823 (invoke "pytest" "sklearn" "-m" "not network")))
71804546
BL		 824 (add-before 'reset-gzip-timestamps 'make-files-writable
825 (lambda* (#:key outputs #:allow-other-keys)
826 ;; Make sure .gz files are writable so that the
827 ;; 'reset-gzip-timestamps' phase can do its work.
828 (let ((out (assoc-ref outputs "out")))
829 (for-each make-file-writable
830 (find-files out "\\.gz$"))
831 #t))))))
be6eb2f1
RW		 832 (inputs
833 `(("openblas" ,openblas)))
834 (native-inputs
4a89bdd1
RW		 835 `(("python-pytest" ,python-pytest)
836 ("python-pandas" ,python-pandas) ;for tests
be6eb2f1
RW		 837 ("python-cython" ,python-cython)))
838 (propagated-inputs
839 `(("python-numpy" ,python-numpy)
840 ("python-scipy" ,python-scipy)))
841 (home-page "http://scikit-learn.org/")
842 (synopsis "Machine Learning in Python")
843 (description
4a89bdd1
RW		 844 "Scikit-learn provides simple and efficient tools for data mining and
845data analysis.")
be6eb2f1
RW		 846 (license license:bsd-3)))
847
848(define-public python2-scikit-learn
7ff3f3d2 849 (package-with-python2 python-scikit-learn))
2dab4188
FT		 850
851(define-public python-autograd
852 (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
853 (revision "0")
854 (version (git-version "0.0.0" revision commit)))
855 (package
856 (name "python-autograd")
857 (home-page "https://github.com/HIPS/autograd")
858 (source (origin
859 (method git-fetch)
860 (uri (git-reference
861 (url home-page)
862 (commit commit)))
863 (sha256
864 (base32
865 "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
866 (file-name (git-file-name name version))))
867 (version version)
868 (build-system python-build-system)
869 (native-inputs
870 `(("python-nose" ,python-nose)
871 ("python-pytest" ,python-pytest)))
872 (propagated-inputs
873 `(("python-future" ,python-future)
874 ("python-numpy" ,python-numpy)))
875 (arguments
876 `(#:phases (modify-phases %standard-phases
877 (replace 'check
878 (lambda _
879 (invoke "py.test" "-v"))))))
880 (synopsis "Efficiently computes derivatives of NumPy code")
881 (description "Autograd can automatically differentiate native Python and
882NumPy code. It can handle a large subset of Python's features, including loops,
883ifs, recursion and closures, and it can even take derivatives of derivatives
884of derivatives. It supports reverse-mode differentiation
885(a.k.a. backpropagation), which means it can efficiently take gradients of
886scalar-valued functions with respect to array-valued arguments, as well as
887forward-mode differentiation, and the two can be composed arbitrarily. The
888main intended application of Autograd is gradient-based optimization.")
889 (license license:expat))))
890
891(define-public python2-autograd
892 (package-with-python2 python-autograd))
112c2c01
FT		 893
894(define-public lightgbm
895 (package
896 (name "lightgbm")
897 (version "2.0.12")
898 (source (origin
899 (method url-fetch)
900 (uri (string-append
901 "https://github.com/Microsoft/LightGBM/archive/v"
902 version ".tar.gz"))
903 (sha256
904 (base32
905 "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
906 (file-name (string-append name "-" version ".tar.gz"))))
907 (native-inputs
908 `(("python-pytest" ,python-pytest)
909 ("python-nose" ,python-nose)))
910 (inputs
911 `(("openmpi" ,openmpi)))
912 (propagated-inputs
913 `(("python-numpy" ,python-numpy)
914 ("python-scipy" ,python-scipy)))
915 (arguments
916 `(#:configure-flags
917 '("-DUSE_MPI=ON")
918 #:phases
919 (modify-phases %standard-phases
920 (replace 'check
921 (lambda* (#:key outputs #:allow-other-keys)
922 (with-directory-excursion ,(string-append "../LightGBM-" version)
923 (invoke "pytest" "tests/c_api_test/test_.py")))))))
924 (build-system cmake-build-system)
925 (home-page "https://github.com/Microsoft/LightGBM")
926 (synopsis "Gradient boosting framework based on decision tree algorithms")
927 (description "LightGBM is a gradient boosting framework that uses tree
928based learning algorithms. It is designed to be distributed and efficient with
929the following advantages:
930
931@itemize
932@item Faster training speed and higher efficiency
933@item Lower memory usage
934@item Better accuracy
935@item Parallel and GPU learning supported (not enabled in this package)
936@item Capable of handling large-scale data
937@end itemize\n")
938 (license license:expat)))
a8fb82a8
FT		 939
940(define-public vowpal-wabbit
941 ;; Language bindings not included.
942 (package
943 (name "vowpal-wabbit")
944 (version "8.5.0")
945 (source (origin
946 (method url-fetch)
947 (uri (string-append
948 "https://github.com/JohnLangford/vowpal_wabbit/archive/"
949 version ".tar.gz"))
950 (sha256
951 (base32
952 "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
953 (file-name (string-append name "-" version ".tar.gz"))))
954 (inputs
955 `(("boost" ,boost)
956 ("zlib" ,zlib)))
957 (arguments
958 `(#:configure-flags
959 (list (string-append "--with-boost="
960 (assoc-ref %build-inputs "boost")))))
961 (build-system gnu-build-system)
962 (home-page "https://github.com/JohnLangford/vowpal_wabbit")
963 (synopsis "Fast machine learning library for online learning")
964 (description "Vowpal Wabbit is a machine learning system with techniques
965such as online, hashing, allreduce, reductions, learning2search, active, and
966interactive learning.")
967 (license license:bsd-3)))
915c6bf6
LC		 968
969(define-public python2-fastlmm
970 (package
971 (name "python2-fastlmm")
972 (version "0.2.21")
973 (source
974 (origin
975 (method url-fetch)
976 (uri (pypi-uri "fastlmm" version ".zip"))
977 (sha256
978 (base32
979 "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
980 (build-system python-build-system)
981 (arguments
237ee6f2
RW		 982 `(#:tests? #f ; some test files are missing
983 #:python ,python-2)) ; only Python 2.7 is supported
915c6bf6
LC		 984 (propagated-inputs
985 `(("python2-numpy" ,python2-numpy)
986 ("python2-scipy" ,python2-scipy)
987 ("python2-matplotlib" ,python2-matplotlib)
988 ("python2-pandas" ,python2-pandas)
989 ("python2-scikit-learn" ,python2-scikit-learn)
990 ("python2-pysnptools" ,python2-pysnptools)))
991 (native-inputs
992 `(("unzip" ,unzip)
993 ("python2-cython" ,python2-cython)
994 ("python2-mock" ,python2-mock)
995 ("python2-nose" ,python2-nose)))
996 (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
997 (synopsis "Perform genome-wide association studies on large data sets")
998 (description
999 "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
1000Models, is a program for performing both single-SNP and SNP-set genome-wide
1001association studies (GWAS) on extremely large data sets.")
