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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>
741115b6
RW		 14;;;
15;;; This file is part of GNU Guix.
16;;;
17;;; GNU Guix is free software; you can redistribute it and/or modify it
18;;; under the terms of the GNU General Public License as published by
19;;; the Free Software Foundation; either version 3 of the License, or (at
20;;; your option) any later version.
21;;;
22;;; GNU Guix is distributed in the hope that it will be useful, but
23;;; WITHOUT ANY WARRANTY; without even the implied warranty of
24;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25;;; GNU General Public License for more details.
26;;;
27;;; You should have received a copy of the GNU General Public License
28;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
29
30(define-module (gnu packages machine-learning)
31 #:use-module ((guix licenses) #:prefix license:)
32 #:use-module (guix packages)
33 #:use-module (guix utils)
34 #:use-module (guix download)
23aab4ab 35 #:use-module (guix svn-download)
c1670a81 36 #:use-module (guix build-system cmake)
741115b6 37 #:use-module (guix build-system gnu)
0a3063d6 38 #:use-module (guix build-system ocaml)
be6eb2f1 39 #:use-module (guix build-system python)
8406138b 40 #:use-module (guix build-system r)
a9b34762 41 #:use-module (guix git-download)
71f80f54 42 #:use-module (gnu packages)
0dfeb285 43 #:use-module (gnu packages adns)
5a14e81e 44 #:use-module (gnu packages algebra)
b9445d0b 45 #:use-module (gnu packages audio)
23aab4ab 46 #:use-module (gnu packages autotools)
b9445d0b 47 #:use-module (gnu packages base)
99260014 48 #:use-module (gnu packages bash)
0931c609 49 #:use-module (gnu packages boost)
be6eb2f1 50 #:use-module (gnu packages check)
0931c609 51 #:use-module (gnu packages compression)
9e37e537 52 #:use-module (gnu packages cran)
4fa16c9a 53 #:use-module (gnu packages databases)
23aab4ab 54 #:use-module (gnu packages dejagnu)
0931c609 55 #:use-module (gnu packages gcc)
b9445d0b 56 #:use-module (gnu packages glib)
f1765b57 57 #:use-module (gnu packages graphviz)
b9445d0b 58 #:use-module (gnu packages gstreamer)
5f0ff6a9 59 #:use-module (gnu packages image)
b9445d0b 60 #:use-module (gnu packages linux)
0931c609 61 #:use-module (gnu packages maths)
112c2c01 62 #:use-module (gnu packages mpi)
0a3063d6 63 #:use-module (gnu packages ocaml)
3929f46c 64 #:use-module (gnu packages onc-rpc)
791c11d6 65 #:use-module (gnu packages perl)
c1670a81 66 #:use-module (gnu packages pkg-config)
0dfeb285 67 #:use-module (gnu packages protobuf)
0931c609 68 #:use-module (gnu packages python)
10451f6b 69 #:use-module (gnu packages python-web)
44d10b1f 70 #:use-module (gnu packages python-xyz)
4fa16c9a 71 #:use-module (gnu packages serialization)
f1765b57 72 #:use-module (gnu packages sphinx)
c1670a81 73 #:use-module (gnu packages statistics)
4fa16c9a 74 #:use-module (gnu packages sqlite)
c1670a81 75 #:use-module (gnu packages swig)
0dfeb285 76 #:use-module (gnu packages tls)
99260014 77 #:use-module (gnu packages web)
5f0ff6a9 78 #:use-module (gnu packages xml)
39bb4937
RW		 79 #:use-module (gnu packages xorg)
80 #:use-module (ice-9 match))
741115b6 81
a9b34762
MM		 82(define-public fann
83 ;; The last release is >100 commits behind, so we package from git.
84 (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
85 (package
86 (name "fann")
87 (version (string-append "2.2.0-1." (string-take commit 8)))
88 (source (origin
89 (method git-fetch)
90 (uri (git-reference
91 (url "https://github.com/libfann/fann.git")
92 (commit commit)))
93 (file-name (string-append name "-" version "-checkout"))
94 (sha256
95 (base32
96 "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
97 (build-system cmake-build-system)
98 (arguments
99 `(#:phases
100 (modify-phases %standard-phases
101 (replace 'check
102 (lambda* (#:key outputs #:allow-other-keys)
103 (let* ((out (assoc-ref outputs "out")))
104 (with-directory-excursion (string-append (getcwd) "/tests")
105 (invoke "./fann_tests"))))))))
106 (home-page "http://leenissen.dk/fann/wp/")
107 (synopsis "Fast Artificial Neural Network")
108 (description
109 "FANN is a free open source neural network library, which implements
110multilayer artificial neural networks in C with support for both fully
111connected and sparsely connected networks.")
112 (license license:lgpl2.1))))
113
741115b6
RW		 114(define-public libsvm
115 (package
116 (name "libsvm")
2cffa2f2 117 (version "3.23")
741115b6
RW		 118 (source
119 (origin
120 (method url-fetch)
d1308c5e
TGR		 121 (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
122 name "-" version ".tar.gz"))
741115b6 123 (sha256
2cffa2f2 124 (base32 "0jpaq0rr92x38p4nk3gjan79ip67m6p80anb28z1d8601miysyi5"))))
741115b6
RW		 125 (build-system gnu-build-system)
126 (arguments
2cffa2f2 127 `(#:tests? #f ; no "check" target
741115b6
RW		 128 #:phases (modify-phases %standard-phases
129 (delete 'configure)
130 (replace
d1308c5e 131 'install ; no ‘install’ target
741115b6
RW		 132 (lambda* (#:key outputs #:allow-other-keys)
133 (let* ((out (assoc-ref outputs "out"))
134 (bin (string-append out "/bin/")))
135 (mkdir-p bin)
136 (for-each (lambda (file)
137 (copy-file file (string-append bin file)))
138 '("svm-train"
139 "svm-predict"
140 "svm-scale")))
141 #t)))))
142 (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
143 (synopsis "Library for Support Vector Machines")
144 (description
145 "LIBSVM is a machine learning library for support vector
146classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
147distribution estimation (one-class SVM). It supports multi-class
148classification.")
149 (license license:bsd-3)))
71f80f54
RW		 150
151(define-public python-libsvm
152 (package (inherit libsvm)
153 (name "python-libsvm")
154 (build-system gnu-build-system)
155 (arguments
2cffa2f2 156 `(#:tests? #f ; no "check" target
71f80f54
RW		 157 #:make-flags '("-C" "python")
158 #:phases
159 (modify-phases %standard-phases
160 (delete 'configure)
161 (replace
d1308c5e 162 'install ; no ‘install’ target
71f80f54
RW		 163 (lambda* (#:key inputs outputs #:allow-other-keys)
164 (let ((site (string-append (assoc-ref outputs "out")
165 "/lib/python"
166 (string-take
167 (string-take-right
168 (assoc-ref inputs "python") 5) 3)
169 "/site-packages/")))
170 (substitute* "python/svm.py"
171 (("../libsvm.so.2") "libsvm.so.2"))
172 (mkdir-p site)
173 (for-each (lambda (file)
174 (copy-file file (string-append site (basename file))))
175 (find-files "python" "\\.py"))
176 (copy-file "libsvm.so.2"
177 (string-append site "libsvm.so.2")))
178 #t)))))
179 (inputs
180 `(("python" ,python)))
181 (synopsis "Python bindings of libSVM")))
0931c609 182
23aab4ab
RW		 183(define-public ghmm
184 ;; The latest release candidate is several years and a couple of fixes have
185 ;; been published since. This is why we download the sources from the SVN
186 ;; repository.
