gnu/packages/machine-learning.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
   4 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
   5 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
   6 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
   7 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
   8 ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
   9 ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
  10 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
  11 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
  12 ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
  13 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
  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)
  35   #:use-module (guix svn-download)
  36   #:use-module (guix build-system cmake)
  37   #:use-module (guix build-system gnu)
  38   #:use-module (guix build-system ocaml)
  39   #:use-module (guix build-system python)
  40   #:use-module (guix build-system r)
  41   #:use-module (guix git-download)
  42   #:use-module (gnu packages)
  43   #:use-module (gnu packages adns)
  44   #:use-module (gnu packages algebra)
  45   #:use-module (gnu packages audio)
  46   #:use-module (gnu packages autotools)
  47   #:use-module (gnu packages base)
  48   #:use-module (gnu packages bash)
  49   #:use-module (gnu packages boost)
  50   #:use-module (gnu packages check)
  51   #:use-module (gnu packages compression)
  52   #:use-module (gnu packages cran)
  53   #:use-module (gnu packages databases)
  54   #:use-module (gnu packages dejagnu)
  55   #:use-module (gnu packages gcc)
  56   #:use-module (gnu packages glib)
  57   #:use-module (gnu packages graphviz)
  58   #:use-module (gnu packages gstreamer)
  59   #:use-module (gnu packages image)
  60   #:use-module (gnu packages linux)
  61   #:use-module (gnu packages maths)
  62   #:use-module (gnu packages mpi)
  63   #:use-module (gnu packages ocaml)
  64   #:use-module (gnu packages onc-rpc)
  65   #:use-module (gnu packages perl)
  66   #:use-module (gnu packages pkg-config)
  67   #:use-module (gnu packages protobuf)
  68   #:use-module (gnu packages python)
  69   #:use-module (gnu packages python-web)
  70   #:use-module (gnu packages python-xyz)
  71   #:use-module (gnu packages serialization)
  72   #:use-module (gnu packages sphinx)
  73   #:use-module (gnu packages statistics)
  74   #:use-module (gnu packages sqlite)
  75   #:use-module (gnu packages swig)
  76   #:use-module (gnu packages tls)
  77   #:use-module (gnu packages web)
  78   #:use-module (gnu packages xml)
  79   #:use-module (gnu packages xorg)
  80   #:use-module (ice-9 match))
  81
  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
 110 multilayer artificial neural networks in C with support for both fully
 111 connected and sparsely connected networks.")
 112       (license license:lgpl2.1))))
 113
 114 (define-public libsvm
 115   (package
 116     (name "libsvm")
 117     (version "3.23")
 118     (source
 119      (origin
 120        (method url-fetch)
 121        (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
 122                            name "-" version ".tar.gz"))
 123        (sha256
 124         (base32 "0jpaq0rr92x38p4nk3gjan79ip67m6p80anb28z1d8601miysyi5"))))
 125     (build-system gnu-build-system)
 126     (arguments
 127      `(#:tests? #f                      ; no "check" target
 128        #:phases (modify-phases %standard-phases
 129                   (delete 'configure)
 130                   (replace
 131                    'install             ; no ‘install’ target
 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
 146 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
 147 distribution estimation (one-class SVM).  It supports multi-class
 148 classification.")
 149     (license license:bsd-3)))
 150
 151 (define-public python-libsvm
 152   (package (inherit libsvm)
 153     (name "python-libsvm")
 154     (build-system gnu-build-system)
 155     (arguments
 156      `(#:tests? #f                      ; no "check" target
 157        #:make-flags '("-C" "python")
 158        #:phases
 159        (modify-phases %standard-phases
 160          (delete 'configure)
 161          (replace
 162           'install                      ; no ‘install’ target
 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")))
 182
 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
 202        `(#:imported-modules (,@%gnu-build-system-modules
 203                              (guix build python-build-system))
 204          #:phases
 205          (modify-phases %standard-phases
 206            (add-after 'unpack 'enter-dir
 207              (lambda _ (chdir "ghmm") #t))
 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 (python-version
 214                                       (assoc-ref inputs "python"))))
 215                  (setenv "PYTHONPATH"
 216                          (string-append (getenv "PYTHONPATH")
 217                                         ":" (assoc-ref outputs "out")
 218                                         "/lib/python" python-version
 219                                         "/site-packages")))
 220                #t))
 221            (add-after 'enter-dir 'fix-runpath
 222              (lambda* (#:key outputs #:allow-other-keys)
 223                (substitute* "ghmmwrapper/setup.py"
 224                  (("^(.*)extra_compile_args = \\[" line indent)
 225                   (string-append indent
 226                                  "extra_link_args = [\"-Wl,-rpath="
 227                                  (assoc-ref outputs "out") "/lib\"],\n"
 228                                  line
 229                                  "\"-Wl,-rpath="
 230                                  (assoc-ref outputs "out")
 231                                  "/lib\", ")))
 232                #t))
 233            (add-after 'enter-dir 'disable-broken-tests
 234              (lambda _
 235                (substitute* "tests/Makefile.am"
 236                  ;; GHMM_SILENT_TESTS is assumed to be a command.
 237                  (("TESTS_ENVIRONMENT.*") "")
 238                  ;; Do not build broken tests.
 239                  (("chmm .*") "")
 240                  (("read_fa .*") "")
 241                  (("mcmc .*") "")
 242                  (("label_higher_order_test.*$")
 243                   "label_higher_order_test\n"))
 244
 245                ;; These Python unittests are broken as there is no gato.
 246                ;; See https://sourceforge.net/p/ghmm/support-requests/3/
 247                (substitute* "ghmmwrapper/ghmmunittests.py"
 248                  (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
 249                    line indent)
 250                   (string-append indent
 251                                  "@unittest.skip(\"Disabled by Guix\")\n"
 252                                  line)))
 253                #t))
 254            (add-after 'disable-broken-tests 'autogen
 255              (lambda _
 256                (invoke "bash" "autogen.sh"))))))
 257       (inputs
 258        `(("python" ,python-2) ; only Python 2 is supported
 259          ("libxml2" ,libxml2)))
 260       (native-inputs
 261        `(("pkg-config" ,pkg-config)
 262          ("dejagnu" ,dejagnu)
 263          ("swig" ,swig)
 264          ("autoconf" ,autoconf)
 265          ("automake" ,automake)
 266          ("libtool" ,libtool)))
 267       (home-page "http://ghmm.org")
 268       (synopsis "Hidden Markov Model library")
 269       (description
 270        "The General Hidden Markov Model library (GHMM) is a C library with
 271 additional Python bindings implementing a wide range of types of @dfn{Hidden
 272 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
 273 training, HMM clustering, HMM mixtures.")
 274       (license license:lgpl2.0+))))
 275
 276 (define-public mcl
 277   (package
 278     (name "mcl")
 279     (version "14.137")
 280     (source (origin
 281               (method url-fetch)
 282               (uri (string-append
 283                     "http://micans.org/mcl/src/mcl-"
 284                     (string-replace-substring version "." "-")
 285                     ".tar.gz"))
 286               (sha256
 287                (base32
 288                 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
 289     (build-system gnu-build-system)
 290     (arguments
 291      `(#:configure-flags (list "--enable-blast")))
 292     (inputs
 293      `(("perl" ,perl)))
 294     (home-page "http://micans.org/mcl/")
 295     (synopsis "Clustering algorithm for graphs")
 296     (description
 297      "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
 298 fast and scalable unsupervised cluster algorithm for graphs (also known as
 299 networks) based on simulation of (stochastic) flow in graphs.")
 300     ;; In the LICENCE file and web page it says "The software is licensed
 301     ;; under the GNU General Public License, version 3.", but in several of
 302     ;; the source code files it suggests GPL3 or later.
 303     ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
 304     (license license:gpl3)))
 305
 306 (define-public ocaml-mcl
 307   (package
 308     (name "ocaml-mcl")
 309     (version "12-068oasis4")
 310     (source
 311      (origin
 312        (method git-fetch)
 313        (uri (git-reference
 314              (url "https://github.com/fhcrc/mcl.git")
 315              (commit version)))
 316        (file-name (git-file-name name version))
 317        (sha256
 318         (base32
 319          "0009dc3h2jp3qg5val452wngpqnbfyhbcxylghq0mrjqxx0jdq5p"))))
 320     (build-system ocaml-build-system)
 321     (arguments
 322      `(#:phases
 323        (modify-phases %standard-phases
 324          (add-before 'configure 'patch-paths
 325            (lambda _
 326              (substitute* "configure"
 327                (("/bin/sh") (which "sh")))
 328              (substitute* "setup.ml"
 329                (("LDFLAGS=-fPIC")
 330                 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))
 331                (("-std=c89") "-std=gnu99")
 332
 333                ;; This is a mutable string, which is no longer supported.  Use
 334                ;; a byte buffer instead.
 335                (("String.make \\(String.length s\\)")
 336                 "Bytes.make (String.length s)")
 337
 338                ;; These two belong together.
 339                (("OASISString.replace_chars")
 340                 "Bytes.to_string (OASISString.replace_chars")
 341                ((" s;")
 342                 " s);"))
 343              (substitute* "myocamlbuild.ml"
 344                (("std=c89") "std=gnu99"))
 345              ;; Since we build with a more recent OCaml, we have to use C99 or
 346              ;; later.  This causes problems with the old C code.
