2051 lines
85 KiB
Scheme
2051 lines
85 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
|
||
;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
|
||
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
|
||
;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
|
||
;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
|
||
;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
|
||
;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
|
||
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
|
||
;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
|
||
;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
|
||
;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
|
||
;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
|
||
;;;
|
||
;;; This file is part of GNU Guix.
|
||
;;;
|
||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||
;;; under the terms of the GNU General Public License as published by
|
||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||
;;; your option) any later version.
|
||
;;;
|
||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||
;;; GNU General Public License for more details.
|
||
;;;
|
||
;;; You should have received a copy of the GNU General Public License
|
||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||
|
||
(define-module (gnu packages machine-learning)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (guix packages)
|
||
#:use-module (guix utils)
|
||
#:use-module (guix download)
|
||
#:use-module (guix svn-download)
|
||
#:use-module (guix build-system asdf)
|
||
#:use-module (guix build-system cmake)
|
||
#:use-module (guix build-system gnu)
|
||
#:use-module (guix build-system ocaml)
|
||
#:use-module (guix build-system python)
|
||
#:use-module (guix build-system r)
|
||
#:use-module (guix git-download)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages adns)
|
||
#:use-module (gnu packages algebra)
|
||
#:use-module (gnu packages audio)
|
||
#:use-module (gnu packages autotools)
|
||
#:use-module (gnu packages base)
|
||
#:use-module (gnu packages bash)
|
||
#:use-module (gnu packages boost)
|
||
#:use-module (gnu packages check)
|
||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages cran)
|
||
#:use-module (gnu packages databases)
|
||
#:use-module (gnu packages dejagnu)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages glib)
|
||
#:use-module (gnu packages graphviz)
|
||
#:use-module (gnu packages gstreamer)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages linux)
|
||
#:use-module (gnu packages lisp)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages mpi)
|
||
#:use-module (gnu packages ocaml)
|
||
#:use-module (gnu packages onc-rpc)
|
||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages protobuf)
|
||
#:use-module (gnu packages python)
|
||
#:use-module (gnu packages python-web)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages serialization)
|
||
#:use-module (gnu packages sphinx)
|
||
#:use-module (gnu packages statistics)
|
||
#:use-module (gnu packages sqlite)
|
||
#:use-module (gnu packages swig)
|
||
#:use-module (gnu packages tls)
|
||
#:use-module (gnu packages web)
|
||
#:use-module (gnu packages xml)
|
||
#:use-module (gnu packages xorg)
|
||
#:use-module (ice-9 match))
|
||
|
||
(define-public fann
|
||
;; The last release is >100 commits behind, so we package from git.
|
||
(let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
|
||
(package
|
||
(name "fann")
|
||
(version (string-append "2.2.0-1." (string-take commit 8)))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/libfann/fann.git")
|
||
(commit commit)))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(sha256
|
||
(base32
|
||
"0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out")))
|
||
(with-directory-excursion (string-append (getcwd) "/tests")
|
||
(invoke "./fann_tests"))))))))
|
||
(home-page "http://leenissen.dk/fann/wp/")
|
||
(synopsis "Fast Artificial Neural Network")
|
||
(description
|
||
"FANN is a free open source neural network library, which implements
|
||
multilayer artificial neural networks in C with support for both fully
|
||
connected and sparsely connected networks.")
|
||
(license license:lgpl2.1))))
|
||
|
||
(define-public libsvm
|
||
(package
|
||
(name "libsvm")
|
||
(version "3.23")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
|
||
name "-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0jpaq0rr92x38p4nk3gjan79ip67m6p80anb28z1d8601miysyi5"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; no "check" target
|
||
#:phases (modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(replace
|
||
'install ; no ‘install’ target
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin/")))
|
||
(mkdir-p bin)
|
||
(for-each (lambda (file)
|
||
(copy-file file (string-append bin file)))
|
||
'("svm-train"
|
||
"svm-predict"
|
||
"svm-scale")))
|
||
#t)))))
|
||
(home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
|
||
(synopsis "Library for Support Vector Machines")
|
||
(description
|
||
"LIBSVM is a machine learning library for support vector
|
||
classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
|
||
distribution estimation (one-class SVM). It supports multi-class
|
||
classification.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-libsvm
|
||
(package (inherit libsvm)
|
||
(name "python-libsvm")
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; no "check" target
|
||
#:make-flags '("-C" "python")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(replace
|
||
'install ; no ‘install’ target
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((site (string-append (assoc-ref outputs "out")
|
||
"/lib/python"
|
||
(string-take
|
||
(string-take-right
|
||
(assoc-ref inputs "python") 5) 3)
|
||
"/site-packages/")))
|
||
(substitute* "python/svm.py"
|
||
(("../libsvm.so.2") "libsvm.so.2"))
|
||
(mkdir-p site)
|
||
(for-each (lambda (file)
|
||
(copy-file file (string-append site (basename file))))
|
||
(find-files "python" "\\.py"))
|
||
(copy-file "libsvm.so.2"
|
||
(string-append site "libsvm.so.2")))
|
||
#t)))))
|
||
(inputs
|
||
`(("python" ,python)))
|
||
(synopsis "Python bindings of libSVM")))
|
||
|
||
(define-public ghmm
|
||
;; The latest release candidate is several years and a couple of fixes have
|
||
;; been published since. This is why we download the sources from the SVN
|
||
;; repository.
|
||
(let ((svn-revision 2341))
|
||
(package
|
||
(name "ghmm")
|
||
(version (string-append "0.9-rc3-0." (number->string svn-revision)))
|
||
(source (origin
|
||
(method svn-fetch)
|
||
(uri (svn-reference
|
||
(url "http://svn.code.sf.net/p/ghmm/code/trunk")
|
||
(revision svn-revision)))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(sha256
|
||
(base32
|
||
"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:imported-modules (,@%gnu-build-system-modules
|
||
(guix build python-build-system))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'enter-dir
|
||
(lambda _ (chdir "ghmm") #t))
|
||
(delete 'check)
|
||
(add-after 'install 'check
|
||
(assoc-ref %standard-phases 'check))
|
||
(add-before 'check 'fix-PYTHONPATH
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((python-version ((@@ (guix build python-build-system)
|
||
get-python-version)
|
||
(assoc-ref inputs "python"))))
|
||
(setenv "PYTHONPATH"
|
||
(string-append (getenv "PYTHONPATH")
|
||
":" (assoc-ref outputs "out")
|
||
"/lib/python" python-version
|
||
"/site-packages")))
|
||
#t))
|
||
(add-after 'enter-dir 'fix-runpath
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(substitute* "ghmmwrapper/setup.py"
|
||
(("^(.*)extra_compile_args = \\[" line indent)
|
||
(string-append indent
|
||
"extra_link_args = [\"-Wl,-rpath="
|
||
(assoc-ref outputs "out") "/lib\"],\n"
|
||
line
|
||
"\"-Wl,-rpath="
|
||
(assoc-ref outputs "out")
|
||
"/lib\", ")))
|
||
#t))
|
||
(add-after 'enter-dir 'disable-broken-tests
|
||
(lambda _
|
||
(substitute* "tests/Makefile.am"
|
||
;; GHMM_SILENT_TESTS is assumed to be a command.
|
||
(("TESTS_ENVIRONMENT.*") "")
|
||
;; Do not build broken tests.
|
||
(("chmm .*") "")
|
||
(("read_fa .*") "")
|
||
(("mcmc .*") "")
|
||
(("label_higher_order_test.*$")
|
||
"label_higher_order_test\n"))
|
||
|
||
;; These Python unittests are broken as there is no gato.
|
||
;; See https://sourceforge.net/p/ghmm/support-requests/3/
|
||
(substitute* "ghmmwrapper/ghmmunittests.py"
|
||
(("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
|
||
line indent)
|
||
(string-append indent
|
||
"@unittest.skip(\"Disabled by Guix\")\n"
|
||
line)))
|
||
#t)))))
|
||
(inputs
|
||
`(("python" ,python-2) ; only Python 2 is supported
|
||
("libxml2" ,libxml2)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("dejagnu" ,dejagnu)
|
||
("swig" ,swig)
|
||
("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)))
|
||
(home-page "http://ghmm.org")
|
||
(synopsis "Hidden Markov Model library")
|
||
(description
|
||
"The General Hidden Markov Model library (GHMM) is a C library with
|
||
additional Python bindings implementing a wide range of types of @dfn{Hidden
|
||
Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
|
||
training, HMM clustering, HMM mixtures.")
|
||
(license license:lgpl2.0+))))
|
||
|
||
(define-public mcl
|
||
(package
|
||
(name "mcl")
|
||
(version "14.137")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://micans.org/mcl/src/mcl-"
|
||
(string-replace-substring version "." "-")
|
||
".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags (list "--enable-blast")))
|
||
(inputs
|
||
`(("perl" ,perl)))
|
||
(home-page "http://micans.org/mcl/")
|
||
(synopsis "Clustering algorithm for graphs")
|
||
(description
|
||
"The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
|
||
fast and scalable unsupervised cluster algorithm for graphs (also known as
|
||
networks) based on simulation of (stochastic) flow in graphs.")