187 (let ((svn-revision 2341))
188 (package
189 (name "ghmm")
190 (version (string-append "0.9-rc3-0." (number->string svn-revision)))
191 (source (origin
192 (method svn-fetch)
193 (uri (svn-reference
194 (url "http://svn.code.sf.net/p/ghmm/code/trunk")
195 (revision svn-revision)))
196 (file-name (string-append name "-" version))
197 (sha256
198 (base32
199 "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
200 (build-system gnu-build-system)
201 (arguments
ced12a7b
RW		 202 `(#:imported-modules (,@%gnu-build-system-modules
203 (guix build python-build-system))
204 #:phases
23aab4ab
RW		 205 (modify-phases %standard-phases
206 (add-after 'unpack 'enter-dir
207 (lambda _ (chdir "ghmm") #t))
ced12a7b
RW		 208 (delete 'check)
209 (add-after 'install 'check
210 (assoc-ref %standard-phases 'check))
211 (add-before 'check 'fix-PYTHONPATH
212 (lambda* (#:key inputs outputs #:allow-other-keys)
213 (let ((python-version ((@@ (guix build python-build-system)
214 get-python-version)
215 (assoc-ref inputs "python"))))
216 (setenv "PYTHONPATH"
217 (string-append (getenv "PYTHONPATH")
218 ":" (assoc-ref outputs "out")
219 "/lib/python" python-version
220 "/site-packages")))
23aab4ab
RW		 221 #t))
222 (add-after 'enter-dir 'fix-runpath
223 (lambda* (#:key outputs #:allow-other-keys)
224 (substitute* "ghmmwrapper/setup.py"
225 (("^(.*)extra_compile_args = \\[" line indent)
226 (string-append indent
227 "extra_link_args = [\"-Wl,-rpath="
228 (assoc-ref outputs "out") "/lib\"],\n"
229 line
230 "\"-Wl,-rpath="
231 (assoc-ref outputs "out")
232 "/lib\", ")))
233 #t))
234 (add-after 'enter-dir 'disable-broken-tests
235 (lambda _
236 (substitute* "tests/Makefile.am"
237 ;; GHMM_SILENT_TESTS is assumed to be a command.
238 (("TESTS_ENVIRONMENT.*") "")
239 ;; Do not build broken tests.
240 (("chmm .*") "")
241 (("read_fa .*") "")
242 (("mcmc .*") "")
243 (("label_higher_order_test.*$")
244 "label_higher_order_test\n"))
245
246 ;; These Python unittests are broken as there is no gato.
247 ;; See https://sourceforge.net/p/ghmm/support-requests/3/
248 (substitute* "ghmmwrapper/ghmmunittests.py"
249 (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
250 line indent)
251 (string-append indent
252 "@unittest.skip(\"Disabled by Guix\")\n"
253 line)))
254 #t))
d10092b8 255 (add-after 'disable-broken-tests 'autogen
23aab4ab 256 (lambda _
3107259f 257 (invoke "bash" "autogen.sh"))))))
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))))
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")
27d6d24e 798 (version "0.20.3")
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
27d6d24e 808 "08aaby5zphfxy83mggg35bwyka7wk91l2qijh8kk0bl08dikq8dl"))))
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")))
4a89bdd1
RW		 824 ;; FIXME: This fails with permission denied
825 (delete 'reset-gzip-timestamps))))
be6eb2f1
RW		 826 (inputs
827 `(("openblas" ,openblas)))
828 (native-inputs
4a89bdd1
RW		 829 `(("python-pytest" ,python-pytest)
830 ("python-pandas" ,python-pandas) ;for tests
be6eb2f1
RW		 831 ("python-cython" ,python-cython)))
832 (propagated-inputs
833 `(("python-numpy" ,python-numpy)
834 ("python-scipy" ,python-scipy)))
835 (home-page "http://scikit-learn.org/")
836 (synopsis "Machine Learning in Python")
837 (description
4a89bdd1
RW		 838 "Scikit-learn provides simple and efficient tools for data mining and
839data analysis.")
be6eb2f1
RW		 840 (license license:bsd-3)))
841
842(define-public python2-scikit-learn
7ff3f3d2 843 (package-with-python2 python-scikit-learn))
2dab4188
FT		 844
845(define-public python-autograd
846 (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
847 (revision "0")
848 (version (git-version "0.0.0" revision commit)))
849 (package
850 (name "python-autograd")
851 (home-page "https://github.com/HIPS/autograd")
852 (source (origin
853 (method git-fetch)
854 (uri (git-reference
855 (url home-page)
856 (commit commit)))
857 (sha256
858 (base32
859 "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
860 (file-name (git-file-name name version))))
861 (version version)
862 (build-system python-build-system)
863 (native-inputs
864 `(("python-nose" ,python-nose)
865 ("python-pytest" ,python-pytest)))
866 (propagated-inputs
867 `(("python-future" ,python-future)
868 ("python-numpy" ,python-numpy)))
869 (arguments
870 `(#:phases (modify-phases %standard-phases
871 (replace 'check
872 (lambda _
873 (invoke "py.test" "-v"))))))
874 (synopsis "Efficiently computes derivatives of NumPy code")
875 (description "Autograd can automatically differentiate native Python and
876NumPy code. It can handle a large subset of Python's features, including loops,
877ifs, recursion and closures, and it can even take derivatives of derivatives
878of derivatives. It supports reverse-mode differentiation
879(a.k.a. backpropagation), which means it can efficiently take gradients of
880scalar-valued functions with respect to array-valued arguments, as well as
881forward-mode differentiation, and the two can be composed arbitrarily. The
882main intended application of Autograd is gradient-based optimization.")
883 (license license:expat))))
884
885(define-public python2-autograd
886 (package-with-python2 python-autograd))
112c2c01
FT		 887
888(define-public lightgbm
889 (package
890 (name "lightgbm")
891 (version "2.0.12")
892 (source (origin
893 (method url-fetch)
894 (uri (string-append
895 "https://github.com/Microsoft/LightGBM/archive/v"
896 version ".tar.gz"))
897 (sha256
898 (base32
899 "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
900 (file-name (string-append name "-" version ".tar.gz"))))
901 (native-inputs
902 `(("python-pytest" ,python-pytest)
903 ("python-nose" ,python-nose)))
904 (inputs
905 `(("openmpi" ,openmpi)))
906 (propagated-inputs
907 `(("python-numpy" ,python-numpy)
908 ("python-scipy" ,python-scipy)))
909 (arguments
910 `(#:configure-flags
911 '("-DUSE_MPI=ON")
912 #:phases
913 (modify-phases %standard-phases
914 (replace 'check
915 (lambda* (#:key outputs #:allow-other-keys)
916 (with-directory-excursion ,(string-append "../LightGBM-" version)
917 (invoke "pytest" "tests/c_api_test/test_.py")))))))
918 (build-system cmake-build-system)
919 (home-page "https://github.com/Microsoft/LightGBM")
920 (synopsis "Gradient boosting framework based on decision tree algorithms")
921 (description "LightGBM is a gradient boosting framework that uses tree
922based learning algorithms. It is designed to be distributed and efficient with
923the following advantages:
924
925@itemize
926@item Faster training speed and higher efficiency
927@item Lower memory usage
928@item Better accuracy
929@item Parallel and GPU learning supported (not enabled in this package)
930@item Capable of handling large-scale data
931@end itemize\n")
932 (license license:expat)))
a8fb82a8
FT		 933
934(define-public vowpal-wabbit
935 ;; Language bindings not included.