1002 (license license:asl2.0)))
b9445d0b
RW		 1003
1004;; There have been no proper releases yet.
1005(define-public kaldi
1006 (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
1007 (revision "1"))
1008 (package
1009 (name "kaldi")
1010 (version (git-version "0" revision commit))
1011 (source (origin
1012 (method git-fetch)
1013 (uri (git-reference
1014 (url "https://github.com/kaldi-asr/kaldi.git")
1015 (commit commit)))
1016 (file-name (git-file-name name version))
1017 (sha256
1018 (base32
1019 "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
1020 (build-system gnu-build-system)
1021 (arguments
1022 `(#:test-target "test"
1023 #:phases
1024 (modify-phases %standard-phases
1025 (add-after 'unpack 'chdir
1026 (lambda _ (chdir "src") #t))
1027 (replace 'configure
1028 (lambda* (#:key build system inputs outputs #:allow-other-keys)
1029 (when (not (or (string-prefix? "x86_64" system)
1030 (string-prefix? "i686" system)))
1031 (substitute* "makefiles/linux_openblas.mk"
1032 (("-msse -msse2") "")))
1033 (substitute* "makefiles/default_rules.mk"
1034 (("/bin/bash") (which "bash")))
1035 (substitute* "Makefile"
1036 (("ext_depend: check_portaudio")
1037 "ext_depend:"))
1038 (substitute* '("online/Makefile"
1039 "onlinebin/Makefile"
1040 "gst-plugin/Makefile")
1041 (("../../tools/portaudio/install")
1042 (assoc-ref inputs "portaudio")))
1043
1044 ;; This `configure' script doesn't support variables passed as
1045 ;; arguments, nor does it support "prefix".
1046 (let ((out (assoc-ref outputs "out"))
1047 (openblas (assoc-ref inputs "openblas"))
1048 (openfst (assoc-ref inputs "openfst")))
1049 (substitute* "configure"
1050 (("check_for_slow_expf;") "")
1051 ;; This affects the RPATH and also serves as the installation
1052 ;; directory.
1053 (("KALDILIBDIR=`pwd`/lib")
1054 (string-append "KALDILIBDIR=" out "/lib")))
1055 (mkdir-p out) ; must exist
1056 (setenv "CONFIG_SHELL" (which "bash"))
1057 (setenv "OPENFST_VER" ,(package-version openfst))
1058 (invoke "./configure"
1059 "--use-cuda=no"
1060 "--shared"
1061 (string-append "--openblas-root=" openblas)
1062 (string-append "--fst-root=" openfst)))))
1063 (add-after 'build 'build-ext-and-gstreamer-plugin
1064 (lambda _
1065 (invoke "make" "-C" "online" "depend")
1066 (invoke "make" "-C" "online")
1067 (invoke "make" "-C" "onlinebin" "depend")
1068 (invoke "make" "-C" "onlinebin")
1069 (invoke "make" "-C" "gst-plugin" "depend")
1070 (invoke "make" "-C" "gst-plugin")
1071 #t))
1072 ;; TODO: also install the executables.
1073 (replace 'install
1074 (lambda* (#:key outputs #:allow-other-keys)
1075 (let* ((out (assoc-ref outputs "out"))
1fdd20c7 1076 (inc (string-append out "/include"))
b9445d0b
RW		 1077 (lib (string-append out "/lib")))
1078 (mkdir-p lib)
1fdd20c7
RW		 1079 ;; The build phase installed symlinks to the actual
1080 ;; libraries. Install the actual targets.
1081 (for-each (lambda (file)
1082 (let ((target (readlink file)))
1083 (delete-file file)
1084 (install-file target lib)))
1085 (find-files lib "\\.so"))
1086 ;; Install headers
1087 (for-each (lambda (file)
1088 (let ((target-dir (string-append inc "/" (dirname file))))
1089 (install-file file target-dir)))
1090 (find-files "." "\\.h"))
1091 (install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
1092 (string-append lib "/gstreamer-1.0"))
b9445d0b
RW		 1093 #t))))))
1094 (inputs
1095 `(("alsa-lib" ,alsa-lib)
1096 ("gfortran" ,gfortran "lib")
1097 ("glib" ,glib)
1098 ("gstreamer" ,gstreamer)
1099 ("jack" ,jack-1)
1100 ("openblas" ,openblas)
1101 ("openfst" ,openfst)
1102 ("portaudio" ,portaudio)
1103 ("python" ,python)))
1104 (native-inputs
1105 `(("glib" ,glib "bin") ; glib-genmarshal
1106 ("grep" ,grep)
1107 ("sed" ,sed)
1108 ("pkg-config" ,pkg-config)
1109 ("which" ,which)))
1110 (home-page "https://kaldi-asr.org/")
1111 (synopsis "Speech recognition toolkit")
1112 (description "Kaldi is an extensible toolkit for speech recognition
1113written in C++.")
1114 (license license:asl2.0))))
99260014
RW		 1115
1116(define-public gst-kaldi-nnet2-online
1117 (let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
1118 (revision "1"))
1119 (package
1120 (name "gst-kaldi-nnet2-online")
1121 (version (git-version "0" revision commit))
1122 (source (origin
1123 (method git-fetch)
1124 (uri (git-reference
1125 (url "https://github.com/alumae/gst-kaldi-nnet2-online.git")
1126 (commit commit)))
1127 (file-name (git-file-name name version))
1128 (sha256
1129 (base32
1130 "0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
1131 (build-system gnu-build-system)
1132 (arguments
1133 `(#:tests? #f ; there are none
1134 #:make-flags
1135 (list (string-append "SHELL="
1136 (assoc-ref %build-inputs "bash") "/bin/bash")
1137 (string-append "KALDI_ROOT="
1138 (assoc-ref %build-inputs "kaldi-src"))
1139 (string-append "KALDILIBDIR="
1140 (assoc-ref %build-inputs "kaldi") "/lib")
1141 "KALDI_FLAVOR=dynamic")
1142 #:phases
1143 (modify-phases %standard-phases
1144 (add-after 'unpack 'chdir
1145 (lambda _ (chdir "src") #t))
1146 (replace 'configure
1147 (lambda* (#:key inputs #:allow-other-keys)
1148 (let ((glib (assoc-ref inputs "glib")))
ad60a348 1149 (setenv "CXXFLAGS" "-fPIC")
99260014
RW		 1150 (setenv "CPLUS_INCLUDE_PATH"
1151 (string-append glib "/include/glib-2.0:"
1152 glib "/lib/glib-2.0/include:"
1153 (assoc-ref inputs "gstreamer")
ad60a348 1154 "/include/gstreamer-1.0")))
99260014
RW		 1155 (substitute* "Makefile"
1156 (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
ad60a348
MB		 1157 (("\\$\\(error Cannot find") "#"))
1158 #t))
99260014
RW		 1159 (add-before 'build 'build-depend
1160 (lambda* (#:key make-flags #:allow-other-keys)
1161 (apply invoke "make" "depend" make-flags)))
1162 (replace 'install
1163 (lambda* (#:key outputs #:allow-other-keys)
1164 (let* ((out (assoc-ref outputs "out"))
1165 (lib (string-append out "/lib/gstreamer-1.0")))
1166 (install-file "libgstkaldinnet2onlinedecoder.so" lib)
1167 #t))))))
1168 (inputs
1169 `(("glib" ,glib)
1170 ("gstreamer" ,gstreamer)
1171 ("jansson" ,jansson)
1172 ("openfst" ,openfst)
1173 ("kaldi" ,kaldi)))
1174 (native-inputs
1175 `(("bash" ,bash)
1176 ("glib:bin" ,glib "bin") ; glib-genmarshal
1177 ("kaldi-src" ,(package-source kaldi))
1178 ("pkg-config" ,pkg-config)))
1179 (home-page "https://kaldi-asr.org/")
1180 (synopsis "Gstreamer plugin for decoding speech")
1181 (description "This package provides a GStreamer plugin that wraps
1182Kaldi's @code{SingleUtteranceNnet2Decoder}. It requires iVector-adapted DNN
1183acoustic models. The iVectors are adapted to the current audio stream
1184automatically.")