|
||
;; In the LICENCE file and web page it says "The software is licensed
|
||
;; under the GNU General Public License, version 3.", but in several of
|
||
;; the source code files it suggests GPL3 or later.
|
||
;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
|
||
(license license:gpl3)))
|
||
|
||
(define-public ocaml-mcl
|
||
(package
|
||
(name "ocaml-mcl")
|
||
(version "12-068oasis4")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/fhcrc/mcl.git")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0009dc3h2jp3qg5val452wngpqnbfyhbcxylghq0mrjqxx0jdq5p"))))
|
||
(build-system ocaml-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'patch-paths
|
||
(lambda _
|
||
(substitute* "configure"
|
||
(("/bin/sh") (which "sh")))
|
||
(substitute* "setup.ml"
|
||
(("LDFLAGS=-fPIC")
|
||
(string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))
|
||
(("-std=c89") "-std=gnu99")
|
||
|
||
;; This is a mutable string, which is no longer supported. Use
|
||
;; a byte buffer instead.
|
||
(("String.make \\(String.length s\\)")
|
||
"Bytes.make (String.length s)")
|
||
|
||
;; These two belong together.
|
||
(("OASISString.replace_chars")
|
||
"Bytes.to_string (OASISString.replace_chars")
|
||
((" s;")
|
||
" s);"))
|
||
(substitute* "myocamlbuild.ml"
|
||
(("std=c89") "std=gnu99"))
|
||
;; Since we build with a more recent OCaml, we have to use C99 or
|
||
;; later. This causes problems with the old C code.
|
||
(substitute* "src/impala/matrix.c"
|
||
(("restrict") "restrict_"))
|
||
#t)))))
|
||
(native-inputs
|
||
`(("ocamlbuild" ,ocamlbuild)))
|
||
(home-page "https://github.com/fhcrc/mcl")
|
||
(synopsis "OCaml wrappers around MCL")
|
||
(description
|
||
"This package provides OCaml bindings for the MCL graph clustering
|
||
algorithm.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public randomjungle
|
||
(package
|
||
(name "randomjungle")
|
||
(version "2.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
|
||
"/randomjungle/randomjungle-" version ".tar_.gz"))
|
||
(patches (search-patches "randomjungle-disable-static-build.patch"))
|
||
(sha256
|
||
(base32
|
||
"12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list "--disable-static"
|
||
(string-append "--with-boost="
|
||
(assoc-ref %build-inputs "boost")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before
|
||
'configure 'set-CXXFLAGS
|
||
(lambda _
|
||
(setenv "CXXFLAGS" "-fpermissive ")
|
||
#t)))))
|
||
(inputs
|
||
`(("boost" ,boost)
|
||
("gsl" ,gsl)
|
||
("libxml2" ,libxml2)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("gfortran:lib" ,gfortran "lib")))
|
||
;; Non-portable assembly instructions are used so building fails on
|
||
;; platforms other than x86_64 or i686.
|
||
(supported-systems '("x86_64-linux" "i686-linux"))
|
||
(home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
|
||
(synopsis "Implementation of the Random Forests machine learning method")
|
||
(description
|
||
"Random Jungle is an implementation of Random Forests. It is supposed to
|
||
analyse high dimensional data. In genetics, it can be used for analysing big
|
||
Genome Wide Association (GWA) data. Random Forests is a powerful machine
|
||
learning method. Most interesting features are variable selection, missing
|
||
value imputation, classifier creation, generalization error estimation and
|
||
sample proximities between pairs of cases.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public openfst
|
||
(package
|
||
(name "openfst")
|
||
(version "1.7.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.openfst.org/twiki/pub/FST/"
|
||
"FstDownload/openfst-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0fqgk8195kz21is09gwzwnrg7fr9526bi9mh4apyskapz27pbhr1"))))
|
||
(build-system gnu-build-system)
|
||
(home-page "http://www.openfst.org")
|
||
(synopsis "Library for weighted finite-state transducers")
|
||
(description "OpenFst is a library for constructing, combining,
|
||
optimizing, and searching weighted finite-state transducers (FSTs).")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public shogun
|
||
(package
|
||
(name "shogun")
|
||
(version "6.1.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"ftp://shogun-toolbox.org/shogun/releases/"
|
||
(version-major+minor version)
|
||
"/sources/shogun-" version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
|
||
(modules '((guix build utils)
|
||
(ice-9 rdelim)))
|
||
(snippet
|
||
'(begin
|
||
;; Remove non-free sources and files referencing them
|
||
(for-each delete-file
|
||
(find-files "src/shogun/classifier/svm/"
|
||
"SVMLight\\.(cpp|h)"))
|
||
(for-each delete-file
|
||
(find-files "examples/undocumented/libshogun/"
|
||
(string-append
|
||
"(classifier_.*svmlight.*|"
|
||
"evaluation_cross_validation_locked_comparison).cpp")))
|
||
;; Remove non-free functions.
|
||
(define (delete-ifdefs file)
|
||
(with-atomic-file-replacement file
|
||
(lambda (in out)
|
||
(let loop ((line (read-line in 'concat))
|
||
(skipping? #f))
|
||
(if (eof-object? line)
|
||
#t
|
||
(let ((skip-next?
|
||
(or (and skipping?
|
||
(not (string-prefix?
|
||
"#endif //USE_SVMLIGHT" line)))
|
||
(string-prefix?
|
||
"#ifdef USE_SVMLIGHT" line))))
|
||
(when (or (not skipping?)
|
||
(and skipping? (not skip-next?)))
|
||
(display line out))
|
||
(loop (read-line in 'concat) skip-next?)))))))
|
||
(for-each delete-ifdefs
|
||
(append
|
||
(find-files "src/shogun/classifier/mkl"
|
||
"^MKLClassification\\.cpp")
|
||
(find-files "src/shogun/classifier/svm"
|
||
"^SVMLightOneClass\\.(cpp|h)")
|
||
(find-files "src/shogun/multiclass"
|
||
"^ScatterSVM\\.(cpp|h)")
|
||
(find-files "src/shogun/kernel/"
|
||
"^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
|
||
(find-files "src/shogun/regression/svr"
|
||
"^(MKLRegression|SVRLight)\\.(cpp|h)")
|
||
(find-files "src/shogun/transfer/domain_adaptation"
|
||
"^DomainAdaptationSVM\\.(cpp|h)")))
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#:tests? #f ;no check target
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'delete-broken-symlinks
|
||
(lambda _
|
||
(for-each delete-file '("applications/arts/data"
|
||
"applications/asp/data"
|
||
"applications/easysvm/data"
|
||
"applications/msplicer/data"
|
||
"applications/ocr/data"
|
||
"examples/meta/data"
|
||
"examples/undocumented/data"))
|
||
#t))
|
||
(add-after 'unpack 'change-R-target-path
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(substitute* '("src/interfaces/r/CMakeLists.txt"
|
||
"examples/meta/r/CMakeLists.txt")
|
||
(("\\$\\{R_COMPONENT_LIB_PATH\\}")
|
||
(string-append (assoc-ref outputs "out")
|
||
"/lib/R/library/")))
|
||
#t))
|
||
(add-after 'unpack 'fix-octave-modules
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(substitute* "src/interfaces/octave/CMakeLists.txt"
|
||
(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
|
||
"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
|
||
;; change target directory
|
||
(("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
|
||
(string-append (assoc-ref outputs "out")
|
||
"/share/octave/packages")))
|
||
(substitute* '("src/interfaces/octave/swig_typemaps.i"
|
||
"src/interfaces/octave/sg_print_functions.cpp")
|
||
;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
|
||
(("octave/config\\.h") "octave/octave-config.h")
|
||
(("octave/oct-obj.h") "octave/ovl.h"))
|
||
#t))
|
||
(add-after 'unpack 'move-rxcpp
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((rxcpp-dir "shogun/third-party/rxcpp"))
|
||
(mkdir-p rxcpp-dir)
|
||
(install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
|
||
#t)))
|
||
(add-before 'build 'set-HOME
|
||
;; $HOME needs to be set at some point during the build phase
|
||
(lambda _ (setenv "HOME" "/tmp") #t)))
|
||
#:configure-flags
|
||
(list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
|
||
"-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
|
||
"-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
|
||
;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
|
||
;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
|
||
;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
|
||
;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
|
||
"-DINTERFACE_OCTAVE=ON"
|
||
"-DINTERFACE_PYTHON=ON"
|
||
"-DINTERFACE_R=ON")))
|
||
(inputs
|
||
`(("python" ,python)
|
||
("numpy" ,python-numpy)
|
||
("r-minimal" ,r-minimal)
|
||
("octave" ,octave-cli)
|
||
("swig" ,swig)
|
||
("eigen" ,eigen)
|
||
("hdf5" ,hdf5)
|
||
("atlas" ,atlas)
|
||
("arpack" ,arpack-ng)
|
||
("lapack" ,lapack)
|
||
("glpk" ,glpk)
|
||
("libxml2" ,libxml2)
|
||
("lzo" ,lzo)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("rxcpp" ,rxcpp)))
|
||
;; Non-portable SSE instructions are used so building fails on platforms
|
||
;; other than x86_64.
