gnu/packages/machine-learning.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017 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 ;;;
   8 ;;; This file is part of GNU Guix.
   9 ;;;
  10 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  11 ;;; under the terms of the GNU General Public License as published by
  12 ;;; the Free Software Foundation; either version 3 of the License, or (at
  13 ;;; your option) any later version.
  14 ;;;
  15 ;;; GNU Guix is distributed in the hope that it will be useful, but
  16 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  17 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 ;;; GNU General Public License for more details.
  19 ;;;
  20 ;;; You should have received a copy of the GNU General Public License
  21 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 (define-module (gnu packages machine-learning)
  24   #:use-module ((guix licenses) #:prefix license:)
  25   #:use-module (guix packages)
  26   #:use-module (guix utils)
  27   #:use-module (guix download)
  28   #:use-module (guix svn-download)
  29   #:use-module (guix build-system cmake)
  30   #:use-module (guix build-system gnu)
  31   #:use-module (guix build-system ocaml)
  32   #:use-module (guix build-system python)
  33   #:use-module (guix build-system r)
  34   #:use-module (gnu packages)
  35   #:use-module (gnu packages autotools)
  36   #:use-module (gnu packages boost)
  37   #:use-module (gnu packages check)
  38   #:use-module (gnu packages compression)
  39   #:use-module (gnu packages cran)
  40   #:use-module (gnu packages dejagnu)
  41   #:use-module (gnu packages gcc)
  42   #:use-module (gnu packages image)
  43   #:use-module (gnu packages maths)
  44   #:use-module (gnu packages ocaml)
  45   #:use-module (gnu packages perl)
  46   #:use-module (gnu packages pkg-config)
  47   #:use-module (gnu packages python)
  48   #:use-module (gnu packages statistics)
  49   #:use-module (gnu packages swig)
  50   #:use-module (gnu packages xml)
  51   #:use-module (gnu packages xorg))
  52
  53 (define-public libsvm
  54   (package
  55     (name "libsvm")
  56     (version "3.22")
  57     (source
  58      (origin
  59        (method url-fetch)
  60        (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
  61                            name "-" version ".tar.gz"))
  62        (sha256
  63         (base32
  64          "0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
  65     (build-system gnu-build-system)
  66     (arguments
  67      `(#:tests? #f ;no "check" target
  68        #:phases (modify-phases %standard-phases
  69                   (delete 'configure)
  70                   (replace
  71                    'install             ; no ‘install’ target
  72                    (lambda* (#:key outputs #:allow-other-keys)
  73                      (let* ((out (assoc-ref outputs "out"))
  74                             (bin (string-append out "/bin/")))
  75                        (mkdir-p bin)
  76                        (for-each (lambda (file)
  77                                    (copy-file file (string-append bin file)))
  78                                  '("svm-train"
  79                                    "svm-predict"
  80                                    "svm-scale")))
  81                      #t)))))
  82     (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
  83     (synopsis "Library for Support Vector Machines")
  84     (description
  85      "LIBSVM is a machine learning library for support vector
  86 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
  87 distribution estimation (one-class SVM).  It supports multi-class
  88 classification.")
  89     (license license:bsd-3)))
  90
  91 (define-public python-libsvm
  92   (package (inherit libsvm)
  93     (name "python-libsvm")
  94     (build-system gnu-build-system)
  95     (arguments
  96      `(#:tests? #f ;no "check" target
  97        #:make-flags '("-C" "python")
  98        #:phases
  99        (modify-phases %standard-phases
 100          (delete 'configure)
 101          (replace
 102           'install                      ; no ‘install’ target
 103           (lambda* (#:key inputs outputs #:allow-other-keys)
 104             (let ((site (string-append (assoc-ref outputs "out")
 105                                        "/lib/python"
 106                                        (string-take
 107                                         (string-take-right
 108                                          (assoc-ref inputs "python") 5) 3)
 109                                        "/site-packages/")))
 110               (substitute* "python/svm.py"
 111                 (("../libsvm.so.2") "libsvm.so.2"))
 112               (mkdir-p site)
 113               (for-each (lambda (file)
 114                           (copy-file file (string-append site (basename file))))
 115                         (find-files "python" "\\.py"))
 116               (copy-file "libsvm.so.2"
 117                          (string-append site "libsvm.so.2")))
 118             #t)))))
 119     (inputs
 120      `(("python" ,python)))
 121     (synopsis "Python bindings of libSVM")))
 122
 123 (define-public ghmm
 124   ;; The latest release candidate is several years and a couple of fixes have
 125   ;; been published since.  This is why we download the sources from the SVN
 126   ;; repository.