936 (package
937 (name "vowpal-wabbit")
938 (version "8.5.0")
939 (source (origin
940 (method url-fetch)
941 (uri (string-append
942 "https://github.com/JohnLangford/vowpal_wabbit/archive/"
943 version ".tar.gz"))
944 (sha256
945 (base32
946 "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
947 (file-name (string-append name "-" version ".tar.gz"))))
948 (inputs
949 `(("boost" ,boost)
950 ("zlib" ,zlib)))
951 (arguments
952 `(#:configure-flags
953 (list (string-append "--with-boost="
954 (assoc-ref %build-inputs "boost")))))
955 (build-system gnu-build-system)
956 (home-page "https://github.com/JohnLangford/vowpal_wabbit")
957 (synopsis "Fast machine learning library for online learning")
958 (description "Vowpal Wabbit is a machine learning system with techniques
959such as online, hashing, allreduce, reductions, learning2search, active, and
960interactive learning.")
961 (license license:bsd-3)))
915c6bf6
LC		 962
963(define-public python2-fastlmm
964 (package
965 (name "python2-fastlmm")
966 (version "0.2.21")
967 (source
968 (origin
969 (method url-fetch)
970 (uri (pypi-uri "fastlmm" version ".zip"))
971 (sha256
972 (base32
973 "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
974 (build-system python-build-system)
975 (arguments
237ee6f2
RW		 976 `(#:tests? #f ; some test files are missing
977 #:python ,python-2)) ; only Python 2.7 is supported
915c6bf6
LC		 978 (propagated-inputs
979 `(("python2-numpy" ,python2-numpy)
980 ("python2-scipy" ,python2-scipy)
981 ("python2-matplotlib" ,python2-matplotlib)
982 ("python2-pandas" ,python2-pandas)
983 ("python2-scikit-learn" ,python2-scikit-learn)
984 ("python2-pysnptools" ,python2-pysnptools)))
985 (native-inputs
986 `(("unzip" ,unzip)
987 ("python2-cython" ,python2-cython)
988 ("python2-mock" ,python2-mock)
989 ("python2-nose" ,python2-nose)))
990 (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
991 (synopsis "Perform genome-wide association studies on large data sets")
992 (description
993 "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
994Models, is a program for performing both single-SNP and SNP-set genome-wide
995association studies (GWAS) on extremely large data sets.")
996 (license license:asl2.0)))
b9445d0b
RW		 997
998;; There have been no proper releases yet.
999(define-public kaldi
1000 (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
1001 (revision "1"))
1002 (package
1003 (name "kaldi")
1004 (version (git-version "0" revision commit))
1005 (source (origin
1006 (method git-fetch)
1007 (uri (git-reference
1008 (url "https://github.com/kaldi-asr/kaldi.git")
1009 (commit commit)))
1010 (file-name (git-file-name name version))
1011 (sha256
1012 (base32
1013 "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
1014 (build-system gnu-build-system)
1015 (arguments
1016 `(#:test-target "test"
1017 #:phases
1018 (modify-phases %standard-phases
1019 (add-after 'unpack 'chdir
1020 (lambda _ (chdir "src") #t))
1021 (replace 'configure
1022 (lambda* (#:key build system inputs outputs #:allow-other-keys)
1023 (when (not (or (string-prefix? "x86_64" system)
1024 (string-prefix? "i686" system)))
1025 (substitute* "makefiles/linux_openblas.mk"
1026 (("-msse -msse2") "")))
1027 (substitute* "makefiles/default_rules.mk"
1028 (("/bin/bash") (which "bash")))
1029 (substitute* "Makefile"
1030 (("ext_depend: check_portaudio")
1031 "ext_depend:"))
1032 (substitute* '("online/Makefile"
1033 "onlinebin/Makefile"
1034 "gst-plugin/Makefile")
1035 (("../../tools/portaudio/install")
1036 (assoc-ref inputs "portaudio")))
1037
1038 ;; This `configure' script doesn't support variables passed as
1039 ;; arguments, nor does it support "prefix".
1040 (let ((out (assoc-ref outputs "out"))
1041 (openblas (assoc-ref inputs "openblas"))
1042 (openfst (assoc-ref inputs "openfst")))
1043 (substitute* "configure"
1044 (("check_for_slow_expf;") "")
1045 ;; This affects the RPATH and also serves as the installation
1046 ;; directory.
1047 (("KALDILIBDIR=`pwd`/lib")
1048 (string-append "KALDILIBDIR=" out "/lib")))
1049 (mkdir-p out) ; must exist
1050 (setenv "CONFIG_SHELL" (which "bash"))
1051 (setenv "OPENFST_VER" ,(package-version openfst))
1052 (invoke "./configure"
1053 "--use-cuda=no"
1054 "--shared"
1055 (string-append "--openblas-root=" openblas)
1056 (string-append "--fst-root=" openfst)))))
1057 (add-after 'build 'build-ext-and-gstreamer-plugin
1058 (lambda _
1059 (invoke "make" "-C" "online" "depend")
1060 (invoke "make" "-C" "online")
1061 (invoke "make" "-C" "onlinebin" "depend")
1062 (invoke "make" "-C" "onlinebin")
1063 (invoke "make" "-C" "gst-plugin" "depend")
1064 (invoke "make" "-C" "gst-plugin")
1065 #t))
1066 ;; TODO: also install the executables.
1067 (replace 'install
1068 (lambda* (#:key outputs #:allow-other-keys)
1069 (let* ((out (assoc-ref outputs "out"))
1fdd20c7 1070 (inc (string-append out "/include"))
b9445d0b
RW		 1071 (lib (string-append out "/lib")))
1072 (mkdir-p lib)
1fdd20c7
RW		 1073 ;; The build phase installed symlinks to the actual
1074 ;; libraries. Install the actual targets.
1075 (for-each (lambda (file)
1076 (let ((target (readlink file)))
1077 (delete-file file)
1078 (install-file target lib)))
1079 (find-files lib "\\.so"))
1080 ;; Install headers
1081 (for-each (lambda (file)
1082 (let ((target-dir (string-append inc "/" (dirname file))))
1083 (install-file file target-dir)))
1084 (find-files "." "\\.h"))
1085 (install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
1086 (string-append lib "/gstreamer-1.0"))
b9445d0b
RW		 1087 #t))))))
1088 (inputs
1089 `(("alsa-lib" ,alsa-lib)
1090 ("gfortran" ,gfortran "lib")
1091 ("glib" ,glib)
1092 ("gstreamer" ,gstreamer)
1093 ("jack" ,jack-1)
1094 ("openblas" ,openblas)
1095 ("openfst" ,openfst)
1096 ("portaudio" ,portaudio)
1097 ("python" ,python)))
1098 (native-inputs
1099 `(("glib" ,glib "bin") ; glib-genmarshal
1100 ("grep" ,grep)
1101 ("sed" ,sed)
1102 ("pkg-config" ,pkg-config)
1103 ("which" ,which)))
1104 (home-page "https://kaldi-asr.org/")
1105 (synopsis "Speech recognition toolkit")
1106 (description "Kaldi is an extensible toolkit for speech recognition
1107written in C++.")
