gnu/packages/machine-learning.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017, 2018 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 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 ;;;
  12 ;;; This file is part of GNU Guix.
  13 ;;;
  14 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  15 ;;; under the terms of the GNU General Public License as published by
  16 ;;; the Free Software Foundation; either version 3 of the License, or (at
  17 ;;; your option) any later version.
  18 ;;;
  19 ;;; GNU Guix is distributed in the hope that it will be useful, but
  20 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  21 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  22 ;;; GNU General Public License for more details.
  23 ;;;
  24 ;;; You should have received a copy of the GNU General Public License
  25 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  26
  27 (define-module (gnu packages machine-learning)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (guix packages)
  30   #:use-module (guix utils)
  31   #:use-module (guix download)
  32   #:use-module (guix svn-download)
  33   #:use-module (guix build-system cmake)
  34   #:use-module (guix build-system gnu)
  35   #:use-module (guix build-system ocaml)
  36   #:use-module (guix build-system python)
  37   #:use-module (guix build-system r)
  38   #:use-module (guix git-download)
  39   #:use-module (gnu packages)
  40   #:use-module (gnu packages algebra)
  41   #:use-module (gnu packages autotools)
  42   #:use-module (gnu packages boost)
  43   #:use-module (gnu packages check)
  44   #:use-module (gnu packages compression)
  45   #:use-module (gnu packages cran)
  46   #:use-module (gnu packages dejagnu)
  47   #:use-module (gnu packages gcc)
  48   #:use-module (gnu packages image)
  49   #:use-module (gnu packages maths)
  50   #:use-module (gnu packages ocaml)
  51   #:use-module (gnu packages perl)
  52   #:use-module (gnu packages pkg-config)
  53   #:use-module (gnu packages python)
  54   #:use-module (gnu packages statistics)
  55   #:use-module (gnu packages swig)
  56   #:use-module (gnu packages xml)
  57   #:use-module (gnu packages xorg))
  58
  59 (define-public fann
  60   ;; The last release is >100 commits behind, so we package from git.
  61   (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
  62     (package
  63       (name "fann")
  64       (version (string-append "2.2.0-1." (string-take commit 8)))
  65       (source (origin
  66                 (method git-fetch)
  67                 (uri (git-reference
  68                       (url "https://github.com/libfann/fann.git")
  69                       (commit commit)))
  70                 (file-name (string-append name "-" version "-checkout"))
  71                 (sha256
  72                  (base32
  73                   "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
  74       (build-system cmake-build-system)
  75       (arguments
  76        `(#:phases
  77          (modify-phases %standard-phases
  78            (replace 'check
  79              (lambda* (#:key outputs #:allow-other-keys)
  80                (let* ((out (assoc-ref outputs "out")))
  81                  (with-directory-excursion (string-append (getcwd) "/tests")
  82                    (invoke "./fann_tests"))))))))
  83       (home-page "http://leenissen.dk/fann/wp/")
  84       (synopsis "Fast Artificial Neural Network")
  85       (description
  86        "FANN is a free open source neural network library, which implements
  87 multilayer artificial neural networks in C with support for both fully
  88 connected and sparsely connected networks.")
  89       (license license:lgpl2.1))))
  90
  91 (define-public libsvm
  92   (package
  93     (name "libsvm")
  94     (version "3.22")
  95     (source
  96      (origin
  97        (method url-fetch)
  98        (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
  99                            name "-" version ".tar.gz"))
 100        (sha256
 101         (base32
 102          "0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
 103     (build-system gnu-build-system)
 104     (arguments
 105      `(#:tests? #f ;no "check" target
 106        #:phases (modify-phases %standard-phases
 107                   (delete 'configure)
 108                   (replace
 109                    'install             ; no ‘install’ target
 110                    (lambda* (#:key outputs #:allow-other-keys)
 111                      (let* ((out (assoc-ref outputs "out"))
 112                             (bin (string-append out "/bin/")))
 113                        (mkdir-p bin)
 114                        (for-each (lambda (file)
 115                                    (copy-file file (string-append bin file)))
 116                                  '("svm-train"
 117                                    "svm-predict"
 118                                    "svm-scale")))
 119                      #t)))))
 120     (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
 121     (synopsis "Library for Support Vector Machines")
 122     (description
 123      "LIBSVM is a machine learning library for support vector
 124 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
 125 distribution estimation (one-class SVM).  It supports multi-class
 126 classification.")