 127   (let ((svn-revision 2341))
 128     (package
 129       (name "ghmm")
 130       (version (string-append "0.9-rc3-0." (number->string svn-revision)))
 131       (source (origin
 132                 (method svn-fetch)
 133                 (uri (svn-reference
 134                       (url "http://svn.code.sf.net/p/ghmm/code/trunk")
 135                       (revision svn-revision)))
 136                 (file-name (string-append name "-" version))
 137                 (sha256
 138                  (base32
 139                   "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
 140       (build-system gnu-build-system)
 141       (arguments
 142        `(#:imported-modules (,@%gnu-build-system-modules
 143                              (guix build python-build-system))
 144          #:phases
 145          (modify-phases %standard-phases
 146            (add-after 'unpack 'enter-dir
 147              (lambda _ (chdir "ghmm") #t))
 148            (delete 'check)
 149            (add-after 'install 'check
 150              (assoc-ref %standard-phases 'check))
 151            (add-before 'check 'fix-PYTHONPATH
 152              (lambda* (#:key inputs outputs #:allow-other-keys)
 153                (let ((python-version ((@@ (guix build python-build-system)
 154                                            get-python-version)
 155                                       (assoc-ref inputs "python"))))
 156                  (setenv "PYTHONPATH"
 157                          (string-append (getenv "PYTHONPATH")
 158                                         ":" (assoc-ref outputs "out")
 159                                         "/lib/python" python-version
 160                                         "/site-packages")))
 161                #t))
 162            (add-after 'enter-dir 'fix-runpath
 163              (lambda* (#:key outputs #:allow-other-keys)
 164                (substitute* "ghmmwrapper/setup.py"
 165                  (("^(.*)extra_compile_args = \\[" line indent)
 166                   (string-append indent
 167                                  "extra_link_args = [\"-Wl,-rpath="
 168                                  (assoc-ref outputs "out") "/lib\"],\n"
 169                                  line
 170                                  "\"-Wl,-rpath="
 171                                  (assoc-ref outputs "out")
 172                                  "/lib\", ")))
 173                #t))
 174            (add-after 'enter-dir 'disable-broken-tests
 175              (lambda _
 176                (substitute* "tests/Makefile.am"
 177                  ;; GHMM_SILENT_TESTS is assumed to be a command.
 178                  (("TESTS_ENVIRONMENT.*") "")
 179                  ;; Do not build broken tests.
 180                  (("chmm .*") "")
 181                  (("read_fa .*") "")
 182                  (("mcmc .*") "")
 183                  (("label_higher_order_test.*$")
 184                   "label_higher_order_test\n"))
 185
 186                ;; These Python unittests are broken as there is no gato.
 187                ;; See https://sourceforge.net/p/ghmm/support-requests/3/
 188                (substitute* "ghmmwrapper/ghmmunittests.py"
 189                  (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
 190                    line indent)
 191                   (string-append indent
 192                                  "@unittest.skip(\"Disabled by Guix\")\n"
 193                                  line)))
 194                #t))
 195            (add-after 'disable-broken-tests 'autogen
 196              (lambda _
 197                (zero? (system* "bash" "autogen.sh")))))))
 198       (inputs
 199        `(("python" ,python-2) ; only Python 2 is supported
 200          ("libxml2" ,libxml2)))
 201       (native-inputs
 202        `(("pkg-config" ,pkg-config)
 203          ("dejagnu" ,dejagnu)
 204          ("swig" ,swig)
 205          ("autoconf" ,autoconf)
 206          ("automake" ,automake)
 207          ("libtool" ,libtool)))
 208       (home-page "http://ghmm.org")
 209       (synopsis "Hidden Markov Model library")
 210       (description
 211        "The General Hidden Markov Model library (GHMM) is a C library with
 212 additional Python bindings implementing a wide range of types of @dfn{Hidden
 213 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
 214 training, HMM clustering, HMM mixtures.")