1108 (license license:asl2.0))))
99260014
RW		 1109
1110(define-public gst-kaldi-nnet2-online
1111 (let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
1112 (revision "1"))
1113 (package
1114 (name "gst-kaldi-nnet2-online")
1115 (version (git-version "0" revision commit))
1116 (source (origin
1117 (method git-fetch)
1118 (uri (git-reference
1119 (url "https://github.com/alumae/gst-kaldi-nnet2-online.git")
1120 (commit commit)))
1121 (file-name (git-file-name name version))
1122 (sha256
1123 (base32
1124 "0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
1125 (build-system gnu-build-system)
1126 (arguments
1127 `(#:tests? #f ; there are none
1128 #:make-flags
1129 (list (string-append "SHELL="
1130 (assoc-ref %build-inputs "bash") "/bin/bash")
1131 (string-append "KALDI_ROOT="
1132 (assoc-ref %build-inputs "kaldi-src"))
1133 (string-append "KALDILIBDIR="
1134 (assoc-ref %build-inputs "kaldi") "/lib")
1135 "KALDI_FLAVOR=dynamic")
1136 #:phases
1137 (modify-phases %standard-phases
1138 (add-after 'unpack 'chdir
1139 (lambda _ (chdir "src") #t))
1140 (replace 'configure
1141 (lambda* (#:key inputs #:allow-other-keys)
1142 (let ((glib (assoc-ref inputs "glib")))
1143 (setenv "CXXFLAGS" "-std=c++11 -fPIC")
1144 (setenv "CPLUS_INCLUDE_PATH"
1145 (string-append glib "/include/glib-2.0:"
1146 glib "/lib/glib-2.0/include:"
1147 (assoc-ref inputs "gstreamer")
1148 "/include/gstreamer-1.0:"
1149 (getenv "CPLUS_INCLUDE_PATH"))))
1150 (substitute* "Makefile"
1151 (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
1152 (("\\$\\(error Cannot find") "#"))))
1153 (add-before 'build 'build-depend
1154 (lambda* (#:key make-flags #:allow-other-keys)
1155 (apply invoke "make" "depend" make-flags)))
1156 (replace 'install
1157 (lambda* (#:key outputs #:allow-other-keys)
1158 (let* ((out (assoc-ref outputs "out"))
1159 (lib (string-append out "/lib/gstreamer-1.0")))
1160 (install-file "libgstkaldinnet2onlinedecoder.so" lib)
1161 #t))))))
1162 (inputs
1163 `(("glib" ,glib)
1164 ("gstreamer" ,gstreamer)
1165 ("jansson" ,jansson)
1166 ("openfst" ,openfst)
1167 ("kaldi" ,kaldi)))
1168 (native-inputs
1169 `(("bash" ,bash)
1170 ("glib:bin" ,glib "bin") ; glib-genmarshal
1171 ("kaldi-src" ,(package-source kaldi))
1172 ("pkg-config" ,pkg-config)))
1173 (home-page "https://kaldi-asr.org/")
1174 (synopsis "Gstreamer plugin for decoding speech")
1175 (description "This package provides a GStreamer plugin that wraps
1176Kaldi's @code{SingleUtteranceNnet2Decoder}. It requires iVector-adapted DNN
1177acoustic models. The iVectors are adapted to the current audio stream
1178automatically.")
1179 (license license:asl2.0))))
10451f6b
RW		 1180
1181(define-public kaldi-gstreamer-server
1182 (let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
1183 (revision "1"))
1184 (package
1185 (name "kaldi-gstreamer-server")
1186 (version (git-version "0" revision commit))
1187 (source (origin
1188 (method git-fetch)
1189 (uri (git-reference
1190 (url "https://github.com/alumae/kaldi-gstreamer-server.git")
1191 (commit commit)))
1192 (file-name (git-file-name name version))
1193 (sha256
1194 (base32
1195 "0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
1196 (build-system gnu-build-system)
1197 (arguments
1198 `(#:tests? #f ; there are no tests that can be run automatically
1199 #:modules ((guix build utils)
1200 (guix build gnu-build-system)
1201 (srfi srfi-26))
1202 #:phases
1203 (modify-phases %standard-phases
1204 (delete 'configure)
1205 (replace 'build
1206 (lambda* (#:key outputs #:allow-other-keys)
1207 ;; Disable hash randomization to ensure the generated .pycs
1208 ;; are reproducible.
1209 (setenv "PYTHONHASHSEED" "0")
1210 (with-directory-excursion "kaldigstserver"
1211 (for-each (lambda (file)
1212 (apply invoke
1213 `("python"
1214 "-m" "compileall"
1215 "-f" ; force rebuild
1216 ,file)))
1217 (find-files "." "\\.py$")))
1218 #t))
1219 (replace 'install
1220 (lambda* (#:key inputs outputs #:allow-other-keys)
1221 (let* ((out (assoc-ref outputs "out"))
1222 (bin (string-append out "/bin"))
1223 (share (string-append out "/share/kaldi-gstreamer-server/")))
1224 ;; Install Python files
1225 (with-directory-excursion "kaldigstserver"
1226 (for-each (cut install-file <> share)
1227 (find-files "." ".*")))
1228
1229 ;; Install sample configuration files
1230 (for-each (cut install-file <> share)
1231 (find-files "." "\\.yaml"))
1232
1233 ;; Install executables
1234 (mkdir-p bin)
1235 (let* ((server (string-append bin "/kaldi-gst-server"))
1236 (client (string-append bin "/kaldi-gst-client"))
1237 (worker (string-append bin "/kaldi-gst-worker"))
1238 (PYTHONPATH (getenv "PYTHONPATH"))
1239 (GST_PLUGIN_PATH (string-append
1240 (assoc-ref inputs "gst-kaldi-nnet2-online")
1241 "/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
1242 (wrap (lambda (wrapper what)
1243 (with-output-to-file wrapper
1244 (lambda _
1245 (format #t
1246 "#!~a
1247export PYTHONPATH=~a
1248export GST_PLUGIN_PATH=~a
1249exec ~a ~a/~a \"$@\"~%"
1250 (which "bash") PYTHONPATH GST_PLUGIN_PATH
1251 (which "python") share what)))
1252 (chmod wrapper #o555))))
1253 (for-each wrap
1254 (list server client worker)
1255 (list "master_server.py"
1256 "client.py"
1257 "worker.py")))
1258 #t))))))
1259 (inputs
1260 `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
1261 ("python2" ,python-2)
1262 ("python2-futures" ,python2-futures)
1263 ("python2-pygobject" ,python2-pygobject)
1264 ("python2-pyyaml" ,python2-pyyaml)
1265 ("python2-tornado" ,python2-tornado)
1266 ("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
1267 (home-page "https://github.com/alumae/kaldi-gstreamer-server")
1268 (synopsis "Real-time full-duplex speech recognition server")
1269 (description "This is a real-time full-duplex speech recognition server,
1270based on the Kaldi toolkit and the GStreamer framework and implemented in
1271Python.")
