1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
4 ;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com>
5 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
6 ;;; Copyright © 2018, 2019, 2020 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 ;;; Copyright © 2019, 2020 Guillaume Le Vaillant <glv@posteo.net>
15 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
16 ;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
17 ;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
19 ;;; This file is part of GNU Guix.
21 ;;; GNU Guix is free software; you can redistribute it and/or modify it
22 ;;; under the terms of the GNU General Public License as published by
23 ;;; the Free Software Foundation; either version 3 of the License, or (at
24 ;;; your option) any later version.
26 ;;; GNU Guix is distributed in the hope that it will be useful, but
27 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
28 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29 ;;; GNU General Public License for more details.
31 ;;; You should have received a copy of the GNU General Public License
32 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
34 (define-module (gnu packages machine-learning)
35 #:use-module ((guix licenses) #:prefix license:)
36 #:use-module (guix packages)
37 #:use-module (guix utils)
38 #:use-module (guix download)
39 #:use-module (guix svn-download)
40 #:use-module (guix build-system asdf)
41 #:use-module (guix build-system cmake)
42 #:use-module (guix build-system gnu)
43 #:use-module (guix build-system ocaml)
44 #:use-module (guix build-system python)
45 #:use-module (guix build-system r)
46 #:use-module (guix git-download)
47 #:use-module (gnu packages)
48 #:use-module (gnu packages adns)
49 #:use-module (gnu packages algebra)
50 #:use-module (gnu packages audio)
51 #:use-module (gnu packages autotools)
52 #:use-module (gnu packages base)
53 #:use-module (gnu packages bash)
54 #:use-module (gnu packages boost)
55 #:use-module (gnu packages check)
56 #:use-module (gnu packages compression)
57 #:use-module (gnu packages cran)
58 #:use-module (gnu packages databases)
59 #:use-module (gnu packages dejagnu)
60 #:use-module (gnu packages gcc)
61 #:use-module (gnu packages glib)
62 #:use-module (gnu packages graphviz)
63 #:use-module (gnu packages gstreamer)
64 #:use-module (gnu packages image)
65 #:use-module (gnu packages linux)
66 #:use-module (gnu packages lisp-xyz)
67 #:use-module (gnu packages maths)
68 #:use-module (gnu packages mpi)
69 #:use-module (gnu packages ocaml)
70 #:use-module (gnu packages onc-rpc)
71 #:use-module (gnu packages perl)
72 #:use-module (gnu packages pkg-config)
73 #:use-module (gnu packages protobuf)
74 #:use-module (gnu packages python)
75 #:use-module (gnu packages python-science)
76 #:use-module (gnu packages python-web)
77 #:use-module (gnu packages python-xyz)
78 #:use-module (gnu packages rpc)
79 #:use-module (gnu packages serialization)
80 #:use-module (gnu packages sphinx)
81 #:use-module (gnu packages statistics)
82 #:use-module (gnu packages sqlite)
83 #:use-module (gnu packages swig)
84 #:use-module (gnu packages web)
85 #:use-module (gnu packages xml)
86 #:use-module (gnu packages xorg)
87 #:use-module (ice-9 match))
90 ;; The last release is >100 commits behind, so we package from git.
91 (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
94 (version (string-append "2.2.0-1." (string-take commit 8)))
98 (url "https://github.com/libfann/fann.git")
100 (file-name (string-append name "-" version "-checkout"))
103 "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
104 (build-system cmake-build-system)
107 (modify-phases %standard-phases
109 (lambda* (#:key outputs #:allow-other-keys)
110 (let* ((out (assoc-ref outputs "out")))
111 (with-directory-excursion (string-append (getcwd) "/tests")
112 (invoke "./fann_tests"))))))))
113 (home-page "http://leenissen.dk/fann/wp/")
114 (synopsis "Fast Artificial Neural Network")
116 "FANN is a neural network library, which implements multilayer
117 artificial neural networks in C with support for both fully connected and
118 sparsely connected networks.")
119 (license license:lgpl2.1))))
121 (define-public libsvm
128 (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
129 name "-" version ".tar.gz"))
131 (base32 "0jpaq0rr92x38p4nk3gjan79ip67m6p80anb28z1d8601miysyi5"))))
132 (build-system gnu-build-system)
134 `(#:tests? #f ; no "check" target
135 #:phases (modify-phases %standard-phases
138 'install ; no ‘install’ target
139 (lambda* (#:key outputs #:allow-other-keys)
140 (let* ((out (assoc-ref outputs "out"))
141 (bin (string-append out "/bin/")))
143 (for-each (lambda (file)
144 (copy-file file (string-append bin file)))
149 (home-page "https://www.csie.ntu.edu.tw/~cjlin/libsvm/")
150 (synopsis "Library for Support Vector Machines")
152 "LIBSVM is a machine learning library for support vector
153 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
154 distribution estimation (one-class SVM). It supports multi-class
156 (license license:bsd-3)))
158 (define-public python-libsvm
159 (package (inherit libsvm)
160 (name "python-libsvm")
161 (build-system gnu-build-system)
163 `(#:tests? #f ; no "check" target
164 #:make-flags '("-C" "python")
166 (modify-phases %standard-phases
169 'install ; no ‘install’ target
170 (lambda* (#:key inputs outputs #:allow-other-keys)
171 (let ((site (string-append (assoc-ref outputs "out")
175 (assoc-ref inputs "python") 5) 3)
177 (substitute* "python/svm.py"
178 (("../libsvm.so.2") "libsvm.so.2"))
180 (for-each (lambda (file)
181 (copy-file file (string-append site (basename file))))
182 (find-files "python" "\\.py"))
183 (copy-file "libsvm.so.2"
184 (string-append site "libsvm.so.2")))
187 `(("python" ,python)))
188 (synopsis "Python bindings of libSVM")))
191 ;; The latest release candidate is several years and a couple of fixes have
192 ;; been published since. This is why we download the sources from the SVN
194 (let ((svn-revision 2341))
197 (version (string-append "0.9-rc3-0." (number->string svn-revision)))
201 (url "http://svn.code.sf.net/p/ghmm/code/trunk")
202 (revision svn-revision)))
203 (file-name (string-append name "-" version "-checkout"))
206 "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
207 (build-system gnu-build-system)
209 `(#:imported-modules (,@%gnu-build-system-modules
210 (guix build python-build-system))
211 #:modules ((guix build python-build-system)
212 ,@%gnu-build-system-modules)
214 (modify-phases %standard-phases
215 (add-after 'unpack 'enter-dir
216 (lambda _ (chdir "ghmm") #t))
218 (add-after 'install 'check
219 (assoc-ref %standard-phases 'check))
220 (add-before 'check 'fix-PYTHONPATH
221 (lambda* (#:key inputs outputs #:allow-other-keys)
222 (let ((python-version (python-version
223 (assoc-ref inputs "python"))))
225 (string-append (getenv "PYTHONPATH")
226 ":" (assoc-ref outputs "out")
227 "/lib/python" python-version
230 (add-after 'enter-dir 'fix-runpath
231 (lambda* (#:key outputs #:allow-other-keys)
232 (substitute* "ghmmwrapper/setup.py"
233 (("^(.*)extra_compile_args = \\[" line indent)
234 (string-append indent
235 "extra_link_args = [\"-Wl,-rpath="
236 (assoc-ref outputs "out") "/lib\"],\n"
239 (assoc-ref outputs "out")
242 (add-after 'enter-dir 'disable-broken-tests
244 (substitute* "tests/Makefile.am"
245 ;; GHMM_SILENT_TESTS is assumed to be a command.
246 (("TESTS_ENVIRONMENT.*") "")
247 ;; Do not build broken tests.
251 (("label_higher_order_test.*$")
252 "label_higher_order_test\n"))
254 ;; These Python unittests are broken as there is no gato.
255 ;; See https://sourceforge.net/p/ghmm/support-requests/3/
256 (substitute* "ghmmwrapper/ghmmunittests.py"
257 (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
259 (string-append indent
260 "@unittest.skip(\"Disabled by Guix\")\n"
264 `(("python" ,python-2) ; only Python 2 is supported
265 ("libxml2" ,libxml2)))
267 `(("pkg-config" ,pkg-config)
270 ("autoconf" ,autoconf)
271 ("automake" ,automake)
272 ("libtool" ,libtool)))
273 (home-page "http://ghmm.org")
274 (synopsis "Hidden Markov Model library")
276 "The General Hidden Markov Model library (GHMM) is a C library with
277 additional Python bindings implementing a wide range of types of @dfn{Hidden
278 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
279 training, HMM clustering, HMM mixtures.")