 347              (substitute* "src/impala/matrix.c"
 348                (("restrict") "restrict_"))
 349              #t)))))
 350     (native-inputs
 351      `(("ocamlbuild" ,ocamlbuild)))
 352     (home-page "https://github.com/fhcrc/mcl")
 353     (synopsis "OCaml wrappers around MCL")
 354     (description
 355      "This package provides OCaml bindings for the MCL graph clustering
 356 algorithm.")
 357     (license license:gpl3)))
 358
 359 (define-public randomjungle
 360   (package
 361     (name "randomjungle")
 362     (version "2.1.0")
 363     (source
 364      (origin
 365        (method url-fetch)
 366        (uri (string-append
 367              "https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
 368              "/randomjungle/randomjungle-" version ".tar_.gz"))
 369        (patches (search-patches "randomjungle-disable-static-build.patch"))
 370        (sha256
 371         (base32
 372          "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
 373     (build-system gnu-build-system)
 374     (arguments
 375      `(#:configure-flags
 376        (list "--disable-static"
 377              (string-append "--with-boost="
 378                             (assoc-ref %build-inputs "boost")))
 379        #:phases
 380        (modify-phases %standard-phases
 381          (add-before
 382           'configure 'set-CXXFLAGS
 383           (lambda _
 384             (setenv "CXXFLAGS" "-fpermissive ")
 385             #t)))))
 386     (inputs
 387      `(("boost" ,boost)
 388        ("gsl" ,gsl)
 389        ("libxml2" ,libxml2)
 390        ("zlib" ,zlib)))
 391     (native-inputs
 392      `(("gfortran" ,gfortran)
 393        ("gfortran:lib" ,gfortran "lib")))
 394     ;; Non-portable assembly instructions are used so building fails on
 395     ;; platforms other than x86_64 or i686.
 396     (supported-systems '("x86_64-linux" "i686-linux"))
 397     (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
 398     (synopsis "Implementation of the Random Forests machine learning method")
 399     (description
 400      "Random Jungle is an implementation of Random Forests.  It is supposed to
 401 analyse high dimensional data.  In genetics, it can be used for analysing big
 402 Genome Wide Association (GWA) data.  Random Forests is a powerful machine
 403 learning method.  Most interesting features are variable selection, missing
 404 value imputation, classifier creation, generalization error estimation and
 405 sample proximities between pairs of cases.")
 406     (license license:gpl3+)))
 407
 408 (define-public openfst
 409   (package
 410     (name "openfst")
 411     (version "1.7.2")
 412     (source (origin
 413               (method url-fetch)
 414               (uri (string-append "http://www.openfst.org/twiki/pub/FST/"
 415                                   "FstDownload/openfst-" version ".tar.gz"))
 416               (sha256
 417                (base32
 418                 "0fqgk8195kz21is09gwzwnrg7fr9526bi9mh4apyskapz27pbhr1"))))
 419     (build-system gnu-build-system)
 420     (home-page "http://www.openfst.org")
 421     (synopsis "Library for weighted finite-state transducers")
 422     (description "OpenFst is a library for constructing, combining,
 423 optimizing, and searching weighted finite-state transducers (FSTs).")
 424     (license license:asl2.0)))
 425
 426 (define-public shogun
 427   (package
 428     (name "shogun")
 429     (version "6.1.3")
 430     (source
 431      (origin
 432        (method url-fetch)
 433        (uri (string-append
 434              "ftp://shogun-toolbox.org/shogun/releases/"
 435              (version-major+minor version)
 436              "/sources/shogun-" version ".tar.bz2"))
 437        (sha256
 438         (base32
 439          "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
 440        (modules '((guix build utils)
 441                   (ice-9 rdelim)))
 442        (snippet
 443         '(begin
 444            ;; Remove non-free sources and files referencing them
 445            (for-each delete-file
 446                      (find-files "src/shogun/classifier/svm/"
 447                                  "SVMLight\\.(cpp|h)"))
 448            (for-each delete-file
 449                      (find-files "examples/undocumented/libshogun/"
 450                                  (string-append
 451                                   "(classifier_.*svmlight.*|"
 452                                   "evaluation_cross_validation_locked_comparison).cpp")))
 453            ;; Remove non-free functions.
 454            (define (delete-ifdefs file)
 455              (with-atomic-file-replacement file
 456                (lambda (in out)
 457                  (let loop ((line (read-line in 'concat))
 458                             (skipping? #f))
 459                    (if (eof-object? line)
 460                        #t
 461                        (let ((skip-next?
 462                               (or (and skipping?
 463                                        (not (string-prefix?
 464                                              "#endif //USE_SVMLIGHT" line)))
 465                                   (string-prefix?
 466                                    "#ifdef USE_SVMLIGHT" line))))
 467                          (when (or (not skipping?)
 468                                    (and skipping? (not skip-next?)))
 469                            (display line out))
 470                          (loop (read-line in 'concat) skip-next?)))))))
 471            (for-each delete-ifdefs
 472                      (append
 473                       (find-files "src/shogun/classifier/mkl"
 474                                   "^MKLClassification\\.cpp")
 475                       (find-files "src/shogun/classifier/svm"
 476                                   "^SVMLightOneClass\\.(cpp|h)")
 477                       (find-files "src/shogun/multiclass"
 478                                   "^ScatterSVM\\.(cpp|h)")
 479                       (find-files "src/shogun/kernel/"
 480                                   "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
 481                       (find-files "src/shogun/regression/svr"
 482                                   "^(MKLRegression|SVRLight)\\.(cpp|h)")
 483                       (find-files "src/shogun/transfer/domain_adaptation"
 484                                   "^DomainAdaptationSVM\\.(cpp|h)")))
 485            #t))))
 486     (build-system cmake-build-system)
 487     (arguments
 488      '(#:tests? #f ;no check target
 489        #:phases
 490        (modify-phases %standard-phases
 491          (add-after 'unpack 'delete-broken-symlinks
 492            (lambda _
 493              (for-each delete-file '("applications/arts/data"
 494                                      "applications/asp/data"
 495                                      "applications/easysvm/data"
 496                                      "applications/msplicer/data"
 497                                      "applications/ocr/data"
 498                                      "examples/meta/data"
 499                                      "examples/undocumented/data"))
 500              #t))
 501          (add-after 'unpack 'change-R-target-path
 502            (lambda* (#:key outputs #:allow-other-keys)
 503              (substitute* '("src/interfaces/r/CMakeLists.txt"
 504                             "examples/meta/r/CMakeLists.txt")
 505                (("\\$\\{R_COMPONENT_LIB_PATH\\}")
 506                 (string-append (assoc-ref outputs "out")
 507                                "/lib/R/library/")))
 508              #t))
 509          (add-after 'unpack 'fix-octave-modules
 510            (lambda* (#:key outputs #:allow-other-keys)
 511              (substitute* "src/interfaces/octave/CMakeLists.txt"
 512                (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
 513                 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
 514                ;; change target directory
 515                (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
 516                 (string-append (assoc-ref outputs "out")
 517                                "/share/octave/packages")))
 518              (substitute* '("src/interfaces/octave/swig_typemaps.i"
 519                             "src/interfaces/octave/sg_print_functions.cpp")
 520                ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
 521                (("octave/config\\.h") "octave/octave-config.h")
 522                (("octave/oct-obj.h") "octave/ovl.h"))
 523              #t))
 524          (add-after 'unpack 'move-rxcpp
 525            (lambda* (#:key inputs #:allow-other-keys)
 526              (let ((rxcpp-dir "shogun/third-party/rxcpp"))
 527                (mkdir-p rxcpp-dir)
 528                (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
 529                #t)))
 530          (add-before 'build 'set-HOME
 531            ;; $HOME needs to be set at some point during the build phase
 532            (lambda _ (setenv "HOME" "/tmp") #t)))
 533        #:configure-flags
 534        (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
 535              "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
 536              "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
 537              ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
 538              ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
 539              ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
 540              ;;"-DINTERFACE_LUA=ON"  ;fails because lua doesn't build pkgconfig file
 541              "-DINTERFACE_OCTAVE=ON"
 542              "-DINTERFACE_PYTHON=ON"
 543              "-DINTERFACE_R=ON")))
 544     (inputs
 545      `(("python" ,python)
 546        ("numpy" ,python-numpy)
 547        ("r-minimal" ,r-minimal)
 548        ("octave" ,octave-cli)
 549        ("swig" ,swig)
 550        ("eigen" ,eigen)
 551        ("hdf5" ,hdf5)
 552        ("atlas" ,atlas)
 553        ("arpack" ,arpack-ng)
 554        ("lapack" ,lapack)
 555        ("glpk" ,glpk)
 556        ("libxml2" ,libxml2)
 557        ("lzo" ,lzo)
 558        ("zlib" ,zlib)))
 559     (native-inputs
 560      `(("pkg-config" ,pkg-config)
 561        ("rxcpp" ,rxcpp)))
 562     ;; Non-portable SSE instructions are used so building fails on platforms
 563     ;; other than x86_64.
 564     (supported-systems '("x86_64-linux"))
 565     (home-page "http://shogun-toolbox.org/")
 566     (synopsis "Machine learning toolbox")
 567     (description
 568      "The Shogun Machine learning toolbox provides a wide range of unified and
 569 efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
 570 combine multiple data representations, algorithm classes, and general purpose
 571 tools.  This enables both rapid prototyping of data pipelines and extensibility
 572 in terms of new algorithms.")