1272 (license license:bsd-2))))
0dfeb285
RW		 1273
1274(define-public grpc
1275 (package
1276 (name "grpc")
1277 (version "1.16.1")
1278 (source (origin
1279 (method git-fetch)
1280 (uri (git-reference
1281 (url "https://github.com/grpc/grpc.git")
1282 (commit (string-append "v" version))))
1283 (file-name (git-file-name name version))
1284 (sha256
1285 (base32
1286 "1jimqz3115f9pli5w6ik9wi7mjc7ix6y7yrq4a1ab9fc3dalj7p2"))))
1287 (build-system cmake-build-system)
1288 (arguments
1289 `(#:tests? #f ; no test target
1290 #:configure-flags
1291 (list "-DgRPC_ZLIB_PROVIDER=package"
1292 "-DgRPC_CARES_PROVIDER=package"
1293 "-DgRPC_SSL_PROVIDER=package"
1294 "-DgRPC_PROTOBUF_PROVIDER=package")))
1295 (inputs
1296 `(("c-ares" ,c-ares-next)
1297 ("openssl" ,openssl)
1298 ("zlib" ,zlib)))
1299 (native-inputs
1300 `(("protobuf" ,protobuf-next)
1301 ("python" ,python-wrapper)))
1302 (home-page "https://grpc.io")
1303 (synopsis "High performance universal RPC framework")
1304 (description "gRPC is a modern open source high performance @dfn{Remote
1305Procedure Call} (RPC) framework that can run in any environment. It can
1306efficiently connect services in and across data centers with pluggable support
1307for load balancing, tracing, health checking and authentication. It is also
1308applicable in last mile of distributed computing to connect devices, mobile
1309applications and browsers to backend services.")
1310 (license license:asl2.0)))
4fa16c9a
RW		 1311
1312;; Note that Tensorflow includes a "third_party" directory, which seems to not
1313;; only contain modified subsets of upstream library source code, but also
1314;; adapter headers provided by Google (such as the fft.h header, which is not
1315;; part of the upstream project code). The Tensorflow code includes headers
1316;; from the "third_party" directory. It does not look like we can replace
1317;; these headers with unmodified upstream files, so we keep them.
1318(define-public tensorflow
1319 (package
1320 (name "tensorflow")
1321 (version "1.9.0")
1322 (source
1323 (origin
1324 (method git-fetch)
1325 (uri (git-reference
1326 (url "https://github.com/tensorflow/tensorflow.git")
1327 (commit (string-append "v" version))))
1328 (file-name (string-append "tensorflow-" version "-checkout"))
1329 (sha256
1330 (base32
1331 "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
1332 (build-system cmake-build-system)
1333 (arguments
1334 `(#:tests? #f ; no "check" target
1335 #:build-type "Release"
1336 #:configure-flags
1337 (let ((protobuf (assoc-ref %build-inputs "protobuf"))
1338 (protobuf:native (assoc-ref %build-inputs "protobuf:native"))
1339 (jsoncpp (assoc-ref %build-inputs "jsoncpp"))
1340 (snappy (assoc-ref %build-inputs "snappy"))
1341 (sqlite (assoc-ref %build-inputs "sqlite")))
1342 (list
1343 ;; Use protobuf from Guix
1344 (string-append "-Dprotobuf_STATIC_LIBRARIES="
1345 protobuf "/lib/libprotobuf.so")
1346 (string-append "-DPROTOBUF_PROTOC_EXECUTABLE="
1347 protobuf:native "/bin/protoc")
1348
1349 ;; Use snappy from Guix
1350 (string-append "-Dsnappy_STATIC_LIBRARIES="
1351 snappy "/lib/libsnappy.so")
1352 ;; Yes, this is not actually the include directory but a prefix...
1353 (string-append "-Dsnappy_INCLUDE_DIR=" snappy)
1354
1355 ;; Use jsoncpp from Guix
1356 (string-append "-Djsoncpp_STATIC_LIBRARIES="
1357 jsoncpp "/lib/libjsoncpp.so")
1358 ;; Yes, this is not actually the include directory but a prefix...
1359 (string-append "-Djsoncpp_INCLUDE_DIR=" jsoncpp)
1360
1361 ;; Use sqlite from Guix
1362 (string-append "-Dsqlite_STATIC_LIBRARIES="
1363 sqlite "/lib/libsqlite.a")
1364
1365 ;; Use system libraries wherever possible. Currently, this
1366 ;; only affects zlib.
1367 "-Dsystemlib_ALL=ON"
1368 "-Dtensorflow_ENABLE_POSITION_INDEPENDENT_CODE=ON"
1369 "-Dtensorflow_BUILD_SHARED_LIB=ON"
1370 "-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=OFF"
1371 "-Dtensorflow_ENABLE_SSL_SUPPORT=OFF"
1372 "-Dtensorflow_BUILD_CONTRIB_KERNELS=OFF"))
1373 #:make-flags
1374 (list "CC=gcc")
1375 #:modules ((ice-9 ftw)
1376 (guix build utils)
1377 (guix build cmake-build-system))
1378 #:phases
1379 (modify-phases %standard-phases
1380 (add-after 'unpack 'set-source-file-times-to-1980
1381 ;; At the end of the tf_python_build_pip_package target, a ZIP
1382 ;; archive should be generated via bdist_wheel, but it fails with
1383 ;; "ZIP does not support timestamps before 1980". Luckily,
1384 ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
1385 ;; 1980.
1386 (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
1387 ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
1388 (add-after 'unpack 'python3.7-compatibility
1389 (lambda _
1390 (substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
1391 "tensorflow/python/lib/core/ndarray_tensor.cc"
1392 "tensorflow/python/lib/core/py_func.cc")
1393 (("PyUnicode_AsUTF8") "(char *)PyUnicode_AsUTF8"))
1394 (substitute* "tensorflow/c/eager/c_api.h"
1395 (("unsigned char async")
1396 "unsigned char is_async"))
1397
1398 ;; Remove dependency on tensorboard, a complicated but probably
1399 ;; optional package.