|
||
(supported-systems '("x86_64-linux"))
|
||
(home-page "http://shogun-toolbox.org/")
|
||
(synopsis "Machine learning toolbox")
|
||
(description
|
||
"The Shogun Machine learning toolbox provides a wide range of unified and
|
||
efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
|
||
combine multiple data representations, algorithm classes, and general purpose
|
||
tools. This enables both rapid prototyping of data pipelines and extensibility
|
||
in terms of new algorithms.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public rxcpp
|
||
(package
|
||
(name "rxcpp")
|
||
(version "4.1.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/ReactiveX/RxCpp.git")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32 "1rdpa3jlc181jd08nk437aar085h28i45s6nzrv65apb3xyyz0ij"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-werror
|
||
(lambda _
|
||
(substitute* (find-files ".")
|
||
(("-Werror") ""))
|
||
#t))
|
||
(replace 'check
|
||
(lambda _
|
||
(invoke "ctest"))))))
|
||
(native-inputs
|
||
`(("catch" ,catch-framework)))
|
||
(home-page "http://reactivex.io/")
|
||
(synopsis "Reactive Extensions for C++")
|
||
(description
|
||
"The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
|
||
values-distributed-in-time. ReactiveX is a library for composing asynchronous
|
||
and event-based programs by using observable sequences.
|
||
|
||
It extends the observer pattern to support sequences of data and/or events and
|
||
adds operators that allow you to compose sequences together declaratively while
|
||
abstracting away concerns about things like low-level threading,
|
||
synchronization, thread-safety, concurrent data structures, and non-blocking
|
||
I/O.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public r-adaptivesparsity
|
||
(package
|
||
(name "r-adaptivesparsity")
|
||
(version "1.6")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "AdaptiveSparsity" version))
|
||
(sha256
|
||
(base32
|
||
"0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
|
||
(properties
|
||
`((upstream-name . "AdaptiveSparsity")))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'link-against-armadillo
|
||
(lambda _
|
||
(substitute* "src/Makevars"
|
||
(("PKG_LIBS=" prefix)
|
||
(string-append prefix "-larmadillo"))))))))
|
||
(propagated-inputs
|
||
`(("r-mass" ,r-mass)
|
||
("r-matrix" ,r-matrix)
|
||
("r-rcpp" ,r-rcpp)
|
||
("r-rcpparmadillo" ,r-rcpparmadillo)))
|
||
(inputs
|
||
`(("armadillo" ,armadillo)))
|
||
(home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
|
||
(synopsis "Adaptive sparsity models")
|
||
(description
|
||
"This package implements the Figueiredo machine learning algorithm for
|
||
adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
|
||
geometric models.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public gemmlowp-for-tensorflow
|
||
;; The commit hash is taken from "tensorflow/workspace.bzl".
|
||
(let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
|
||
(revision "2"))
|
||
(package
|
||
(name "gemmlowp")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://mirror.bazel.build/"
|
||
"github.com/google/gemmlowp/archive/"
|
||
commit ".zip"))
|
||
(file-name (string-append "gemmlowp-" version ".zip"))
|
||
(sha256
|
||
(base32
|
||
"0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list ,@(match (%current-system)
|
||
((or "x86_64-linux" "i686-linux")
|
||
'("-DCMAKE_CXX_FLAGS=-msse2"))
|
||
(_ '())))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
;; This directory contains the CMakeLists.txt.
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "contrib") #t))
|
||
;; There is no install target
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib/"))
|
||
(inc (string-append out "/include/")))
|
||
(install-file "../build/libeight_bit_int_gemm.so" lib)
|
||
(for-each (lambda (dir)
|
||
(let ((target (string-append inc "/" dir)))
|
||
(mkdir-p target)
|
||
(for-each (lambda (h)
|
||
(install-file h target))
|
||
(find-files (string-append "../" dir)
|
||
"\\.h$"))))
|
||
'("meta" "profiling" "public" "fixedpoint"
|
||
"eight_bit_int_gemm" "internal"))
|
||
#t))))))
|
||
(native-inputs
|
||
`(("unzip" ,unzip)))
|
||
(home-page "https://github.com/google/gemmlowp")
|
||
(synopsis "Small self-contained low-precision GEMM library")
|
||
(description
|
||
"This is a small self-contained low-precision @dfn{general matrix
|
||
multiplication} (GEMM) library. It is not a full linear algebra library.
|
||
Low-precision means that the input and output matrix entries are integers on
|
||
at most 8 bits. To avoid overflow, results are internally accumulated on more
|
||
than 8 bits, and at the end only some significant 8 bits are kept.")
|
||
(license license:asl2.0))))
|
||
|
||
(define-public dlib
|
||
(package
|
||
(name "dlib")
|
||
(version "19.7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://dlib.net/files/dlib-" version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Delete ~13MB of bundled dependencies.
|
||
(delete-file-recursively "dlib/external")
|
||
(delete-file-recursively "docs/dlib/external")
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'disable-asserts
|
||
(lambda _
|
||
;; config.h recommends explicitly enabling or disabling asserts
|
||
;; when building as a shared library. By default neither is set.
|
||
(substitute* "dlib/config.h"
|
||
(("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
|
||
#t))
|
||
(add-after 'disable-asserts 'disable-failing-tests
|
||
(lambda _
|
||
;; One test times out on MIPS, so we need to disable it.
|
||
;; Others are flaky on some platforms.
|
||
(let* ((system ,(or (%current-target-system)
|
||
(%current-system)))
|
||
(disabled-tests (cond
|
||
((string-prefix? "mips64" system)
|
||
'("object_detector" ; timeout
|
||
"data_io"))
|
||
((string-prefix? "armhf" system)
|
||
'("learning_to_track"))
|
||
((string-prefix? "i686" system)
|
||
'("optimization"))
|
||
(else '()))))
|
||
(for-each
|
||
(lambda (test)
|
||
(substitute* "dlib/test/makefile"
|
||
(((string-append "SRC \\+= " test "\\.cpp")) "")))
|
||
disabled-tests)
|
||
#t)))
|
||
(replace 'check
|
||
(lambda _
|
||
;; No test target, so we build and run the unit tests here.
|
||
(let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
|
||
(with-directory-excursion test-dir
|
||
(invoke "make" "-j" (number->string (parallel-job-count)))
|
||
(invoke "./dtest" "--runall"))
|
||
#t)))
|
||
(add-after 'install 'delete-static-library
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(delete-file (string-append (assoc-ref outputs "out")
|
||
"/lib/libdlib.a"))
|
||
#t)))))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
;; For tests.
|
||
("libnsl" ,libnsl)))
|
||
(inputs
|
||
`(("giflib" ,giflib)
|
||
("lapack" ,lapack)
|
||
("libjpeg" ,libjpeg)
|
||
("libpng" ,libpng)
|
||
("libx11" ,libx11)
|
||
("openblas" ,openblas)
|
||
("zlib" ,zlib)))
|
||
(synopsis
|
||
"Toolkit for making machine learning and data analysis applications in C++")
|
||
(description
|
||
"Dlib is a modern C++ toolkit containing machine learning algorithms and
|
||
tools. It is used in both industry and academia in a wide range of domains
|
||
including robotics, embedded devices, mobile phones, and large high performance
|
||
computing environments.")
|
||
(home-page "http://dlib.net")
|
||
(license license:boost1.0)))
|
||
|
||
(define-public python-scikit-learn
|
||
(package
|
||
(name "python-scikit-learn")
|
||
(version "0.20.3")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/scikit-learn/scikit-learn.git")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"08aaby5zphfxy83mggg35bwyka7wk91l2qijh8kk0bl08dikq8dl"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-ext
|
||
(lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
|
||
(replace 'check
|
||
(lambda _
|
||
;; Restrict OpenBLAS threads to prevent segfaults while testing!
|
||
(setenv "OPENBLAS_NUM_THREADS" "1")
|
||
|
||
;; Some tests require write access to $HOME.
|
||
(setenv "HOME" "/tmp")
|
||
|
||
(invoke "pytest" "sklearn" "-m" "not network")))
|
||
(add-before 'reset-gzip-timestamps 'make-files-writable
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Make sure .gz files are writable so that the
|
||
;; 'reset-gzip-timestamps' phase can do its work.