 127     (license license:bsd-3)))
 128
 129 (define-public python-libsvm
 130   (package (inherit libsvm)
 131     (name "python-libsvm")
 132     (build-system gnu-build-system)
 133     (arguments
 134      `(#:tests? #f ;no "check" target
 135        #:make-flags '("-C" "python")
 136        #:phases
 137        (modify-phases %standard-phases
 138          (delete 'configure)
 139          (replace
 140           'install                      ; no ‘install’ target
 141           (lambda* (#:key inputs outputs #:allow-other-keys)
 142             (let ((site (string-append (assoc-ref outputs "out")
 143                                        "/lib/python"
 144                                        (string-take
 145                                         (string-take-right
 146                                          (assoc-ref inputs "python") 5) 3)
 147                                        "/site-packages/")))
 148               (substitute* "python/svm.py"
 149                 (("../libsvm.so.2") "libsvm.so.2"))
 150               (mkdir-p site)
 151               (for-each (lambda (file)
 152                           (copy-file file (string-append site (basename file))))
 153                         (find-files "python" "\\.py"))
 154               (copy-file "libsvm.so.2"
 155                          (string-append site "libsvm.so.2")))
 156             #t)))))
 157     (inputs
 158      `(("python" ,python)))
 159     (synopsis "Python bindings of libSVM")))
 160
 161 (define-public ghmm
 162   ;; The latest release candidate is several years and a couple of fixes have
 163   ;; been published since.  This is why we download the sources from the SVN
 164   ;; repository.
 165   (let ((svn-revision 2341))
 166     (package
 167       (name "ghmm")
 168       (version (string-append "0.9-rc3-0." (number->string svn-revision)))
 169       (source (origin
 170                 (method svn-fetch)
 171                 (uri (svn-reference
 172                       (url "http://svn.code.sf.net/p/ghmm/code/trunk")
 173                       (revision svn-revision)))
 174                 (file-name (string-append name "-" version))
 175                 (sha256
 176                  (base32
 177                   "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
 178       (build-system gnu-build-system)
 179       (arguments
 180        `(#:imported-modules (,@%gnu-build-system-modules
 181                              (guix build python-build-system))
 182          #:phases
 183          (modify-phases %standard-phases
 184            (add-after 'unpack 'enter-dir
 185              (lambda _ (chdir "ghmm") #t))
 186            (delete 'check)
 187            (add-after 'install 'check
 188              (assoc-ref %standard-phases 'check))
 189            (add-before 'check 'fix-PYTHONPATH
 190              (lambda* (#:key inputs outputs #:allow-other-keys)
 191                (let ((python-version ((@@ (guix build python-build-system)
 192                                            get-python-version)
 193                                       (assoc-ref inputs "python"))))
 194                  (setenv "PYTHONPATH"
 195                          (string-append (getenv "PYTHONPATH")
 196                                         ":" (assoc-ref outputs "out")
 197                                         "/lib/python" python-version
 198                                         "/site-packages")))
 199                #t))
 200            (add-after 'enter-dir 'fix-runpath
 201              (lambda* (#:key outputs #:allow-other-keys)
 202                (substitute* "ghmmwrapper/setup.py"
 203                  (("^(.*)extra_compile_args = \\[" line indent)
 204                   (string-append indent
 205                                  "extra_link_args = [\"-Wl,-rpath="
 206                                  (assoc-ref outputs "out") "/lib\"],\n"
 207                                  line
 208                                  "\"-Wl,-rpath="
 209                                  (assoc-ref outputs "out")
 210                                  "/lib\", ")))
 211                #t))
 212            (add-after 'enter-dir 'disable-broken-tests
 213              (lambda _
 214                (substitute* "tests/Makefile.am"
 215                  ;; GHMM_SILENT_TESTS is assumed to be a command.
 216                  (("TESTS_ENVIRONMENT.*") "")
 217                  ;; Do not build broken tests.
 218                  (("chmm .*") "")
 219                  (("read_fa .*") "")
 220                  (("mcmc .*") "")
 221                  (("label_higher_order_test.*$")
 222                   "label_higher_order_test\n"))
 223
 224                ;; These Python unittests are broken as there is no gato.
