2909 lines
121 KiB
Scheme
2909 lines
121 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2016, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
|
||
;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com>
|
||
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
|
||
;;; Copyright © 2018, 2019, 2020 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, 2020 Guillaume Le Vaillant <glv@posteo.net>
|
||
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
|
||
;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
|
||
;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
|
||
;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
|
||
;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
|
||
;;;
|
||
;;; 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 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 cmake)
|
||
#:use-module (gnu packages cpp)
|
||
#: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 libffi)
|
||
#:use-module (gnu packages linux)
|
||
#:use-module (gnu packages llvm)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages mpi)
|
||
#:use-module (gnu packages ninja)
|
||
#:use-module (gnu packages ocaml)
|
||
#:use-module (gnu packages onc-rpc)
|
||
#:use-module (gnu packages parallel)
|
||
#: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-build)
|
||
#:use-module (gnu packages python-check)
|
||
#:use-module (gnu packages python-science)
|
||
#:use-module (gnu packages python-web)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages rpc)
|
||
#: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")
|
||
(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 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 "https://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))
|
||
#:modules ((guix build python-build-system)
|
||
,@%gnu-build-system-modules)
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'enter-dir
|
||
(lambda _ (chdir "ghmm")))
|
||
(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\", ")))))
|
||
(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))))))))
|
||
(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")
|
||
(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* "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 "1.7.9")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.openfst.org/twiki/pub/FST/"
|
||
"FstDownload/openfst-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1pmx1yhn2gknj0an0zwqmzgwjaycapi896244np50a8y3nrsw6ck"))))
|
||
(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 "https://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
|
||
combines 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 onnx
|
||
(package
|
||
(name "onnx")
|
||
(version "1.9.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/onnx/onnx")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32
|
||
"1xnii361f68x0masxgfc4ai7hh3wlxxk56aznwf4m4yr6wqx47ml"))
|
||
(file-name (git-file-name name version))
|
||
(patches (search-patches "onnx-use-system-googletest.patch"
|
||
"onnx-shared-libraries.patch"
|
||
"onnx-skip-model-downloads.patch"))
|
||
(modules '((guix build utils)))
|
||
(snippet '(delete-file-recursively "third_party"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
'(#:phases (modify-phases %standard-phases
|
||
(add-before 'build 'pass-cmake-arguments
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Pass options to the CMake-based build process.
|
||
(define out
|
||
(assoc-ref outputs "out"))
|
||
|
||
(define args
|
||
;; Copy arguments from 'cmake-build-system', plus ask
|
||
;; for shared libraries.
|
||
(list "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
|
||
(string-append "-DCMAKE_INSTALL_PREFIX=" out)
|
||
"-DCMAKE_INSTALL_LIBDIR=lib"
|
||
"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
|
||
(string-append "-DCMAKE_INSTALL_RPATH=" out
|
||
"/lib")
|
||
"-DCMAKE_VERBOSE_MAKEFILE=ON"
|
||
|
||
"-DBUILD_SHARED_LIBS=ON"))
|
||
|
||
;; This environment variable is honored by 'setup.py',
|
||
;; which passes it down to 'cmake'.
|
||
(setenv "CMAKE_ARGS" (string-join args))
|
||
|
||
;; This one is honored by 'setup.py' and passed to 'make
|
||
;; -j'.
|
||
(setenv "MAX_JOBS"
|
||
(number->string (parallel-job-count)))))
|
||
(add-before 'check 'make-test-directory-writable
|
||
(lambda _
|
||
;; Make things writable for tests.
|
||
(setenv "HOME" (getcwd))
|
||
(for-each make-file-writable
|
||
(find-files "onnx/examples" "."
|
||
#:directories? #t))))
|
||
(add-after 'install 'install-from-cmake
|
||
(lambda _
|
||
;; Run "make install" in the build tree 'setup.py'
|
||
;; created for CMake so that libonnx.so,
|
||
;; libonnx_proto.so, etc. are installed.
|
||
(invoke "make" "install"
|
||
"-C" ".setuptools-cmake-build"))))))
|
||
(native-inputs
|
||
`(("cmake" ,cmake)
|
||
("googletest" ,googletest)
|
||
("pybind11" ,pybind11)
|
||
("python-coverage" ,python-coverage)
|
||
("python-nbval" ,python-nbval)
|
||
("python-pytest" ,python-pytest)
|
||
("python-pytest-runner" ,python-pytest-runner)))
|
||
(inputs
|
||
`(("protobuf" ,protobuf)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-protobuf" ,python-protobuf)
|
||
("python-six" ,python-six)
|
||
("python-tabulate" ,python-tabulate)
|
||
("python-typing-extensions"
|
||
,python-typing-extensions)))
|
||
(home-page "https://onnx.ai/")
|
||
(synopsis "Open Neural Network Exchange")
|
||
(description
|
||
"Open Neural Network Exchange (ONNX) provides an open source format for
|
||
AI models, both deep learning and traditional ML. It defines an extensible
|
||
computation graph model, as well as definitions of built-in operators and
|
||
standard data types.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-onnx
|
||
;; This used to be called "python-onnx" because it provided nothing but
|
||
;; Python bindings. The package now provides shared libraries and C++
|
||
;; headers, hence the name change.