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(for-each make-file-writable
|
||
(find-files out "\\.gz$"))
|
||
#t))))))
|
||
(inputs
|
||
`(("openblas" ,openblas)))
|
||
(native-inputs
|
||
`(("python-pytest" ,python-pytest)
|
||
("python-pandas" ,python-pandas) ;for tests
|
||
("python-cython" ,python-cython)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-scipy" ,python-scipy)))
|
||
(home-page "http://scikit-learn.org/")
|
||
(synopsis "Machine Learning in Python")
|
||
(description
|
||
"Scikit-learn provides simple and efficient tools for data mining and
|
||
data analysis.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python2-scikit-learn
|
||
(package-with-python2 python-scikit-learn))
|
||
|
||
(define-public python-autograd
|
||
(let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
|
||
(revision "0")
|
||
(version (git-version "0.0.0" revision commit)))
|
||
(package
|
||
(name "python-autograd")
|
||
(home-page "https://github.com/HIPS/autograd")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url home-page)
|
||
(commit commit)))
|
||
(sha256
|
||
(base32
|
||
"189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
|
||
(file-name (git-file-name name version))))
|
||
(version version)
|
||
(build-system python-build-system)
|
||
(native-inputs
|
||
`(("python-nose" ,python-nose)
|
||
("python-pytest" ,python-pytest)))
|
||
(propagated-inputs
|
||
`(("python-future" ,python-future)
|
||
("python-numpy" ,python-numpy)))
|
||
(arguments
|
||
`(#:phases (modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda _
|
||
(invoke "py.test" "-v"))))))
|
||
(synopsis "Efficiently computes derivatives of NumPy code")
|
||
(description "Autograd can automatically differentiate native Python and
|
||
NumPy code. It can handle a large subset of Python's features, including loops,
|
||
ifs, recursion and closures, and it can even take derivatives of derivatives
|
||
of derivatives. It supports reverse-mode differentiation
|
||
(a.k.a. backpropagation), which means it can efficiently take gradients of
|
||
scalar-valued functions with respect to array-valued arguments, as well as
|
||
forward-mode differentiation, and the two can be composed arbitrarily. The
|
||
main intended application of Autograd is gradient-based optimization.")
|
||
(license license:expat))))
|
||
|
||
(define-public python2-autograd
|
||
(package-with-python2 python-autograd))
|
||
|
||
(define-public lightgbm
|
||
(package
|
||
(name "lightgbm")
|
||
(version "2.0.12")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://github.com/Microsoft/LightGBM/archive/v"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
|
||
(file-name (string-append name "-" version ".tar.gz"))))
|
||
(native-inputs
|
||
`(("python-pytest" ,python-pytest)
|
||
("python-nose" ,python-nose)))
|
||
(inputs
|
||
`(("openmpi" ,openmpi)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-scipy" ,python-scipy)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
'("-DUSE_MPI=ON")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(with-directory-excursion ,(string-append "../LightGBM-" version)
|
||
(invoke "pytest" "tests/c_api_test/test_.py")))))))
|
||
(build-system cmake-build-system)
|
||
(home-page "https://github.com/Microsoft/LightGBM")
|
||
(synopsis "Gradient boosting framework based on decision tree algorithms")
|
||
(description "LightGBM is a gradient boosting framework that uses tree
|
||
based learning algorithms. It is designed to be distributed and efficient with
|
||
the following advantages:
|
||
|
||
@itemize
|
||
@item Faster training speed and higher efficiency
|
||
@item Lower memory usage
|
||
@item Better accuracy
|
||
@item Parallel and GPU learning supported (not enabled in this package)
|
||
@item Capable of handling large-scale data
|
||
@end itemize\n")
|
||
(license license:expat)))
|
||
|
||
(define-public vowpal-wabbit
|
||
;; Language bindings not included.
|
||
(package
|
||
(name "vowpal-wabbit")
|
||
(version "8.5.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://github.com/JohnLangford/vowpal_wabbit/archive/"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
|
||
(file-name (string-append name "-" version ".tar.gz"))))
|
||
(inputs
|
||
`(("boost" ,boost)
|
||
("zlib" ,zlib)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "--with-boost="
|
||
(assoc-ref %build-inputs "boost")))))
|
||
(build-system gnu-build-system)
|
||
(home-page "https://github.com/JohnLangford/vowpal_wabbit")
|
||
(synopsis "Fast machine learning library for online learning")
|
||
(description "Vowpal Wabbit is a machine learning system with techniques
|
||
such as online, hashing, allreduce, reductions, learning2search, active, and
|
||
interactive learning.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python2-fastlmm
|
||
(package
|
||
(name "python2-fastlmm")
|
||
(version "0.2.21")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "fastlmm" version ".zip"))
|
||
(sha256
|
||
(base32
|
||
"1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; some test files are missing
|
||
#:python ,python-2)) ; only Python 2.7 is supported
|
||
(propagated-inputs
|
||
`(("python2-numpy" ,python2-numpy)
|
||
("python2-scipy" ,python2-scipy)
|
||
("python2-matplotlib" ,python2-matplotlib)
|
||
("python2-pandas" ,python2-pandas)
|
||
("python2-scikit-learn" ,python2-scikit-learn)
|
||
("python2-pysnptools" ,python2-pysnptools)))
|
||
(native-inputs
|
||
`(("unzip" ,unzip)
|
||
("python2-cython" ,python2-cython)
|
||
("python2-mock" ,python2-mock)
|
||
("python2-nose" ,python2-nose)))
|
||
(home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
|
||
(synopsis "Perform genome-wide association studies on large data sets")
|
||
(description
|
||
"FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
|
||
Models, is a program for performing both single-SNP and SNP-set genome-wide
|
||
association studies (GWAS) on extremely large data sets.")
|
||
(license license:asl2.0)))
|
||
|
||
;; There have been no proper releases yet.
|
||
(define-public kaldi
|
||
(let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
|
||
(revision "1"))
|
||
(package
|
||
(name "kaldi")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/kaldi-asr/kaldi.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:test-target "test"
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "src") #t))
|
||
(replace 'configure
|
||
(lambda* (#:key build system inputs outputs #:allow-other-keys)
|
||
(when (not (or (string-prefix? "x86_64" system)
|
||
(string-prefix? "i686" system)))
|
||
(substitute* "makefiles/linux_openblas.mk"
|
||
(("-msse -msse2") "")))
|
||
(substitute* "makefiles/default_rules.mk"
|
||
(("/bin/bash") (which "bash")))
|
||
(substitute* "Makefile"
|
||
(("ext_depend: check_portaudio")
|
||
"ext_depend:"))
|
||
(substitute* '("online/Makefile"
|
||
"onlinebin/Makefile"
|
||
"gst-plugin/Makefile")
|
||
(("../../tools/portaudio/install")
|
||
(assoc-ref inputs "portaudio")))
|
||
|
||
;; This `configure' script doesn't support variables passed as
|
||
;; arguments, nor does it support "prefix".
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(openblas (assoc-ref inputs "openblas"))
|
||
(openfst (assoc-ref inputs "openfst")))
|
||
(substitute* "configure"
|
||
(("check_for_slow_expf;") "")
|
||
;; This affects the RPATH and also serves as the installation
|
||
;; directory.
|
||
(("KALDILIBDIR=`pwd`/lib")
|
||
(string-append "KALDILIBDIR=" out "/lib")))
|
||
(mkdir-p out) ; must exist
|
||
(setenv "CONFIG_SHELL" (which "bash"))
|
||
(setenv "OPENFST_VER" ,(package-version openfst))
|
||
(invoke "./configure"
|
||
"--use-cuda=no"
|
||
"--shared"
|
||
(string-append "--openblas-root=" openblas)
|
||
(string-append "--fst-root=" openfst)))))
|
||
(add-after 'build 'build-ext-and-gstreamer-plugin
|
||
(lambda _
|
||
(invoke "make" "-C" "online" "depend")
|
||
(invoke "make" "-C" "online")
|
||
(invoke "make" "-C" "onlinebin" "depend")
|
||
(invoke "make" "-C" "onlinebin")
|
||
(invoke "make" "-C" "gst-plugin" "depend")
|
||
(invoke "make" "-C" "gst-plugin")
|
||
#t))
|
||
;; TODO: also install the executables.
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(inc (string-append out "/include"))
|
||
(lib (string-append out "/lib")))
|
||
(mkdir-p lib)
|
||
;; The build phase installed symlinks to the actual
|
||
;; libraries. Install the actual targets.
|
||
(for-each (lambda (file)
|
||
(let ((target (readlink file)))
|
||
(delete-file file)
|
||
(install-file target lib)))
|
||
(find-files lib "\\.so"))
|
||
;; Install headers
|
||
(for-each (lambda (file)
|
||
(let ((target-dir (string-append inc "/" (dirname file))))
|
||
(install-file file target-dir)))
|
||
(find-files "." "\\.h"))
|
||
(install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
|
||
(string-append lib "/gstreamer-1.0"))
|
||
#t))))))
|
||
(inputs
|
||
`(("alsa-lib" ,alsa-lib)
|
||
("gfortran" ,gfortran "lib")
|
||
("glib" ,glib)
|
||
("gstreamer" ,gstreamer)
|
||
("jack" ,jack-1)
|
||
("openblas" ,openblas)
|
||
("openfst" ,openfst)
|
||
("portaudio" ,portaudio)
|
||
("python" ,python)))
|
||
(native-inputs
|
||
`(("glib" ,glib "bin") ; glib-genmarshal
|
||
("grep" ,grep)
|
||
("sed" ,sed)
|
||
("pkg-config" ,pkg-config)
|
||
("which" ,which)))
|
||
(home-page "https://kaldi-asr.org/")
|
||
(synopsis "Speech recognition toolkit")
|
||
(description "Kaldi is an extensible toolkit for speech recognition
|
||
written in C++.")