280 (license license:lgpl2.0+))))
289 "http://micans.org/mcl/src/mcl-"
290 (string-replace-substring version "." "-")
294 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
295 (build-system gnu-build-system)
297 `(#:configure-flags (list "--enable-blast")))
300 (home-page "http://micans.org/mcl/")
301 (synopsis "Clustering algorithm for graphs")
303 "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
304 fast and scalable unsupervised cluster algorithm for graphs (also known as
305 networks) based on simulation of (stochastic) flow in graphs.")
306 ;; In the LICENCE file and web page it says "The software is licensed
307 ;; under the GNU General Public License, version 3.", but in several of
308 ;; the source code files it suggests GPL3 or later.
309 ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
310 (license license:gpl3)))
312 (define-public ocaml-mcl
315 (version "12-068oasis4")
320 (url "https://github.com/fhcrc/mcl.git")
322 (file-name (git-file-name name version))
325 "0009dc3h2jp3qg5val452wngpqnbfyhbcxylghq0mrjqxx0jdq5p"))))
326 (build-system ocaml-build-system)
329 (modify-phases %standard-phases
330 (add-before 'configure 'patch-paths
332 (substitute* "configure"
333 (("/bin/sh") (which "sh")))
334 (substitute* "setup.ml"
336 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))
337 (("-std=c89") "-std=gnu99")
339 ;; This is a mutable string, which is no longer supported. Use
340 ;; a byte buffer instead.
341 (("String.make \\(String.length s\\)")
342 "Bytes.make (String.length s)")
344 ;; These two belong together.
345 (("OASISString.replace_chars")
346 "Bytes.to_string (OASISString.replace_chars")
349 (substitute* "myocamlbuild.ml"
350 (("std=c89") "std=gnu99"))
351 ;; Since we build with a more recent OCaml, we have to use C99 or
352 ;; later. This causes problems with the old C code.
353 (substitute* "src/impala/matrix.c"
354 (("restrict") "restrict_"))
357 `(("ocamlbuild" ,ocamlbuild)))
358 (home-page "https://github.com/fhcrc/mcl")
359 (synopsis "OCaml wrappers around MCL")
361 "This package provides OCaml bindings for the MCL graph clustering
363 (license license:gpl3)))
365 (define-public randomjungle
367 (name "randomjungle")
373 "https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
374 "/randomjungle/randomjungle-" version ".tar_.gz"))
375 (patches (search-patches "randomjungle-disable-static-build.patch"))
378 "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
379 (build-system gnu-build-system)
382 (list "--disable-static"
383 (string-append "--with-boost="
384 (assoc-ref %build-inputs "boost")))
386 (modify-phases %standard-phases
388 'configure 'set-CXXFLAGS
390 (setenv "CXXFLAGS" "-fpermissive ")
398 `(("gfortran" ,gfortran)
399 ("gfortran:lib" ,gfortran "lib")))
400 ;; Non-portable assembly instructions are used so building fails on
401 ;; platforms other than x86_64 or i686.
402 (supported-systems '("x86_64-linux" "i686-linux"))
403 (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
404 (synopsis "Implementation of the Random Forests machine learning method")
406 "Random Jungle is an implementation of Random Forests. It is supposed to
407 analyse high dimensional data. In genetics, it can be used for analysing big
408 Genome Wide Association (GWA) data. Random Forests is a powerful machine
409 learning method. Most interesting features are variable selection, missing
410 value imputation, classifier creation, generalization error estimation and
411 sample proximities between pairs of cases.")
412 (license license:gpl3+)))
414 (define-public openfst
420 (uri (string-append "http://www.openfst.org/twiki/pub/FST/"
421 "FstDownload/openfst-" version ".tar.gz"))
424 "0fqgk8195kz21is09gwzwnrg7fr9526bi9mh4apyskapz27pbhr1"))))
425 (build-system gnu-build-system)
426 (home-page "http://www.openfst.org")
427 (synopsis "Library for weighted finite-state transducers")
428 (description "OpenFst is a library for constructing, combining,
429 optimizing, and searching weighted finite-state transducers (FSTs).")
430 (license license:asl2.0)))
432 (define-public shogun
440 "ftp://shogun-toolbox.org/shogun/releases/"
441 (version-major+minor version)
442 "/sources/shogun-" version ".tar.bz2"))
445 "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
446 (modules '((guix build utils)
450 ;; Remove non-free sources and files referencing them
451 (for-each delete-file
452 (find-files "src/shogun/classifier/svm/"
453 "SVMLight\\.(cpp|h)"))
454 (for-each delete-file
455 (find-files "examples/undocumented/libshogun/"
457 "(classifier_.*svmlight.*|"
458 "evaluation_cross_validation_locked_comparison).cpp")))
459 ;; Remove non-free functions.
460 (define (delete-ifdefs file)
461 (with-atomic-file-replacement file
463 (let loop ((line (read-line in 'concat))
465 (if (eof-object? line)
470 "#endif //USE_SVMLIGHT" line)))
472 "#ifdef USE_SVMLIGHT" line))))
473 (when (or (not skipping?)
474 (and skipping? (not skip-next?)))
476 (loop (read-line in 'concat) skip-next?)))))))
477 (for-each delete-ifdefs
479 (find-files "src/shogun/classifier/mkl"
480 "^MKLClassification\\.cpp")
481 (find-files "src/shogun/classifier/svm"
482 "^SVMLightOneClass\\.(cpp|h)")
483 (find-files "src/shogun/multiclass"
484 "^ScatterSVM\\.(cpp|h)")
485 (find-files "src/shogun/kernel/"
486 "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
487 (find-files "src/shogun/regression/svr"
488 "^(MKLRegression|SVRLight)\\.(cpp|h)")
489 (find-files "src/shogun/transfer/domain_adaptation"
490 "^DomainAdaptationSVM\\.(cpp|h)")))
492 (build-system cmake-build-system)
494 '(#:tests? #f ;no check target
496 (modify-phases %standard-phases
497 (add-after 'unpack 'delete-broken-symlinks
499 (for-each delete-file '("applications/arts/data"
500 "applications/asp/data"
501 "applications/easysvm/data"
502 "applications/msplicer/data"
503 "applications/ocr/data"
505 "examples/undocumented/data"))
507 (add-after 'unpack 'change-R-target-path
508 (lambda* (#:key outputs #:allow-other-keys)
509 (substitute* '("src/interfaces/r/CMakeLists.txt"
510 "examples/meta/r/CMakeLists.txt")
511 (("\\$\\{R_COMPONENT_LIB_PATH\\}")
512 (string-append (assoc-ref outputs "out")
515 (add-after 'unpack 'fix-octave-modules
516 (lambda* (#:key outputs #:allow-other-keys)
517 (substitute* "src/interfaces/octave/CMakeLists.txt"
518 (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
519 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
520 ;; change target directory
521 (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
522 (string-append (assoc-ref outputs "out")
523 "/share/octave/packages")))
524 (substitute* '("src/interfaces/octave/swig_typemaps.i"
525 "src/interfaces/octave/sg_print_functions.cpp")
526 ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
527 (("octave/config\\.h") "octave/octave-config.h")
528 (("octave/oct-obj.h") "octave/ovl.h"))
530 (add-after 'unpack 'move-rxcpp
531 (lambda* (#:key inputs #:allow-other-keys)
532 (let ((rxcpp-dir "shogun/third-party/rxcpp"))
534 (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
536 (add-before 'build 'set-HOME
537 ;; $HOME needs to be set at some point during the build phase
538 (lambda _ (setenv "HOME" "/tmp") #t)))
540 (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
541 "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
542 "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
543 ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
544 ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
545 ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
546 ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
547 "-DINTERFACE_OCTAVE=ON"
548 "-DINTERFACE_PYTHON=ON"
549 "-DINTERFACE_R=ON")))
552 ("numpy" ,python-numpy)
553 ("r-minimal" ,r-minimal)
554 ("octave" ,octave-cli)
559 ("arpack" ,arpack-ng)
566 `(("pkg-config" ,pkg-config)
568 ;; Non-portable SSE instructions are used so building fails on platforms
569 ;; other than x86_64.
570 (supported-systems '("x86_64-linux"))
571 (home-page "https://shogun-toolbox.org/")
572 (synopsis "Machine learning toolbox")
574 "The Shogun Machine learning toolbox provides a wide range of unified and
575 efficient Machine Learning (ML) methods. The toolbox seamlessly
576 combines multiple data representations, algorithm classes, and general purpose
577 tools. This enables both rapid prototyping of data pipelines and extensibility
578 in terms of new algorithms.")
579 (license license:gpl3+)))
589 (url "https://github.com/ReactiveX/RxCpp.git")
590 (commit (string-append "v" version))))
592 (base32 "1rdpa3jlc181jd08nk437aar085h28i45s6nzrv65apb3xyyz0ij"))
593 (file-name (git-file-name name version))))
594 (build-system cmake-build-system)
597 (modify-phases %standard-phases
598 (add-after 'unpack 'remove-werror
600 (substitute* (find-files ".")