 215       (license license:lgpl2.0+))))
 216
 217 (define-public mcl
 218   (package
 219     (name "mcl")
 220     (version "14.137")
 221     (source (origin
 222               (method url-fetch)
 223               (uri (string-append
 224                     "http://micans.org/mcl/src/mcl-"
 225                     (string-replace-substring version "." "-")
 226                     ".tar.gz"))
 227               (sha256
 228                (base32
 229                 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
 230     (build-system gnu-build-system)
 231     (arguments
 232      `(#:configure-flags (list "--enable-blast")))
 233     (inputs
 234      `(("perl" ,perl)))
 235     (home-page "http://micans.org/mcl/")
 236     (synopsis "Clustering algorithm for graphs")
 237     (description
 238      "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
 239 fast and scalable unsupervised cluster algorithm for graphs (also known as
 240 networks) based on simulation of (stochastic) flow in graphs.")
 241     ;; In the LICENCE file and web page it says "The software is licensed
 242     ;; under the GNU General Public License, version 3.", but in several of
 243     ;; the source code files it suggests GPL3 or later.
 244     ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
 245     (license license:gpl3)))
 246
 247 (define-public ocaml-mcl
 248   (package
 249     (name "ocaml-mcl")
 250     (version "12-068oasis4")
 251     (source
 252      (origin
 253        (method url-fetch)
 254        (uri (string-append
 255              "https://github.com/fhcrc/mcl/archive/"
 256              version ".tar.gz"))
 257        (file-name (string-append name "-" version ".tar.gz"))
 258        (sha256
 259         (base32
 260          "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
 261     (build-system ocaml-build-system)
 262     (arguments
 263      `(#:phases
 264        (modify-phases %standard-phases
 265          (add-before 'configure 'patch-paths
 266            (lambda _
 267              (substitute* "configure"
 268                (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
 269              (substitute* "setup.ml"
 270                (("LDFLAGS=-fPIC")
 271                 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
 272              #t)))))
 273     (home-page "https://github.com/fhcrc/mcl")
 274     (synopsis "OCaml wrappers around MCL")
 275     (description
 276      "This package provides OCaml bindings for the MCL graph clustering
 277 algorithm.")
 278     (license license:gpl3)))
 279
 280 (define-public ocaml4.01-mcl
 281   (package-with-ocaml4.01 ocaml-mcl))
 282
 283 (define-public randomjungle
 284   (package
 285     (name "randomjungle")
 286     (version "2.1.0")
 287     (source
 288      (origin
 289        (method url-fetch)
 290        (uri (string-append
 291              "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
 292              "randomjungle-" version ".tar_.gz"))
 293        (sha256
 294         (base32
 295          "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
 296     (build-system gnu-build-system)
 297     (arguments
 298      `(#:configure-flags
 299        (list (string-append "--with-boost="
 300                             (assoc-ref %build-inputs "boost")))
 301        #:phases
 302        (modify-phases %standard-phases
 303          (add-before
 304           'configure 'set-CXXFLAGS
 305           (lambda _
 306             (setenv "CXXFLAGS" "-fpermissive ")
 307             #t)))))
 308     (inputs
 309      `(("boost" ,boost)
 310        ("gsl" ,gsl)
 311        ("libxml2" ,libxml2)
 312        ("zlib" ,zlib)))
 313     (native-inputs
 314      `(("gfortran" ,gfortran)
 315        ("gfortran:lib" ,gfortran "lib")))
 316     ;; Non-portable assembly instructions are used so building fails on
 317     ;; platforms other than x86_64 or i686.
 318     (supported-systems '("x86_64-linux" "i686-linux"))
 319     (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
 320     (synopsis "Implementation of the Random Forests machine learning method")
 321     (description
 322      "Random Jungle is an implementation of Random Forests.  It is supposed to
 323 analyse high dimensional data.  In genetics, it can be used for analysing big
 324 Genome Wide Association (GWA) data.  Random Forests is a powerful machine
 325 learning method.  Most interesting features are variable selection, missing
 326 value imputation, classifier creation, generalization error estimation and
 327 sample proximities between pairs of cases.")