|
||
(license license:asl2.0))))
|
||
|
||
(define-public gst-kaldi-nnet2-online
|
||
(let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
|
||
(revision "1"))
|
||
(package
|
||
(name "gst-kaldi-nnet2-online")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/alumae/gst-kaldi-nnet2-online.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; there are none
|
||
#:make-flags
|
||
(list (string-append "SHELL="
|
||
(assoc-ref %build-inputs "bash") "/bin/bash")
|
||
(string-append "KALDI_ROOT="
|
||
(assoc-ref %build-inputs "kaldi-src"))
|
||
(string-append "KALDILIBDIR="
|
||
(assoc-ref %build-inputs "kaldi") "/lib")
|
||
"KALDI_FLAVOR=dynamic")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "src") #t))
|
||
(replace 'configure
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((glib (assoc-ref inputs "glib")))
|
||
(setenv "CXXFLAGS" "-std=c++11 -fPIC")
|
||
(setenv "CPLUS_INCLUDE_PATH"
|
||
(string-append glib "/include/glib-2.0:"
|
||
glib "/lib/glib-2.0/include:"
|
||
(assoc-ref inputs "gstreamer")
|
||
"/include/gstreamer-1.0:"
|
||
(getenv "CPLUS_INCLUDE_PATH"))))
|
||
(substitute* "Makefile"
|
||
(("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
|
||
(("\\$\\(error Cannot find") "#"))))
|
||
(add-before 'build 'build-depend
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "depend" make-flags)))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib/gstreamer-1.0")))
|
||
(install-file "libgstkaldinnet2onlinedecoder.so" lib)
|
||
#t))))))
|
||
(inputs
|
||
`(("glib" ,glib)
|
||
("gstreamer" ,gstreamer)
|
||
("jansson" ,jansson)
|
||
("openfst" ,openfst)
|
||
("kaldi" ,kaldi)))
|
||
(native-inputs
|
||
`(("bash" ,bash)
|
||
("glib:bin" ,glib "bin") ; glib-genmarshal
|
||
("kaldi-src" ,(package-source kaldi))
|
||
("pkg-config" ,pkg-config)))
|
||
(home-page "https://kaldi-asr.org/")
|
||
(synopsis "Gstreamer plugin for decoding speech")
|
||
(description "This package provides a GStreamer plugin that wraps
|
||
Kaldi's @code{SingleUtteranceNnet2Decoder}. It requires iVector-adapted DNN
|
||
acoustic models. The iVectors are adapted to the current audio stream
|
||
automatically.")
|
||
(license license:asl2.0))))
|
||
|
||
(define-public kaldi-gstreamer-server
|
||
(let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
|
||
(revision "1"))
|
||
(package
|
||
(name "kaldi-gstreamer-server")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/alumae/kaldi-gstreamer-server.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; there are no tests that can be run automatically
|
||
#:modules ((guix build utils)
|
||
(guix build gnu-build-system)
|
||
(srfi srfi-26))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(replace 'build
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Disable hash randomization to ensure the generated .pycs
|
||
;; are reproducible.
|
||
(setenv "PYTHONHASHSEED" "0")
|
||
(with-directory-excursion "kaldigstserver"
|
||
(for-each (lambda (file)
|
||
(apply invoke
|
||
`("python"
|
||
"-m" "compileall"
|
||
"-f" ; force rebuild
|
||
,file)))
|
||
(find-files "." "\\.py$")))
|
||
#t))
|
||
(replace 'install
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin"))
|
||
(share (string-append out "/share/kaldi-gstreamer-server/")))
|
||
;; Install Python files
|
||
(with-directory-excursion "kaldigstserver"
|
||
(for-each (cut install-file <> share)
|
||
(find-files "." ".*")))
|
||
|
||
;; Install sample configuration files
|
||
(for-each (cut install-file <> share)
|
||
(find-files "." "\\.yaml"))
|
||
|
||
;; Install executables
|
||
(mkdir-p bin)
|
||
(let* ((server (string-append bin "/kaldi-gst-server"))
|
||
(client (string-append bin "/kaldi-gst-client"))
|
||
(worker (string-append bin "/kaldi-gst-worker"))
|
||
(PYTHONPATH (getenv "PYTHONPATH"))
|
||
(GST_PLUGIN_PATH (string-append
|
||
(assoc-ref inputs "gst-kaldi-nnet2-online")
|
||
"/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
|
||
(wrap (lambda (wrapper what)
|
||
(with-output-to-file wrapper
|
||
(lambda _
|
||
(format #t
|
||
"#!~a
|
||
export PYTHONPATH=~a
|
||
export GST_PLUGIN_PATH=~a
|
||
exec ~a ~a/~a \"$@\"~%"
|
||
(which "bash") PYTHONPATH GST_PLUGIN_PATH
|
||
(which "python") share what)))
|
||
(chmod wrapper #o555))))
|
||
(for-each wrap
|
||
(list server client worker)
|
||
(list "master_server.py"
|
||
"client.py"
|
||
"worker.py")))
|
||
#t))))))
|
||
(inputs
|
||
`(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
|
||
("python2" ,python-2)
|
||
("python2-futures" ,python2-futures)
|
||
("python2-pygobject" ,python2-pygobject)
|
||
("python2-pyyaml" ,python2-pyyaml)
|
||
("python2-tornado" ,python2-tornado)
|
||
("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
|
||
(home-page "https://github.com/alumae/kaldi-gstreamer-server")
|
||
(synopsis "Real-time full-duplex speech recognition server")
|
||
(description "This is a real-time full-duplex speech recognition server,
|
||
based on the Kaldi toolkit and the GStreamer framework and implemented in
|
||
Python.")
|
||
(license license:bsd-2))))
|
||
|
||
(define-public grpc
|
||
(package
|
||
(name "grpc")
|
||
(version "1.16.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/grpc/grpc.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1jimqz3115f9pli5w6ik9wi7mjc7ix6y7yrq4a1ab9fc3dalj7p2"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; no test target
|
||
#:configure-flags
|
||
(list "-DgRPC_ZLIB_PROVIDER=package"
|
||
"-DgRPC_CARES_PROVIDER=package"
|
||
"-DgRPC_SSL_PROVIDER=package"
|
||
"-DgRPC_PROTOBUF_PROVIDER=package")))
|
||
(inputs
|
||
`(("c-ares" ,c-ares-next)
|
||
("openssl" ,openssl)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("protobuf" ,protobuf-next)
|
||
("python" ,python-wrapper)))
|
||
(home-page "https://grpc.io")
|
||
(synopsis "High performance universal RPC framework")
|
||
(description "gRPC is a modern open source high performance @dfn{Remote
|
||
Procedure Call} (RPC) framework that can run in any environment. It can
|
||
efficiently connect services in and across data centers with pluggable support
|
||
for load balancing, tracing, health checking and authentication. It is also
|
||
applicable in last mile of distributed computing to connect devices, mobile
|
||
applications and browsers to backend services.")
|
||
(license license:asl2.0)))
|
||
|
||
;; Note that Tensorflow includes a "third_party" directory, which seems to not
|
||
;; only contain modified subsets of upstream library source code, but also
|
||
;; adapter headers provided by Google (such as the fft.h header, which is not
|
||
;; part of the upstream project code). The Tensorflow code includes headers
|
||
;; from the "third_party" directory. It does not look like we can replace
|
||
;; these headers with unmodified upstream files, so we keep them.
|
||
(define-public tensorflow
|
||
(package
|
||
(name "tensorflow")
|
||
(version "1.9.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tensorflow/tensorflow.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (string-append "tensorflow-" version "-checkout"))
|
||
(sha256
|
||
(base32
|
||
"0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; no "check" target
|
||
#:build-type "Release"
|
||
#:configure-flags
|
||
(let ((protobuf (assoc-ref %build-inputs "protobuf"))
|
||
(protobuf:native (assoc-ref %build-inputs "protobuf:native"))
|
||
(jsoncpp (assoc-ref %build-inputs "jsoncpp"))
|
||
(snappy (assoc-ref %build-inputs "snappy"))
|
||
(sqlite (assoc-ref %build-inputs "sqlite")))
|
||
(list
|
||
;; Use protobuf from Guix
|
||
(string-append "-Dprotobuf_STATIC_LIBRARIES="
|
||
protobuf "/lib/libprotobuf.so")
|
||
(string-append "-DPROTOBUF_PROTOC_EXECUTABLE="
|
||
protobuf:native "/bin/protoc")
|
||
|
||
;; Use snappy from Guix
|
||
(string-append "-Dsnappy_STATIC_LIBRARIES="
|
||
snappy "/lib/libsnappy.so")
|
||
;; Yes, this is not actually the include directory but a prefix...
|
||
(string-append "-Dsnappy_INCLUDE_DIR=" snappy)
|
||
|
||
;; Use jsoncpp from Guix
|
||
(string-append "-Djsoncpp_STATIC_LIBRARIES="
|
||
jsoncpp "/lib/libjsoncpp.so")
|
||
;; Yes, this is not actually the include directory but a prefix...
|
||
(string-append "-Djsoncpp_INCLUDE_DIR=" jsoncpp)
|
||
|
||
;; Use sqlite from Guix
|
||
(string-append "-Dsqlite_STATIC_LIBRARIES="
|
||
sqlite "/lib/libsqlite.a")
|
||
|
||
;; Use system libraries wherever possible. Currently, this
|
||
;; only affects zlib.