605 (invoke "ctest"))))))
607 `(("catch" ,catch-framework)))
608 (home-page "http://reactivex.io/")
609 (synopsis "Reactive Extensions for C++")
611 "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
612 values-distributed-in-time. ReactiveX is a library for composing asynchronous
613 and event-based programs by using observable sequences.
615 It extends the observer pattern to support sequences of data and/or events and
616 adds operators that allow you to compose sequences together declaratively while
617 abstracting away concerns about things like low-level threading,
618 synchronization, thread-safety, concurrent data structures, and non-blocking
620 (license license:asl2.0)))
622 (define-public r-adaptivesparsity
624 (name "r-adaptivesparsity")
628 (uri (cran-uri "AdaptiveSparsity" version))
631 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
633 `((upstream-name . "AdaptiveSparsity")))
634 (build-system r-build-system)
637 (modify-phases %standard-phases
638 (add-after 'unpack 'link-against-armadillo
640 (substitute* "src/Makevars"
641 (("PKG_LIBS=" prefix)
642 (string-append prefix "-larmadillo"))))))))
645 ("r-matrix" ,r-matrix)
647 ("r-rcpparmadillo" ,r-rcpparmadillo)))
649 `(("armadillo" ,armadillo)))
650 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
651 (synopsis "Adaptive sparsity models")
653 "This package implements the Figueiredo machine learning algorithm for
654 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
656 (license license:lgpl3+)))
658 (define-public gemmlowp-for-tensorflow
659 ;; The commit hash is taken from "tensorflow/workspace.bzl".
660 (let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
664 (version (git-version "0" revision commit))
667 (uri (string-append "https://mirror.bazel.build/"
668 "github.com/google/gemmlowp/archive/"
670 (file-name (string-append "gemmlowp-" version ".zip"))
673 "0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
674 (build-system cmake-build-system)
677 (list ,@(match (%current-system)
678 ((or "x86_64-linux" "i686-linux")
679 '("-DCMAKE_CXX_FLAGS=-msse2"))
682 (modify-phases %standard-phases
683 ;; This directory contains the CMakeLists.txt.
684 (add-after 'unpack 'chdir
685 (lambda _ (chdir "contrib") #t))
686 ;; There is no install target
688 (lambda* (#:key outputs #:allow-other-keys)
689 (let* ((out (assoc-ref outputs "out"))
690 (lib (string-append out "/lib/"))
691 (inc (string-append out "/include/")))
692 (install-file "../build/libeight_bit_int_gemm.so" lib)
693 (for-each (lambda (dir)
694 (let ((target (string-append inc "/" dir)))
696 (for-each (lambda (h)
697 (install-file h target))
698 (find-files (string-append "../" dir)
700 '("meta" "profiling" "public" "fixedpoint"
701 "eight_bit_int_gemm" "internal"))
705 (home-page "https://github.com/google/gemmlowp")
706 (synopsis "Small self-contained low-precision GEMM library")
708 "This is a small self-contained low-precision @dfn{general matrix
709 multiplication} (GEMM) library. It is not a full linear algebra library.
710 Low-precision means that the input and output matrix entries are integers on
711 at most 8 bits. To avoid overflow, results are internally accumulated on more
712 than 8 bits, and at the end only some significant 8 bits are kept.")
713 (license license:asl2.0))))
722 "http://dlib.net/files/dlib-" version ".tar.bz2"))
725 "139jyi19qz37wwmmy48gil9d1kkh2r3w3bwdzabha6ayxmba96nz"))
726 (modules '((guix build utils)))
729 ;; Delete ~13MB of bundled dependencies.
730 (delete-file-recursively "dlib/external")
731 (delete-file-recursively "docs/dlib/external")
733 (build-system cmake-build-system)
736 (modify-phases %standard-phases
737 (add-after 'unpack 'disable-asserts
739 ;; config.h recommends explicitly enabling or disabling asserts
740 ;; when building as a shared library. By default neither is set.
741 (substitute* "dlib/config.h"
742 (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
744 (add-after 'disable-asserts 'disable-failing-tests
746 ;; One test times out on MIPS, so we need to disable it.
747 ;; Others are flaky on some platforms.
748 (let* ((system ,(or (%current-target-system)
750 (disabled-tests (cond
751 ((string-prefix? "mips64" system)
752 '("object_detector" ; timeout
754 ((string-prefix? "armhf" system)
755 '("learning_to_track"))
756 ((string-prefix? "i686" system)
761 (substitute* "dlib/test/makefile"
762 (((string-append "SRC \\+= " test "\\.cpp")) "")))
767 ;; No test target, so we build and run the unit tests here.
768 (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
769 (with-directory-excursion test-dir
770 (invoke "make" "-j" (number->string (parallel-job-count)))
771 (invoke "./dtest" "--runall"))
773 (add-after 'install 'delete-static-library
774 (lambda* (#:key outputs #:allow-other-keys)
775 (delete-file (string-append (assoc-ref outputs "out")
779 `(("pkg-config" ,pkg-config)
785 ("libjpeg" ,libjpeg-turbo)
788 ("openblas" ,openblas)
791 "Toolkit for making machine learning and data analysis applications in C++")
793 "Dlib is a modern C++ toolkit containing machine learning algorithms and
794 tools. It is used in both industry and academia in a wide range of domains
795 including robotics, embedded devices, mobile phones, and large high performance
796 computing environments.")
797 (home-page "http://dlib.net")
798 (license license:boost1.0)))
800 (define-public python-scikit-learn
802 (name "python-scikit-learn")
808 (url "https://github.com/scikit-learn/scikit-learn.git")
810 (file-name (git-file-name name version))
813 "1xqxv210gsmjw094vc5ghq2y9lmm74qkk22pq6flcjzj51b86jxf"))))
814 (build-system python-build-system)
817 (modify-phases %standard-phases
818 (add-after 'build 'build-ext
819 (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
822 ;; Restrict OpenBLAS threads to prevent segfaults while testing!
823 (setenv "OPENBLAS_NUM_THREADS" "1")
825 ;; Some tests require write access to $HOME.
826 (setenv "HOME" "/tmp")
828 (invoke "pytest" "sklearn" "-m" "not network")))
829 (add-before 'reset-gzip-timestamps 'make-files-writable
830 (lambda* (#:key outputs #:allow-other-keys)
831 ;; Make sure .gz files are writable so that the
832 ;; 'reset-gzip-timestamps' phase can do its work.
833 (let ((out (assoc-ref outputs "out")))
834 (for-each make-file-writable
835 (find-files out "\\.gz$"))
838 `(("openblas" ,openblas)))
840 `(("python-pytest" ,python-pytest)
841 ("python-pandas" ,python-pandas) ;for tests
842 ("python-cython" ,python-cython)))
844 `(("python-numpy" ,python-numpy)
845 ("python-scipy" ,python-scipy)
846 ("python-joblib" ,python-joblib)))
847 (home-page "https://scikit-learn.org/")
848 (synopsis "Machine Learning in Python")
850 "Scikit-learn provides simple and efficient tools for data mining and
852 (properties `((python2-variant . ,(delay python2-scikit-learn))))
853 (license license:bsd-3)))
855 ;; scikit-learn 0.22 and later only supports Python 3, so we stick with
856 ;; an older version here.
857 (define-public python2-scikit-learn
858 (let ((base (package-with-python2 (strip-python2-variant python-scikit-learn))))
865 (url "https://github.com/scikit-learn/scikit-learn.git")
867 (file-name (git-file-name "python-scikit-learn" version))
870 "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))))))
872 (define-public python-scikit-rebate
874 (name "python-scikit-rebate")
878 (uri (pypi-uri "skrebate" version))
881 "1h7qs9gjxpzqabzhb8rmpv3jpmi5iq41kqdibg48299h94iikiw7"))))
882 (build-system python-build-system)
883 ;; Pandas is only needed to run the tests.
885 `(("python-pandas" ,python-pandas)))
887 `(("python-numpy" ,python-numpy)
888 ("python-scipy" ,python-scipy)
889 ("python-scikit-learn" ,python-scikit-learn)
890 ("python-joblib" ,python-joblib)))
891 (home-page "https://epistasislab.github.io/scikit-rebate/")
892 (synopsis "Relief-based feature selection algorithms for Python")
893 (description "Scikit-rebate is a scikit-learn-compatible Python
894 implementation of ReBATE, a suite of Relief-based feature selection algorithms
895 for Machine Learning. These algorithms excel at identifying features that are
896 predictive of the outcome in supervised learning problems, and are especially
897 good at identifying feature interactions that are normally overlooked by
898 standard feature selection algorithms.")