 573     (license license:gpl3+)))
 574
 575 (define-public rxcpp
 576   (package
 577     (name "rxcpp")
 578     (version "4.1.0")
 579     (source
 580      (origin
 581        (method git-fetch)
 582        (uri (git-reference
 583              (url "https://github.com/ReactiveX/RxCpp.git")
 584              (commit (string-append "v" version))))
 585        (sha256
 586         (base32 "1rdpa3jlc181jd08nk437aar085h28i45s6nzrv65apb3xyyz0ij"))
 587        (file-name (git-file-name name version))))
 588     (build-system cmake-build-system)
 589     (arguments
 590      `(#:phases
 591        (modify-phases %standard-phases
 592          (add-after 'unpack 'remove-werror
 593            (lambda _
 594              (substitute* (find-files ".")
 595                (("-Werror") ""))
 596              #t))
 597          (replace 'check
 598            (lambda _
 599              (invoke "ctest"))))))
 600     (native-inputs
 601      `(("catch" ,catch-framework)))
 602     (home-page "http://reactivex.io/")
 603     (synopsis "Reactive Extensions for C++")
 604     (description
 605      "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
 606 values-distributed-in-time.  ReactiveX is a library for composing asynchronous
 607 and event-based programs by using observable sequences.
 608
 609 It extends the observer pattern to support sequences of data and/or events and
 610 adds operators that allow you to compose sequences together declaratively while
 611 abstracting away concerns about things like low-level threading,
 612 synchronization, thread-safety, concurrent data structures, and non-blocking
 613 I/O.")
 614     (license license:asl2.0)))
 615
 616 (define-public r-adaptivesparsity
 617   (package
 618     (name "r-adaptivesparsity")
 619     (version "1.6")
 620     (source (origin
 621               (method url-fetch)
 622               (uri (cran-uri "AdaptiveSparsity" version))
 623               (sha256
 624                (base32
 625                 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
 626     (properties
 627      `((upstream-name . "AdaptiveSparsity")))
 628     (build-system r-build-system)
 629     (arguments
 630      `(#:phases
 631        (modify-phases %standard-phases
 632          (add-after 'unpack 'link-against-armadillo
 633            (lambda _
 634              (substitute* "src/Makevars"
 635                (("PKG_LIBS=" prefix)
 636                 (string-append prefix "-larmadillo"))))))))
 637     (propagated-inputs
 638      `(("r-mass" ,r-mass)
 639        ("r-matrix" ,r-matrix)
 640        ("r-rcpp" ,r-rcpp)
 641        ("r-rcpparmadillo" ,r-rcpparmadillo)))
 642     (inputs
 643      `(("armadillo" ,armadillo)))
 644     (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
 645     (synopsis "Adaptive sparsity models")
 646     (description
 647      "This package implements the Figueiredo machine learning algorithm for
 648 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
 649 geometric models.")
 650     (license license:lgpl3+)))
 651
 652 (define-public gemmlowp-for-tensorflow
 653   ;; The commit hash is taken from "tensorflow/workspace.bzl".
 654   (let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
 655         (revision "2"))
 656     (package
 657       (name "gemmlowp")
 658       (version (git-version "0" revision commit))
 659       (source (origin
 660                 (method url-fetch)
 661                 (uri (string-append "https://mirror.bazel.build/"
 662                                     "github.com/google/gemmlowp/archive/"
 663                                     commit ".zip"))
 664                 (file-name (string-append "gemmlowp-" version ".zip"))
 665                 (sha256
 666                  (base32
 667                   "0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
 668       (build-system cmake-build-system)
 669       (arguments
 670        `(#:configure-flags
 671          (list ,@(match (%current-system)
 672                    ((or "x86_64-linux" "i686-linux")
 673                     '("-DCMAKE_CXX_FLAGS=-msse2"))
 674                    (_ '())))
 675          #:phases
 676          (modify-phases %standard-phases
 677            ;; This directory contains the CMakeLists.txt.
 678            (add-after 'unpack 'chdir
 679              (lambda _ (chdir "contrib") #t))
 680            ;; There is no install target
 681            (replace 'install
 682              (lambda* (#:key outputs #:allow-other-keys)
 683                (let* ((out (assoc-ref outputs "out"))
 684                       (lib (string-append out "/lib/"))
 685                       (inc (string-append out "/include/")))
 686                  (install-file "../build/libeight_bit_int_gemm.so" lib)
 687                  (for-each (lambda (dir)
 688                              (let ((target (string-append inc "/" dir)))
 689                                (mkdir-p target)
 690                                (for-each (lambda (h)
 691                                            (install-file h target))
 692                                          (find-files (string-append "../" dir)
 693                                                      "\\.h$"))))
 694                            '("meta" "profiling" "public" "fixedpoint"
 695                              "eight_bit_int_gemm" "internal"))
 696                  #t))))))
 697       (native-inputs
 698        `(("unzip" ,unzip)))
 699       (home-page "https://github.com/google/gemmlowp")
 700       (synopsis "Small self-contained low-precision GEMM library")
 701       (description
 702        "This is a small self-contained low-precision @dfn{general matrix
 703 multiplication} (GEMM) library.  It is not a full linear algebra library.
 704 Low-precision means that the input and output matrix entries are integers on
 705 at most 8 bits.  To avoid overflow, results are internally accumulated on more
 706 than 8 bits, and at the end only some significant 8 bits are kept.")
 707       (license license:asl2.0))))
 708
 709 (define-public dlib
 710   (package
 711     (name "dlib")
 712     (version "19.7")
 713     (source (origin
 714               (method url-fetch)
 715               (uri (string-append
 716                     "http://dlib.net/files/dlib-" version ".tar.bz2"))
 717               (sha256
 718                (base32
 719                 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
 720               (modules '((guix build utils)))
 721               (snippet
 722                '(begin
 723                   ;; Delete ~13MB of bundled dependencies.
 724                   (delete-file-recursively "dlib/external")
 725                   (delete-file-recursively "docs/dlib/external")
 726                   #t))))
 727     (build-system cmake-build-system)
 728     (arguments
 729      `(#:phases
 730        (modify-phases %standard-phases
 731          (add-after 'unpack 'disable-asserts
 732            (lambda _
 733              ;; config.h recommends explicitly enabling or disabling asserts
 734              ;; when building as a shared library. By default neither is set.
 735              (substitute* "dlib/config.h"
 736                (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
 737              #t))
 738          (add-after 'disable-asserts 'disable-failing-tests
 739            (lambda _
 740              ;; One test times out on MIPS, so we need to disable it.
 741              ;; Others are flaky on some platforms.
 742              (let* ((system ,(or (%current-target-system)
 743                                  (%current-system)))
 744                     (disabled-tests (cond
 745                                      ((string-prefix? "mips64" system)
 746                                       '("object_detector" ; timeout
 747                                         "data_io"))
 748                                      ((string-prefix? "armhf" system)
 749                                       '("learning_to_track"))
 750                                      ((string-prefix? "i686" system)
 751                                       '("optimization"))
 752                                      (else '()))))
 753                (for-each
 754                 (lambda (test)
 755                   (substitute* "dlib/test/makefile"
 756                     (((string-append "SRC \\+= " test "\\.cpp")) "")))
 757                 disabled-tests)
 758                #t)))
 759          (replace 'check
 760            (lambda _
 761              ;; No test target, so we build and run the unit tests here.
 762              (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
 763                (with-directory-excursion test-dir
 764                  (invoke "make" "-j" (number->string (parallel-job-count)))
 765                  (invoke "./dtest" "--runall"))
 766                #t)))
 767          (add-after 'install 'delete-static-library
 768            (lambda* (#:key outputs #:allow-other-keys)
 769              (delete-file (string-append (assoc-ref outputs "out")
 770                                          "/lib/libdlib.a"))
 771              #t)))))
 772     (native-inputs
 773      `(("pkg-config" ,pkg-config)
 774        ;; For tests.
 775        ("libnsl" ,libnsl)))
 776     (inputs
 777      `(("giflib" ,giflib)
 778        ("lapack" ,lapack)
 779        ("libjpeg" ,libjpeg)
 780        ("libpng" ,libpng)
 781        ("libx11" ,libx11)
 782        ("openblas" ,openblas)
 783        ("zlib" ,zlib)))
 784     (synopsis
 785      "Toolkit for making machine learning and data analysis applications in C++")
 786     (description
 787      "Dlib is a modern C++ toolkit containing machine learning algorithms and
 788 tools.  It is used in both industry and academia in a wide range of domains
 789 including robotics, embedded devices, mobile phones, and large high performance
 790 computing environments.")
 791     (home-page "http://dlib.net")
 792     (license license:boost1.0)))
 793
 794 (define-public python-scikit-learn
 795   (package
 796     (name "python-scikit-learn")
 797     (version "0.20.3")
 798     (source
 799      (origin
 800        (method git-fetch)
 801        (uri (git-reference
 802              (url "https://github.com/scikit-learn/scikit-learn.git")
 803              (commit version)))
 804        (file-name (git-file-name name version))
 805        (sha256
 806         (base32
 807          "08aaby5zphfxy83mggg35bwyka7wk91l2qijh8kk0bl08dikq8dl"))))
 808     (build-system python-build-system)
 809     (arguments
 810      `(#:phases
 811        (modify-phases %standard-phases
 812          (add-after 'build 'build-ext
 813            (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
 814          (replace 'check
 815            (lambda _
 816              ;; Restrict OpenBLAS threads to prevent segfaults while testing!
 817              (setenv "OPENBLAS_NUM_THREADS" "1")
 818
 819              ;; Some tests require write access to $HOME.