1185 (license license:asl2.0))))
10451f6b
RW		 1186
1187(define-public kaldi-gstreamer-server
1188 (let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
1189 (revision "1"))
1190 (package
1191 (name "kaldi-gstreamer-server")
1192 (version (git-version "0" revision commit))
1193 (source (origin
1194 (method git-fetch)
1195 (uri (git-reference
1196 (url "https://github.com/alumae/kaldi-gstreamer-server.git")
1197 (commit commit)))
1198 (file-name (git-file-name name version))
1199 (sha256
1200 (base32
1201 "0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
1202 (build-system gnu-build-system)
1203 (arguments
1204 `(#:tests? #f ; there are no tests that can be run automatically
1205 #:modules ((guix build utils)
1206 (guix build gnu-build-system)
1207 (srfi srfi-26))
1208 #:phases
1209 (modify-phases %standard-phases
1210 (delete 'configure)
1211 (replace 'build
1212 (lambda* (#:key outputs #:allow-other-keys)
1213 ;; Disable hash randomization to ensure the generated .pycs
1214 ;; are reproducible.
1215 (setenv "PYTHONHASHSEED" "0")
1216 (with-directory-excursion "kaldigstserver"
1217 (for-each (lambda (file)
1218 (apply invoke
1219 `("python"
1220 "-m" "compileall"
1221 "-f" ; force rebuild
1222 ,file)))
1223 (find-files "." "\\.py$")))
1224 #t))
1225 (replace 'install
1226 (lambda* (#:key inputs outputs #:allow-other-keys)
1227 (let* ((out (assoc-ref outputs "out"))
1228 (bin (string-append out "/bin"))
1229 (share (string-append out "/share/kaldi-gstreamer-server/")))
1230 ;; Install Python files
1231 (with-directory-excursion "kaldigstserver"
1232 (for-each (cut install-file <> share)
1233 (find-files "." ".*")))
1234
1235 ;; Install sample configuration files
1236 (for-each (cut install-file <> share)
1237 (find-files "." "\\.yaml"))
1238
1239 ;; Install executables
1240 (mkdir-p bin)
1241 (let* ((server (string-append bin "/kaldi-gst-server"))
1242 (client (string-append bin "/kaldi-gst-client"))
1243 (worker (string-append bin "/kaldi-gst-worker"))
1244 (PYTHONPATH (getenv "PYTHONPATH"))
1245 (GST_PLUGIN_PATH (string-append
1246 (assoc-ref inputs "gst-kaldi-nnet2-online")
1247 "/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
1248 (wrap (lambda (wrapper what)
1249 (with-output-to-file wrapper
1250 (lambda _
1251 (format #t
1252 "#!~a
1253export PYTHONPATH=~a
1254export GST_PLUGIN_PATH=~a
1255exec ~a ~a/~a \"$@\"~%"
1256 (which "bash") PYTHONPATH GST_PLUGIN_PATH
1257 (which "python") share what)))
1258 (chmod wrapper #o555))))
1259 (for-each wrap
1260 (list server client worker)
1261 (list "master_server.py"
1262 "client.py"
1263 "worker.py")))
1264 #t))))))
1265 (inputs
1266 `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
1267 ("python2" ,python-2)
1268 ("python2-futures" ,python2-futures)
1269 ("python2-pygobject" ,python2-pygobject)
1270 ("python2-pyyaml" ,python2-pyyaml)
1271 ("python2-tornado" ,python2-tornado)
1272 ("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
1273 (home-page "https://github.com/alumae/kaldi-gstreamer-server")
1274 (synopsis "Real-time full-duplex speech recognition server")
1275 (description "This is a real-time full-duplex speech recognition server,
1276based on the Kaldi toolkit and the GStreamer framework and implemented in
1277Python.")
1278 (license license:bsd-2))))
0dfeb285
RW		 1279
1280(define-public grpc
1281 (package
1282 (name "grpc")
1283 (version "1.16.1")
1284 (source (origin
1285 (method git-fetch)
1286 (uri (git-reference
1287 (url "https://github.com/grpc/grpc.git")
1288 (commit (string-append "v" version))))
1289 (file-name (git-file-name name version))
1290 (sha256
1291 (base32
1292 "1jimqz3115f9pli5w6ik9wi7mjc7ix6y7yrq4a1ab9fc3dalj7p2"))))
1293 (build-system cmake-build-system)
1294 (arguments
1295 `(#:tests? #f ; no test target
1296 #:configure-flags
1297 (list "-DgRPC_ZLIB_PROVIDER=package"
1298 "-DgRPC_CARES_PROVIDER=package"
1299 "-DgRPC_SSL_PROVIDER=package"
1300 "-DgRPC_PROTOBUF_PROVIDER=package")))
1301 (inputs
c1cb85bf 1302 `(("c-ares" ,c-ares/cmake)
0dfeb285
RW		 1303 ("openssl" ,openssl)
1304 ("zlib" ,zlib)))
1305 (native-inputs
7373eb83 1306 `(("protobuf" ,protobuf)
0dfeb285
RW		 1307 ("python" ,python-wrapper)))
1308 (home-page "https://grpc.io")
1309 (synopsis "High performance universal RPC framework")
0effc65c
MB		 1310 (description "gRPC is a modern high performance @dfn{Remote Procedure Call}
1311(RPC) framework that can run in any environment. It can efficiently connect
1312services in and across data centers with pluggable support for load balancing,
1313tracing, health checking and authentication. It is also applicable in last
1314mile of distributed computing to connect devices, mobile applications and
1315browsers to backend services.")