899 (license license:expat)))
901 (define-public python-autograd
902 (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
904 (version (git-version "0.0.0" revision commit)))
906 (name "python-autograd")
907 (home-page "https://github.com/HIPS/autograd")
915 "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
916 (file-name (git-file-name name version))))
918 (build-system python-build-system)
920 `(("python-nose" ,python-nose)
921 ("python-pytest" ,python-pytest)))
923 `(("python-future" ,python-future)
924 ("python-numpy" ,python-numpy)))
926 `(#:phases (modify-phases %standard-phases
929 (invoke "py.test" "-v"))))))
930 (synopsis "Efficiently computes derivatives of NumPy code")
931 (description "Autograd can automatically differentiate native Python and
932 NumPy code. It can handle a large subset of Python's features, including loops,
933 ifs, recursion and closures, and it can even take derivatives of derivatives
934 of derivatives. It supports reverse-mode differentiation
935 (a.k.a. backpropagation), which means it can efficiently take gradients of
936 scalar-valued functions with respect to array-valued arguments, as well as
937 forward-mode differentiation, and the two can be composed arbitrarily. The
938 main intended application of Autograd is gradient-based optimization.")
939 (license license:expat))))
941 (define-public python2-autograd
942 (package-with-python2 python-autograd))
944 (define-public lightgbm
951 (url "https://github.com/Microsoft/LightGBM")
952 (commit (string-append "v" version))))
955 "0jlvyn7k81dzrh9ij3zw576wbgiwmmr26rzpdxjn1dbpc3njpvzi"))
956 (file-name (git-file-name name version))))
958 `(("python-pytest" ,python-pytest)
959 ("python-nose" ,python-nose)))
961 `(("openmpi" ,openmpi)))
963 `(("python-numpy" ,python-numpy)
964 ("python-scipy" ,python-scipy)))
969 (modify-phases %standard-phases
972 (with-directory-excursion "../source"
973 (invoke "pytest" "tests/c_api_test/test_.py")))))))
974 (build-system cmake-build-system)
975 (home-page "https://github.com/Microsoft/LightGBM")
976 (synopsis "Gradient boosting framework based on decision tree algorithms")
977 (description "LightGBM is a gradient boosting framework that uses tree
978 based learning algorithms. It is designed to be distributed and efficient with
979 the following advantages:
982 @item Faster training speed and higher efficiency
983 @item Lower memory usage
984 @item Better accuracy
985 @item Parallel and GPU learning supported (not enabled in this package)
986 @item Capable of handling large-scale data
988 (license license:expat)))
990 (define-public vowpal-wabbit
991 ;; Language bindings not included.
993 (name "vowpal-wabbit")
998 (url "https://github.com/JohnLangford/vowpal_wabbit")
1002 "04bwzk6ifgnz3fmzid8b7avxf9n5pnx9xcjm61nkjng1vv0bpj8x"))
1003 (file-name (git-file-name name version))))
1009 (list (string-append "--with-boost="
1010 (assoc-ref %build-inputs "boost")))
1012 (modify-phases %standard-phases
1013 (add-after 'unpack 'make-files-writable
1015 (for-each make-file-writable (find-files "." ".*")) #t)))))
1016 (build-system gnu-build-system)
1017 (home-page "https://github.com/JohnLangford/vowpal_wabbit")
1018 (synopsis "Fast machine learning library for online learning")
1019 (description "Vowpal Wabbit is a machine learning system with techniques
1020 such as online, hashing, allreduce, reductions, learning2search, active, and
1021 interactive learning.")
1022 (license license:bsd-3)))
1024 (define-public python2-fastlmm
1026 (name "python2-fastlmm")
1031 (uri (pypi-uri "fastlmm" version ".zip"))
1034 "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
1035 (build-system python-build-system)
1037 `(#:tests? #f ; some test files are missing
1038 #:python ,python-2)) ; only Python 2.7 is supported
1040 `(("python2-numpy" ,python2-numpy)
1041 ("python2-scipy" ,python2-scipy)
1042 ("python2-matplotlib" ,python2-matplotlib)
1043 ("python2-pandas" ,python2-pandas)
1044 ("python2-scikit-learn" ,python2-scikit-learn)
1045 ("python2-pysnptools" ,python2-pysnptools)))
1048 ("python2-cython" ,python2-cython)
1049 ("python2-mock" ,python2-mock)
1050 ("python2-nose" ,python2-nose)))
1051 (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
1052 (synopsis "Perform genome-wide association studies on large data sets")
1054 "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
1055 Models, is a program for performing both single-SNP and SNP-set genome-wide
1056 association studies (GWAS) on extremely large data sets.")
1057 (license license:asl2.0)))
1059 ;; There have been no proper releases yet.
1060 (define-public kaldi
1061 (let ((commit "d4791c0f3fc1a09c042dac365e120899ee2ad21e")
1065 (version (git-version "0" revision commit))
1069 (url "https://github.com/kaldi-asr/kaldi.git")
1071 (file-name (git-file-name name version))
1074 "07k80my6f19mhrkwbzhjsnpf9871wmrwkl0ym468i830w67qyjrz"))))
1075 (build-system gnu-build-system)
1077 `(#:test-target "test"
1079 (modify-phases %standard-phases
1080 (add-after 'unpack 'chdir
1081 (lambda _ (chdir "src") #t))
1083 (lambda* (#:key build system inputs outputs #:allow-other-keys)
1084 (when (not (or (string-prefix? "x86_64" system)
1085 (string-prefix? "i686" system)))
1086 (substitute* "makefiles/linux_openblas.mk"
1087 (("-msse -msse2") "")))
1088 (substitute* "makefiles/default_rules.mk"
1089 (("/bin/bash") (which "bash")))
1090 (substitute* "Makefile"
1091 (("ext_depend: check_portaudio")
1093 (substitute* '("online/Makefile"
1094 "onlinebin/Makefile"
1095 "gst-plugin/Makefile")
1096 (("../../tools/portaudio/install")
1097 (assoc-ref inputs "portaudio")))
1099 ;; This `configure' script doesn't support variables passed as
1100 ;; arguments, nor does it support "prefix".
1101 (let ((out (assoc-ref outputs "out"))
1102 (openblas (assoc-ref inputs "openblas"))
1103 (openfst (assoc-ref inputs "openfst")))
1104 (substitute* "configure"
1105 (("check_for_slow_expf;") "")
1106 ;; This affects the RPATH and also serves as the installation
1108 (("KALDILIBDIR=`pwd`/lib")
1109 (string-append "KALDILIBDIR=" out "/lib")))
1110 (mkdir-p out) ; must exist
1111 (setenv "CONFIG_SHELL" (which "bash"))
1112 (setenv "OPENFST_VER" ,(package-version openfst))
1113 (invoke "./configure"
1116 (string-append "--openblas-root=" openblas)
1117 (string-append "--fst-root=" openfst)))))
1118 (add-after 'build 'build-ext-and-gstreamer-plugin
1120 (invoke "make" "-C" "online" "depend")
1121 (invoke "make" "-C" "online")
1122 (invoke "make" "-C" "onlinebin" "depend")
1123 (invoke "make" "-C" "onlinebin")
1124 (invoke "make" "-C" "gst-plugin" "depend")
1125 (invoke "make" "-C" "gst-plugin")
1127 ;; TODO: also install the executables.
1129 (lambda* (#:key outputs #:allow-other-keys)
1130 (let* ((out (assoc-ref outputs "out"))
1131 (inc (string-append out "/include"))
1132 (lib (string-append out "/lib")))
1134 ;; The build phase installed symlinks to the actual
1135 ;; libraries. Install the actual targets.