 820              (setenv "HOME" "/tmp")
 821
 822              (invoke "pytest" "sklearn" "-m" "not network")))
 823          ;; FIXME: This fails with permission denied
 824          (delete 'reset-gzip-timestamps))))
 825     (inputs
 826      `(("openblas" ,openblas)))
 827     (native-inputs
 828      `(("python-pytest" ,python-pytest)
 829        ("python-pandas" ,python-pandas) ;for tests
 830        ("python-cython" ,python-cython)))
 831     (propagated-inputs
 832      `(("python-numpy" ,python-numpy)
 833        ("python-scipy" ,python-scipy)))
 834     (home-page "http://scikit-learn.org/")
 835     (synopsis "Machine Learning in Python")
 836     (description
 837      "Scikit-learn provides simple and efficient tools for data mining and
 838 data analysis.")
 839     (license license:bsd-3)))
 840
 841 (define-public python2-scikit-learn
 842   (package-with-python2 python-scikit-learn))
 843
 844 (define-public python-autograd
 845   (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
 846          (revision "0")
 847          (version (git-version "0.0.0" revision commit)))
 848     (package
 849       (name "python-autograd")
 850       (home-page "https://github.com/HIPS/autograd")
 851       (source (origin
 852                 (method git-fetch)
 853                 (uri (git-reference
 854                       (url home-page)
 855                       (commit commit)))
 856                 (sha256
 857                  (base32
 858                   "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
 859                 (file-name (git-file-name name version))))
 860       (version version)
 861       (build-system python-build-system)
 862       (native-inputs
 863        `(("python-nose" ,python-nose)
 864          ("python-pytest" ,python-pytest)))
 865       (propagated-inputs
 866        `(("python-future" ,python-future)
 867          ("python-numpy" ,python-numpy)))
 868       (arguments
 869        `(#:phases (modify-phases %standard-phases
 870                     (replace 'check
 871                       (lambda _
 872                         (invoke "py.test" "-v"))))))
 873       (synopsis "Efficiently computes derivatives of NumPy code")
 874       (description "Autograd can automatically differentiate native Python and
 875 NumPy code.  It can handle a large subset of Python's features, including loops,
 876 ifs, recursion and closures, and it can even take derivatives of derivatives
 877 of derivatives.  It supports reverse-mode differentiation
 878 (a.k.a. backpropagation), which means it can efficiently take gradients of
 879 scalar-valued functions with respect to array-valued arguments, as well as
 880 forward-mode differentiation, and the two can be composed arbitrarily.  The
 881 main intended application of Autograd is gradient-based optimization.")
 882       (license license:expat))))
 883
 884 (define-public python2-autograd
 885   (package-with-python2 python-autograd))
 886
 887 (define-public lightgbm
 888   (package
 889     (name "lightgbm")
 890     (version "2.0.12")
 891     (source (origin
 892               (method url-fetch)
 893               (uri (string-append
 894                     "https://github.com/Microsoft/LightGBM/archive/v"
 895                     version ".tar.gz"))
 896               (sha256
 897                (base32
 898                 "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
 899               (file-name (string-append name "-" version ".tar.gz"))))
 900     (native-inputs
 901      `(("python-pytest" ,python-pytest)
 902        ("python-nose" ,python-nose)))
 903     (inputs
 904      `(("openmpi" ,openmpi)))
 905     (propagated-inputs
 906      `(("python-numpy" ,python-numpy)
 907        ("python-scipy" ,python-scipy)))
 908     (arguments
 909      `(#:configure-flags
 910        '("-DUSE_MPI=ON")
 911        #:phases
 912        (modify-phases %standard-phases
 913          (replace 'check
 914            (lambda* (#:key outputs #:allow-other-keys)
 915              (with-directory-excursion ,(string-append "../LightGBM-" version)
 916                (invoke "pytest" "tests/c_api_test/test_.py")))))))
 917     (build-system cmake-build-system)
 918     (home-page "https://github.com/Microsoft/LightGBM")
 919     (synopsis "Gradient boosting framework based on decision tree algorithms")
 920     (description "LightGBM is a gradient boosting framework that uses tree
 921 based learning algorithms.  It is designed to be distributed and efficient with
 922 the following advantages:
 923
 924 @itemize
 925 @item Faster training speed and higher efficiency
 926 @item Lower memory usage
 927 @item Better accuracy
 928 @item Parallel and GPU learning supported (not enabled in this package)
 929 @item Capable of handling large-scale data
 930 @end itemize\n")
 931     (license license:expat)))
 932
 933 (define-public vowpal-wabbit
 934   ;; Language bindings not included.
 935   (package
 936     (name "vowpal-wabbit")
 937     (version "8.5.0")
 938     (source (origin
 939               (method url-fetch)
 940               (uri (string-append
 941                     "https://github.com/JohnLangford/vowpal_wabbit/archive/"
 942                     version ".tar.gz"))
 943               (sha256
 944                (base32
 945                 "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
 946               (file-name (string-append name "-" version ".tar.gz"))))
 947     (inputs
 948      `(("boost" ,boost)
 949        ("zlib" ,zlib)))
 950     (arguments
 951      `(#:configure-flags
 952        (list (string-append "--with-boost="
 953                             (assoc-ref %build-inputs "boost")))))
 954     (build-system gnu-build-system)
 955     (home-page "https://github.com/JohnLangford/vowpal_wabbit")
 956     (synopsis "Fast machine learning library for online learning")
 957     (description "Vowpal Wabbit is a machine learning system with techniques
 958 such as online, hashing, allreduce, reductions, learning2search, active, and
 959 interactive learning.")
 960     (license license:bsd-3)))
 961
 962 (define-public python2-fastlmm
 963   (package
 964     (name "python2-fastlmm")
 965     (version "0.2.21")
 966     (source
 967      (origin
 968        (method url-fetch)
 969        (uri (pypi-uri "fastlmm" version ".zip"))
 970        (sha256
 971         (base32
 972          "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
 973     (build-system python-build-system)
 974     (arguments
 975      `(#:tests? #f ; some test files are missing
 976        #:python ,python-2)) ; only Python 2.7 is supported
 977     (propagated-inputs
 978      `(("python2-numpy" ,python2-numpy)
 979        ("python2-scipy" ,python2-scipy)
 980        ("python2-matplotlib" ,python2-matplotlib)
 981        ("python2-pandas" ,python2-pandas)
 982        ("python2-scikit-learn" ,python2-scikit-learn)
 983        ("python2-pysnptools" ,python2-pysnptools)))
 984     (native-inputs
 985      `(("unzip" ,unzip)
 986        ("python2-cython" ,python2-cython)
 987        ("python2-mock" ,python2-mock)
 988        ("python2-nose" ,python2-nose)))
 989     (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
 990     (synopsis "Perform genome-wide association studies on large data sets")
 991     (description
 992      "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
 993 Models, is a program for performing both single-SNP and SNP-set genome-wide
 994 association studies (GWAS) on extremely large data sets.")
 995     (license license:asl2.0)))
 996
 997 ;; There have been no proper releases yet.
 998 (define-public kaldi
 999   (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
1000         (revision "1"))
1001     (package
1002       (name "kaldi")
1003       (version (git-version "0" revision commit))
1004       (source (origin
1005                 (method git-fetch)
1006                 (uri (git-reference
1007                       (url "https://github.com/kaldi-asr/kaldi.git")
1008                       (commit commit)))
1009                 (file-name (git-file-name name version))
1010                 (sha256
1011                  (base32
1012                   "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
1013       (build-system gnu-build-system)
1014       (arguments
1015        `(#:test-target "test"
1016          #:phases
1017          (modify-phases %standard-phases
1018            (add-after 'unpack 'chdir
1019              (lambda _ (chdir "src") #t))
1020            (replace 'configure
1021              (lambda* (#:key build system inputs outputs #:allow-other-keys)
1022                (when (not (or (string-prefix? "x86_64" system)
1023                               (string-prefix? "i686" system)))
1024                  (substitute* "makefiles/linux_openblas.mk"
1025                    (("-msse -msse2") "")))
1026                (substitute* "makefiles/default_rules.mk"
1027                  (("/bin/bash") (which "bash")))
1028                (substitute* "Makefile"
1029                  (("ext_depend: check_portaudio")
1030                   "ext_depend:"))
1031                (substitute* '("online/Makefile"
1032                               "onlinebin/Makefile"
1033                               "gst-plugin/Makefile")
1034                  (("../../tools/portaudio/install")
1035                   (assoc-ref inputs "portaudio")))
1036
1037                ;; This `configure' script doesn't support variables passed as
1038                ;; arguments, nor does it support "prefix".
1039                (let ((out (assoc-ref outputs "out"))
1040                      (openblas (assoc-ref inputs "openblas"))
1041                      (openfst (assoc-ref inputs "openfst")))
1042                  (substitute* "configure"
1043                    (("check_for_slow_expf;") "")
1044                    ;; This affects the RPATH and also serves as the installation
1045                    ;; directory.
1046                    (("KALDILIBDIR=`pwd`/lib")
1047                     (string-append "KALDILIBDIR=" out "/lib")))
1048                  (mkdir-p out) ; must exist
1049                  (setenv "CONFIG_SHELL" (which "bash"))
1050                  (setenv "OPENFST_VER" ,(package-version openfst))
1051                  (invoke "./configure"
1052                          "--use-cuda=no"
1053                          "--shared"
1054                          (string-append "--openblas-root=" openblas)
1055                          (string-append "--fst-root=" openfst)))))
1056            (add-after 'build 'build-ext-and-gstreamer-plugin
1057              (lambda _
1058                (invoke "make" "-C" "online" "depend")
1059                (invoke "make" "-C" "online")
1060                (invoke "make" "-C" "onlinebin" "depend")
1061                (invoke "make" "-C" "onlinebin")
1062                (invoke "make" "-C" "gst-plugin" "depend")
1063                (invoke "make" "-C" "gst-plugin")
1064                #t))
1065            ;; TODO: also install the executables.