0dfeb285 1316 (license license:asl2.0)))
4fa16c9a
RW		 1317
1318;; Note that Tensorflow includes a "third_party" directory, which seems to not
1319;; only contain modified subsets of upstream library source code, but also
1320;; adapter headers provided by Google (such as the fft.h header, which is not
1321;; part of the upstream project code). The Tensorflow code includes headers
1322;; from the "third_party" directory. It does not look like we can replace
1323;; these headers with unmodified upstream files, so we keep them.
1324(define-public tensorflow
1325 (package
1326 (name "tensorflow")
1327 (version "1.9.0")
1328 (source
1329 (origin
1330 (method git-fetch)
1331 (uri (git-reference
1332 (url "https://github.com/tensorflow/tensorflow.git")
1333 (commit (string-append "v" version))))
1334 (file-name (string-append "tensorflow-" version "-checkout"))
1335 (sha256
1336 (base32
1337 "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
1338 (build-system cmake-build-system)
1339 (arguments
1340 `(#:tests? #f ; no "check" target
1341 #:build-type "Release"
1342 #:configure-flags
1343 (let ((protobuf (assoc-ref %build-inputs "protobuf"))
1344 (protobuf:native (assoc-ref %build-inputs "protobuf:native"))
1345 (jsoncpp (assoc-ref %build-inputs "jsoncpp"))
1346 (snappy (assoc-ref %build-inputs "snappy"))
1347 (sqlite (assoc-ref %build-inputs "sqlite")))
1348 (list
1349 ;; Use protobuf from Guix
1350 (string-append "-Dprotobuf_STATIC_LIBRARIES="
1351 protobuf "/lib/libprotobuf.so")
1352 (string-append "-DPROTOBUF_PROTOC_EXECUTABLE="
1353 protobuf:native "/bin/protoc")
1354
1355 ;; Use snappy from Guix
1356 (string-append "-Dsnappy_STATIC_LIBRARIES="
1357 snappy "/lib/libsnappy.so")
1358 ;; Yes, this is not actually the include directory but a prefix...
1359 (string-append "-Dsnappy_INCLUDE_DIR=" snappy)
1360
1361 ;; Use jsoncpp from Guix
1362 (string-append "-Djsoncpp_STATIC_LIBRARIES="
1363 jsoncpp "/lib/libjsoncpp.so")
1364 ;; Yes, this is not actually the include directory but a prefix...
1365 (string-append "-Djsoncpp_INCLUDE_DIR=" jsoncpp)
1366
1367 ;; Use sqlite from Guix
1368 (string-append "-Dsqlite_STATIC_LIBRARIES="
1369 sqlite "/lib/libsqlite.a")
1370
1371 ;; Use system libraries wherever possible. Currently, this
1372 ;; only affects zlib.
1373 "-Dsystemlib_ALL=ON"
1374 "-Dtensorflow_ENABLE_POSITION_INDEPENDENT_CODE=ON"
1375 "-Dtensorflow_BUILD_SHARED_LIB=ON"
1376 "-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=OFF"
1377 "-Dtensorflow_ENABLE_SSL_SUPPORT=OFF"
1378 "-Dtensorflow_BUILD_CONTRIB_KERNELS=OFF"))
1379 #:make-flags
1380 (list "CC=gcc")
1381 #:modules ((ice-9 ftw)
1382 (guix build utils)
1383 (guix build cmake-build-system))
1384 #:phases
1385 (modify-phases %standard-phases
1386 (add-after 'unpack 'set-source-file-times-to-1980
1387 ;; At the end of the tf_python_build_pip_package target, a ZIP
1388 ;; archive should be generated via bdist_wheel, but it fails with
1389 ;; "ZIP does not support timestamps before 1980". Luckily,
1390 ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
1391 ;; 1980.
1392 (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
1393 ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
1394 (add-after 'unpack 'python3.7-compatibility
1395 (lambda _
1396 (substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
1397 "tensorflow/python/lib/core/ndarray_tensor.cc"
1398 "tensorflow/python/lib/core/py_func.cc")
1399 (("PyUnicode_AsUTF8") "(char *)PyUnicode_AsUTF8"))
1400 (substitute* "tensorflow/c/eager/c_api.h"
1401 (("unsigned char async")
1402 "unsigned char is_async"))
1403
1404 ;; Remove dependency on tensorboard, a complicated but probably
1405 ;; optional package.
1406 (substitute* "tensorflow/tools/pip_package/setup.py"
1407 ((".*'tensorboard >.*") ""))
1408 #t))
1409 (add-after 'python3.7-compatibility 'chdir
1410 (lambda _ (chdir "tensorflow/contrib/cmake") #t))
1411 (add-after 'chdir 'disable-downloads
1412 (lambda* (#:key inputs #:allow-other-keys)
1413 (substitute* (find-files "external" "\\.cmake$")
1414 (("GIT_REPOSITORY.*") "")
1415 (("GIT_TAG.*") "")
1416 (("PREFIX ")
1417 "DOWNLOAD_COMMAND \"\"\nPREFIX "))
1418
1419 ;; Use packages from Guix
1420 (let ((grpc (assoc-ref inputs "grpc")))
1421 (substitute* "CMakeLists.txt"
1422 ;; Sqlite
1423 (("include\\(sqlite\\)") "")
1424 (("\\$\\{sqlite_STATIC_LIBRARIES\\}")
1425 (string-append (assoc-ref inputs "sqlite")
1426 "/lib/libsqlite3.so"))
1427 (("sqlite_copy_headers_to_destination") "")
1428
1429 ;; PNG
1430 (("include\\(png\\)") "")
1431 (("\\$\\{png_STATIC_LIBRARIES\\}")
1432 (string-append (assoc-ref inputs "libpng")
1433 "/lib/libpng16.so"))
1434 (("png_copy_headers_to_destination") "")
1435
1436 ;; JPEG
1437 (("include\\(jpeg\\)") "")
1438 (("\\$\\{jpeg_STATIC_LIBRARIES\\}")
1439 (string-append (assoc-ref inputs "libjpeg")
1440 "/lib/libjpeg.so"))
1441 (("jpeg_copy_headers_to_destination") "")
1442
1443 ;; GIF
1444 (("include\\(gif\\)") "")
1445 (("\\$\\{gif_STATIC_LIBRARIES\\}")
1446 (string-append (assoc-ref inputs "giflib")
1447 "/lib/libgif.so"))
1448 (("gif_copy_headers_to_destination") "")
1449
1450 ;; lmdb
1451 (("include\\(lmdb\\)") "")
1452 (("\\$\\{lmdb_STATIC_LIBRARIES\\}")
1453 (string-append (assoc-ref inputs "lmdb")
1454 "/lib/liblmdb.so"))
1455 (("lmdb_copy_headers_to_destination") "")
1456
1457 ;; Protobuf
1458 (("include\\(protobuf\\)") "")
1459 (("protobuf_copy_headers_to_destination") "")
1460 (("^ +protobuf") "")
1461
1462 ;; gRPC
1463 (("include\\(grpc\\)")
1464 "find_package(grpc REQUIRED NAMES gRPC)")
1465 (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES grpc\\)") "")
1466
1467 ;; Eigen
1468 (("include\\(eigen\\)")
1469 (string-append "find_package(eigen REQUIRED NAMES Eigen3)
1470set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
1471 (assoc-ref inputs "eigen") "/include/eigen3)"))
1472 (("^ +eigen") "")
1473
1474 ;; snappy
1475 (("include\\(snappy\\)")
1476 "add_definitions(-DTF_USE_SNAPPY)")
1477 (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES snappy\\)") "")
1478
1479 ;; jsoncpp
1480 (("include\\(jsoncpp\\)") "")
1481 (("^ +jsoncpp") ""))
1482
1483 (substitute* "tf_core_framework.cmake"
1484 ((" grpc") "")
1485 (("\\$\\{GRPC_BUILD\\}/grpc_cpp_plugin")
1486 (which "grpc_cpp_plugin"))
1487 ;; Link with gRPC libraries
1488 (("add_library\\(tf_protos_cc.*" m)
1489 (string-append m
1490 (format #f "\ntarget_link_libraries(tf_protos_cc PRIVATE \
1491~a/lib/libgrpc++_unsecure.a \
1492~a/lib/libgrpc_unsecure.a \
1493~a/lib/libaddress_sorting.a \
1494~a/lib/libgpr.a \
1495~a//lib/libcares.so
1496)\n"
1497 grpc grpc grpc grpc
1498 (assoc-ref inputs "c-ares"))))))
1499 (substitute* "tf_tools.cmake"
1500 (("add_dependencies\\(\\$\\{proto_text.*") ""))
1501 ;; Remove dependency on bundled grpc
1502 (substitute* "tf_core_distributed_runtime.cmake"
1503 (("tf_core_cpu grpc") "tf_core_cpu"))
1504
1505 ;; This directory is a dependency of many targets.