|
||
"-Dsystemlib_ALL=ON"
|
||
"-Dtensorflow_ENABLE_POSITION_INDEPENDENT_CODE=ON"
|
||
"-Dtensorflow_BUILD_SHARED_LIB=ON"
|
||
"-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=OFF"
|
||
"-Dtensorflow_ENABLE_SSL_SUPPORT=OFF"
|
||
"-Dtensorflow_BUILD_CONTRIB_KERNELS=OFF"))
|
||
#:make-flags
|
||
(list "CC=gcc")
|
||
#:modules ((ice-9 ftw)
|
||
(guix build utils)
|
||
(guix build cmake-build-system))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'set-source-file-times-to-1980
|
||
;; At the end of the tf_python_build_pip_package target, a ZIP
|
||
;; archive should be generated via bdist_wheel, but it fails with
|
||
;; "ZIP does not support timestamps before 1980". Luckily,
|
||
;; SOURCE_DATE_EPOCH is respected, which we set to some time in
|
||
;; 1980.
|
||
(lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
|
||
;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
|
||
(add-after 'unpack 'python3.7-compatibility
|
||
(lambda _
|
||
(substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
|
||
"tensorflow/python/lib/core/ndarray_tensor.cc"
|
||
"tensorflow/python/lib/core/py_func.cc")
|
||
(("PyUnicode_AsUTF8") "(char *)PyUnicode_AsUTF8"))
|
||
(substitute* "tensorflow/c/eager/c_api.h"
|
||
(("unsigned char async")
|
||
"unsigned char is_async"))
|
||
|
||
;; Remove dependency on tensorboard, a complicated but probably
|
||
;; optional package.
|
||
(substitute* "tensorflow/tools/pip_package/setup.py"
|
||
((".*'tensorboard >.*") ""))
|
||
#t))
|
||
(add-after 'python3.7-compatibility 'chdir
|
||
(lambda _ (chdir "tensorflow/contrib/cmake") #t))
|
||
(add-after 'chdir 'disable-downloads
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(substitute* (find-files "external" "\\.cmake$")
|
||
(("GIT_REPOSITORY.*") "")
|
||
(("GIT_TAG.*") "")
|
||
(("PREFIX ")
|
||
"DOWNLOAD_COMMAND \"\"\nPREFIX "))
|
||
|
||
;; Use packages from Guix
|
||
(let ((grpc (assoc-ref inputs "grpc")))
|
||
(substitute* "CMakeLists.txt"
|
||
;; Sqlite
|
||
(("include\\(sqlite\\)") "")
|
||
(("\\$\\{sqlite_STATIC_LIBRARIES\\}")
|
||
(string-append (assoc-ref inputs "sqlite")
|
||
"/lib/libsqlite3.so"))
|
||
(("sqlite_copy_headers_to_destination") "")
|
||
|
||
;; PNG
|
||
(("include\\(png\\)") "")
|
||
(("\\$\\{png_STATIC_LIBRARIES\\}")
|
||
(string-append (assoc-ref inputs "libpng")
|
||
"/lib/libpng16.so"))
|
||
(("png_copy_headers_to_destination") "")
|
||
|
||
;; JPEG
|
||
(("include\\(jpeg\\)") "")
|
||
(("\\$\\{jpeg_STATIC_LIBRARIES\\}")
|
||
(string-append (assoc-ref inputs "libjpeg")
|
||
"/lib/libjpeg.so"))
|
||
(("jpeg_copy_headers_to_destination") "")
|
||
|
||
;; GIF
|
||
(("include\\(gif\\)") "")
|
||
(("\\$\\{gif_STATIC_LIBRARIES\\}")
|
||
(string-append (assoc-ref inputs "giflib")
|
||
"/lib/libgif.so"))
|
||
(("gif_copy_headers_to_destination") "")
|
||
|
||
;; lmdb
|
||
(("include\\(lmdb\\)") "")
|
||
(("\\$\\{lmdb_STATIC_LIBRARIES\\}")
|
||
(string-append (assoc-ref inputs "lmdb")
|
||
"/lib/liblmdb.so"))
|
||
(("lmdb_copy_headers_to_destination") "")
|
||
|
||
;; Protobuf
|
||
(("include\\(protobuf\\)") "")
|
||
(("protobuf_copy_headers_to_destination") "")
|
||
(("^ +protobuf") "")
|
||
|
||
;; gRPC
|
||
(("include\\(grpc\\)")
|
||
"find_package(grpc REQUIRED NAMES gRPC)")
|
||
(("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES grpc\\)") "")
|
||
|
||
;; Eigen
|
||
(("include\\(eigen\\)")
|
||
(string-append "find_package(eigen REQUIRED NAMES Eigen3)
|
||
set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
|
||
(assoc-ref inputs "eigen") "/include/eigen3)"))
|
||
(("^ +eigen") "")
|
||
|
||
;; snappy
|
||
(("include\\(snappy\\)")
|
||
"add_definitions(-DTF_USE_SNAPPY)")
|
||
(("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES snappy\\)") "")
|
||
|
||
;; jsoncpp
|
||
(("include\\(jsoncpp\\)") "")
|
||
(("^ +jsoncpp") ""))
|
||
|
||
(substitute* "tf_core_framework.cmake"
|
||
((" grpc") "")
|
||
(("\\$\\{GRPC_BUILD\\}/grpc_cpp_plugin")
|
||
(which "grpc_cpp_plugin"))
|
||
;; Link with gRPC libraries
|
||
(("add_library\\(tf_protos_cc.*" m)
|
||
(string-append m
|
||
(format #f "\ntarget_link_libraries(tf_protos_cc PRIVATE \
|
||
~a/lib/libgrpc++_unsecure.a \
|
||
~a/lib/libgrpc_unsecure.a \
|
||
~a/lib/libaddress_sorting.a \
|
||
~a/lib/libgpr.a \
|
||
~a//lib/libcares.so
|
||
)\n"
|
||
grpc grpc grpc grpc
|
||
(assoc-ref inputs "c-ares"))))))
|
||
(substitute* "tf_tools.cmake"
|
||
(("add_dependencies\\(\\$\\{proto_text.*") ""))
|
||
;; Remove dependency on bundled grpc
|
||
(substitute* "tf_core_distributed_runtime.cmake"
|
||
(("tf_core_cpu grpc") "tf_core_cpu"))
|
||
|
||
;; This directory is a dependency of many targets.
|
||
(mkdir-p "protobuf")
|
||
#t))
|
||
(add-after 'configure 'unpack-third-party-sources
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; This is needed to configure bundled packages properly.
|
||
(setenv "CONFIG_SHELL" (which "bash"))
|
||
(for-each
|
||
(lambda (name)
|
||
(let* ((what (assoc-ref inputs (string-append name "-src")))
|
||
(name* (string-map (lambda (c)
|
||
(if (char=? c #\-)
|
||
#\_ c)) name))
|
||
(where (string-append "../build/" name* "/src/" name*)))
|
||
(cond
|
||
((string-suffix? ".zip" what)
|
||
(mkdir-p where)
|
||
(with-directory-excursion where
|
||
(invoke "unzip" what)))
|
||
((string-suffix? ".tar.gz" what)
|
||
(mkdir-p where)
|
||
(invoke "tar" "xf" what
|
||
"-C" where "--strip-components=1"))
|
||
(else
|
||
(let ((parent (dirname where)))
|
||
(mkdir-p parent)
|
||
(with-directory-excursion parent
|
||
(when (file-exists? name*)
|
||
(delete-file-recursively name*))
|
||
(copy-recursively what name*)
|
||
(map make-file-writable
|
||
(find-files name* ".*"))))))))
|
||
(list "boringssl"
|
||
"cub"
|
||
"double-conversion"
|
||
"farmhash"
|
||
"fft2d"
|
||
"highwayhash"
|
||
"nsync"
|
||
"re2"))
|
||
|
||
(rename-file "../build/cub/src/cub/cub-1.8.0/"
|
||
"../build/cub/src/cub/cub/")
|
||
#t))
|
||
(add-after 'unpack 'fix-python-build
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(mkdir-p "protobuf-src")
|
||
(invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
|
||
"-C" "protobuf-src" "--strip-components=1")
|
||
(mkdir-p "eigen-src")
|
||
(invoke "tar" "xf" (assoc-ref inputs "eigen:src")
|
||
"-C" "eigen-src" "--strip-components=1")
|
||
|
||
(substitute* "tensorflow/contrib/cmake/tf_python.cmake"
|
||
;; Ensure that all Python dependencies can be found at build time.
|
||
(("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
|
||
(string-append m ":" (getenv "PYTHONPATH")))
|
||
;; Take protobuf source files from our source package.
|
||
(("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
|
||
(string-append (getcwd) "/protobuf-src/src/google")))
|
||
|
||
(substitute* '("tensorflow/contrib/cmake/tf_shared_lib.cmake"
|
||
"tensorflow/contrib/cmake/tf_python.cmake")
|
||
;; Take Eigen source files from our source package.
|
||
(("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/eigen/src/eigen/")
|
||
(string-append (getcwd) "/eigen-src/"))
|
||
;; Take Eigen headers from our own package.
|
||
(("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
|
||
(string-append (assoc-ref inputs "eigen") "/include/eigen3")))
|
||
|
||
;; Correct the RUNPATH of ops libraries generated for Python.