1066            (replace 'install
1067              (lambda* (#:key outputs #:allow-other-keys)
1068                (let* ((out (assoc-ref outputs "out"))
1069                       (inc (string-append out "/include"))
1070                       (lib (string-append out "/lib")))
1071                  (mkdir-p lib)
1072                  ;; The build phase installed symlinks to the actual
1073                  ;; libraries.  Install the actual targets.
1074                  (for-each (lambda (file)
1075                              (let ((target (readlink file)))
1076                                (delete-file file)
1077                                (install-file target lib)))
1078                            (find-files lib "\\.so"))
1079                  ;; Install headers
1080                  (for-each (lambda (file)
1081                              (let ((target-dir (string-append inc "/" (dirname file))))
1082                                (install-file file target-dir)))
1083                            (find-files "." "\\.h"))
1084                  (install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
1085                                (string-append lib "/gstreamer-1.0"))
1086                  #t))))))
1087       (inputs
1088        `(("alsa-lib" ,alsa-lib)
1089          ("gfortran" ,gfortran "lib")
1090          ("glib" ,glib)
1091          ("gstreamer" ,gstreamer)
1092          ("jack" ,jack-1)
1093          ("openblas" ,openblas)
1094          ("openfst" ,openfst)
1095          ("portaudio" ,portaudio)
1096          ("python" ,python)))
1097       (native-inputs
1098        `(("glib" ,glib "bin")             ; glib-genmarshal
1099          ("grep" ,grep)
1100          ("sed" ,sed)
1101          ("pkg-config" ,pkg-config)
1102          ("which" ,which)))
1103       (home-page "https://kaldi-asr.org/")
1104       (synopsis "Speech recognition toolkit")
1105       (description "Kaldi is an extensible toolkit for speech recognition
1106 written in C++.")
1107       (license license:asl2.0))))
1108
1109 (define-public gst-kaldi-nnet2-online
1110   (let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
1111         (revision "1"))
1112     (package
1113       (name "gst-kaldi-nnet2-online")
1114       (version (git-version "0" revision commit))
1115       (source (origin
1116                 (method git-fetch)
1117                 (uri (git-reference
1118                       (url "https://github.com/alumae/gst-kaldi-nnet2-online.git")
1119                       (commit commit)))
1120                 (file-name (git-file-name name version))
1121                 (sha256
1122                  (base32
1123                   "0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
1124       (build-system gnu-build-system)
1125       (arguments
1126        `(#:tests? #f                    ; there are none
1127          #:make-flags
1128          (list (string-append "SHELL="
1129                               (assoc-ref %build-inputs "bash") "/bin/bash")
1130                (string-append "KALDI_ROOT="
1131                               (assoc-ref %build-inputs "kaldi-src"))
1132                (string-append "KALDILIBDIR="
1133                               (assoc-ref %build-inputs "kaldi") "/lib")
1134                "KALDI_FLAVOR=dynamic")
1135          #:phases
1136          (modify-phases %standard-phases
1137            (add-after 'unpack 'chdir
1138              (lambda _ (chdir "src") #t))
1139            (replace 'configure
1140              (lambda* (#:key inputs #:allow-other-keys)
1141                (let ((glib (assoc-ref inputs "glib")))
1142                  (setenv "CXXFLAGS" "-std=c++11 -fPIC")
1143                  (setenv "CPLUS_INCLUDE_PATH"
1144                          (string-append glib "/include/glib-2.0:"
1145                                         glib "/lib/glib-2.0/include:"
1146                                         (assoc-ref inputs "gstreamer")
1147                                         "/include/gstreamer-1.0:"
1148                                         (getenv "CPLUS_INCLUDE_PATH"))))
1149                (substitute* "Makefile"
1150                  (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
1151                  (("\\$\\(error Cannot find") "#"))))
1152            (add-before 'build 'build-depend
1153              (lambda* (#:key make-flags #:allow-other-keys)
1154                (apply invoke "make" "depend" make-flags)))
1155            (replace 'install
1156              (lambda* (#:key outputs #:allow-other-keys)
1157                (let* ((out (assoc-ref outputs "out"))
1158                       (lib (string-append out "/lib/gstreamer-1.0")))
1159                  (install-file "libgstkaldinnet2onlinedecoder.so" lib)
1160                  #t))))))
1161       (inputs
1162        `(("glib" ,glib)
1163          ("gstreamer" ,gstreamer)
1164          ("jansson" ,jansson)
1165          ("openfst" ,openfst)
1166          ("kaldi" ,kaldi)))
1167       (native-inputs
1168        `(("bash" ,bash)
1169          ("glib:bin" ,glib "bin")       ; glib-genmarshal
1170          ("kaldi-src" ,(package-source kaldi))
1171          ("pkg-config" ,pkg-config)))
1172       (home-page "https://kaldi-asr.org/")
1173       (synopsis "Gstreamer plugin for decoding speech")
1174       (description "This package provides a GStreamer plugin that wraps
1175 Kaldi's @code{SingleUtteranceNnet2Decoder}.  It requires iVector-adapted DNN
1176 acoustic models.  The iVectors are adapted to the current audio stream
1177 automatically.")
1178       (license license:asl2.0))))
1179
1180 (define-public kaldi-gstreamer-server
1181   (let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
1182         (revision "1"))
1183     (package
1184       (name "kaldi-gstreamer-server")
1185       (version (git-version "0" revision commit))
1186       (source (origin
1187                 (method git-fetch)
1188                 (uri (git-reference
1189                       (url "https://github.com/alumae/kaldi-gstreamer-server.git")
1190                       (commit commit)))
1191                 (file-name (git-file-name name version))
1192                 (sha256
1193                  (base32
1194                   "0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
1195       (build-system gnu-build-system)
1196       (arguments
1197        `(#:tests? #f ; there are no tests that can be run automatically
1198          #:modules ((guix build utils)
1199                     (guix build gnu-build-system)
1200                     (srfi srfi-26))
1201          #:phases
1202          (modify-phases %standard-phases
1203            (delete 'configure)
1204            (replace 'build
1205              (lambda* (#:key outputs #:allow-other-keys)
1206                ;; Disable hash randomization to ensure the generated .pycs
1207                ;; are reproducible.
1208                (setenv "PYTHONHASHSEED" "0")
1209                (with-directory-excursion "kaldigstserver"
1210                  (for-each (lambda (file)
1211                              (apply invoke
1212                                     `("python"
1213                                       "-m" "compileall"
1214                                       "-f" ; force rebuild
1215                                       ,file)))
1216                            (find-files "." "\\.py$")))
1217                #t))
1218            (replace 'install
1219              (lambda* (#:key inputs outputs #:allow-other-keys)
1220                (let* ((out (assoc-ref outputs "out"))
1221                       (bin (string-append out "/bin"))
1222                       (share (string-append out "/share/kaldi-gstreamer-server/")))
1223                  ;; Install Python files
1224                  (with-directory-excursion "kaldigstserver"
1225                    (for-each (cut install-file <> share)
1226                              (find-files "." ".*")))
1227
1228                  ;; Install sample configuration files
1229                  (for-each (cut install-file <> share)
1230                            (find-files "." "\\.yaml"))
1231
1232                  ;; Install executables
1233                  (mkdir-p bin)
1234                  (let* ((server (string-append bin "/kaldi-gst-server"))
1235                         (client (string-append bin "/kaldi-gst-client"))
1236                         (worker (string-append bin "/kaldi-gst-worker"))
1237                         (PYTHONPATH (getenv "PYTHONPATH"))
1238                         (GST_PLUGIN_PATH (string-append
1239                                           (assoc-ref inputs "gst-kaldi-nnet2-online")
1240                                           "/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
1241                         (wrap (lambda (wrapper what)
1242                                 (with-output-to-file wrapper
1243                                   (lambda _
1244                                     (format #t
1245                                             "#!~a
1246 export PYTHONPATH=~a
1247 export GST_PLUGIN_PATH=~a
1248 exec ~a ~a/~a \"$@\"~%"
1249                                             (which "bash") PYTHONPATH GST_PLUGIN_PATH
1250                                             (which "python") share what)))
1251                                 (chmod wrapper #o555))))
1252                    (for-each wrap
1253                              (list server client worker)
1254                              (list "master_server.py"
1255                                    "client.py"
1256                                    "worker.py")))
1257                  #t))))))
1258       (inputs
1259        `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
1260          ("python2" ,python-2)
1261          ("python2-futures" ,python2-futures)
1262          ("python2-pygobject" ,python2-pygobject)
1263          ("python2-pyyaml" ,python2-pyyaml)
1264          ("python2-tornado" ,python2-tornado)
1265          ("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
1266       (home-page "https://github.com/alumae/kaldi-gstreamer-server")
1267       (synopsis "Real-time full-duplex speech recognition server")
1268       (description "This is a real-time full-duplex speech recognition server,
1269 based on the Kaldi toolkit and the GStreamer framework and implemented in
1270 Python.")
1271       (license license:bsd-2))))
1272
1273 (define-public grpc
1274   (package
1275     (name "grpc")
1276     (version "1.16.1")
1277     (source (origin
1278               (method git-fetch)
1279               (uri (git-reference
1280                     (url "https://github.com/grpc/grpc.git")
1281                     (commit (string-append "v" version))))
1282               (file-name (git-file-name name version))
1283               (sha256
1284                (base32
1285                 "1jimqz3115f9pli5w6ik9wi7mjc7ix6y7yrq4a1ab9fc3dalj7p2"))))
1286     (build-system cmake-build-system)
1287     (arguments
1288      `(#:tests? #f ; no test target
1289        #:configure-flags
1290        (list "-DgRPC_ZLIB_PROVIDER=package"
1291              "-DgRPC_CARES_PROVIDER=package"
1292              "-DgRPC_SSL_PROVIDER=package"
1293              "-DgRPC_PROTOBUF_PROVIDER=package")))
1294     (inputs
1295      `(("c-ares" ,c-ares)
1296        ("openssl" ,openssl)
1297        ("zlib" ,zlib)))
1298     (native-inputs
1299      `(("protobuf" ,protobuf-next)
1300        ("python" ,python-wrapper)))
1301     (home-page "https://grpc.io")
1302     (synopsis "High performance universal RPC framework")
1303     (description "gRPC is a modern open source high performance @dfn{Remote
1304 Procedure Call} (RPC) framework that can run in any environment.  It can
1305 efficiently connect services in and across data centers with pluggable support
1306 for load balancing, tracing, health checking and authentication.  It is also
1307 applicable in last mile of distributed computing to connect devices, mobile
1308 applications and browsers to backend services.")