1506 (mkdir-p "protobuf")
1507 #t))
1508 (add-after 'configure 'unpack-third-party-sources
1509 (lambda* (#:key inputs #:allow-other-keys)
1510 ;; This is needed to configure bundled packages properly.
1511 (setenv "CONFIG_SHELL" (which "bash"))
1512 (for-each
1513 (lambda (name)
1514 (let* ((what (assoc-ref inputs (string-append name "-src")))
1515 (name* (string-map (lambda (c)
1516 (if (char=? c #\-)
1517 #\_ c)) name))
1518 (where (string-append "../build/" name* "/src/" name*)))
1519 (cond
1520 ((string-suffix? ".zip" what)
1521 (mkdir-p where)
1522 (with-directory-excursion where
1523 (invoke "unzip" what)))
1524 ((string-suffix? ".tar.gz" what)
1525 (mkdir-p where)
1526 (invoke "tar" "xf" what
1527 "-C" where "--strip-components=1"))
1528 (else
1529 (let ((parent (dirname where)))
1530 (mkdir-p parent)
1531 (with-directory-excursion parent
1532 (when (file-exists? name*)
1533 (delete-file-recursively name*))
1534 (copy-recursively what name*)
1535 (map make-file-writable
1536 (find-files name* ".*"))))))))
1537 (list "boringssl"
1538 "cub"
1539 "double-conversion"
1540 "farmhash"
1541 "fft2d"
1542 "highwayhash"
1543 "nsync"
1544 "re2"))
1545
1546 (rename-file "../build/cub/src/cub/cub-1.8.0/"
1547 "../build/cub/src/cub/cub/")
1548 #t))
1549 (add-after 'unpack 'fix-python-build
1550 (lambda* (#:key inputs outputs #:allow-other-keys)
1551 (mkdir-p "protobuf-src")
1552 (invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
1553 "-C" "protobuf-src" "--strip-components=1")
1554 (mkdir-p "eigen-src")
1555 (invoke "tar" "xf" (assoc-ref inputs "eigen:src")
1556 "-C" "eigen-src" "--strip-components=1")
1557
1558 (substitute* "tensorflow/contrib/cmake/tf_python.cmake"
1559 ;; Ensure that all Python dependencies can be found at build time.
1560 (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
1561 (string-append m ":" (getenv "PYTHONPATH")))
1562 ;; Take protobuf source files from our source package.
1563 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
1564 (string-append (getcwd) "/protobuf-src/src/google")))
1565
1566 (substitute* '("tensorflow/contrib/cmake/tf_shared_lib.cmake"
1567 "tensorflow/contrib/cmake/tf_python.cmake")
1568 ;; Take Eigen source files from our source package.
1569 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/eigen/src/eigen/")
1570 (string-append (getcwd) "/eigen-src/"))
1571 ;; Take Eigen headers from our own package.
1572 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
1573 (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
1574
1575 ;; Correct the RUNPATH of ops libraries generated for Python.
1576 ;; TODO: this doesn't work :(
1577 ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1578 ;; warning: RUNPATH contains bogus entries: ("/tmp/guix-build-tensorflow-1.9.0.drv-0/source/tensorflow/contrib/build")
1579 ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1580 ;; error: depends on 'libpywrap_tensorflow_internal.so', which
1581 ;; cannot be found in RUNPATH ...
1582 (substitute* "tensorflow/contrib/cmake/tf_cc_ops.cmake"
1583 (("set_target_properties.*")
1584 (string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
1585COMPILE_FLAGS ${target_compile_flags} \
1586INSTALL_RPATH_USE_LINK_PATH TRUE \
1587INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
1588 #t))
1589 (add-after 'build 'build-pip-package
1590 (lambda* (#:key outputs #:allow-other-keys)
1591 (setenv "LDFLAGS"
1592 (string-append "-Wl,-rpath="
1593 (assoc-ref outputs "out") "/lib"))
1594 (invoke "make" "tf_python_build_pip_package")
1595 #t))
1596 (add-after 'build-pip-package 'install-python
1597 (lambda* (#:key outputs #:allow-other-keys)
1598 (let ((out (assoc-ref outputs "out"))
1599 (wheel (car (find-files "../build/tf_python/dist/" "\\.whl$"))))
1600 (invoke "python" "-m" "pip" "install" wheel
1601 (string-append "--prefix=" out))
1602
1603 ;; XXX: broken RUNPATH, see fix-python-build phase.
1604 (delete-file
1605 (string-append
1606 out "/lib/python3.7/site-packages/tensorflow/contrib/"
1607 "seq2seq/python/ops/lib_beam_search_ops.so"))
1608 #t))))))
1609 (native-inputs
1610 `(("pkg-config" ,pkg-config)
7373eb83
MB		 1611 ("protobuf:native" ,protobuf-3.6) ; protoc
1612 ("protobuf:src" ,(package-source protobuf-3.6))
4fa16c9a 1613 ("eigen:src" ,(package-source eigen-for-tensorflow))
0fdec2a3
MB		 1614 ;; install_pip_packages.sh wants setuptools 39.1.0 specifically.