|
||
;; TODO: this doesn't work :(
|
||
;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
|
||
;; warning: RUNPATH contains bogus entries: ("/tmp/guix-build-tensorflow-1.9.0.drv-0/source/tensorflow/contrib/build")
|
||
;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
|
||
;; error: depends on 'libpywrap_tensorflow_internal.so', which
|
||
;; cannot be found in RUNPATH ...
|
||
(substitute* "tensorflow/contrib/cmake/tf_cc_ops.cmake"
|
||
(("set_target_properties.*")
|
||
(string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
|
||
COMPILE_FLAGS ${target_compile_flags} \
|
||
INSTALL_RPATH_USE_LINK_PATH TRUE \
|
||
INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
|
||
#t))
|
||
(add-after 'build 'build-pip-package
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(setenv "LDFLAGS"
|
||
(string-append "-Wl,-rpath="
|
||
(assoc-ref outputs "out") "/lib"))
|
||
(invoke "make" "tf_python_build_pip_package")
|
||
#t))
|
||
(add-after 'build-pip-package 'install-python
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(wheel (car (find-files "../build/tf_python/dist/" "\\.whl$"))))
|
||
(invoke "python" "-m" "pip" "install" wheel
|
||
(string-append "--prefix=" out))
|
||
|
||
;; XXX: broken RUNPATH, see fix-python-build phase.
|
||
(delete-file
|
||
(string-append
|
||
out "/lib/python3.7/site-packages/tensorflow/contrib/"
|
||
"seq2seq/python/ops/lib_beam_search_ops.so"))
|
||
#t))))))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("protobuf:native" ,protobuf-next) ; protoc
|
||
("protobuf:src" ,(package-source protobuf-next))
|
||
("eigen:src" ,(package-source eigen-for-tensorflow))
|
||
;; The commit hashes and URLs for third-party source code are taken
|
||
;; from "tensorflow/workspace.bzl".
|
||
("boringssl-src"
|
||
,(let ((commit "ee7aa02")
|
||
(revision "1"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://boringssl.googlesource.com/boringssl")
|
||
(commit commit)))
|
||
(file-name (string-append "boringssl-0-" revision
|
||
(string-take commit 7)
|
||
"-checkout"))
|
||
(sha256
|
||
(base32
|
||
"1jf693q0nw0adsic6cgmbdx6g7wr4rj4vxa8j1hpn792fqhd8wgw")))))
|
||
("cub-src"
|
||
,(let ((version "1.8.0"))
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://mirror.bazel.build/github.com/NVlabs/"
|
||
"cub/archive/" version ".zip"))
|
||
(file-name (string-append "cub-" version ".zip"))
|
||
(sha256
|
||
(base32
|
||
"1hsqikqridb90dkxkjr2918dcry6pfh46ccnwrzawl56aamhdykb")))))
|
||
("double-conversion-src"
|
||
,(let ((commit "5664746")
|
||
(revision "1"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/google/double-conversion.git")
|
||
(commit commit)))
|
||
(file-name
|
||
(git-file-name "double-conversion"
|
||
(string-append "0-" revision "."
|
||
(string-take commit 7))))
|
||
(sha256
|
||
(base32
|
||
"1h5lppqqxcvdg5jq42i5msgwx20ryij3apvmndflngrgdpc04gn1")))))
|
||
("farmhash-src"
|
||
,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://mirror.bazel.build/github.com/google/farmhash/archive/"
|
||
commit ".tar.gz"))
|
||
(file-name (string-append "farmhash-0-" (string-take commit 7)
|
||
".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
|
||
;; The license notice on the home page at
|
||
;; http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html says:
|
||
;; Copyright Takuya OOURA, 1996-2001
|
||
;;
|
||
;; You may use, copy, modify and distribute this code for any purpose
|
||
;; (include commercial use) and without fee. Please refer to this
|
||
;; package when you modify this code.
|
||
;;
|
||
;; We take the identical tarball from the Bazel mirror, because the URL
|
||
;; at the home page is not versioned and might change.
|
||
("fft2d-src"
|
||
,(origin
|
||
(method url-fetch)
|
||
(uri "https://mirror.bazel.build/www.kurims.kyoto-u.ac.jp/~ooura/fft.tgz")
|
||
(file-name "fft2d.tar.gz")
|
||
(sha256
|
||
(base32
|
||
"15jjkfvhqvl2c0753d2di8hz0pyzn598g74wqy79awdrf1y67fsj"))))
|
||
("highwayhash-src"
|
||
,(let ((commit "be5edafc2e1a455768e260ccd68ae7317b6690ee")
|
||
(revision "1"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/google/highwayhash.git")
|
||
(commit commit)))
|
||
(file-name (string-append "highwayhash-0-" revision
|
||
(string-take commit 7)
|
||
"-checkout"))
|
||
(sha256
|
||
(base32
|
||
"154jwf98cyy54hldr94pgjn85zynly3abpnc1avmb8a18lzwjyb6")))))
|
||
("nsync-src"
|
||
,(let ((version "0559ce013feac8db639ee1bf776aca0325d28777")
|
||
(revision "1"))
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://mirror.bazel.build/"
|
||
"github.com/google/nsync/archive/"
|
||
version ".tar.gz"))
|
||
(file-name (string-append "nsync-0." revision
|
||
"-" (string-take version 7)
|
||
".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0qdkyqym34x739mmzv97ah5r7ph462v5xkxqxvidmcfqbi64b132")))))
|
||
("re2-src"
|
||
,(let ((commit "e7efc48")
|
||
(revision "1"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/google/re2")
|
||
(commit commit)))
|
||
(file-name (string-append "re2-0-" revision
|
||
(string-take commit 7)
|
||
"-checkout"))
|
||
(sha256
|
||
(base32
|
||
"161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign")))))
|
||
("googletest" ,googletest)
|
||
("swig" ,swig)
|
||
("unzip" ,unzip)))
|
||
(propagated-inputs
|
||
`(("python-absl-py" ,python-absl-py)
|
||
("python-astor" ,python-astor)
|
||
("python-gast" ,python-gast)
|
||
("python-grpcio" ,python-grpcio)
|
||
("python-numpy" ,python-numpy)
|
||
("python-protobuf" ,python-protobuf-next)
|
||
("python-six" ,python-six)
|
||
("python-termcolo" ,python-termcolor)
|
||
("python-wheel" ,python-wheel)))
|
||
(inputs
|
||
`(("c-ares" ,c-ares-next)
|
||
("eigen" ,eigen-for-tensorflow)
|
||
("gemmlowp" ,gemmlowp-for-tensorflow)
|
||
("lmdb" ,lmdb)
|
||
("libjpeg" ,libjpeg)
|
||
("libpng" ,libpng)
|
||
("giflib" ,giflib)
|
||
("grpc" ,grpc)
|
||
("jsoncpp" ,jsoncpp-for-tensorflow)
|
||
("snappy" ,snappy)
|
||
("sqlite" ,sqlite)
|
||
("protobuf" ,protobuf-next)
|
||
("python" ,python-wrapper)
|
||
("zlib" ,zlib)))
|
||
(home-page "https://tensorflow.org")
|
||
(synopsis "Machine learning framework")
|
||
(description
|
||
"TensorFlow is a flexible platform for building and training machine
|
||
learning models. It provides a library for high performance numerical
|
||
computation and includes high level Python APIs, including both a sequential
|
||
API for beginners that allows users to build models quickly by plugging
|
||
together building blocks and a subclassing API with an imperative style for
|
||
advanced research.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-iml
|
||
(package
|
||
(name "python-iml")
|
||
(version "0.6.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "iml" version))
|
||
(sha256
|
||
(base32
|
||
"1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
|
||
(build-system python-build-system)
|
||
(propagated-inputs
|
||
`(("ipython" ,python-ipython)
|
||
("nose" ,python-nose)
|
||
("numpy" ,python-numpy)
|
||
("pandas" ,python-pandas)
|
||
("scipy" ,python-scipy)))
|
||
(home-page "http://github.com/interpretable-ml/iml")
|
||
(synopsis "Interpretable Machine Learning (iML) package")
|
||
(description "Interpretable ML (iML) is a set of data type objects,
|
||
visualizations, and interfaces that can be used by any method designed to
|
||
explain the predictions of machine learning models (or really the output of
|
||
any function). It currently contains the interface and IO code from the Shap
|
||
project, and it will potentially also do the same for the Lime project.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-keras-applications
|
||
(package
|
||
(name "python-keras-applications")
|
||
(version "1.0.8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "Keras_Applications" version))
|
||
(sha256
|
||
(base32
|
||
"1rcz31ca4axa6kzhjx4lwqxbg4wvlljkj8qj9a7p9sfd5fhzjyam"))))
|
||
(build-system python-build-system)
|
||
;; The tests require Keras, but this package is needed to build Keras.