1309     (license license:asl2.0)))
1310
1311 ;; Note that Tensorflow includes a "third_party" directory, which seems to not
1312 ;; only contain modified subsets of upstream library source code, but also
1313 ;; adapter headers provided by Google (such as the fft.h header, which is not
1314 ;; part of the upstream project code).  The Tensorflow code includes headers
1315 ;; from the "third_party" directory.  It does not look like we can replace
1316 ;; these headers with unmodified upstream files, so we keep them.
1317 (define-public tensorflow
1318   (package
1319     (name "tensorflow")
1320     (version "1.9.0")
1321     (source
1322      (origin
1323        (method git-fetch)
1324        (uri (git-reference
1325              (url "https://github.com/tensorflow/tensorflow.git")
1326              (commit (string-append "v" version))))
1327        (file-name (string-append "tensorflow-" version "-checkout"))
1328        (sha256
1329         (base32
1330          "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
1331     (build-system cmake-build-system)
1332     (arguments
1333      `(#:tests? #f                      ; no "check" target
1334        #:build-type "Release"
1335        #:configure-flags
1336        (let ((protobuf (assoc-ref %build-inputs "protobuf"))
1337              (protobuf:native (assoc-ref %build-inputs "protobuf:native"))
1338              (jsoncpp (assoc-ref %build-inputs "jsoncpp"))
1339              (snappy (assoc-ref %build-inputs "snappy"))
1340              (sqlite (assoc-ref %build-inputs "sqlite")))
1341          (list
1342           ;; Use protobuf from Guix
1343           (string-append "-Dprotobuf_STATIC_LIBRARIES="
1344                          protobuf "/lib/libprotobuf.so")
1345           (string-append "-DPROTOBUF_PROTOC_EXECUTABLE="
1346                          protobuf:native "/bin/protoc")
1347
1348           ;; Use snappy from Guix
1349           (string-append "-Dsnappy_STATIC_LIBRARIES="
1350                          snappy "/lib/libsnappy.so")
1351           ;; Yes, this is not actually the include directory but a prefix...
1352           (string-append "-Dsnappy_INCLUDE_DIR=" snappy)
1353
1354           ;; Use jsoncpp from Guix
1355           (string-append "-Djsoncpp_STATIC_LIBRARIES="
1356                          jsoncpp "/lib/libjsoncpp.so")
1357           ;; Yes, this is not actually the include directory but a prefix...
1358           (string-append "-Djsoncpp_INCLUDE_DIR=" jsoncpp)
1359
1360           ;; Use sqlite from Guix
1361           (string-append "-Dsqlite_STATIC_LIBRARIES="
1362                          sqlite "/lib/libsqlite.a")
1363
1364           ;; Use system libraries wherever possible.  Currently, this
1365           ;; only affects zlib.
1366           "-Dsystemlib_ALL=ON"
1367           "-Dtensorflow_ENABLE_POSITION_INDEPENDENT_CODE=ON"
1368           "-Dtensorflow_BUILD_SHARED_LIB=ON"
1369           "-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=OFF"
1370           "-Dtensorflow_ENABLE_SSL_SUPPORT=OFF"
1371           "-Dtensorflow_BUILD_CONTRIB_KERNELS=OFF"))
1372        #:make-flags
1373        (list "CC=gcc")
1374        #:modules ((ice-9 ftw)
1375                   (guix build utils)
1376                   (guix build cmake-build-system))
1377        #:phases
1378        (modify-phases %standard-phases
1379          (add-after 'unpack 'set-source-file-times-to-1980
1380            ;; At the end of the tf_python_build_pip_package target, a ZIP
1381            ;; archive should be generated via bdist_wheel, but it fails with
1382            ;; "ZIP does not support timestamps before 1980".  Luckily,
1383            ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
1384            ;; 1980.
1385            (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
1386          ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
1387          (add-after 'unpack 'python3.7-compatibility
1388            (lambda _
1389              (substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
1390                             "tensorflow/python/lib/core/ndarray_tensor.cc"
1391                             "tensorflow/python/lib/core/py_func.cc")
1392                (("PyUnicode_AsUTF8") "(char *)PyUnicode_AsUTF8"))
1393              (substitute* "tensorflow/c/eager/c_api.h"
1394                (("unsigned char async")
1395                 "unsigned char is_async"))
1396
1397              ;; Remove dependency on tensorboard, a complicated but probably
1398              ;; optional package.
1399              (substitute* "tensorflow/tools/pip_package/setup.py"
1400                ((".*'tensorboard >.*") ""))
1401              #t))
1402          (add-after 'python3.7-compatibility 'chdir
1403            (lambda _ (chdir "tensorflow/contrib/cmake") #t))
1404          (add-after 'chdir 'disable-downloads
1405            (lambda* (#:key inputs #:allow-other-keys)
1406              (substitute* (find-files "external" "\\.cmake$")
1407                (("GIT_REPOSITORY.*") "")
1408                (("GIT_TAG.*") "")
1409                (("PREFIX ")
1410                 "DOWNLOAD_COMMAND \"\"\nPREFIX "))
1411
1412              ;; Use packages from Guix
1413              (let ((grpc (assoc-ref inputs "grpc")))
1414                (substitute* "CMakeLists.txt"
1415                  ;; Sqlite
1416                  (("include\\(sqlite\\)") "")
1417                  (("\\$\\{sqlite_STATIC_LIBRARIES\\}")
1418                   (string-append (assoc-ref inputs "sqlite")
1419                                  "/lib/libsqlite3.so"))
1420                  (("sqlite_copy_headers_to_destination") "")
1421
1422                  ;; PNG
1423                  (("include\\(png\\)") "")
1424                  (("\\$\\{png_STATIC_LIBRARIES\\}")
1425                   (string-append (assoc-ref inputs "libpng")
1426                                  "/lib/libpng16.so"))
1427                  (("png_copy_headers_to_destination") "")
1428
1429                  ;; JPEG
1430                  (("include\\(jpeg\\)") "")
1431                  (("\\$\\{jpeg_STATIC_LIBRARIES\\}")
1432                   (string-append (assoc-ref inputs "libjpeg")
1433                                  "/lib/libjpeg.so"))
1434                  (("jpeg_copy_headers_to_destination") "")
1435
1436                  ;; GIF
1437                  (("include\\(gif\\)") "")
1438                  (("\\$\\{gif_STATIC_LIBRARIES\\}")
1439                   (string-append (assoc-ref inputs "giflib")
1440                                  "/lib/libgif.so"))
1441                  (("gif_copy_headers_to_destination") "")
1442
1443                  ;; lmdb
1444                  (("include\\(lmdb\\)") "")
1445                  (("\\$\\{lmdb_STATIC_LIBRARIES\\}")
1446                   (string-append (assoc-ref inputs "lmdb")
1447                                  "/lib/liblmdb.so"))
1448                  (("lmdb_copy_headers_to_destination") "")
1449
1450                  ;; Protobuf
1451                  (("include\\(protobuf\\)") "")
1452                  (("protobuf_copy_headers_to_destination") "")
1453                  (("^ +protobuf") "")
1454
1455                  ;; gRPC
1456                  (("include\\(grpc\\)")
1457                   "find_package(grpc REQUIRED NAMES gRPC)")
1458                  (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES grpc\\)") "")
1459
1460                  ;; Eigen
1461                  (("include\\(eigen\\)")
1462                   (string-append "find_package(eigen REQUIRED NAMES Eigen3)
1463 set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
1464                                  (assoc-ref inputs "eigen") "/include/eigen3)"))
1465                  (("^ +eigen") "")
1466
1467                  ;; snappy
1468                  (("include\\(snappy\\)")
1469                   "add_definitions(-DTF_USE_SNAPPY)")
1470                  (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES snappy\\)") "")
1471
1472                  ;; jsoncpp
1473                  (("include\\(jsoncpp\\)") "")
1474                  (("^ +jsoncpp") ""))
1475
1476                (substitute* "tf_core_framework.cmake"
1477                  ((" grpc") "")
1478                  (("\\$\\{GRPC_BUILD\\}/grpc_cpp_plugin")
1479                   (which "grpc_cpp_plugin"))
1480                  ;; Link with gRPC libraries
1481                  (("add_library\\(tf_protos_cc.*" m)
1482                   (string-append m
1483                                  (format #f "\ntarget_link_libraries(tf_protos_cc PRIVATE \
1484 ~a/lib/libgrpc++_unsecure.a \
1485 ~a/lib/libgrpc_unsecure.a \
1486 ~a/lib/libaddress_sorting.a \
1487 ~a/lib/libgpr.a \
1488 ~a//lib/libcares.so
1489 )\n"
1490                                          grpc grpc grpc grpc
1491                                          (assoc-ref inputs "c-ares"))))))
1492              (substitute* "tf_tools.cmake"
1493                (("add_dependencies\\(\\$\\{proto_text.*") ""))
1494              ;; Remove dependency on bundled grpc
1495              (substitute* "tf_core_distributed_runtime.cmake"
1496                (("tf_core_cpu grpc") "tf_core_cpu"))
1497
1498              ;; This directory is a dependency of many targets.