 225                ;; See https://sourceforge.net/p/ghmm/support-requests/3/
 226                (substitute* "ghmmwrapper/ghmmunittests.py"
 227                  (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
 228                    line indent)
 229                   (string-append indent
 230                                  "@unittest.skip(\"Disabled by Guix\")\n"
 231                                  line)))
 232                #t))
 233            (add-after 'disable-broken-tests 'autogen
 234              (lambda _
 235                (zero? (system* "bash" "autogen.sh")))))))
 236       (inputs
 237        `(("python" ,python-2) ; only Python 2 is supported
 238          ("libxml2" ,libxml2)))
 239       (native-inputs
 240        `(("pkg-config" ,pkg-config)
 241          ("dejagnu" ,dejagnu)
 242          ("swig" ,swig)
 243          ("autoconf" ,autoconf)
 244          ("automake" ,automake)
 245          ("libtool" ,libtool)))
 246       (home-page "http://ghmm.org")
 247       (synopsis "Hidden Markov Model library")
 248       (description
 249        "The General Hidden Markov Model library (GHMM) is a C library with
 250 additional Python bindings implementing a wide range of types of @dfn{Hidden
 251 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
 252 training, HMM clustering, HMM mixtures.")
 253       (license license:lgpl2.0+))))
 254
 255 (define-public mcl
 256   (package
 257     (name "mcl")
 258     (version "14.137")
 259     (source (origin
 260               (method url-fetch)
 261               (uri (string-append
 262                     "http://micans.org/mcl/src/mcl-"
 263                     (string-replace-substring version "." "-")
 264                     ".tar.gz"))
 265               (sha256
 266                (base32
 267                 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
 268     (build-system gnu-build-system)
 269     (arguments
 270      `(#:configure-flags (list "--enable-blast")))
 271     (inputs
 272      `(("perl" ,perl)))
 273     (home-page "http://micans.org/mcl/")
 274     (synopsis "Clustering algorithm for graphs")
 275     (description
 276      "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
 277 fast and scalable unsupervised cluster algorithm for graphs (also known as
 278 networks) based on simulation of (stochastic) flow in graphs.")
 279     ;; In the LICENCE file and web page it says "The software is licensed
 280     ;; under the GNU General Public License, version 3.", but in several of
 281     ;; the source code files it suggests GPL3 or later.
 282     ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
 283     (license license:gpl3)))
 284
 285 (define-public ocaml-mcl
 286   (package
 287     (name "ocaml-mcl")
 288     (version "12-068oasis4")
 289     (source
 290      (origin
 291        (method url-fetch)
 292        (uri (string-append
 293              "https://github.com/fhcrc/mcl/archive/"
 294              version ".tar.gz"))
 295        (file-name (string-append name "-" version ".tar.gz"))
 296        (sha256
 297         (base32
 298          "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
 299     (build-system ocaml-build-system)
 300     (arguments
 301      `(#:phases
 302        (modify-phases %standard-phases
 303          (add-before 'configure 'patch-paths
 304            (lambda _
 305              (substitute* "configure"
 306                (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
 307              (substitute* "setup.ml"
 308                (("LDFLAGS=-fPIC")
 309                 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
 310              #t)))))
 311     (home-page "https://github.com/fhcrc/mcl")
 312     (synopsis "OCaml wrappers around MCL")
 313     (description
 314      "This package provides OCaml bindings for the MCL graph clustering
 315 algorithm.")
 316     (license license:gpl3)))
 317
 318 (define-public ocaml4.01-mcl
 319   (package-with-ocaml4.01 ocaml-mcl))
 320
 321 (define-public randomjungle
 322   (package
 323     (name "randomjungle")
 324     (version "2.1.0")
 325     (source
 326      (origin
 327        (method url-fetch)
 328        (uri (string-append
 329              "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
 330              "randomjungle-" version ".tar_.gz"))
 331        (sha256
 332         (base32
 333          "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
 334     (build-system gnu-build-system)
 335     (arguments
 336      `(#:configure-flags
 337        (list (string-append "--with-boost="
 338                             (assoc-ref %build-inputs "boost")))
 339        #:phases
 340        (modify-phases %standard-phases
 341          (add-before
 342           'configure 'set-CXXFLAGS
 343           (lambda _
 344             (setenv "CXXFLAGS" "-fpermissive ")
 345             #t)))))
 346     (inputs
 347      `(("boost" ,boost)
 348        ("gsl" ,gsl)
 349        ("libxml2" ,libxml2)
 350        ("zlib" ,zlib)))
 351     (native-inputs
 352      `(("gfortran" ,gfortran)
 353        ("gfortran:lib" ,gfortran "lib")))
 354     ;; Non-portable assembly instructions are used so building fails on
 355     ;; platforms other than x86_64 or i686.