 328     (license license:gpl3+)))
 329
 330 (define-public shogun
 331   (package
 332     (name "shogun")
 333     (version "4.0.0")
 334     (source
 335      (origin
 336        (method url-fetch)
 337        (uri (string-append
 338              "ftp://shogun-toolbox.org/shogun/releases/"
 339              (version-major+minor version)
 340              "/sources/shogun-" version ".tar.bz2"))
 341        (sha256
 342         (base32
 343          "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
 344        (modules '((guix build utils)
 345                   (ice-9 rdelim)))
 346        (snippet
 347         '(begin
 348            ;; Remove non-free sources and files referencing them
 349            (for-each delete-file
 350                      (find-files "src/shogun/classifier/svm/"
 351                                  "SVMLight\\.(cpp|h)"))
 352            (for-each delete-file
 353                      (find-files "examples/undocumented/libshogun/"
 354                                  (string-append
 355                                   "(classifier_.*svmlight.*|"
 356                                   "evaluation_cross_validation_locked_comparison).cpp")))
 357            ;; Remove non-free functions.
 358            (define (delete-ifdefs file)
 359              (with-atomic-file-replacement file
 360                (lambda (in out)
 361                  (let loop ((line (read-line in 'concat))
 362                             (skipping? #f))
 363                    (if (eof-object? line)
 364                        #t
 365                        (let ((skip-next?
 366                               (or (and skipping?
 367                                        (not (string-prefix?
 368                                              "#endif //USE_SVMLIGHT" line)))
 369                                   (string-prefix?
 370                                    "#ifdef USE_SVMLIGHT" line))))
 371                          (when (or (not skipping?)
 372                                    (and skipping? (not skip-next?)))
 373                            (display line out))
 374                          (loop (read-line in 'concat) skip-next?)))))))
 375            (for-each delete-ifdefs (find-files "src/shogun/kernel/"
 376                                                "^Kernel\\.(cpp|h)"))))))
 377     (build-system cmake-build-system)
 378     (arguments
 379      '(#:tests? #f ;no check target
 380        #:phases
 381        (modify-phases %standard-phases
 382          (add-after 'unpack 'delete-broken-symlinks
 383            (lambda _
 384              (for-each delete-file '("applications/arts/data"
 385                                      "applications/asp/data"
 386                                      "applications/easysvm/data"
 387                                      "applications/msplicer/data"
 388                                      "applications/ocr/data"
 389                                      "examples/documented/data"
 390                                      "examples/documented/matlab_static"
 391                                      "examples/documented/octave_static"
 392                                      "examples/undocumented/data"
 393                                      "examples/undocumented/matlab_static"
 394                                      "examples/undocumented/octave_static"
 395                                      "tests/integration/data"
 396                                      "tests/integration/matlab_static"
 397                                      "tests/integration/octave_static"
 398                                      "tests/integration/python_modular/tests"))
 399              #t))
 400          (add-after 'unpack 'change-R-target-path
 401            (lambda* (#:key outputs #:allow-other-keys)
 402              (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
 403                             "src/interfaces/r_static/CMakeLists.txt"
 404                             "examples/undocumented/r_modular/CMakeLists.txt")
 405                (("\\$\\{R_COMPONENT_LIB_PATH\\}")
 406                 (string-append (assoc-ref outputs "out")
 407                                "/lib/R/library/")))
 408              #t))
 409          (add-after 'unpack 'fix-octave-modules
 410            (lambda* (#:key outputs #:allow-other-keys)
 411              (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
 412                             "src/interfaces/octave_static/CMakeLists.txt")
 413                (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
 414                 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
 415
 416              ;; change target directory
 417              (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
 418                (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
 419                 (string-append (assoc-ref outputs "out")
 420                                "/share/octave/packages")))
 421              #t))
 422          (add-before 'build 'set-HOME
 423            ;; $HOME needs to be set at some point during the build phase
 424            (lambda _ (setenv "HOME" "/tmp") #t)))
 425        #:configure-flags
 426        (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
 427              "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
 428              ;;"-DJavaModular=ON" ;requires unpackaged jblas
 429              ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
 430              ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
 431              ;;"-DLuaModular=ON"  ;fails because lua doesn't build pkgconfig file
 432              "-DOctaveModular=ON"
 433              "-DOctaveStatic=ON"
 434              "-DPythonModular=ON"
 435              "-DPythonStatic=ON"
 436              "-DRModular=ON"
 437              "-DRStatic=ON"
 438              "-DCmdLineStatic=ON")))
 439     (inputs
 440      `(("python" ,python)
 441        ("numpy" ,python-numpy)
 442        ("r-minimal" ,r-minimal)
 443        ("octave" ,octave)
 444        ("swig" ,swig)
 445        ("hdf5" ,hdf5)
 446        ("atlas" ,atlas)
 447        ("arpack" ,arpack-ng)
 448        ("lapack" ,lapack)
 449        ("glpk" ,glpk)
 450        ("libxml2" ,libxml2)
 451        ("lzo" ,lzo)
 452        ("zlib" ,zlib)))
 453     (native-inputs
 454      `(("pkg-config" ,pkg-config)))
 455     ;; Non-portable SSE instructions are used so building fails on platforms
 456     ;; other than x86_64.