1499              (mkdir-p "protobuf")
1500              #t))
1501          (add-after 'configure 'unpack-third-party-sources
1502            (lambda* (#:key inputs #:allow-other-keys)
1503              ;; This is needed to configure bundled packages properly.
1504              (setenv "CONFIG_SHELL" (which "bash"))
1505              (for-each
1506               (lambda (name)
1507                 (let* ((what  (assoc-ref inputs (string-append name "-src")))
1508                        (name* (string-map (lambda (c)
1509                                             (if (char=? c #\-)
1510                                                 #\_ c)) name))
1511                        (where (string-append "../build/" name* "/src/" name*)))
1512                   (cond
1513                    ((string-suffix? ".zip" what)
1514                     (mkdir-p where)
1515                     (with-directory-excursion where
1516                       (invoke "unzip" what)))
1517                    ((string-suffix? ".tar.gz" what)
1518                     (mkdir-p where)
1519                     (invoke "tar" "xf" what
1520                             "-C" where "--strip-components=1"))
1521                    (else
1522                     (let ((parent (dirname where)))
1523                       (mkdir-p parent)
1524                       (with-directory-excursion parent
1525                         (when (file-exists? name*)
1526                           (delete-file-recursively name*))
1527                         (copy-recursively what name*)
1528                         (map make-file-writable
1529                              (find-files name* ".*"))))))))
1530               (list "boringssl"
1531                     "cub"
1532                     "double-conversion"
1533                     "farmhash"
1534                     "fft2d"
1535                     "highwayhash"
1536                     "nsync"
1537                     "re2"))
1538
1539              (rename-file "../build/cub/src/cub/cub-1.8.0/"
1540                           "../build/cub/src/cub/cub/")
1541              #t))
1542          (add-after 'unpack 'fix-python-build
1543            (lambda* (#:key inputs outputs #:allow-other-keys)
1544              (mkdir-p "protobuf-src")
1545              (invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
1546                      "-C" "protobuf-src" "--strip-components=1")
1547              (mkdir-p "eigen-src")
1548              (invoke "tar" "xf" (assoc-ref inputs "eigen:src")
1549                      "-C" "eigen-src" "--strip-components=1")
1550
1551              (substitute* "tensorflow/contrib/cmake/tf_python.cmake"
1552                ;; Ensure that all Python dependencies can be found at build time.
1553                (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
1554                 (string-append m ":" (getenv "PYTHONPATH")))
1555                ;; Take protobuf source files from our source package.
1556                (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
1557                 (string-append (getcwd) "/protobuf-src/src/google")))
1558
1559              (substitute* '("tensorflow/contrib/cmake/tf_shared_lib.cmake"
1560                             "tensorflow/contrib/cmake/tf_python.cmake")
1561                ;; Take Eigen source files from our source package.
1562                (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/eigen/src/eigen/")
1563                 (string-append (getcwd) "/eigen-src/"))
1564                ;; Take Eigen headers from our own package.
1565                (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
1566                 (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
1567
1568              ;; Correct the RUNPATH of ops libraries generated for Python.
1569              ;; TODO: this doesn't work :(
1570              ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1571              ;; warning: RUNPATH contains bogus entries: ("/tmp/guix-build-tensorflow-1.9.0.drv-0/source/tensorflow/contrib/build")
1572              ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1573              ;; error: depends on 'libpywrap_tensorflow_internal.so', which
1574              ;; cannot be found in RUNPATH ...
1575              (substitute* "tensorflow/contrib/cmake/tf_cc_ops.cmake"
1576                (("set_target_properties.*")
1577                 (string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
1578 COMPILE_FLAGS ${target_compile_flags} \
1579 INSTALL_RPATH_USE_LINK_PATH TRUE \
1580 INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
1581              #t))
1582          (add-after 'build 'build-pip-package
1583            (lambda* (#:key outputs #:allow-other-keys)
1584              (setenv "LDFLAGS"
1585                      (string-append "-Wl,-rpath="
1586                                     (assoc-ref outputs "out") "/lib"))
1587              (invoke "make" "tf_python_build_pip_package")
1588              #t))
1589          (add-after 'build-pip-package 'install-python
1590            (lambda* (#:key outputs #:allow-other-keys)
1591              (let ((out (assoc-ref outputs "out"))
1592                    (wheel (car (find-files "../build/tf_python/dist/" "\\.whl$"))))
1593                (invoke "python" "-m" "pip" "install" wheel
1594                        (string-append "--prefix=" out))
1595
1596                ;; XXX: broken RUNPATH, see fix-python-build phase.
1597                (delete-file
1598                 (string-append
1599                  out "/lib/python3.7/site-packages/tensorflow/contrib/"
1600                  "seq2seq/python/ops/lib_beam_search_ops.so"))
1601                #t))))))
1602     (native-inputs
1603      `(("pkg-config" ,pkg-config)
1604        ("protobuf:native" ,protobuf-next) ; protoc
1605        ("protobuf:src" ,(package-source protobuf-next))
1606        ("eigen:src" ,(package-source eigen-for-tensorflow))
1607        ;; The commit hashes and URLs for third-party source code are taken
1608        ;; from "tensorflow/workspace.bzl".
1609        ("boringssl-src"
1610         ,(let ((commit "ee7aa02")
1611                (revision "1"))
1612            (origin
1613              (method git-fetch)
1614              (uri (git-reference
1615                    (url "https://boringssl.googlesource.com/boringssl")
1616                    (commit commit)))
1617              (file-name (string-append "boringssl-0-" revision
1618                                        (string-take commit 7)
1619                                        "-checkout"))
1620              (sha256
1621               (base32
1622                "1jf693q0nw0adsic6cgmbdx6g7wr4rj4vxa8j1hpn792fqhd8wgw")))))
1623        ("cub-src"
1624         ,(let ((version "1.8.0"))
1625            (origin
1626              (method url-fetch)
1627              (uri (string-append "https://mirror.bazel.build/github.com/NVlabs/"
1628                                  "cub/archive/" version ".zip"))
1629              (file-name (string-append "cub-" version ".zip"))
1630              (sha256
1631               (base32
1632                "1hsqikqridb90dkxkjr2918dcry6pfh46ccnwrzawl56aamhdykb")))))
1633        ("double-conversion-src"
1634         ,(let ((commit "5664746")
1635                (revision "1"))
1636            (origin
1637              (method git-fetch)
1638              (uri (git-reference
1639                    (url "https://github.com/google/double-conversion.git")
1640                    (commit commit)))
1641              (file-name
1642               (git-file-name "double-conversion"
1643                              (string-append "0-" revision "."
1644                                             (string-take commit 7))))
1645              (sha256
1646               (base32
1647                "1h5lppqqxcvdg5jq42i5msgwx20ryij3apvmndflngrgdpc04gn1")))))
1648        ("farmhash-src"
1649         ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
1650            (origin
1651              (method url-fetch)
1652              (uri (string-append
1653                    "https://mirror.bazel.build/github.com/google/farmhash/archive/"
1654                    commit ".tar.gz"))
1655              (file-name (string-append "farmhash-0-" (string-take commit 7)
1656                                        ".tar.gz"))
1657              (sha256
1658               (base32
1659                "185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
1660        ;; The license notice on the home page at
1661        ;; http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html says:
1662        ;;   Copyright Takuya OOURA, 1996-2001
1663        ;;
1664        ;;   You may use, copy, modify and distribute this code for any purpose
1665        ;;   (include commercial use) and without fee. Please refer to this
1666        ;;   package when you modify this code.
1667        ;;
1668        ;; We take the identical tarball from the Bazel mirror, because the URL
1669        ;; at the home page is not versioned and might change.