 356     (supported-systems '("x86_64-linux" "i686-linux"))
 357     (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
 358     (synopsis "Implementation of the Random Forests machine learning method")
 359     (description
 360      "Random Jungle is an implementation of Random Forests.  It is supposed to
 361 analyse high dimensional data.  In genetics, it can be used for analysing big
 362 Genome Wide Association (GWA) data.  Random Forests is a powerful machine
 363 learning method.  Most interesting features are variable selection, missing
 364 value imputation, classifier creation, generalization error estimation and
 365 sample proximities between pairs of cases.")
 366     (license license:gpl3+)))
 367
 368 (define-public shogun
 369   (package
 370     (name "shogun")
 371     (version "6.1.3")
 372     (source
 373      (origin
 374        (method url-fetch)
 375        (uri (string-append
 376              "ftp://shogun-toolbox.org/shogun/releases/"
 377              (version-major+minor version)
 378              "/sources/shogun-" version ".tar.bz2"))
 379        (sha256
 380         (base32
 381          "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
 382        (modules '((guix build utils)
 383                   (ice-9 rdelim)))
 384        (snippet
 385         '(begin
 386            ;; Remove non-free sources and files referencing them
 387            (for-each delete-file
 388                      (find-files "src/shogun/classifier/svm/"
 389                                  "SVMLight\\.(cpp|h)"))
 390            (for-each delete-file
 391                      (find-files "examples/undocumented/libshogun/"
 392                                  (string-append
 393                                   "(classifier_.*svmlight.*|"
 394                                   "evaluation_cross_validation_locked_comparison).cpp")))
 395            ;; Remove non-free functions.
 396            (define (delete-ifdefs file)
 397              (with-atomic-file-replacement file
 398                (lambda (in out)
 399                  (let loop ((line (read-line in 'concat))
 400                             (skipping? #f))
 401                    (if (eof-object? line)
 402                        #t
 403                        (let ((skip-next?
 404                               (or (and skipping?
 405                                        (not (string-prefix?
 406                                              "#endif //USE_SVMLIGHT" line)))
 407                                   (string-prefix?
 408                                    "#ifdef USE_SVMLIGHT" line))))
 409                          (when (or (not skipping?)
 410                                    (and skipping? (not skip-next?)))
 411                            (display line out))
 412                          (loop (read-line in 'concat) skip-next?)))))))
 413            (for-each delete-ifdefs
 414                      (append
 415                       (find-files "src/shogun/classifier/mkl"
 416                                   "^MKLClassification\\.cpp")
 417                       (find-files "src/shogun/classifier/svm"
 418                                   "^SVMLightOneClass\\.(cpp|h)")
 419                       (find-files "src/shogun/multiclass"
 420                                   "^ScatterSVM\\.(cpp|h)")
 421                       (find-files "src/shogun/kernel/"
 422                                   "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
 423                       (find-files "src/shogun/regression/svr"
 424                                   "^(MKLRegression|SVRLight)\\.(cpp|h)")
 425                       (find-files "src/shogun/transfer/domain_adaptation"
 426                                   "^DomainAdaptationSVM\\.(cpp|h)")))
 427            #t))))
 428     (build-system cmake-build-system)
 429     (arguments
 430      '(#:tests? #f ;no check target
 431        #:phases
 432        (modify-phases %standard-phases
 433          (add-after 'unpack 'delete-broken-symlinks
 434            (lambda _
 435              (for-each delete-file '("applications/arts/data"
 436                                      "applications/asp/data"
 437                                      "applications/easysvm/data"
 438                                      "applications/msplicer/data"
 439                                      "applications/ocr/data"
 440                                      "examples/meta/data"
 441                                      "examples/undocumented/data"))
 442              #t))
 443          (add-after 'unpack 'change-R-target-path
 444            (lambda* (#:key outputs #:allow-other-keys)
 445              (substitute* '("src/interfaces/r/CMakeLists.txt"
 446                             "examples/meta/r/CMakeLists.txt")