1400 (substitute* "tensorflow/tools/pip_package/setup.py"
1401 ((".*'tensorboard >.*") ""))
1402 #t))
1403 (add-after 'python3.7-compatibility 'chdir
1404 (lambda _ (chdir "tensorflow/contrib/cmake") #t))
1405 (add-after 'chdir 'disable-downloads
1406 (lambda* (#:key inputs #:allow-other-keys)
1407 (substitute* (find-files "external" "\\.cmake$")
1408 (("GIT_REPOSITORY.*") "")
1409 (("GIT_TAG.*") "")
1410 (("PREFIX ")
1411 "DOWNLOAD_COMMAND \"\"\nPREFIX "))
1412
1413 ;; Use packages from Guix
1414 (let ((grpc (assoc-ref inputs "grpc")))
1415 (substitute* "CMakeLists.txt"
1416 ;; Sqlite
1417 (("include\\(sqlite\\)") "")
1418 (("\\$\\{sqlite_STATIC_LIBRARIES\\}")
1419 (string-append (assoc-ref inputs "sqlite")
1420 "/lib/libsqlite3.so"))
1421 (("sqlite_copy_headers_to_destination") "")
1422
1423 ;; PNG
1424 (("include\\(png\\)") "")
1425 (("\\$\\{png_STATIC_LIBRARIES\\}")
1426 (string-append (assoc-ref inputs "libpng")
1427 "/lib/libpng16.so"))
1428 (("png_copy_headers_to_destination") "")
1429
1430 ;; JPEG
1431 (("include\\(jpeg\\)") "")
1432 (("\\$\\{jpeg_STATIC_LIBRARIES\\}")
1433 (string-append (assoc-ref inputs "libjpeg")
1434 "/lib/libjpeg.so"))
1435 (("jpeg_copy_headers_to_destination") "")
1436
1437 ;; GIF
1438 (("include\\(gif\\)") "")
1439 (("\\$\\{gif_STATIC_LIBRARIES\\}")
1440 (string-append (assoc-ref inputs "giflib")
1441 "/lib/libgif.so"))
1442 (("gif_copy_headers_to_destination") "")
1443
1444 ;; lmdb
1445 (("include\\(lmdb\\)") "")
1446 (("\\$\\{lmdb_STATIC_LIBRARIES\\}")
1447 (string-append (assoc-ref inputs "lmdb")
1448 "/lib/liblmdb.so"))
1449 (("lmdb_copy_headers_to_destination") "")
1450
1451 ;; Protobuf
1452 (("include\\(protobuf\\)") "")
1453 (("protobuf_copy_headers_to_destination") "")
1454 (("^ +protobuf") "")
1455
1456 ;; gRPC
1457 (("include\\(grpc\\)")
1458 "find_package(grpc REQUIRED NAMES gRPC)")
1459 (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES grpc\\)") "")
1460
1461 ;; Eigen
1462 (("include\\(eigen\\)")
1463 (string-append "find_package(eigen REQUIRED NAMES Eigen3)
1464set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
1465 (assoc-ref inputs "eigen") "/include/eigen3)"))
1466 (("^ +eigen") "")
1467
1468 ;; snappy
1469 (("include\\(snappy\\)")
1470 "add_definitions(-DTF_USE_SNAPPY)")
1471 (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES snappy\\)") "")
1472
1473 ;; jsoncpp
1474 (("include\\(jsoncpp\\)") "")
1475 (("^ +jsoncpp") ""))
1476
1477 (substitute* "tf_core_framework.cmake"
1478 ((" grpc") "")
1479 (("\\$\\{GRPC_BUILD\\}/grpc_cpp_plugin")
1480 (which "grpc_cpp_plugin"))
1481 ;; Link with gRPC libraries
1482 (("add_library\\(tf_protos_cc.*" m)
1483 (string-append m
1484 (format #f "\ntarget_link_libraries(tf_protos_cc PRIVATE \
1485~a/lib/libgrpc++_unsecure.a \
1486~a/lib/libgrpc_unsecure.a \
1487~a/lib/libaddress_sorting.a \
1488~a/lib/libgpr.a \
1489~a//lib/libcares.so
1490)\n"
1491 grpc grpc grpc grpc
1492 (assoc-ref inputs "c-ares"))))))
1493 (substitute* "tf_tools.cmake"
1494 (("add_dependencies\\(\\$\\{proto_text.*") ""))
1495 ;; Remove dependency on bundled grpc
1496 (substitute* "tf_core_distributed_runtime.cmake"
1497 (("tf_core_cpu grpc") "tf_core_cpu"))
1498
1499 ;; This directory is a dependency of many targets.
1500 (mkdir-p "protobuf")
1501 #t))
1502 (add-after 'configure 'unpack-third-party-sources
1503 (lambda* (#:key inputs #:allow-other-keys)
1504 ;; This is needed to configure bundled packages properly.
1505 (setenv "CONFIG_SHELL" (which "bash"))
1506 (for-each
1507 (lambda (name)
1508 (let* ((what (assoc-ref inputs (string-append name "-src")))
1509 (name* (string-map (lambda (c)
1510 (if (char=? c #\-)
1511 #\_ c)) name))
1512 (where (string-append "../build/" name* "/src/" name*)))
1513 (cond
1514 ((string-suffix? ".zip" what)
1515 (mkdir-p where)
1516 (with-directory-excursion where
1517 (invoke "unzip" what)))
1518 ((string-suffix? ".tar.gz" what)
1519 (mkdir-p where)
1520 (invoke "tar" "xf" what
1521 "-C" where "--strip-components=1"))
1522 (else
1523 (let ((parent (dirname where)))
1524 (mkdir-p parent)
1525 (with-directory-excursion parent
1526 (when (file-exists? name*)
1527 (delete-file-recursively name*))
1528 (copy-recursively what name*)
1529 (map make-file-writable
1530 (find-files name* ".*"))))))))
1531 (list "boringssl"
1532 "cub"
1533 "double-conversion"
1534 "farmhash"
1535 "fft2d"
1536 "highwayhash"
1537 "nsync"
1538 "re2"))
1539
1540 (rename-file "../build/cub/src/cub/cub-1.8.0/"
1541 "../build/cub/src/cub/cub/")
1542 #t))
1543 (add-after 'unpack 'fix-python-build
1544 (lambda* (#:key inputs outputs #:allow-other-keys)
1545 (mkdir-p "protobuf-src")
1546 (invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
1547 "-C" "protobuf-src" "--strip-components=1")
1548 (mkdir-p "eigen-src")
1549 (invoke "tar" "xf" (assoc-ref inputs "eigen:src")
1550 "-C" "eigen-src" "--strip-components=1")
1551
1552 (substitute* "tensorflow/contrib/cmake/tf_python.cmake"
1553 ;; Ensure that all Python dependencies can be found at build time.
1554 (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
1555 (string-append m ":" (getenv "PYTHONPATH")))
1556 ;; Take protobuf source files from our source package.
1557 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
1558 (string-append (getcwd) "/protobuf-src/src/google")))
1559
1560 (substitute* '("tensorflow/contrib/cmake/tf_shared_lib.cmake"
1561 "tensorflow/contrib/cmake/tf_python.cmake")
1562 ;; Take Eigen source files from our source package.
1563 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/eigen/src/eigen/")
1564 (string-append (getcwd) "/eigen-src/"))
1565 ;; Take Eigen headers from our own package.
1566 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
1567 (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
1568
1569 ;; Correct the RUNPATH of ops libraries generated for Python.
1570 ;; TODO: this doesn't work :(
1571 ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1572 ;; warning: RUNPATH contains bogus entries: ("/tmp/guix-build-tensorflow-1.9.0.drv-0/source/tensorflow/contrib/build")
1573 ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1574 ;; error: depends on 'libpywrap_tensorflow_internal.so', which
1575 ;; cannot be found in RUNPATH ...