1670        ("fft2d-src"
1671         ,(origin
1672            (method url-fetch)
1673            (uri "https://mirror.bazel.build/www.kurims.kyoto-u.ac.jp/~ooura/fft.tgz")
1674            (file-name "fft2d.tar.gz")
1675            (sha256
1676             (base32
1677              "15jjkfvhqvl2c0753d2di8hz0pyzn598g74wqy79awdrf1y67fsj"))))
1678        ("highwayhash-src"
1679         ,(let ((commit "be5edafc2e1a455768e260ccd68ae7317b6690ee")
1680                (revision "1"))
1681            (origin
1682              (method git-fetch)
1683              (uri (git-reference
1684                    (url "https://github.com/google/highwayhash.git")
1685                    (commit commit)))
1686              (file-name (string-append "highwayhash-0-" revision
1687                                        (string-take commit 7)
1688                                        "-checkout"))
1689              (sha256
1690               (base32
1691                "154jwf98cyy54hldr94pgjn85zynly3abpnc1avmb8a18lzwjyb6")))))
1692        ("nsync-src"
1693         ,(let ((version "0559ce013feac8db639ee1bf776aca0325d28777")
1694                (revision "1"))
1695            (origin
1696              (method url-fetch)
1697              (uri (string-append "https://mirror.bazel.build/"
1698                                  "github.com/google/nsync/archive/"
1699                                  version ".tar.gz"))
1700              (file-name (string-append "nsync-0." revision
1701                                        "-" (string-take version 7)
1702                                        ".tar.gz"))
1703              (sha256
1704               (base32
1705                "0qdkyqym34x739mmzv97ah5r7ph462v5xkxqxvidmcfqbi64b132")))))
1706        ("re2-src"
1707         ,(let ((commit "e7efc48")
1708                (revision "1"))
1709            (origin
1710              (method git-fetch)
1711              (uri (git-reference
1712                    (url "https://github.com/google/re2")
1713                    (commit commit)))
1714              (file-name (string-append "re2-0-" revision
1715                                        (string-take commit 7)
1716                                        "-checkout"))
1717              (sha256
1718               (base32
1719                "161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign")))))
1720        ("googletest" ,googletest)
1721        ("swig" ,swig)
1722        ("unzip" ,unzip)))
1723     (propagated-inputs
1724      `(("python-absl-py" ,python-absl-py)
1725        ("python-astor" ,python-astor)
1726        ("python-gast" ,python-gast)
1727        ("python-grpcio" ,python-grpcio)
1728        ("python-numpy" ,python-numpy)
1729        ("python-protobuf" ,python-protobuf-next)
1730        ("python-six" ,python-six)
1731        ("python-termcolo" ,python-termcolor)
1732        ("python-wheel" ,python-wheel)))
1733     (inputs
1734      `(("c-ares" ,c-ares)
1735        ("eigen" ,eigen-for-tensorflow)
1736        ("gemmlowp" ,gemmlowp-for-tensorflow)
1737        ("lmdb" ,lmdb)
1738        ("libjpeg" ,libjpeg)
1739        ("libpng" ,libpng)
1740        ("giflib" ,giflib)
1741        ("grpc" ,grpc)
1742        ("jsoncpp" ,jsoncpp-for-tensorflow)
1743        ("snappy" ,snappy)
1744        ("sqlite" ,sqlite)
1745        ("protobuf" ,protobuf-next)
1746        ("python" ,python-wrapper)
1747        ("zlib" ,zlib)))
1748     (home-page "https://tensorflow.org")
1749     (synopsis "Machine learning framework")
1750     (description
1751      "TensorFlow is a flexible platform for building and training machine
1752 learning models.  It provides a library for high performance numerical
1753 computation and includes high level Python APIs, including both a sequential
1754 API for beginners that allows users to build models quickly by plugging
1755 together building blocks and a subclassing API with an imperative style for
1756 advanced research.")
1757     (license license:asl2.0)))
1758
1759 (define-public python-iml
1760   (package
1761     (name "python-iml")
1762     (version "0.6.2")
1763     (source
1764      (origin
1765        (method url-fetch)
1766        (uri (pypi-uri "iml" version))
1767        (sha256
1768         (base32
1769          "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
1770     (build-system python-build-system)
1771     (propagated-inputs
1772      `(("ipython" ,python-ipython)
1773        ("nose" ,python-nose)
1774        ("numpy" ,python-numpy)
1775        ("pandas" ,python-pandas)
1776        ("scipy" ,python-scipy)))
1777     (home-page "http://github.com/interpretable-ml/iml")
1778     (synopsis "Interpretable Machine Learning (iML) package")
1779     (description "Interpretable ML (iML) is a set of data type objects,
1780 visualizations, and interfaces that can be used by any method designed to
1781 explain the predictions of machine learning models (or really the output of
1782 any function).  It currently contains the interface and IO code from the Shap
1783 project, and it will potentially also do the same for the Lime project.")
1784     (license license:expat)))
1785
1786 (define-public python-keras-applications
1787   (package
1788     (name "python-keras-applications")
1789     (version "1.0.8")
1790     (source
1791      (origin
1792        (method url-fetch)
1793        (uri (pypi-uri "Keras_Applications" version))
1794        (sha256
1795         (base32
1796          "1rcz31ca4axa6kzhjx4lwqxbg4wvlljkj8qj9a7p9sfd5fhzjyam"))))
1797     (build-system python-build-system)
1798     ;; The tests require Keras, but this package is needed to build Keras.
1799     (arguments '(#:tests? #f))
1800     (propagated-inputs
1801      `(("python-h5py" ,python-h5py)
1802        ("python-numpy" ,python-numpy)))
1803     (native-inputs
1804      `(("python-pytest" ,python-pytest)
1805        ("python-pytest-cov" ,python-pytest-cov)
1806        ("python-pytest-pep8" ,python-pytest-pep8)
1807        ("python-pytest-xdist" ,python-pytest-xdist)))
1808     (home-page "https://github.com/keras-team/keras-applications")
1809     (synopsis "Reference implementations of popular deep learning models")
1810     (description
1811      "This package provides reference implementations of popular deep learning
1812 models for use with the Keras deep learning framework.")
1813     (license license:expat)))
1814
1815 (define-public python-keras-preprocessing
1816   (package
1817     (name "python-keras-preprocessing")
1818     (version "1.1.0")
1819     (source
1820      (origin
1821        (method url-fetch)
1822        (uri (pypi-uri "Keras_Preprocessing" version))
1823        (sha256
1824         (base32
1825          "1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as"))))
1826     (build-system python-build-system)
1827     (propagated-inputs
1828      `(("python-numpy" ,python-numpy)
1829        ("python-six" ,python-six)))
1830     (native-inputs
1831      `(("python-pandas" ,python-pandas)
1832        ("python-pillow" ,python-pillow)
1833        ("python-pytest" ,python-pytest)
1834        ("python-pytest-cov" ,python-pytest-cov)
1835        ("python-pytest-xdist" ,python-pytest-xdist)
1836        ("tensorflow" ,tensorflow)))
1837     (home-page "https://github.com/keras-team/keras-preprocessing/")
1838     (synopsis "Data preprocessing and augmentation for deep learning models")
1839     (description
1840      "Keras Preprocessing is the data preprocessing and data augmentation
1841 module of the Keras deep learning library.  It provides utilities for working
1842 with image data, text data, and sequence data.")
1843     (license license:expat)))
1844
1845 (define-public python-keras
1846   (package
1847     (name "python-keras")
1848     (version "2.2.4")
1849     (source
1850      (origin
1851        (method url-fetch)
1852        (uri (pypi-uri "Keras" version))
1853        (sha256
1854         (base32
1855          "1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh"))))
1856     (build-system python-build-system)
1857     (arguments
1858      `(#:phases
1859        (modify-phases %standard-phases
1860          (add-after 'unpack 'remove-tests-for-unavailable-features
1861            (lambda _
1862              (delete-file "keras/backend/theano_backend.py")
1863              (delete-file "keras/backend/cntk_backend.py")
1864              (delete-file "tests/keras/backend/backend_test.py")
1865
1866              ;; FIXME: This doesn't work because Tensorflow is missing the
1867              ;; coder ops library.
1868              (delete-file "tests/keras/test_callbacks.py")
1869              #t))
1870          (replace 'check
1871            (lambda _
1872              ;; These tests attempt to download data files from the internet.
1873              (delete-file "tests/integration_tests/test_datasets.py")
1874              (delete-file "tests/integration_tests/imagenet_utils_test.py")
1875
1876              (setenv "PYTHONPATH"
1877                      (string-append (getcwd) "/build/lib:"
1878                                     (getenv "PYTHONPATH")))
1879              (invoke "py.test" "-v"
1880                      "-p" "no:cacheprovider"
1881                      "--ignore" "keras/utils"))))))
1882     (propagated-inputs
1883      `(("python-h5py" ,python-h5py)
1884        ("python-keras-applications" ,python-keras-applications)
1885        ("python-keras-preprocessing" ,python-keras-preprocessing)
1886        ("python-numpy" ,python-numpy)
1887        ("python-pydot" ,python-pydot)
1888        ("python-pyyaml" ,python-pyyaml)
1889        ("python-scipy" ,python-scipy)
1890        ("python-six" ,python-six)
1891        ("tensorflow" ,tensorflow)
1892        ("graphviz" ,graphviz)))
1893     (native-inputs
1894      `(("python-pandas" ,python-pandas)
1895        ("python-pytest" ,python-pytest)
1896        ("python-pytest-cov" ,python-pytest-cov)
1897        ("python-pytest-pep8" ,python-pytest-pep8)
1898        ("python-pytest-timeout" ,python-pytest-timeout)
1899        ("python-pytest-xdist" ,python-pytest-xdist)
1900        ("python-sphinx" ,python-sphinx)
1901        ("python-requests" ,python-requests)))
1902     (home-page "https://github.com/keras-team/keras")
1903     (synopsis "High-level deep learning framework")
1904     (description "Keras is a high-level neural networks API, written in Python
1905 and capable of running on top of TensorFlow.  It was developed with a focus on
1906 enabling fast experimentation.  Use Keras if you need a deep learning library
1907 that:
1908
1909 @itemize
1910 @item Allows for easy and fast prototyping (through user friendliness,
1911   modularity, and extensibility).
1912 @item Supports both convolutional networks and recurrent networks, as well as
1913   combinations of the two.
1914 @item Runs seamlessly on CPU and GPU.
1915 @end itemize\n")
1916     (license license:expat)))