1615 ("python-setuptools" ,python-setuptools-for-tensorflow)
1616
4fa16c9a
RW		 1617 ;; The commit hashes and URLs for third-party source code are taken
1618 ;; from "tensorflow/workspace.bzl".
1619 ("boringssl-src"
1620 ,(let ((commit "ee7aa02")
1621 (revision "1"))
1622 (origin
1623 (method git-fetch)
1624 (uri (git-reference
1625 (url "https://boringssl.googlesource.com/boringssl")
1626 (commit commit)))
1627 (file-name (string-append "boringssl-0-" revision
1628 (string-take commit 7)
1629 "-checkout"))
1630 (sha256
1631 (base32
1632 "1jf693q0nw0adsic6cgmbdx6g7wr4rj4vxa8j1hpn792fqhd8wgw")))))
1633 ("cub-src"
1634 ,(let ((version "1.8.0"))
1635 (origin
1636 (method url-fetch)
1637 (uri (string-append "https://mirror.bazel.build/github.com/NVlabs/"
1638 "cub/archive/" version ".zip"))
1639 (file-name (string-append "cub-" version ".zip"))
1640 (sha256
1641 (base32
1642 "1hsqikqridb90dkxkjr2918dcry6pfh46ccnwrzawl56aamhdykb")))))
1643 ("double-conversion-src"
1644 ,(let ((commit "5664746")
1645 (revision "1"))
1646 (origin
1647 (method git-fetch)
1648 (uri (git-reference
1649 (url "https://github.com/google/double-conversion.git")
1650 (commit commit)))
1651 (file-name
1652 (git-file-name "double-conversion"
1653 (string-append "0-" revision "."
1654 (string-take commit 7))))
1655 (sha256
1656 (base32
1657 "1h5lppqqxcvdg5jq42i5msgwx20ryij3apvmndflngrgdpc04gn1")))))
1658 ("farmhash-src"
1659 ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
1660 (origin
1661 (method url-fetch)
1662 (uri (string-append
1663 "https://mirror.bazel.build/github.com/google/farmhash/archive/"
1664 commit ".tar.gz"))
1665 (file-name (string-append "farmhash-0-" (string-take commit 7)
1666 ".tar.gz"))
1667 (sha256
1668 (base32
1669 "185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
1670 ;; The license notice on the home page at
1671 ;; http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html says:
1672 ;; Copyright Takuya OOURA, 1996-2001
1673 ;;
1674 ;; You may use, copy, modify and distribute this code for any purpose
1675 ;; (include commercial use) and without fee. Please refer to this
1676 ;; package when you modify this code.
1677 ;;
1678 ;; We take the identical tarball from the Bazel mirror, because the URL
1679 ;; at the home page is not versioned and might change.
1680 ("fft2d-src"
1681 ,(origin
1682 (method url-fetch)
1683 (uri "https://mirror.bazel.build/www.kurims.kyoto-u.ac.jp/~ooura/fft.tgz")
1684 (file-name "fft2d.tar.gz")
1685 (sha256
1686 (base32
1687 "15jjkfvhqvl2c0753d2di8hz0pyzn598g74wqy79awdrf1y67fsj"))))
1688 ("highwayhash-src"
1689 ,(let ((commit "be5edafc2e1a455768e260ccd68ae7317b6690ee")
1690 (revision "1"))
1691 (origin
1692 (method git-fetch)
1693 (uri (git-reference
1694 (url "https://github.com/google/highwayhash.git")
1695 (commit commit)))
1696 (file-name (string-append "highwayhash-0-" revision
1697 (string-take commit 7)
1698 "-checkout"))
1699 (sha256
1700 (base32
1701 "154jwf98cyy54hldr94pgjn85zynly3abpnc1avmb8a18lzwjyb6")))))
1702 ("nsync-src"
1703 ,(let ((version "0559ce013feac8db639ee1bf776aca0325d28777")
1704 (revision "1"))
1705 (origin
1706 (method url-fetch)
1707 (uri (string-append "https://mirror.bazel.build/"
1708 "github.com/google/nsync/archive/"
1709 version ".tar.gz"))
1710 (file-name (string-append "nsync-0." revision
1711 "-" (string-take version 7)
1712 ".tar.gz"))
1713 (sha256
1714 (base32
1715 "0qdkyqym34x739mmzv97ah5r7ph462v5xkxqxvidmcfqbi64b132")))))
1716 ("re2-src"
1717 ,(let ((commit "e7efc48")
1718 (revision "1"))
1719 (origin
1720 (method git-fetch)
1721 (uri (git-reference
1722 (url "https://github.com/google/re2")
1723 (commit commit)))
1724 (file-name (string-append "re2-0-" revision
1725 (string-take commit 7)
1726 "-checkout"))
1727 (sha256
1728 (base32
1729 "161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign")))))
1730 ("googletest" ,googletest)
1731 ("swig" ,swig)
1732 ("unzip" ,unzip)))
1733 (propagated-inputs
1734 `(("python-absl-py" ,python-absl-py)
1735 ("python-astor" ,python-astor)
1736 ("python-gast" ,python-gast)
1737 ("python-grpcio" ,python-grpcio)
1738 ("python-numpy" ,python-numpy)
7373eb83 1739 ("python-protobuf" ,python-protobuf-3.6)
4fa16c9a
RW		 1740 ("python-six" ,python-six)
1741 ("python-termcolo" ,python-termcolor)
1742 ("python-wheel" ,python-wheel)))
1743 (inputs
3b458d54 1744 `(("c-ares" ,c-ares)
4fa16c9a
RW		 1745 ("eigen" ,eigen-for-tensorflow)
1746 ("gemmlowp" ,gemmlowp-for-tensorflow)
1747 ("lmdb" ,lmdb)
1748 ("libjpeg" ,libjpeg)
1749 ("libpng" ,libpng)
1750 ("giflib" ,giflib)
1751 ("grpc" ,grpc)
1752 ("jsoncpp" ,jsoncpp-for-tensorflow)
1753 ("snappy" ,snappy)
1754 ("sqlite" ,sqlite)
7373eb83 1755 ("protobuf" ,protobuf-3.6)
4fa16c9a
RW		 1756 ("python" ,python-wrapper)
1757 ("zlib" ,zlib)))
1758 (home-page "https://tensorflow.org")
1759 (synopsis "Machine learning framework")
1760 (description
1761 "TensorFlow is a flexible platform for building and training machine
1762learning models. It provides a library for high performance numerical
1763computation and includes high level Python APIs, including both a sequential
1764API for beginners that allows users to build models quickly by plugging
1765together building blocks and a subclassing API with an imperative style for
1766advanced research.")