 447                (("\\$\\{R_COMPONENT_LIB_PATH\\}")
 448                 (string-append (assoc-ref outputs "out")
 449                                "/lib/R/library/")))
 450              #t))
 451          (add-after 'unpack 'fix-octave-modules
 452            (lambda* (#:key outputs #:allow-other-keys)
 453              (substitute* "src/interfaces/octave/CMakeLists.txt"
 454                (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
 455                 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
 456                ;; change target directory
 457                (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
 458                 (string-append (assoc-ref outputs "out")
 459                                "/share/octave/packages")))
 460              (substitute* '("src/interfaces/octave/swig_typemaps.i"
 461                             "src/interfaces/octave/sg_print_functions.cpp")
 462                ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
 463                (("octave/config\\.h") "octave/octave-config.h")
 464                (("octave/oct-obj.h") "octave/ovl.h"))
 465              #t))
 466          (add-after 'unpack 'move-rxcpp
 467            (lambda* (#:key inputs #:allow-other-keys)
 468              (let ((rxcpp-dir "shogun/third-party/rxcpp"))
 469                (mkdir-p rxcpp-dir)
 470                (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
 471                #t)))
 472          (add-before 'build 'set-HOME
 473            ;; $HOME needs to be set at some point during the build phase
 474            (lambda _ (setenv "HOME" "/tmp") #t)))
 475        #:configure-flags
 476        (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
 477              "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
 478              "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
 479              ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
 480              ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
 481              ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
 482              ;;"-DINTERFACE_LUA=ON"  ;fails because lua doesn't build pkgconfig file
 483              "-DINTERFACE_OCTAVE=ON"
 484              "-DINTERFACE_PYTHON=ON"
 485              "-DINTERFACE_R=ON")))
 486     (inputs
 487      `(("python" ,python)
 488        ("numpy" ,python-numpy)
 489        ("r-minimal" ,r-minimal)
 490        ("octave" ,octave)
 491        ("swig" ,swig)
 492        ("eigen" ,eigen)
 493        ("hdf5" ,hdf5)
 494        ("atlas" ,atlas)
 495        ("arpack" ,arpack-ng)
 496        ("lapack" ,lapack)
 497        ("glpk" ,glpk)
 498        ("libxml2" ,libxml2)
 499        ("lzo" ,lzo)
 500        ("zlib" ,zlib)))
 501     (native-inputs
 502      `(("pkg-config" ,pkg-config)
 503        ("rxcpp" ,rxcpp)))
 504     ;; Non-portable SSE instructions are used so building fails on platforms
 505     ;; other than x86_64.
 506     (supported-systems '("x86_64-linux"))
 507     (home-page "http://shogun-toolbox.org/")
 508     (synopsis "Machine learning toolbox")
 509     (description
 510      "The Shogun Machine learning toolbox provides a wide range of unified and
 511 efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
 512 combine multiple data representations, algorithm classes, and general purpose
 513 tools.  This enables both rapid prototyping of data pipelines and extensibility
 514 in terms of new algorithms.")
 515     (license license:gpl3+)))
 516
 517 (define-public rxcpp
 518   (package
 519     (name "rxcpp")
 520     (version "4.0.0")
 521     (source
 522      (origin
 523        (method url-fetch)
 524        (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
 525                            version ".tar.gz"))
 526        (sha256
 527         (base32
 528          "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
 529        (file-name (string-append name "-" version ".tar.gz"))))
 530     (build-system cmake-build-system)
 531     (arguments
 532      `(#:phases
 533        (modify-phases %standard-phases
 534          (add-after 'unpack 'remove-werror
 535            (lambda _
 536              (substitute* (find-files ".")
 537                (("-Werror") ""))
 538              #t))
 539          (replace 'check
 540            (lambda _
 541              (invoke "ctest"))))))
 542     (native-inputs
 543      `(("catch" ,catch-framework)))
 544     (home-page "http://reactivex.io/")
 545     (synopsis "Reactive Extensions for C++")
 546     (description
 547      "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
 548 values-distributed-in-time.  ReactiveX is a library for composing asynchronous
 549 and event-based programs by using observable sequences.