1136 (for-each (lambda (file)
1137 (let ((target (readlink file)))
1139 (install-file target lib)))
1140 (find-files lib "\\.so"))
1142 (for-each (lambda (file)
1143 (let ((target-dir (string-append inc "/" (dirname file))))
1144 (install-file file target-dir)))
1145 (find-files "." "\\.h"))
1146 (install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
1147 (string-append lib "/gstreamer-1.0"))
1150 `(("alsa-lib" ,alsa-lib)
1151 ("gfortran" ,gfortran "lib")
1153 ("gstreamer" ,gstreamer)
1155 ("openblas" ,openblas)
1156 ("openfst" ,openfst)
1157 ("portaudio" ,portaudio)
1158 ("python" ,python)))
1160 `(("glib" ,glib "bin") ; glib-genmarshal
1163 ("pkg-config" ,pkg-config)
1165 (home-page "https://kaldi-asr.org/")
1166 (synopsis "Speech recognition toolkit")
1167 (description "Kaldi is an extensible toolkit for speech recognition
1169 (license license:asl2.0))))
1171 (define-public gst-kaldi-nnet2-online
1172 (let ((commit "cb227ef43b66a9835c14eb0ad39e08ee03c210ad")
1175 (name "gst-kaldi-nnet2-online")
1176 (version (git-version "0" revision commit))
1180 (url "https://github.com/alumae/gst-kaldi-nnet2-online.git")
1182 (file-name (git-file-name name version))
1185 "1i6ffwiavxx07ri0lxix6s8q0r31x7i4xxvhys5jxkixf5q34w8g"))))
1186 (build-system gnu-build-system)
1188 `(#:tests? #f ; there are none
1190 (list (string-append "SHELL="
1191 (assoc-ref %build-inputs "bash") "/bin/bash")
1192 (string-append "KALDI_ROOT="
1193 (assoc-ref %build-inputs "kaldi-src"))
1194 (string-append "KALDILIBDIR="
1195 (assoc-ref %build-inputs "kaldi") "/lib")
1196 "KALDI_FLAVOR=dynamic")
1198 (modify-phases %standard-phases
1199 (add-after 'unpack 'chdir
1200 (lambda _ (chdir "src") #t))
1202 (lambda* (#:key inputs #:allow-other-keys)
1203 (let ((glib (assoc-ref inputs "glib")))
1204 (setenv "CXXFLAGS" "-fPIC")
1205 (setenv "CPLUS_INCLUDE_PATH"
1206 (string-append glib "/include/glib-2.0:"
1207 glib "/lib/glib-2.0/include:"
1208 (assoc-ref inputs "gstreamer")
1209 "/include/gstreamer-1.0")))
1210 (substitute* "Makefile"
1211 (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
1212 (("\\$\\(error Cannot find") "#"))
1214 (add-before 'build 'build-depend
1215 (lambda* (#:key make-flags #:allow-other-keys)
1216 (apply invoke "make" "depend" make-flags)))
1218 (lambda* (#:key outputs #:allow-other-keys)
1219 (let* ((out (assoc-ref outputs "out"))
1220 (lib (string-append out "/lib/gstreamer-1.0")))
1221 (install-file "libgstkaldinnet2onlinedecoder.so" lib)
1225 ("gstreamer" ,gstreamer)
1226 ("jansson" ,jansson)
1227 ("openfst" ,openfst)
1231 ("glib:bin" ,glib "bin") ; glib-genmarshal
1232 ("kaldi-src" ,(package-source kaldi))
1233 ("pkg-config" ,pkg-config)))
1234 (home-page "https://kaldi-asr.org/")
1235 (synopsis "Gstreamer plugin for decoding speech")
1236 (description "This package provides a GStreamer plugin that wraps
1237 Kaldi's @code{SingleUtteranceNnet2Decoder}. It requires iVector-adapted DNN
1238 acoustic models. The iVectors are adapted to the current audio stream
1240 (license license:asl2.0))))
1242 (define-public kaldi-gstreamer-server
1243 ;; This is the tip of the py3 branch
1244 (let ((commit "f68cab490be7eb0da2af1475fbc16655f50a60cb")
1247 (name "kaldi-gstreamer-server")
1248 (version (git-version "0" revision commit))
1252 (url "https://github.com/alumae/kaldi-gstreamer-server.git")
1254 (file-name (git-file-name name version))
1257 "17lh1368vkg8ngrcbn2phvigzlmalrqg6djx2gg61qq1a0nj87dm"))))
1258 (build-system gnu-build-system)
1260 `(#:tests? #f ; there are no tests that can be run automatically
1261 #:modules ((guix build utils)
1262 (guix build gnu-build-system)
1265 (modify-phases %standard-phases
1268 (lambda* (#:key outputs #:allow-other-keys)
1269 ;; Disable hash randomization to ensure the generated .pycs
1270 ;; are reproducible.
1271 (setenv "PYTHONHASHSEED" "0")
1272 (with-directory-excursion "kaldigstserver"
1273 ;; See https://github.com/alumae/kaldi-gstreamer-server/issues/232
1274 (substitute* "master_server.py"
1275 (("\\.replace\\('\\\\.*") ")"))
1277 ;; This is a Python 2 file
1278 (delete-file "decoder_test.py")
1279 (delete-file "test-buffer.py")
1281 (for-each (lambda (file)
1285 "-f" ; force rebuild
1287 (find-files "." "\\.py$")))
1290 (lambda* (#:key inputs outputs #:allow-other-keys)
1291 (let* ((out (assoc-ref outputs "out"))
1292 (bin (string-append out "/bin"))
1293 (share (string-append out "/share/kaldi-gstreamer-server/")))
1294 ;; Install Python files
1295 (with-directory-excursion "kaldigstserver"
1296 (for-each (cut install-file <> share)
1297 (find-files "." ".*")))
1299 ;; Install sample configuration files
1300 (for-each (cut install-file <> share)
1301 (find-files "." "\\.yaml"))
1303 ;; Install executables
1305 (let* ((server (string-append bin "/kaldi-gst-server"))
1306 (client (string-append bin "/kaldi-gst-client"))
1307 (worker (string-append bin "/kaldi-gst-worker"))
1308 (PYTHONPATH (getenv "PYTHONPATH"))
1309 (GST_PLUGIN_PATH (string-append
1310 (assoc-ref inputs "gst-kaldi-nnet2-online")
1311 "/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
1312 (wrap (lambda (wrapper what)
1313 (with-output-to-file wrapper
1317 export PYTHONPATH=~a
1318 export GST_PLUGIN_PATH=~a
1319 exec ~a ~a/~a \"$@\"~%"
1320 (which "bash") PYTHONPATH GST_PLUGIN_PATH
1321 (which "python") share what)))
1322 (chmod wrapper #o555))))
1324 (list server client worker)
1325 (list "master_server.py"
1330 `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
1331 ("python" ,python-wrapper)
1332 ("python-pygobject" ,python-pygobject)
1333 ("python-pyyaml" ,python-pyyaml)
1334 ("python-tornado" ,python-tornado-6)))
1335 (home-page "https://github.com/alumae/kaldi-gstreamer-server")
1336 (synopsis "Real-time full-duplex speech recognition server")
1337 (description "This is a real-time full-duplex speech recognition server,
1338 based on the Kaldi toolkit and the GStreamer framework and implemented in
1340 (license license:bsd-2))))
1342 ;; Note that Tensorflow includes a "third_party" directory, which seems to not
1343 ;; only contain modified subsets of upstream library source code, but also
1344 ;; adapter headers provided by Google (such as the fft.h header, which is not
1345 ;; part of the upstream project code). The Tensorflow code includes headers
1346 ;; from the "third_party" directory. It does not look like we can replace
1347 ;; these headers with unmodified upstream files, so we keep them.
1348 (define-public tensorflow
1356 (url "https://github.com/tensorflow/tensorflow.git")
1357 (commit (string-append "v" version))))
1358 (file-name (string-append "tensorflow-" version "-checkout"))
1361 "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
1362 (build-system cmake-build-system)
1364 `(#:tests? #f ; no "check" target
1365 #:build-type "Release"
1367 (let ((protobuf (assoc-ref %build-inputs "protobuf"))
1368 (protobuf:native (assoc-ref %build-inputs "protobuf:native"))
1369 (jsoncpp (assoc-ref %build-inputs "jsoncpp"))
1370 (snappy (assoc-ref %build-inputs "snappy"))
1371 (sqlite (assoc-ref %build-inputs "sqlite")))
1373 ;; Use protobuf from Guix
1374 (string-append "-Dprotobuf_STATIC_LIBRARIES="
1375 protobuf "/lib/libprotobuf.so")
1376 (string-append "-DPROTOBUF_PROTOC_EXECUTABLE="
1377 protobuf:native "/bin/protoc")
1379 ;; Use snappy from Guix
1380 (string-append "-Dsnappy_STATIC_LIBRARIES="
1381 snappy "/lib/libsnappy.so")
1382 ;; Yes, this is not actually the include directory but a prefix...
1383 (string-append "-Dsnappy_INCLUDE_DIR=" snappy)
1385 ;; Use jsoncpp from Guix
1386 (string-append "-Djsoncpp_STATIC_LIBRARIES="
1387 jsoncpp "/lib/libjsoncpp.so")
1388 ;; Yes, this is not actually the include directory but a prefix...
1389 (string-append "-Djsoncpp_INCLUDE_DIR=" jsoncpp)
1391 ;; Use sqlite from Guix
1392 (string-append "-Dsqlite_STATIC_LIBRARIES="
1393 sqlite "/lib/libsqlite.a")
1395 ;; Use system libraries wherever possible. Currently, this
1396 ;; only affects zlib.