1576 (substitute* "tensorflow/contrib/cmake/tf_cc_ops.cmake"
1577 (("set_target_properties.*")
1578 (string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
1579COMPILE_FLAGS ${target_compile_flags} \
1580INSTALL_RPATH_USE_LINK_PATH TRUE \
1581INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
1582 #t))
1583 (add-after 'build 'build-pip-package
1584 (lambda* (#:key outputs #:allow-other-keys)
1585 (setenv "LDFLAGS"
1586 (string-append "-Wl,-rpath="
1587 (assoc-ref outputs "out") "/lib"))
1588 (invoke "make" "tf_python_build_pip_package")
1589 #t))
1590 (add-after 'build-pip-package 'install-python
1591 (lambda* (#:key outputs #:allow-other-keys)
1592 (let ((out (assoc-ref outputs "out"))
1593 (wheel (car (find-files "../build/tf_python/dist/" "\\.whl$"))))
1594 (invoke "python" "-m" "pip" "install" wheel
1595 (string-append "--prefix=" out))
1596
1597 ;; XXX: broken RUNPATH, see fix-python-build phase.
1598 (delete-file
1599 (string-append
1600 out "/lib/python3.7/site-packages/tensorflow/contrib/"
1601 "seq2seq/python/ops/lib_beam_search_ops.so"))
1602 #t))))))
1603 (native-inputs
1604 `(("pkg-config" ,pkg-config)
1605 ("protobuf:native" ,protobuf-next) ; protoc
1606 ("protobuf:src" ,(package-source protobuf-next))
1607 ("eigen:src" ,(package-source eigen-for-tensorflow))
1608 ;; The commit hashes and URLs for third-party source code are taken
1609 ;; from "tensorflow/workspace.bzl".
1610 ("boringssl-src"
1611 ,(let ((commit "ee7aa02")
1612 (revision "1"))
1613 (origin
1614 (method git-fetch)
1615 (uri (git-reference
1616 (url "https://boringssl.googlesource.com/boringssl")
1617 (commit commit)))
1618 (file-name (string-append "boringssl-0-" revision
1619 (string-take commit 7)
1620 "-checkout"))
1621 (sha256
1622 (base32
1623 "1jf693q0nw0adsic6cgmbdx6g7wr4rj4vxa8j1hpn792fqhd8wgw")))))
1624 ("cub-src"
1625 ,(let ((version "1.8.0"))
1626 (origin
1627 (method url-fetch)
1628 (uri (string-append "https://mirror.bazel.build/github.com/NVlabs/"
1629 "cub/archive/" version ".zip"))
1630 (file-name (string-append "cub-" version ".zip"))
1631 (sha256
1632 (base32
1633 "1hsqikqridb90dkxkjr2918dcry6pfh46ccnwrzawl56aamhdykb")))))
1634 ("double-conversion-src"
1635 ,(let ((commit "5664746")
1636 (revision "1"))
1637 (origin
1638 (method git-fetch)
1639 (uri (git-reference
1640 (url "https://github.com/google/double-conversion.git")
1641 (commit commit)))
1642 (file-name
1643 (git-file-name "double-conversion"
1644 (string-append "0-" revision "."
1645 (string-take commit 7))))
1646 (sha256
1647 (base32
1648 "1h5lppqqxcvdg5jq42i5msgwx20ryij3apvmndflngrgdpc04gn1")))))
1649 ("farmhash-src"
1650 ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
1651 (origin
1652 (method url-fetch)
1653 (uri (string-append
1654 "https://mirror.bazel.build/github.com/google/farmhash/archive/"
1655 commit ".tar.gz"))
1656 (file-name (string-append "farmhash-0-" (string-take commit 7)
1657 ".tar.gz"))
1658 (sha256
1659 (base32
1660 "185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
1661 ;; The license notice on the home page at
1662 ;; http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html says:
1663 ;; Copyright Takuya OOURA, 1996-2001
1664 ;;
1665 ;; You may use, copy, modify and distribute this code for any purpose
1666 ;; (include commercial use) and without fee. Please refer to this
1667 ;; package when you modify this code.
1668 ;;
1669 ;; We take the identical tarball from the Bazel mirror, because the URL
1670 ;; at the home page is not versioned and might change.
1671 ("fft2d-src"
1672 ,(origin
1673 (method url-fetch)
1674 (uri "https://mirror.bazel.build/www.kurims.kyoto-u.ac.jp/~ooura/fft.tgz")
1675 (file-name "fft2d.tar.gz")
1676 (sha256
1677 (base32
1678 "15jjkfvhqvl2c0753d2di8hz0pyzn598g74wqy79awdrf1y67fsj"))))
1679 ("highwayhash-src"
1680 ,(let ((commit "be5edafc2e1a455768e260ccd68ae7317b6690ee")
1681 (revision "1"))
1682 (origin
1683 (method git-fetch)
1684 (uri (git-reference
1685 (url "https://github.com/google/highwayhash.git")
1686 (commit commit)))
1687 (file-name (string-append "highwayhash-0-" revision
1688 (string-take commit 7)
1689 "-checkout"))
1690 (sha256
1691 (base32
1692 "154jwf98cyy54hldr94pgjn85zynly3abpnc1avmb8a18lzwjyb6")))))
1693 ("nsync-src"
1694 ,(let ((version "0559ce013feac8db639ee1bf776aca0325d28777")
1695 (revision "1"))
1696 (origin
1697 (method url-fetch)
1698 (uri (string-append "https://mirror.bazel.build/"
1699 "github.com/google/nsync/archive/"
1700 version ".tar.gz"))
1701 (file-name (string-append "nsync-0." revision
1702 "-" (string-take version 7)
1703 ".tar.gz"))
1704 (sha256
1705 (base32
1706 "0qdkyqym34x739mmzv97ah5r7ph462v5xkxqxvidmcfqbi64b132")))))
1707 ("re2-src"
1708 ,(let ((commit "e7efc48")
1709 (revision "1"))
1710 (origin
1711 (method git-fetch)
1712 (uri (git-reference
1713 (url "https://github.com/google/re2")
1714 (commit commit)))
1715 (file-name (string-append "re2-0-" revision
1716 (string-take commit 7)
1717 "-checkout"))
1718 (sha256
1719 (base32
1720 "161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign")))))
1721 ("googletest" ,googletest)
1722 ("swig" ,swig)
1723 ("unzip" ,unzip)))
1724 (propagated-inputs
1725 `(("python-absl-py" ,python-absl-py)
1726 ("python-astor" ,python-astor)
1727 ("python-gast" ,python-gast)
1728 ("python-grpcio" ,python-grpcio)
1729 ("python-numpy" ,python-numpy)
1730 ("python-protobuf" ,python-protobuf-next)
1731 ("python-six" ,python-six)
1732 ("python-termcolo" ,python-termcolor)
1733 ("python-wheel" ,python-wheel)))
1734 (inputs
1735 `(("c-ares" ,c-ares-next)
1736 ("eigen" ,eigen-for-tensorflow)
1737 ("gemmlowp" ,gemmlowp-for-tensorflow)
1738 ("lmdb" ,lmdb)
1739 ("libjpeg" ,libjpeg)
1740 ("libpng" ,libpng)
1741 ("giflib" ,giflib)
1742 ("grpc" ,grpc)
1743 ("jsoncpp" ,jsoncpp-for-tensorflow)
1744 ("snappy" ,snappy)
1745 ("sqlite" ,sqlite)
1746 ("protobuf" ,protobuf-next)
1747 ("python" ,python-wrapper)
1748 ("zlib" ,zlib)))
1749 (home-page "https://tensorflow.org")
1750 (synopsis "Machine learning framework")
1751 (description
1752 "TensorFlow is a flexible platform for building and training machine
1753learning models. It provides a library for high performance numerical
1754computation and includes high level Python APIs, including both a sequential
1755API for beginners that allows users to build models quickly by plugging
1756together building blocks and a subclassing API with an imperative style for
1757advanced research.")