 550
 551 It extends the observer pattern to support sequences of data and/or events and
 552 adds operators that allow you to compose sequences together declaratively while
 553 abstracting away concerns about things like low-level threading,
 554 synchronization, thread-safety, concurrent data structures, and non-blocking
 555 I/O.")
 556     (license license:asl2.0)))
 557
 558 (define-public r-adaptivesparsity
 559   (package
 560     (name "r-adaptivesparsity")
 561     (version "1.4")
 562     (source (origin
 563               (method url-fetch)
 564               (uri (cran-uri "AdaptiveSparsity" version))
 565               (sha256
 566                (base32
 567                 "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z"))))
 568     (properties
 569      `((upstream-name . "AdaptiveSparsity")))
 570     (build-system r-build-system)
 571     (arguments
 572      `(#:phases
 573        (modify-phases %standard-phases
 574          (add-after 'unpack 'link-against-armadillo
 575            (lambda _
 576              (substitute* "src/Makevars"
 577                (("PKG_LIBS=" prefix)
 578                 (string-append prefix "-larmadillo"))))))))
 579     (propagated-inputs
 580      `(("r-rcpp" ,r-rcpp)
 581        ("r-rcpparmadillo" ,r-rcpparmadillo)))
 582     (inputs
 583      `(("armadillo" ,armadillo)))
 584     (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
 585     (synopsis "Adaptive sparsity models")
 586     (description
 587      "This package implements the Figueiredo machine learning algorithm for
 588 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
 589 geometric models.")
 590     (license license:lgpl3+)))
 591
 592 (define-public r-kernlab
 593   (package
 594     (name "r-kernlab")
 595     (version "0.9-26")
 596     (source
 597      (origin
 598        (method url-fetch)
 599        (uri (cran-uri "kernlab" version))
 600        (sha256
 601         (base32
 602          "0xv0slf3ggw3sswsi34416lb1g3h1pqkrr2h7r1n1kvgii3l0jcm"))))
 603     (build-system r-build-system)
 604     (home-page "https://cran.r-project.org/web/packages/kernlab")
 605     (synopsis "Kernel-based machine learning tools")
 606     (description
 607      "This package provides kernel-based machine learning methods for
 608 classification, regression, clustering, novelty detection, quantile regression
 609 and dimensionality reduction.  Among other methods @code{kernlab} includes
 610 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
 611 and a QP solver.")
 612     (license license:gpl2)))
 613
 614 (define-public dlib
 615   (package
 616     (name "dlib")
 617     (version "19.7")
 618     (source (origin
 619               (method url-fetch)
 620               (uri (string-append
 621                     "http://dlib.net/files/dlib-" version ".tar.bz2"))
 622               (sha256
 623                (base32
 624                 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
 625               (modules '((guix build utils)))
 626               (snippet
 627                '(begin
 628                   ;; Delete ~13MB of bundled dependencies.
 629                   (delete-file-recursively "dlib/external")
 630                   (delete-file-recursively "docs/dlib/external")
 631                   #t))))
 632     (build-system cmake-build-system)
 633     (arguments
 634      `(#:phases
 635        (modify-phases %standard-phases
 636          (add-after 'unpack 'disable-asserts
 637            (lambda _
 638              ;; config.h recommends explicitly enabling or disabling asserts
 639              ;; when building as a shared library. By default neither is set.
 640              (substitute* "dlib/config.h"
 641                (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
 642              #t))
 643          (add-after 'disable-asserts 'disable-failing-tests
 644            (lambda _
 645              ;; One test times out on MIPS, so we need to disable it.
 646              ;; Others are flaky on some platforms.
 647              (let* ((system ,(or (%current-target-system)
 648                                  (%current-system)))
 649                     (disabled-tests (cond
 650                                      ((string-prefix? "mips64" system)
 651                                       '("object_detector" ; timeout
 652                                         "data_io"))
 653                                      ((string-prefix? "armhf" system)
 654                                       '("learning_to_track"))
 655                                      ((string-prefix? "i686" system)
 656                                       '("optimization"))
 657                                      (else '()))))
 658                (for-each
 659                 (lambda (test)
 660                   (substitute* "dlib/test/makefile"
 661                     (((string-append "SRC \\+= " test "\\.cpp")) "")))
 662                 disabled-tests)
 663                #t)))
 664          (replace 'check
 665            (lambda _
 666              ;; No test target, so we build and run the unit tests here.