1397 "-Dsystemlib_ALL=ON"
1398 "-Dtensorflow_ENABLE_POSITION_INDEPENDENT_CODE=ON"
1399 "-Dtensorflow_BUILD_SHARED_LIB=ON"
1400 "-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=OFF"
1401 "-Dtensorflow_ENABLE_SSL_SUPPORT=OFF"
1402 "-Dtensorflow_BUILD_CONTRIB_KERNELS=OFF"))
1405 #:modules ((ice-9 ftw)
1407 (guix build cmake-build-system)
1408 ((guix build python-build-system)
1409 #:select (python-version)))
1410 #:imported-modules (,@%cmake-build-system-modules
1411 (guix build python-build-system))
1413 (modify-phases %standard-phases
1414 (add-after 'unpack 'set-source-file-times-to-1980
1415 ;; At the end of the tf_python_build_pip_package target, a ZIP
1416 ;; archive should be generated via bdist_wheel, but it fails with
1417 ;; "ZIP does not support timestamps before 1980". Luckily,
1418 ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
1420 (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
1421 ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
1422 (add-after 'unpack 'python3.7-compatibility
1424 (substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
1425 "tensorflow/python/lib/core/ndarray_tensor.cc"
1426 "tensorflow/python/lib/core/py_func.cc")
1427 (("PyUnicode_AsUTF8") "(char *)PyUnicode_AsUTF8"))
1428 (substitute* "tensorflow/c/eager/c_api.h"
1429 (("unsigned char async")
1430 "unsigned char is_async"))
1432 ;; Remove dependency on tensorboard, a complicated but probably
1433 ;; optional package.
1434 (substitute* "tensorflow/tools/pip_package/setup.py"
1435 ((".*'tensorboard >.*") ""))
1437 ;; Fix the build with python-3.8, taken from rejected upstream patch:
1438 ;; https://github.com/tensorflow/tensorflow/issues/34197
1439 (substitute* (find-files "tensorflow/python" ".*\\.cc$")
1440 (("(nullptr,)(\\ +/. tp_print)" _ _ tp_print)
1441 (string-append "NULL, " tp_print)))
1443 (add-after 'python3.7-compatibility 'chdir
1444 (lambda _ (chdir "tensorflow/contrib/cmake") #t))
1445 (add-after 'chdir 'disable-downloads
1446 (lambda* (#:key inputs #:allow-other-keys)
1447 (substitute* (find-files "external" "\\.cmake$")
1448 (("GIT_REPOSITORY.*") "")
1451 "DOWNLOAD_COMMAND \"\"\nPREFIX "))
1453 ;; Use packages from Guix
1454 (let ((grpc (assoc-ref inputs "grpc")))
1455 (substitute* "CMakeLists.txt"
1457 (("include\\(sqlite\\)") "")
1458 (("\\$\\{sqlite_STATIC_LIBRARIES\\}")
1459 (string-append (assoc-ref inputs "sqlite")
1460 "/lib/libsqlite3.so"))
1461 (("sqlite_copy_headers_to_destination") "")
1464 (("include\\(png\\)") "")
1465 (("\\$\\{png_STATIC_LIBRARIES\\}")
1466 (string-append (assoc-ref inputs "libpng")
1467 "/lib/libpng16.so"))
1468 (("png_copy_headers_to_destination") "")
1471 (("include\\(jpeg\\)") "")
1472 (("\\$\\{jpeg_STATIC_LIBRARIES\\}")
1473 (string-append (assoc-ref inputs "libjpeg")
1475 (("jpeg_copy_headers_to_destination") "")
1478 (("include\\(gif\\)") "")
1479 (("\\$\\{gif_STATIC_LIBRARIES\\}")
1480 (string-append (assoc-ref inputs "giflib")
1482 (("gif_copy_headers_to_destination") "")
1485 (("include\\(lmdb\\)") "")
1486 (("\\$\\{lmdb_STATIC_LIBRARIES\\}")
1487 (string-append (assoc-ref inputs "lmdb")
1489 (("lmdb_copy_headers_to_destination") "")
1492 (("include\\(protobuf\\)") "")
1493 (("protobuf_copy_headers_to_destination") "")
1494 (("^ +protobuf") "")
1497 (("include\\(grpc\\)")
1498 "find_package(grpc REQUIRED NAMES gRPC)")
1499 (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES grpc\\)") "")
1502 (("include\\(eigen\\)")
1503 (string-append "find_package(eigen REQUIRED NAMES Eigen3)
1504 set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
1505 (assoc-ref inputs "eigen") "/include/eigen3)"))
1509 (("include\\(snappy\\)")
1510 "add_definitions(-DTF_USE_SNAPPY)")
1511 (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES snappy\\)") "")
1514 (("include\\(jsoncpp\\)") "")
1515 (("^ +jsoncpp") ""))
1517 (substitute* "tf_core_framework.cmake"
1519 (("\\$\\{GRPC_BUILD\\}/grpc_cpp_plugin")
1520 (which "grpc_cpp_plugin"))
1521 ;; Link with gRPC libraries
1522 (("add_library\\(tf_protos_cc.*" m)
1524 (format #f "\ntarget_link_libraries(tf_protos_cc PRIVATE \
1525 ~a/lib/libgrpc++_unsecure.a \
1526 ~a/lib/libgrpc_unsecure.a \
1527 ~a/lib/libaddress_sorting.a \
1532 (assoc-ref inputs "c-ares"))))))
1533 (substitute* "tf_tools.cmake"
1534 (("add_dependencies\\(\\$\\{proto_text.*") ""))
1535 ;; Remove dependency on bundled grpc
1536 (substitute* "tf_core_distributed_runtime.cmake"
1537 (("tf_core_cpu grpc") "tf_core_cpu"))
1539 ;; This directory is a dependency of many targets.
1540 (mkdir-p "protobuf")
1542 (add-after 'configure 'unpack-third-party-sources
1543 (lambda* (#:key inputs #:allow-other-keys)
1544 ;; This is needed to configure bundled packages properly.
1545 (setenv "CONFIG_SHELL" (which "bash"))
1548 (let* ((what (assoc-ref inputs (string-append name "-src")))
1549 (name* (string-map (lambda (c)
1552 (where (string-append "../build/" name* "/src/" name*)))
1554 ((string-suffix? ".zip" what)
1556 (with-directory-excursion where
1557 (invoke "unzip" what)))
1558 ((string-suffix? ".tar.gz" what)
1560 (invoke "tar" "xf" what
1561 "-C" where "--strip-components=1"))
1563 (let ((parent (dirname where)))
1565 (with-directory-excursion parent
1566 (when (file-exists? name*)
1567 (delete-file-recursively name*))
1568 (copy-recursively what name*)
1569 (map make-file-writable
1570 (find-files name* ".*"))))))))
1580 (rename-file "../build/cub/src/cub/cub-1.8.0/"
1581 "../build/cub/src/cub/cub/")
1583 (add-after 'unpack 'fix-python-build
1584 (lambda* (#:key inputs outputs #:allow-other-keys)
1585 (mkdir-p "protobuf-src")
1586 (invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
1587 "-C" "protobuf-src" "--strip-components=1")
1588 (mkdir-p "eigen-src")
1589 (invoke "tar" "xf" (assoc-ref inputs "eigen:src")
1590 "-C" "eigen-src" "--strip-components=1")
1592 (substitute* "tensorflow/contrib/cmake/tf_python.cmake"
1593 ;; Ensure that all Python dependencies can be found at build time.
1594 (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
1595 (string-append m ":" (getenv "PYTHONPATH")))
1596 ;; Take protobuf source files from our source package.
1597 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
1598 (string-append (getcwd) "/protobuf-src/src/google")))
1600 (substitute* '("tensorflow/contrib/cmake/tf_shared_lib.cmake"
1601 "tensorflow/contrib/cmake/tf_python.cmake")
1602 ;; Take Eigen source files from our source package.
1603 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/eigen/src/eigen/")
1604 (string-append (getcwd) "/eigen-src/"))
1605 ;; Take Eigen headers from our own package.
1606 (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
1607 (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
1609 ;; Correct the RUNPATH of ops libraries generated for Python.
1610 ;; TODO: this doesn't work :(
1611 ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1612 ;; warning: RUNPATH contains bogus entries: ("/tmp/guix-build-tensorflow-1.9.0.drv-0/source/tensorflow/contrib/build")
1613 ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1614 ;; error: depends on 'libpywrap_tensorflow_internal.so', which
1615 ;; cannot be found in RUNPATH ...