1758 (license license:asl2.0)))
d60b064d
NG		 1759
1760(define-public python-iml
1761 (package
1762 (name "python-iml")
1763 (version "0.6.2")
1764 (source
1765 (origin
1766 (method url-fetch)
1767 (uri (pypi-uri "iml" version))
1768 (sha256
1769 (base32
1770 "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
1771 (build-system python-build-system)
1772 (propagated-inputs
1773 `(("ipython" ,python-ipython)
1774 ("nose" ,python-nose)
1775 ("numpy" ,python-numpy)
1776 ("pandas" ,python-pandas)
1777 ("scipy" ,python-scipy)))
1778 (home-page "http://github.com/interpretable-ml/iml")
1779 (synopsis "Interpretable Machine Learning (iML) package")
1780 (description "Interpretable ML (iML) is a set of data type objects,
1781visualizations, and interfaces that can be used by any method designed to
1782explain the predictions of machine learning models (or really the output of
1783any function). It currently contains the interface and IO code from the Shap
1784project, and it will potentially also do the same for the Lime project.")
1785 (license license:expat)))
d93ad191
RW		 1786
1787(define-public python-keras-applications
1788 (package
1789 (name "python-keras-applications")
1790 (version "1.0.8")
1791 (source
1792 (origin
1793 (method url-fetch)
1794 (uri (pypi-uri "Keras_Applications" version))
1795 (sha256
1796 (base32
1797 "1rcz31ca4axa6kzhjx4lwqxbg4wvlljkj8qj9a7p9sfd5fhzjyam"))))
1798 (build-system python-build-system)
1799 ;; The tests require Keras, but this package is needed to build Keras.
1800 (arguments '(#:tests? #f))
1801 (propagated-inputs
1802 `(("python-h5py" ,python-h5py)
1803 ("python-numpy" ,python-numpy)))
1804 (native-inputs
1805 `(("python-pytest" ,python-pytest)
1806 ("python-pytest-cov" ,python-pytest-cov)
1807 ("python-pytest-pep8" ,python-pytest-pep8)
1808 ("python-pytest-xdist" ,python-pytest-xdist)))
1809 (home-page "https://github.com/keras-team/keras-applications")
1810 (synopsis "Reference implementations of popular deep learning models")
1811 (description
1812 "This package provides reference implementations of popular deep learning
1813models for use with the Keras deep learning framework.")
1814 (license license:expat)))
4abc5066
RW		 1815
1816(define-public python-keras-preprocessing
1817 (package
1818 (name "python-keras-preprocessing")
1819 (version "1.1.0")
1820 (source
1821 (origin
1822 (method url-fetch)
1823 (uri (pypi-uri "Keras_Preprocessing" version))
1824 (sha256
1825 (base32
1826 "1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as"))))
1827 (build-system python-build-system)
1828 (propagated-inputs
1829 `(("python-numpy" ,python-numpy)
1830 ("python-six" ,python-six)))
1831 (native-inputs
1832 `(("python-pandas" ,python-pandas)
1833 ("python-pillow" ,python-pillow)
1834 ("python-pytest" ,python-pytest)
1835 ("python-pytest-cov" ,python-pytest-cov)
1836 ("python-pytest-xdist" ,python-pytest-xdist)
1837 ("tensorflow" ,tensorflow)))
1838 (home-page "https://github.com/keras-team/keras-preprocessing/")
1839 (synopsis "Data preprocessing and augmentation for deep learning models")
1840 (description
1841 "Keras Preprocessing is the data preprocessing and data augmentation
1842module of the Keras deep learning library. It provides utilities for working
1843with image data, text data, and sequence data.")
1844 (license license:expat)))
f1765b57
RW		 1845
1846(define-public python-keras
1847 (package
1848 (name "python-keras")
1849 (version "2.2.4")
1850 (source
1851 (origin
1852 (method url-fetch)
1853 (uri (pypi-uri "Keras" version))
1854 (sha256
1855 (base32
1856 "1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh"))))
1857 (build-system python-build-system)
1858 (arguments
1859 `(#:phases
1860 (modify-phases %standard-phases
1861 (add-after 'unpack 'remove-tests-for-unavailable-features
1862 (lambda _
1863 (delete-file "keras/backend/theano_backend.py")
1864 (delete-file "keras/backend/cntk_backend.py")
1865 (delete-file "tests/keras/backend/backend_test.py")
1866
1867 ;; FIXME: This doesn't work because Tensorflow is missing the
1868 ;; coder ops library.
1869 (delete-file "tests/keras/test_callbacks.py")
1870 #t))
1871 (replace 'check
1872 (lambda _
1873 ;; These tests attempt to download data files from the internet.
1874 (delete-file "tests/integration_tests/test_datasets.py")
1875 (delete-file "tests/integration_tests/imagenet_utils_test.py")
1876
1877 (setenv "PYTHONPATH"
1878 (string-append (getcwd) "/build/lib:"
1879 (getenv "PYTHONPATH")))
1880 (invoke "py.test" "-v"
1881 "-p" "no:cacheprovider"
1882 "--ignore" "keras/utils"))))))
1883 (propagated-inputs
1884 `(("python-h5py" ,python-h5py)
1885 ("python-keras-applications" ,python-keras-applications)
1886 ("python-keras-preprocessing" ,python-keras-preprocessing)
1887 ("python-numpy" ,python-numpy)
1888 ("python-pydot" ,python-pydot)
1889 ("python-pyyaml" ,python-pyyaml)
1890 ("python-scipy" ,python-scipy)
1891 ("python-six" ,python-six)
1892 ("tensorflow" ,tensorflow)
1893 ("graphviz" ,graphviz)))
1894 (native-inputs
1895 `(("python-pandas" ,python-pandas)
1896 ("python-pytest" ,python-pytest)
1897 ("python-pytest-cov" ,python-pytest-cov)
1898 ("python-pytest-pep8" ,python-pytest-pep8)
1899 ("python-pytest-timeout" ,python-pytest-timeout)
1900 ("python-pytest-xdist" ,python-pytest-xdist)
1901 ("python-sphinx" ,python-sphinx)
1902 ("python-requests" ,python-requests)))
1903 (home-page "https://github.com/keras-team/keras")
1904 (synopsis "High-level deep learning framework")
1905 (description "Keras is a high-level neural networks API, written in Python
1906and capable of running on top of TensorFlow. It was developed with a focus on
1907enabling fast experimentation. Use Keras if you need a deep learning library
1908that:
1909
1910@itemize
1911@item Allows for easy and fast prototyping (through user friendliness,
1912 modularity, and extensibility).
1913@item Supports both convolutional networks and recurrent networks, as well as
1914 combinations of the two.
1915@item Runs seamlessly on CPU and GPU.
1916@end itemize\n")
1917 (license license:expat)))
jackhill's copy of GNU Guix: https://guix.gnu.org/