 667              (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
 668                (with-directory-excursion test-dir
 669                  (and (zero? (system* "make" "-j" (number->string (parallel-job-count))))
 670                       (zero? (system* "./dtest" "--runall")))))))
 671          (add-after 'install 'delete-static-library
 672            (lambda* (#:key outputs #:allow-other-keys)
 673              (delete-file (string-append (assoc-ref outputs "out")
 674                                          "/lib/libdlib.a"))
 675              #t)))))
 676     (native-inputs
 677      `(("pkg-config" ,pkg-config)))
 678     (inputs
 679      `(("giflib" ,giflib)
 680        ("lapack" ,lapack)
 681        ("libjpeg" ,libjpeg)
 682        ("libpng" ,libpng)
 683        ("libx11" ,libx11)
 684        ("openblas" ,openblas)
 685        ("zlib" ,zlib)))
 686     (synopsis
 687      "Toolkit for making machine learning and data analysis applications in C++")
 688     (description
 689      "Dlib is a modern C++ toolkit containing machine learning algorithms and
 690 tools.  It is used in both industry and academia in a wide range of domains
 691 including robotics, embedded devices, mobile phones, and large high performance
 692 computing environments.")
 693     (home-page "http://dlib.net")
 694     (license license:boost1.0)))
 695
 696 (define-public python-scikit-learn
 697   (package
 698     (name "python-scikit-learn")
 699     (version "0.19.1")
 700     (source
 701      (origin
 702        (method url-fetch)
 703        (uri (string-append
 704              "https://github.com/scikit-learn/scikit-learn/archive/"
 705              version ".tar.gz"))
 706        (file-name (string-append name "-" version ".tar.gz"))
 707        (sha256
 708         (base32
 709          "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))
 710        (patches (search-patches
 711                 "python-scikit-learn-fix-test-non-determinism.patch"))))
 712     (build-system python-build-system)
 713     (arguments
 714      `(#:phases
 715        (modify-phases %standard-phases
 716          (delete 'check)
 717          (add-after 'install 'check
 718            ;; Running tests from the source directory requires
 719            ;; an "inplace" build with paths relative to CWD.
 720            ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing
 721            ;; Use the installed version instead.
 722            (lambda* (#:key inputs outputs #:allow-other-keys)
 723              (add-installed-pythonpath inputs outputs)
 724              ;; some tests require access to "$HOME"
 725              (setenv "HOME" "/tmp")
 726              ;; Step out of the source directory just to be sure.
 727              (chdir "..")
 728              (zero? (system* "nosetests" "-v" "sklearn")))))))
 729     (inputs
 730      `(("openblas" ,openblas)))
 731     (native-inputs
 732      `(("python-nose" ,python-nose)
 733        ("python-cython" ,python-cython)))
 734     (propagated-inputs
 735      `(("python-numpy" ,python-numpy)
 736        ("python-scipy" ,python-scipy)))
 737     (home-page "http://scikit-learn.org/")
 738     (synopsis "Machine Learning in Python")
 739     (description
 740      "Scikit-learn provides simple and efficient tools for data
 741 mining and data analysis.")
 742     (license license:bsd-3)))
 743
 744 (define-public python2-scikit-learn
 745   (package-with-python2 python-scikit-learn))
 746
 747 (define-public python-autograd
 748   (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
 749          (revision "0")
 750          (version (git-version "0.0.0" revision commit)))
 751     (package
 752       (name "python-autograd")
 753       (home-page "https://github.com/HIPS/autograd")
 754       (source (origin
 755                 (method git-fetch)
 756                 (uri (git-reference
 757                       (url home-page)
 758                       (commit commit)))
 759                 (sha256
 760                  (base32
 761                   "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
 762                 (file-name (git-file-name name version))))
 763       (version version)
 764       (build-system python-build-system)
 765       (native-inputs
 766        `(("python-nose" ,python-nose)
 767          ("python-pytest" ,python-pytest)))
 768       (propagated-inputs
 769        `(("python-future" ,python-future)
 770          ("python-numpy" ,python-numpy)))
 771       (arguments
 772        `(#:phases (modify-phases %standard-phases
 773                     (replace 'check
 774                       (lambda _
 775                         (invoke "py.test" "-v"))))))
 776       (synopsis "Efficiently computes derivatives of NumPy code")
 777       (description "Autograd can automatically differentiate native Python and
 778 NumPy code.  It can handle a large subset of Python's features, including loops,
 779 ifs, recursion and closures, and it can even take derivatives of derivatives
 780 of derivatives.  It supports reverse-mode differentiation
 781 (a.k.a. backpropagation), which means it can efficiently take gradients of
 782 scalar-valued functions with respect to array-valued arguments, as well as
 783 forward-mode differentiation, and the two can be composed arbitrarily.  The
 784 main intended application of Autograd is gradient-based optimization.")
 785       (license license:expat))))
 786
 787 (define-public python2-autograd
 788   (package-with-python2 python-autograd))