1767 (license license:asl2.0)))
d60b064d
NG		 1768
1769(define-public python-iml
1770 (package
1771 (name "python-iml")
1772 (version "0.6.2")
1773 (source
1774 (origin
1775 (method url-fetch)
1776 (uri (pypi-uri "iml" version))
1777 (sha256
1778 (base32
1779 "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
1780 (build-system python-build-system)
1781 (propagated-inputs
1782 `(("ipython" ,python-ipython)
1783 ("nose" ,python-nose)
1784 ("numpy" ,python-numpy)
1785 ("pandas" ,python-pandas)
1786 ("scipy" ,python-scipy)))
1787 (home-page "http://github.com/interpretable-ml/iml")
1788 (synopsis "Interpretable Machine Learning (iML) package")
1789 (description "Interpretable ML (iML) is a set of data type objects,
1790visualizations, and interfaces that can be used by any method designed to
1791explain the predictions of machine learning models (or really the output of
1792any function). It currently contains the interface and IO code from the Shap
1793project, and it will potentially also do the same for the Lime project.")
1794 (license license:expat)))
d93ad191
RW		 1795
1796(define-public python-keras-applications
1797 (package
1798 (name "python-keras-applications")
1799 (version "1.0.8")
1800 (source
1801 (origin
1802 (method url-fetch)
1803 (uri (pypi-uri "Keras_Applications" version))
1804 (sha256
1805 (base32
1806 "1rcz31ca4axa6kzhjx4lwqxbg4wvlljkj8qj9a7p9sfd5fhzjyam"))))
1807 (build-system python-build-system)
1808 ;; The tests require Keras, but this package is needed to build Keras.
1809 (arguments '(#:tests? #f))
1810 (propagated-inputs
1811 `(("python-h5py" ,python-h5py)
1812 ("python-numpy" ,python-numpy)))
1813 (native-inputs
1814 `(("python-pytest" ,python-pytest)
1815 ("python-pytest-cov" ,python-pytest-cov)
1816 ("python-pytest-pep8" ,python-pytest-pep8)
1817 ("python-pytest-xdist" ,python-pytest-xdist)))
1818 (home-page "https://github.com/keras-team/keras-applications")
1819 (synopsis "Reference implementations of popular deep learning models")
1820 (description
1821 "This package provides reference implementations of popular deep learning
1822models for use with the Keras deep learning framework.")
1823 (license license:expat)))
4abc5066
RW		 1824
1825(define-public python-keras-preprocessing
1826 (package
1827 (name "python-keras-preprocessing")
1828 (version "1.1.0")
1829 (source
1830 (origin
1831 (method url-fetch)
1832 (uri (pypi-uri "Keras_Preprocessing" version))
1833 (sha256
1834 (base32
1835 "1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as"))))
1836 (build-system python-build-system)
1837 (propagated-inputs
1838 `(("python-numpy" ,python-numpy)
1839 ("python-six" ,python-six)))
1840 (native-inputs
1841 `(("python-pandas" ,python-pandas)
1842 ("python-pillow" ,python-pillow)
1843 ("python-pytest" ,python-pytest)
1844 ("python-pytest-cov" ,python-pytest-cov)
1845 ("python-pytest-xdist" ,python-pytest-xdist)
1846 ("tensorflow" ,tensorflow)))
1847 (home-page "https://github.com/keras-team/keras-preprocessing/")
1848 (synopsis "Data preprocessing and augmentation for deep learning models")
1849 (description
1850 "Keras Preprocessing is the data preprocessing and data augmentation
1851module of the Keras deep learning library. It provides utilities for working
1852with image data, text data, and sequence data.")
1853 (license license:expat)))
f1765b57
RW		 1854
1855(define-public python-keras
1856 (package
1857 (name "python-keras")
1858 (version "2.2.4")
1859 (source
1860 (origin
1861 (method url-fetch)
1862 (uri (pypi-uri "Keras" version))
b16e0827 1863 (patches (search-patches "python-keras-integration-test.patch"))
f1765b57
RW		 1864 (sha256
1865 (base32
1866 "1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh"))))
1867 (build-system python-build-system)
1868 (arguments
1869 `(#:phases
1870 (modify-phases %standard-phases
1871 (add-after 'unpack 'remove-tests-for-unavailable-features
1872 (lambda _
1873 (delete-file "keras/backend/theano_backend.py")
1874 (delete-file "keras/backend/cntk_backend.py")
1875 (delete-file "tests/keras/backend/backend_test.py")
1876
1877 ;; FIXME: This doesn't work because Tensorflow is missing the
1878 ;; coder ops library.
1879 (delete-file "tests/keras/test_callbacks.py")
1880 #t))
1881 (replace 'check
1882 (lambda _
1883 ;; These tests attempt to download data files from the internet.
1884 (delete-file "tests/integration_tests/test_datasets.py")
1885 (delete-file "tests/integration_tests/imagenet_utils_test.py")
1886
1887 (setenv "PYTHONPATH"
1888 (string-append (getcwd) "/build/lib:"
1889 (getenv "PYTHONPATH")))
1890 (invoke "py.test" "-v"
1891 "-p" "no:cacheprovider"
1892 "--ignore" "keras/utils"))))))
1893 (propagated-inputs
1894 `(("python-h5py" ,python-h5py)
1895 ("python-keras-applications" ,python-keras-applications)
1896 ("python-keras-preprocessing" ,python-keras-preprocessing)
1897 ("python-numpy" ,python-numpy)
1898 ("python-pydot" ,python-pydot)
1899 ("python-pyyaml" ,python-pyyaml)
1900 ("python-scipy" ,python-scipy)
1901 ("python-six" ,python-six)
1902 ("tensorflow" ,tensorflow)
1903 ("graphviz" ,graphviz)))
1904 (native-inputs
1905 `(("python-pandas" ,python-pandas)
1906 ("python-pytest" ,python-pytest)
1907 ("python-pytest-cov" ,python-pytest-cov)
1908 ("python-pytest-pep8" ,python-pytest-pep8)
1909 ("python-pytest-timeout" ,python-pytest-timeout)
1910 ("python-pytest-xdist" ,python-pytest-xdist)
1911 ("python-sphinx" ,python-sphinx)
1912 ("python-requests" ,python-requests)))
1913 (home-page "https://github.com/keras-team/keras")
1914 (synopsis "High-level deep learning framework")
1915 (description "Keras is a high-level neural networks API, written in Python
1916and capable of running on top of TensorFlow. It was developed with a focus on
1917enabling fast experimentation. Use Keras if you need a deep learning library
1918that:
1919
1920@itemize
1921@item Allows for easy and fast prototyping (through user friendliness,
1922 modularity, and extensibility).
1923@item Supports both convolutional networks and recurrent networks, as well as
1924 combinations of the two.
1925@item Runs seamlessly on CPU and GPU.