1616 (substitute* "tensorflow/contrib/cmake/tf_cc_ops.cmake"
1617 (("set_target_properties.*")
1618 (string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
1619 COMPILE_FLAGS ${target_compile_flags} \
1620 INSTALL_RPATH_USE_LINK_PATH TRUE \
1621 INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
1623 (add-after 'build 'build-pip-package
1624 (lambda* (#:key outputs #:allow-other-keys)
1626 (string-append "-Wl,-rpath="
1627 (assoc-ref outputs "out") "/lib"))
1628 (invoke "make" "tf_python_build_pip_package")
1630 (add-after 'build-pip-package 'install-python
1631 (lambda* (#:key inputs outputs #:allow-other-keys)
1632 (let ((out (assoc-ref outputs "out"))
1633 (wheel (car (find-files "../build/tf_python/dist/" "\\.whl$")))
1634 (python-version (python-version
1635 (assoc-ref inputs "python"))))
1636 (invoke "python" "-m" "pip" "install" wheel
1637 (string-append "--prefix=" out))
1639 ;; XXX: broken RUNPATH, see fix-python-build phase.
1642 out "/lib/python" python-version
1643 "/site-packages/tensorflow/contrib/"
1644 "seq2seq/python/ops/lib_beam_search_ops.so"))
1647 `(("pkg-config" ,pkg-config)
1648 ("protobuf:native" ,protobuf-3.6) ; protoc
1649 ("protobuf:src" ,(package-source protobuf-3.6))
1650 ("eigen:src" ,(package-source eigen-for-tensorflow))
1651 ;; install_pip_packages.sh wants setuptools 39.1.0 specifically.
1652 ("python-setuptools" ,python-setuptools-for-tensorflow)
1654 ;; The commit hashes and URLs for third-party source code are taken
1655 ;; from "tensorflow/workspace.bzl".
1657 ,(let ((commit "ee7aa02")
1662 (url "https://boringssl.googlesource.com/boringssl")
1664 (file-name (string-append "boringssl-0-" revision
1665 (string-take commit 7)
1669 "1jf693q0nw0adsic6cgmbdx6g7wr4rj4vxa8j1hpn792fqhd8wgw")))))
1671 ,(let ((version "1.8.0"))
1674 (uri (string-append "https://mirror.bazel.build/github.com/NVlabs/"
1675 "cub/archive/" version ".zip"))
1676 (file-name (string-append "cub-" version ".zip"))
1679 "1hsqikqridb90dkxkjr2918dcry6pfh46ccnwrzawl56aamhdykb")))))
1680 ("double-conversion-src"
1681 ,(let ((commit "5664746")
1686 (url "https://github.com/google/double-conversion.git")
1689 (git-file-name "double-conversion"
1690 (string-append "0-" revision "."
1691 (string-take commit 7))))
1694 "1h5lppqqxcvdg5jq42i5msgwx20ryij3apvmndflngrgdpc04gn1")))))
1696 ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
1700 "https://mirror.bazel.build/github.com/google/farmhash/archive/"
1702 (file-name (string-append "farmhash-0-" (string-take commit 7)
1706 "185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
1707 ;; The license notice on the home page at
1708 ;; http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html says:
1709 ;; Copyright Takuya OOURA, 1996-2001
1711 ;; You may use, copy, modify and distribute this code for any purpose
1712 ;; (include commercial use) and without fee. Please refer to this
1713 ;; package when you modify this code.
1715 ;; We take the identical tarball from the Bazel mirror, because the URL
1716 ;; at the home page is not versioned and might change.
1720 (uri "https://mirror.bazel.build/www.kurims.kyoto-u.ac.jp/~ooura/fft.tgz")
1721 (file-name "fft2d.tar.gz")
1724 "15jjkfvhqvl2c0753d2di8hz0pyzn598g74wqy79awdrf1y67fsj"))))
1726 ,(let ((commit "be5edafc2e1a455768e260ccd68ae7317b6690ee")
1731 (url "https://github.com/google/highwayhash.git")
1733 (file-name (string-append "highwayhash-0-" revision
1734 (string-take commit 7)
1738 "154jwf98cyy54hldr94pgjn85zynly3abpnc1avmb8a18lzwjyb6")))))
1740 ,(let ((version "0559ce013feac8db639ee1bf776aca0325d28777")
1744 (uri (string-append "https://mirror.bazel.build/"
1745 "github.com/google/nsync/archive/"
1747 (file-name (string-append "nsync-0." revision
1748 "-" (string-take version 7)
1752 "0qdkyqym34x739mmzv97ah5r7ph462v5xkxqxvidmcfqbi64b132")))))
1754 ,(let ((commit "e7efc48")
1759 (url "https://github.com/google/re2")
1761 (file-name (string-append "re2-0-" revision
1762 (string-take commit 7)
1766 "161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign")))))
1767 ("googletest" ,googletest)
1771 `(("python-absl-py" ,python-absl-py)
1772 ("python-astor" ,python-astor)
1773 ("python-gast" ,python-gast)
1774 ("python-grpcio" ,python-grpcio)
1775 ("python-numpy" ,python-numpy)
1776 ("python-protobuf" ,python-protobuf-3.6)
1777 ("python-six" ,python-six)
1778 ("python-termcolo" ,python-termcolor)
1779 ("python-wheel" ,python-wheel)))
1781 `(("c-ares" ,c-ares)
1782 ("eigen" ,eigen-for-tensorflow)
1783 ("gemmlowp" ,gemmlowp-for-tensorflow)
1785 ("libjpeg" ,libjpeg-turbo)
1788 ("grpc" ,grpc-1.16.1 "static")
1789 ("grpc:bin" ,grpc-1.16.1)
1790 ("jsoncpp" ,jsoncpp-for-tensorflow)
1793 ("protobuf" ,protobuf-3.6)
1794 ("python" ,python-wrapper)
1796 (home-page "https://tensorflow.org")
1797 (synopsis "Machine learning framework")
1799 "TensorFlow is a flexible platform for building and training machine
1800 learning models. It provides a library for high performance numerical
1801 computation and includes high level Python APIs, including both a sequential
1802 API for beginners that allows users to build models quickly by plugging
1803 together building blocks and a subclassing API with an imperative style for
1804 advanced research.")
1805 (license license:asl2.0)))
1807 (define-public python-iml
1814 (uri (pypi-uri "iml" version))
1817 "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
1818 (build-system python-build-system)
1820 `(("ipython" ,python-ipython)
1821 ("numpy" ,python-numpy)
1822 ("pandas" ,python-pandas)
1823 ("scipy" ,python-scipy)))
1825 `(("nose" ,python-nose)))
1826 (home-page "https://github.com/interpretable-ml/iml")
1827 (synopsis "Interpretable Machine Learning (iML) package")
1828 (description "Interpretable ML (iML) is a set of data type objects,
1829 visualizations, and interfaces that can be used by any method designed to
1830 explain the predictions of machine learning models (or really the output of
1831 any function). It currently contains the interface and IO code from the Shap
1832 project, and it will potentially also do the same for the Lime project.")
1833 (license license:expat)))
1835 (define-public python-keras-applications
1837 (name "python-keras-applications")
1842 (uri (pypi-uri "Keras_Applications" version))
1845 "1rcz31ca4axa6kzhjx4lwqxbg4wvlljkj8qj9a7p9sfd5fhzjyam"))))
1846 (build-system python-build-system)
1847 ;; The tests require Keras, but this package is needed to build Keras.
1848 (arguments '(#:tests? #f))
1850 `(("python-h5py" ,python-h5py)
1851 ("python-numpy" ,python-numpy)))
1853 `(("python-pytest" ,python-pytest)
1854 ("python-pytest-cov" ,python-pytest-cov)
1855 ("python-pytest-pep8" ,python-pytest-pep8)
1856 ("python-pytest-xdist" ,python-pytest-xdist)))
1857 (home-page "https://github.com/keras-team/keras-applications")
1858 (synopsis "Reference implementations of popular deep learning models")
1860 "This package provides reference implementations of popular deep learning
1861 models for use with the Keras deep learning framework.")
1862 (license license:expat)))
1864 (define-public python-keras-preprocessing
1866 (name "python-keras-preprocessing")
1871 (uri (pypi-uri "Keras_Preprocessing" version))
1874 "1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as"))))
1875 (build-system python-build-system)
1877 `(("python-numpy" ,python-numpy)
1878 ("python-six" ,python-six)))
1880 `(("python-pandas" ,python-pandas)
1881 ("python-pillow" ,python-pillow)
1882 ("python-pytest" ,python-pytest)
1883 ("python-pytest-cov" ,python-pytest-cov)
1884 ("python-pytest-xdist" ,python-pytest-xdist)
1885 ("tensorflow" ,tensorflow)))
1886 (home-page "https://github.com/keras-team/keras-preprocessing/")
1887 (synopsis "Data preprocessing and augmentation for deep learning models")
1889 "Keras Preprocessing is the data preprocessing and data augmentation
1890 module of the Keras deep learning library. It provides utilities for working
1891 with image data, text data, and sequence data.")