|
||
(arguments '(#:tests? #f))
|
||
(propagated-inputs
|
||
`(("python-h5py" ,python-h5py)
|
||
("python-numpy" ,python-numpy)))
|
||
(native-inputs
|
||
`(("python-pytest" ,python-pytest)
|
||
("python-pytest-cov" ,python-pytest-cov)
|
||
("python-pytest-pep8" ,python-pytest-pep8)
|
||
("python-pytest-xdist" ,python-pytest-xdist)))
|
||
(home-page "https://github.com/keras-team/keras-applications")
|
||
(synopsis "Reference implementations of popular deep learning models")
|
||
(description
|
||
"This package provides reference implementations of popular deep learning
|
||
models for use with the Keras deep learning framework.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-keras-preprocessing
|
||
(package
|
||
(name "python-keras-preprocessing")
|
||
(version "1.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "Keras_Preprocessing" version))
|
||
(sha256
|
||
(base32
|
||
"1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as"))))
|
||
(build-system python-build-system)
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-six" ,python-six)))
|
||
(native-inputs
|
||
`(("python-pandas" ,python-pandas)
|
||
("python-pillow" ,python-pillow)
|
||
("python-pytest" ,python-pytest)
|
||
("python-pytest-cov" ,python-pytest-cov)
|
||
("python-pytest-xdist" ,python-pytest-xdist)
|
||
("tensorflow" ,tensorflow)))
|
||
(home-page "https://github.com/keras-team/keras-preprocessing/")
|
||
(synopsis "Data preprocessing and augmentation for deep learning models")
|
||
(description
|
||
"Keras Preprocessing is the data preprocessing and data augmentation
|
||
module of the Keras deep learning library. It provides utilities for working
|
||
with image data, text data, and sequence data.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-keras
|
||
(package
|
||
(name "python-keras")
|
||
(version "2.2.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "Keras" version))
|
||
(sha256
|
||
(base32
|
||
"1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-tests-for-unavailable-features
|
||
(lambda _
|
||
(delete-file "keras/backend/theano_backend.py")
|
||
(delete-file "keras/backend/cntk_backend.py")
|
||
(delete-file "tests/keras/backend/backend_test.py")
|
||
|
||
;; FIXME: This doesn't work because Tensorflow is missing the
|
||
;; coder ops library.
|
||
(delete-file "tests/keras/test_callbacks.py")
|
||
#t))
|
||
(replace 'check
|
||
(lambda _
|
||
;; These tests attempt to download data files from the internet.
|
||
(delete-file "tests/integration_tests/test_datasets.py")
|
||
(delete-file "tests/integration_tests/imagenet_utils_test.py")
|
||
|
||
(setenv "PYTHONPATH"
|
||
(string-append (getcwd) "/build/lib:"
|
||
(getenv "PYTHONPATH")))
|
||
(invoke "py.test" "-v"
|
||
"-p" "no:cacheprovider"
|
||
"--ignore" "keras/utils"))))))
|
||
(propagated-inputs
|
||
`(("python-h5py" ,python-h5py)
|
||
("python-keras-applications" ,python-keras-applications)
|
||
("python-keras-preprocessing" ,python-keras-preprocessing)
|
||
("python-numpy" ,python-numpy)
|
||
("python-pydot" ,python-pydot)
|
||
("python-pyyaml" ,python-pyyaml)
|
||
("python-scipy" ,python-scipy)
|
||
("python-six" ,python-six)
|
||
("tensorflow" ,tensorflow)
|
||
("graphviz" ,graphviz)))
|
||
(native-inputs
|
||
`(("python-pandas" ,python-pandas)
|
||
("python-pytest" ,python-pytest)
|
||
("python-pytest-cov" ,python-pytest-cov)
|
||
("python-pytest-pep8" ,python-pytest-pep8)
|
||
("python-pytest-timeout" ,python-pytest-timeout)
|
||
("python-pytest-xdist" ,python-pytest-xdist)
|
||
("python-sphinx" ,python-sphinx)
|
||
("python-requests" ,python-requests)))
|
||
(home-page "https://github.com/keras-team/keras")
|
||
(synopsis "High-level deep learning framework")
|
||
(description "Keras is a high-level neural networks API, written in Python
|
||
and capable of running on top of TensorFlow. It was developed with a focus on
|
||
enabling fast experimentation. Use Keras if you need a deep learning library
|
||
that:
|
||
|
||
@itemize
|
||
@item Allows for easy and fast prototyping (through user friendliness,
|
||
modularity, and extensibility).
|
||
@item Supports both convolutional networks and recurrent networks, as well as
|
||
combinations of the two.
|
||
@item Runs seamlessly on CPU and GPU.
|
||
@end itemize\n")
|
||
(license license:expat)))
|
||
|
||
(define-public sbcl-cl-libsvm-format
|
||
(let ((commit "3300f84fd8d9f5beafc114f543f9d83417c742fb")
|
||
(revision "0"))
|
||
(package
|
||
(name "sbcl-cl-libsvm-format")
|
||
(version (git-version "0.1.0" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/masatoi/cl-libsvm-format.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0284aj84xszhkhlivaigf9qj855fxad3mzmv3zfr0qzb5k0nzwrg"))))
|
||
(build-system asdf-build-system/sbcl)
|
||
(native-inputs
|
||
`(("prove" ,sbcl-prove)
|
||
("prove-asdf" ,sbcl-prove-asdf)))
|
||
(inputs
|
||
`(("alexandria" ,sbcl-alexandria)))
|
||
(synopsis "LibSVM data format reader for Common Lisp")
|
||
(description
|
||
"This Common Lisp library provides a fast reader for data in LibSVM
|
||
format.")
|
||
(home-page "https://github.com/masatoi/cl-libsvm-format")
|
||
(license license:expat))))
|
||
|
||
(define-public cl-libsvm-format
|
||
(sbcl-package->cl-source-package sbcl-cl-libsvm-format))
|
||
|
||
(define-public ecl-cl-libsvm-format
|
||
(sbcl-package->ecl-package sbcl-cl-libsvm-format))
|
||
|
||
(define-public sbcl-cl-online-learning
|
||
(let ((commit "fc7a34f4f161cd1c7dd747d2ed8f698947781423")
|
||
(revision "0"))
|
||
(package
|
||
(name "sbcl-cl-online-learning")
|
||
(version (git-version "0.5" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/masatoi/cl-online-learning.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"14x95rlg80ay5hv645ki57pqvy12v28hz4k1w0f6bsfi2rmpxchq"))))
|
||
(build-system asdf-build-system/sbcl)
|
||
(native-inputs
|
||
`(("prove" ,sbcl-prove)
|
||
("prove-asdf" ,sbcl-prove-asdf)))
|
||
(inputs
|
||
`(("cl-libsvm-format" ,sbcl-cl-libsvm-format)
|
||
("cl-store" ,sbcl-cl-store)))
|
||
(arguments
|
||
`(;; FIXME: Tests pass but then the check phase crashes
|
||
#:tests? #f))
|
||
(synopsis "Online Machine Learning for Common Lisp")
|
||
(description
|
||
"This library contains a collection of machine learning algorithms for
|
||
online linear classification written in Common Lisp.")
|
||
(home-page "https://github.com/masatoi/cl-online-learning")
|
||
(license license:expat))))
|
||
|
||
(define-public cl-online-learning
|
||
(sbcl-package->cl-source-package sbcl-cl-online-learning))
|
||
|
||
(define-public ecl-cl-online-learning
|
||
(sbcl-package->ecl-package sbcl-cl-online-learning))
|
||
|
||
(define-public sbcl-cl-random-forest
|
||
(let ((commit "85fbdd4596d40e824f70f1b7cf239cf544e49d51")
|
||
(revision "0"))
|
||
(package
|
||
(name "sbcl-cl-random-forest")
|
||
(version (git-version "0.1" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/masatoi/cl-random-forest.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"097xv60i1ndz68sg9p4pc7c5gvyp9i1xgw966b4wwfq3x6hbz421"))))
|
||
(build-system asdf-build-system/sbcl)
|
||
(native-inputs
|
||
`(("prove" ,sbcl-prove)
|
||
("prove-asdf" ,sbcl-prove-asdf)
|
||
("trivial-garbage" ,sbcl-trivial-garbage)))
|
||
(inputs
|
||
`(("alexandria" ,sbcl-alexandria)
|
||
("cl-libsvm-format" ,sbcl-cl-libsvm-format)
|
||
("cl-online-learning" ,sbcl-cl-online-learning)
|
||
("lparallel" ,sbcl-lparallel)))
|
||
(arguments
|
||
`(;; The tests download data from the Internet
|
||
#:tests? #f
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'add-sb-cltl2-dependency
|
||
(lambda _
|
||
;; sb-cltl2 is required by lparallel when using sbcl, but it is
|
||
;; not loaded automatically.
|
||
(substitute* "cl-random-forest.asd"
|
||
(("\\(in-package :cl-user\\)")
|
||
"(in-package :cl-user) #+sbcl (require :sb-cltl2)"))
|
||
#t)))))
|
||
(synopsis "Random Forest and Global Refinement for Common Lisp")
|
||
(description
|
||
"CL-random-forest is an implementation of Random Forest for multiclass
|
||
classification and univariate regression written in Common Lisp. It also
|
||
includes an implementation of Global Refinement of Random Forest.")
|
||
(home-page "https://github.com/masatoi/cl-random-forest")
|
||
(license license:expat))))
|
||
|
||
(define-public cl-random-forest
|
||
(sbcl-package->cl-source-package sbcl-cl-random-forest))
|
||
|
||
(define-public ecl-cl-random-forest
|
||
(sbcl-package->ecl-package sbcl-cl-random-forest))
|