 457     (supported-systems '("x86_64-linux"))
 458     (home-page "http://shogun-toolbox.org/")
 459     (synopsis "Machine learning toolbox")
 460     (description
 461      "The Shogun Machine learning toolbox provides a wide range of unified and
 462 efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
 463 combine multiple data representations, algorithm classes, and general purpose
 464 tools.  This enables both rapid prototyping of data pipelines and extensibility
 465 in terms of new algorithms.")
 466     (license license:gpl3+)))
 467
 468 (define-public r-adaptivesparsity
 469   (package
 470     (name "r-adaptivesparsity")
 471     (version "1.4")
 472     (source (origin
 473               (method url-fetch)
 474               (uri (cran-uri "AdaptiveSparsity" version))
 475               (sha256
 476                (base32
 477                 "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z"))))
 478     (properties
 479      `((upstream-name . "AdaptiveSparsity")))
 480     (build-system r-build-system)
 481     (arguments
 482      `(#:phases
 483        (modify-phases %standard-phases
 484          (add-after 'unpack 'link-against-armadillo
 485            (lambda _
 486              (substitute* "src/Makevars"
 487                (("PKG_LIBS=" prefix)
 488                 (string-append prefix "-larmadillo"))))))))
 489     (propagated-inputs
 490      `(("r-rcpp" ,r-rcpp)
 491        ("r-rcpparmadillo" ,r-rcpparmadillo)))
 492     (inputs
 493      `(("armadillo" ,armadillo)))
 494     (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
 495     (synopsis "Adaptive sparsity models")
 496     (description
 497      "This package implements the Figueiredo machine learning algorithm for
 498 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
 499 geometric models.")
 500     (license license:lgpl3+)))
 501
 502 (define-public r-kernlab
 503   (package
 504     (name "r-kernlab")
 505     (version "0.9-25")
 506     (source
 507      (origin
 508        (method url-fetch)
 509        (uri (cran-uri "kernlab" version))
 510        (sha256
 511         (base32
 512          "0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr"))))
 513     (build-system r-build-system)
 514     (home-page "https://cran.r-project.org/web/packages/kernlab")
 515     (synopsis "Kernel-based machine learning tools")
 516     (description
 517      "This package provides kernel-based machine learning methods for
 518 classification, regression, clustering, novelty detection, quantile regression
 519 and dimensionality reduction.  Among other methods @code{kernlab} includes
 520 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
 521 and a QP solver.")
 522     (license license:gpl2)))
 523
 524 (define-public dlib
 525   (package
 526     (name "dlib")
 527     (version "19.7")
 528     (source (origin
 529               (method url-fetch)
 530               (uri (string-append
 531                     "http://dlib.net/files/dlib-" version ".tar.bz2"))
 532               (sha256
 533                (base32
 534                 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
 535               (modules '((guix build utils)))
 536               (snippet
 537                '(begin
 538                   ;; Delete ~13MB of bundled dependencies.
 539                   (delete-file-recursively "dlib/external")
 540                   (delete-file-recursively "docs/dlib/external")
 541                   #t))))
 542     (build-system cmake-build-system)
 543     (arguments
 544      `(#:phases
 545        (modify-phases %standard-phases
 546          (add-after 'unpack 'disable-asserts
 547            (lambda _
 548              ;; config.h recommends explicitly enabling or disabling asserts
 549              ;; when building as a shared library. By default neither is set.