1892 (license license:expat)))
1894 (define-public python-keras
1896 (name "python-keras")
1901 (uri (pypi-uri "Keras" version))
1902 (patches (search-patches "python-keras-integration-test.patch"))
1905 "1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh"))))
1906 (build-system python-build-system)
1909 (modify-phases %standard-phases
1910 (add-after 'unpack 'remove-tests-for-unavailable-features
1912 (delete-file "keras/backend/theano_backend.py")
1913 (delete-file "keras/backend/cntk_backend.py")
1914 (delete-file "tests/keras/backend/backend_test.py")
1916 ;; FIXME: This doesn't work because Tensorflow is missing the
1917 ;; coder ops library.
1918 (delete-file "tests/keras/test_callbacks.py")
1922 ;; These tests attempt to download data files from the internet.
1923 (delete-file "tests/integration_tests/test_datasets.py")
1924 (delete-file "tests/integration_tests/imagenet_utils_test.py")
1926 (setenv "PYTHONPATH"
1927 (string-append (getcwd) "/build/lib:"
1928 (getenv "PYTHONPATH")))
1929 (invoke "py.test" "-v"
1930 "-p" "no:cacheprovider"
1931 "--ignore" "keras/utils"))))))
1933 `(("python-h5py" ,python-h5py)
1934 ("python-keras-applications" ,python-keras-applications)
1935 ("python-keras-preprocessing" ,python-keras-preprocessing)
1936 ("python-numpy" ,python-numpy)
1937 ("python-pydot" ,python-pydot)
1938 ("python-pyyaml" ,python-pyyaml)
1939 ("python-scipy" ,python-scipy)
1940 ("python-six" ,python-six)
1941 ("tensorflow" ,tensorflow)
1942 ("graphviz" ,graphviz)))
1944 `(("python-pandas" ,python-pandas)
1945 ("python-pytest" ,python-pytest)
1946 ("python-pytest-cov" ,python-pytest-cov)
1947 ("python-pytest-pep8" ,python-pytest-pep8)
1948 ("python-pytest-timeout" ,python-pytest-timeout)
1949 ("python-pytest-xdist" ,python-pytest-xdist)
1950 ("python-sphinx" ,python-sphinx)
1951 ("python-requests" ,python-requests)))
1952 (home-page "https://github.com/keras-team/keras")
1953 (synopsis "High-level deep learning framework")
1954 (description "Keras is a high-level neural networks API, written in Python
1955 and capable of running on top of TensorFlow. It was developed with a focus on
1956 enabling fast experimentation. Use Keras if you need a deep learning library
1960 @item Allows for easy and fast prototyping (through user friendliness,
1961 modularity, and extensibility).
1962 @item Supports both convolutional networks and recurrent networks, as well as
1963 combinations of the two.
1964 @item Runs seamlessly on CPU and GPU.
1966 (license license:expat)))
1968 (define-public sbcl-cl-libsvm-format
1969 (let ((commit "3300f84fd8d9f5beafc114f543f9d83417c742fb")
1972 (name "sbcl-cl-libsvm-format")
1973 (version (git-version "0.1.0" revision commit))
1978 (url "https://github.com/masatoi/cl-libsvm-format.git")
1980 (file-name (git-file-name name version))
1983 "0284aj84xszhkhlivaigf9qj855fxad3mzmv3zfr0qzb5k0nzwrg"))))
1984 (build-system asdf-build-system/sbcl)
1986 `(("prove" ,sbcl-prove)
1987 ("prove-asdf" ,sbcl-prove-asdf)))
1989 `(("alexandria" ,sbcl-alexandria)))
1990 (synopsis "LibSVM data format reader for Common Lisp")
1992 "This Common Lisp library provides a fast reader for data in LibSVM
1994 (home-page "https://github.com/masatoi/cl-libsvm-format")
1995 (license license:expat))))
1997 (define-public cl-libsvm-format
1998 (sbcl-package->cl-source-package sbcl-cl-libsvm-format))
2000 (define-public ecl-cl-libsvm-format
2001 (sbcl-package->ecl-package sbcl-cl-libsvm-format))
2003 (define-public sbcl-cl-online-learning
2004 (let ((commit "fc7a34f4f161cd1c7dd747d2ed8f698947781423")
2007 (name "sbcl-cl-online-learning")
2008 (version (git-version "0.5" revision commit))
2013 (url "https://github.com/masatoi/cl-online-learning.git")
2015 (file-name (git-file-name name version))
2018 "14x95rlg80ay5hv645ki57pqvy12v28hz4k1w0f6bsfi2rmpxchq"))))
2019 (build-system asdf-build-system/sbcl)
2021 `(("prove" ,sbcl-prove)
2022 ("prove-asdf" ,sbcl-prove-asdf)))
2024 `(("cl-libsvm-format" ,sbcl-cl-libsvm-format)
2025 ("cl-store" ,sbcl-cl-store)))
2027 `(;; FIXME: Tests pass but then the check phase crashes
2029 (synopsis "Online Machine Learning for Common Lisp")
2031 "This library contains a collection of machine learning algorithms for
2032 online linear classification written in Common Lisp.")
2033 (home-page "https://github.com/masatoi/cl-online-learning")
2034 (license license:expat))))
2036 (define-public cl-online-learning
2037 (sbcl-package->cl-source-package sbcl-cl-online-learning))
2039 (define-public ecl-cl-online-learning
2040 (sbcl-package->ecl-package sbcl-cl-online-learning))
2042 (define-public sbcl-cl-random-forest
2043 (let ((commit "85fbdd4596d40e824f70f1b7cf239cf544e49d51")
2046 (name "sbcl-cl-random-forest")
2047 (version (git-version "0.1" revision commit))
2052 (url "https://github.com/masatoi/cl-random-forest.git")
2054 (file-name (git-file-name name version))
2057 "097xv60i1ndz68sg9p4pc7c5gvyp9i1xgw966b4wwfq3x6hbz421"))))
2058 (build-system asdf-build-system/sbcl)
2060 `(("prove" ,sbcl-prove)
2061 ("prove-asdf" ,sbcl-prove-asdf)
2062 ("trivial-garbage" ,sbcl-trivial-garbage)))
2064 `(("alexandria" ,sbcl-alexandria)
2065 ("cl-libsvm-format" ,sbcl-cl-libsvm-format)
2066 ("cl-online-learning" ,sbcl-cl-online-learning)
2067 ("lparallel" ,sbcl-lparallel)))
2069 `(#:tests? #f)) ; The tests download data from the Internet
2070 (synopsis "Random Forest and Global Refinement for Common Lisp")
2072 "CL-random-forest is an implementation of Random Forest for multiclass
2073 classification and univariate regression written in Common Lisp. It also
2074 includes an implementation of Global Refinement of Random Forest.")
2075 (home-page "https://github.com/masatoi/cl-random-forest")
2076 (license license:expat))))
2078 (define-public cl-random-forest
2079 (sbcl-package->cl-source-package sbcl-cl-random-forest))
2081 (define-public ecl-cl-random-forest
2082 (sbcl-package->ecl-package sbcl-cl-random-forest))
2085 (let ((version "0.0.0") ; no proper version tag
2086 (commit "ca528e32fea9ca8f2b16053cff17160290fc84ce")
2090 (version (git-version version revision commit))
2095 (url "https://github.com/facebookincubator/gloo.git")
2097 (file-name (git-file-name name version))
2100 "1q9f80zy75f6njrzrqkmhc0g3qxs4gskr7ns2jdqanxa2ww7a99w"))))
2101 (build-system cmake-build-system)
2103 `(("googletest" ,googletest)))
2105 `(#:configure-flags '("-DBUILD_TEST=1")
2107 (modify-phases %standard-phases
2110 (invoke "make" "gloo_test")
2112 (synopsis "Collective communications library")
2114 "Gloo is a collective communications library. It comes with a
2115 number of collective algorithms useful for machine learning applications.
2116 These include a barrier, broadcast, and allreduce.")
2117 (home-page "https://github.com/facebookincubator/gloo")
2118 (license license:bsd-3))))
2120 (define-public python-umap-learn
2122 (name "python-umap-learn")
2127 (uri (pypi-uri "umap-learn" version))
2130 "02ada2yy6km6zgk2836kg1c97yrcpalvan34p8c57446finnpki1"))))
2131 (build-system python-build-system)
2133 `(("python-joblib" ,python-joblib)
2134 ("python-nose" ,python-nose)))
2136 `(("python-numba" ,python-numba)
2137 ("python-numpy" ,python-numpy)
2138 ("python-scikit-learn" ,python-scikit-learn)
2139 ("python-scipy" ,python-scipy)))
2140 (home-page "https://github.com/lmcinnes/umap")
2142 "Uniform Manifold Approximation and Projection")
2144 "Uniform Manifold Approximation and Projection is a dimension reduction
2145 technique that can be used for visualisation similarly to t-SNE, but also for
2146 general non-linear dimension reduction.")
2147 (license license:bsd-3)))