1926@end itemize\n")
1927 (license license:expat)))
6e760872
GLV		 1928
1929(define-public sbcl-cl-libsvm-format
1930 (let ((commit "3300f84fd8d9f5beafc114f543f9d83417c742fb")
1931 (revision "0"))
1932 (package
1933 (name "sbcl-cl-libsvm-format")
1934 (version (git-version "0.1.0" revision commit))
1935 (source
1936 (origin
1937 (method git-fetch)
1938 (uri (git-reference
1939 (url "https://github.com/masatoi/cl-libsvm-format.git")
1940 (commit commit)))
1941 (file-name (git-file-name name version))
1942 (sha256
1943 (base32
1944 "0284aj84xszhkhlivaigf9qj855fxad3mzmv3zfr0qzb5k0nzwrg"))))
1945 (build-system asdf-build-system/sbcl)
1946 (native-inputs
1947 `(("prove" ,sbcl-prove)
1948 ("prove-asdf" ,sbcl-prove-asdf)))
1949 (inputs
1950 `(("alexandria" ,sbcl-alexandria)))
1951 (synopsis "LibSVM data format reader for Common Lisp")
1952 (description
1953 "This Common Lisp library provides a fast reader for data in LibSVM
1954format.")
1955 (home-page "https://github.com/masatoi/cl-libsvm-format")
1956 (license license:expat))))
1957
1958(define-public cl-libsvm-format
1959 (sbcl-package->cl-source-package sbcl-cl-libsvm-format))
1960
1961(define-public ecl-cl-libsvm-format
1962 (sbcl-package->ecl-package sbcl-cl-libsvm-format))
7a15aab8
GLV		 1963
1964(define-public sbcl-cl-online-learning
1965 (let ((commit "fc7a34f4f161cd1c7dd747d2ed8f698947781423")
1966 (revision "0"))
1967 (package
1968 (name "sbcl-cl-online-learning")
1969 (version (git-version "0.5" revision commit))
1970 (source
1971 (origin
1972 (method git-fetch)
1973 (uri (git-reference
1974 (url "https://github.com/masatoi/cl-online-learning.git")
1975 (commit commit)))
1976 (file-name (git-file-name name version))
1977 (sha256
1978 (base32
1979 "14x95rlg80ay5hv645ki57pqvy12v28hz4k1w0f6bsfi2rmpxchq"))))
1980 (build-system asdf-build-system/sbcl)
1981 (native-inputs
1982 `(("prove" ,sbcl-prove)
1983 ("prove-asdf" ,sbcl-prove-asdf)))
1984 (inputs
1985 `(("cl-libsvm-format" ,sbcl-cl-libsvm-format)
1986 ("cl-store" ,sbcl-cl-store)))
1987 (arguments
1988 `(;; FIXME: Tests pass but then the check phase crashes
1989 #:tests? #f))
1990 (synopsis "Online Machine Learning for Common Lisp")
1991 (description
1992 "This library contains a collection of machine learning algorithms for
1993online linear classification written in Common Lisp.")
1994 (home-page "https://github.com/masatoi/cl-online-learning")
1995 (license license:expat))))
1996
1997(define-public cl-online-learning
1998 (sbcl-package->cl-source-package sbcl-cl-online-learning))
1999
2000(define-public ecl-cl-online-learning
2001 (sbcl-package->ecl-package sbcl-cl-online-learning))
5a65fede
GLV		 2002
2003(define-public sbcl-cl-random-forest
2004 (let ((commit "85fbdd4596d40e824f70f1b7cf239cf544e49d51")
2005 (revision "0"))
2006 (package
2007 (name "sbcl-cl-random-forest")
2008 (version (git-version "0.1" revision commit))
2009 (source
2010 (origin
2011 (method git-fetch)
2012 (uri (git-reference
2013 (url "https://github.com/masatoi/cl-random-forest.git")
2014 (commit commit)))
2015 (file-name (git-file-name name version))
2016 (sha256
2017 (base32
2018 "097xv60i1ndz68sg9p4pc7c5gvyp9i1xgw966b4wwfq3x6hbz421"))))
2019 (build-system asdf-build-system/sbcl)
2020 (native-inputs
2021 `(("prove" ,sbcl-prove)
2022 ("prove-asdf" ,sbcl-prove-asdf)
2023 ("trivial-garbage" ,sbcl-trivial-garbage)))
2024 (inputs
2025 `(("alexandria" ,sbcl-alexandria)
2026 ("cl-libsvm-format" ,sbcl-cl-libsvm-format)
2027 ("cl-online-learning" ,sbcl-cl-online-learning)
2028 ("lparallel" ,sbcl-lparallel)))
2029 (arguments
2030 `(;; The tests download data from the Internet
2031 #:tests? #f
2032 #:phases
2033 (modify-phases %standard-phases
2034 (add-after 'unpack 'add-sb-cltl2-dependency
2035 (lambda _
2036 ;; sb-cltl2 is required by lparallel when using sbcl, but it is
2037 ;; not loaded automatically.
2038 (substitute* "cl-random-forest.asd"
2039 (("\\(in-package :cl-user\\)")
2040 "(in-package :cl-user) #+sbcl (require :sb-cltl2)"))
2041 #t)))))
2042 (synopsis "Random Forest and Global Refinement for Common Lisp")
2043 (description
2044 "CL-random-forest is an implementation of Random Forest for multiclass
2045classification and univariate regression written in Common Lisp. It also
2046includes an implementation of Global Refinement of Random Forest.")
2047 (home-page "https://github.com/masatoi/cl-random-forest")
2048 (license license:expat))))
2049
2050(define-public cl-random-forest
2051 (sbcl-package->cl-source-package sbcl-cl-random-forest))
2052
2053(define-public ecl-cl-random-forest
2054 (sbcl-package->ecl-package sbcl-cl-random-forest))
58b13287
GL		 2055
2056(define-public gloo
2057 (let ((version "0.0.0") ; no proper version tag
2058 (commit "ca528e32fea9ca8f2b16053cff17160290fc84ce")
2059 (revision "0"))
2060 (package
2061 (name "gloo")
2062 (version (git-version version revision commit))
2063 (source
2064 (origin
2065 (method git-fetch)
2066 (uri (git-reference
2067 (url "https://github.com/facebookincubator/gloo.git")
2068 (commit commit)))
2069 (file-name (git-file-name name version))
2070 (sha256
2071 (base32
2072 "1q9f80zy75f6njrzrqkmhc0g3qxs4gskr7ns2jdqanxa2ww7a99w"))))
2073 (build-system cmake-build-system)
2074 (native-inputs
2075 `(("googletest" ,googletest)))
2076 (arguments
2077 `(#:configure-flags '("-DBUILD_TEST=1")
2078 #:phases
2079 (modify-phases %standard-phases
2080 (replace 'check
2081 (lambda _
2082 (invoke "make" "gloo_test")
2083 #t)))))
2084 (synopsis "Collective communications library")
2085 (description
2086 "Gloo is a collective communications library. It comes with a
2087number of collective algorithms useful for machine learning applications.
2088These include a barrier, broadcast, and allreduce.")
2089 (home-page "https://github.com/facebookincubator/gloo")
2090 (license license:bsd-3))))
jackhill's copy of GNU Guix: https://guix.gnu.org/