 550              (substitute* "dlib/config.h"
 551                (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
 552              #t))
 553          (add-after 'disable-asserts 'disable-failing-tests
 554            (lambda _
 555              ;; One test times out on MIPS, so we need to disable it.
 556              ;; Others are flaky on some platforms.
 557              (let* ((system ,(or (%current-target-system)
 558                                  (%current-system)))
 559                     (disabled-tests (cond
 560                                      ((string-prefix? "mips64" system)
 561                                       '("object_detector" ; timeout
 562                                         "data_io"))
 563                                      ((string-prefix? "armhf" system)
 564                                       '("learning_to_track"))
 565                                      ((string-prefix? "i686" system)
 566                                       '("optimization"))
 567                                      (else '()))))
 568                (for-each
 569                 (lambda (test)
 570                   (substitute* "dlib/test/makefile"
 571                     (((string-append "SRC \\+= " test "\\.cpp")) "")))
 572                 disabled-tests)
 573                #t)))
 574          (replace 'check
 575            (lambda _
 576              ;; No test target, so we build and run the unit tests here.
 577              (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
 578                (with-directory-excursion test-dir
 579                  (and (zero? (system* "make" "-j" (number->string (parallel-job-count))))
 580                       (zero? (system* "./dtest" "--runall")))))))
 581          (add-after 'install 'delete-static-library
 582            (lambda* (#:key outputs #:allow-other-keys)
 583              (delete-file (string-append (assoc-ref outputs "out")
 584                                          "/lib/libdlib.a"))
 585              #t)))))
 586     (native-inputs
 587      `(("pkg-config" ,pkg-config)))
 588     (inputs
 589      `(("giflib" ,giflib)
 590        ("lapack" ,lapack)
 591        ("libjpeg" ,libjpeg)
 592        ("libpng" ,libpng)
 593        ("libx11" ,libx11)
 594        ("openblas" ,openblas)
 595        ("zlib" ,zlib)))
 596     (synopsis
 597      "Toolkit for making machine learning and data analysis applications in C++")
 598     (description
 599      "Dlib is a modern C++ toolkit containing machine learning algorithms and
 600 tools.  It is used in both industry and academia in a wide range of domains
 601 including robotics, embedded devices, mobile phones, and large high performance
 602 computing environments.")
 603     (home-page "http://dlib.net")
 604     (license license:boost1.0)))
 605
 606 (define-public python-scikit-learn
 607   (package
 608     (name "python-scikit-learn")
 609     (version "0.19.1")
 610     (source
 611      (origin
 612        (method url-fetch)
 613        (uri (string-append
 614              "https://github.com/scikit-learn/scikit-learn/archive/"
 615              version ".tar.gz"))
 616        (file-name (string-append name "-" version ".tar.gz"))
 617        (sha256
 618         (base32
 619          "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))
 620        (patches (search-patches
 621                 "python-scikit-learn-fix-test-non-determinism.patch"))))
 622     (build-system python-build-system)
 623     (arguments
 624      `(#:phases
 625        (modify-phases %standard-phases
 626          (delete 'check)
 627          (add-after 'install 'check
 628            ;; Running tests from the source directory requires
 629            ;; an "inplace" build with paths relative to CWD.
 630            ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing
 631            ;; Use the installed version instead.
 632            (lambda* (#:key inputs outputs #:allow-other-keys)
 633              (add-installed-pythonpath inputs outputs)
 634              ;; some tests require access to "$HOME"
 635              (setenv "HOME" "/tmp")
 636              ;; Step out of the source directory just to be sure.
 637              (chdir "..")
 638              (zero? (system* "nosetests" "-v" "sklearn")))))))
 639     (inputs
 640      `(("openblas" ,openblas)))
 641     (native-inputs
 642      `(("python-nose" ,python-nose)
 643        ("python-cython" ,python-cython)))
 644     (propagated-inputs
 645      `(("python-numpy" ,python-numpy)
 646        ("python-scipy" ,python-scipy)))
 647     (home-page "http://scikit-learn.org/")
 648     (synopsis "Machine Learning in Python")
 649     (description
 650      "Scikit-learn provides simple and efficient tools for data
 651 mining and data analysis.")
 652     (license license:bsd-3)))
 653
 654 (define-public python2-scikit-learn
 655   (package-with-python2 python-scikit-learn))