|
||
(deprecated-package "python-onnx" onnx))
|
||
|
||
(define-public onnx-optimizer
|
||
(package
|
||
(name "onnx-optimizer")
|
||
;; Note: 0.2.x is *more* recent than 1.5.0.
|
||
(version "0.2.6")
|
||
(home-page "https://github.com/onnx/optimizer")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url home-page)
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32
|
||
"1wkqqdxcxpfbf8zpbdfdd3zz5jkw775g31gyykj11z4y6pp659l6"))
|
||
(file-name (git-file-name name version))
|
||
(patches (search-patches "onnx-optimizer-system-library.patch"))
|
||
(modules '((guix build utils)))
|
||
(snippet '(delete-file-recursively "third_party"))))
|
||
(build-system python-build-system)
|
||
(arguments (package-arguments onnx)) ;reuse build system tweaks
|
||
(native-inputs
|
||
`(("cmake" ,cmake)
|
||
("python-pytest" ,python-pytest)
|
||
("python-pytest-runner" ,python-pytest-runner)
|
||
("python-nbval" ,python-nbval)
|
||
("python-coverage" ,python-coverage)))
|
||
(inputs
|
||
`(("onnx" ,onnx)
|
||
("protobuf" ,protobuf)
|
||
("pybind11" ,pybind11)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)))
|
||
(synopsis "Library to optimize ONNX models")
|
||
(description
|
||
"This package provides a C++ and Python library for performing arbitrary
|
||
optimizations on ONNX models, as well as a growing list of prepackaged
|
||
optimization passes.
|
||
|
||
Not all possible optimizations can be directly implemented on ONNX graphs---
|
||
some will need additional backend-specific information---but many can, and the
|
||
aim is to provide all such passes along with ONNX so that they can be re-used
|
||
with a single function call.")
|
||
(license license:expat)))
|
||
|
||
(define-public rxcpp
|
||
(package
|
||
(name "rxcpp")
|
||
(version "4.1.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/ReactiveX/RxCpp")
|
||
(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 gemmlowp
|
||
(let ((commit "f9959600daa42992baace8a49544a00a743ce1b6")
|
||
(version "0.1")
|
||
(revision "1"))
|
||
(package
|
||
(name "gemmlowp")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/google/gemmlowp")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1hzfhlhzcb827aza6a7drydc67dw5fm3qfqilb9ibskan8dsf0c6"))))
|
||
(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 "/gemmlowp/" dir)))
|
||
(for-each (lambda (h)
|
||
(install-file h target))
|
||
(find-files (string-append "../" dir)
|
||
"\\.h$"))))
|
||
'("meta" "profiling" "public" "fixedpoint"
|
||
"eight_bit_int_gemm" "internal"))))))))
|
||
(build-system cmake-build-system)
|
||
(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 gemmlowp-for-tensorflow
|
||
;; The commit hash is taken from "tensorflow/workspace.bzl".
|
||
(let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
|
||
(revision "2"))
|
||
(package
|
||
(inherit 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"))))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments gemmlowp)
|
||
((#:phases phases)
|
||
`(modify-phases ,phases
|
||
(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)
|
||
;; Note: Install headers straight into
|
||
;; $includedir instead of $includedir/gemmlowp.
|
||
(let ((target (string-append inc "/" dir)))
|
||
(for-each (lambda (h)
|
||
(install-file h target))
|
||
(find-files (string-append "../" dir)
|
||
"\\.h$"))))
|
||
'("meta" "profiling" "public" "fixedpoint"
|
||
"eight_bit_int_gemm" "internal")))))))))
|
||
(native-inputs
|
||
`(("unzip" ,unzip)))
|
||
(properties '((hidden? . #t))))))
|
||
|
||
(define-public dlib
|
||
(package
|
||
(name "dlib")
|
||
(version "19.20")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://dlib.net/files/dlib-" version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"139jyi19qz37wwmmy48gil9d1kkh2r3w3bwdzabha6ayxmba96nz"))
|
||
(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
|
||
`(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
|
||
#: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))))))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
;; For tests.
|
||
("libnsl" ,libnsl)))
|
||
(inputs
|
||
`(("giflib" ,giflib)
|
||
("lapack" ,lapack)
|
||
("libjpeg" ,libjpeg-turbo)
|
||
("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 "0.24.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/scikit-learn/scikit-learn")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0hm92biqwwc87bqnr56lwa5bz77lr7k9q21rdwksnfzq3vsdp2nm"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-ext
|
||
(lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))
|
||
(replace 'check
|
||
(lambda _
|
||
;; Restrict OpenBLAS threads to prevent segfaults while testing!
|
||
(setenv "OPENBLAS_NUM_THREADS" "1")
|
||
|
||
;; Some tests require write access to $HOME.
|
||
(setenv "HOME" "/tmp")
|
||
|
||
(invoke "pytest" "sklearn" "-m" "not network")))
|
||
(add-before 'reset-gzip-timestamps 'make-files-writable
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Make sure .gz files are writable so that the
|
||
;; 'reset-gzip-timestamps' phase can do its work.
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(for-each make-file-writable
|
||
(find-files out "\\.gz$"))))))))
|
||
(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-threadpoolctl" ,python-threadpoolctl)
|
||
("python-scipy" ,python-scipy)
|
||
("python-joblib" ,python-joblib)))
|
||
(home-page "https://scikit-learn.org/")
|
||
(synopsis "Machine Learning in Python")
|
||
(description
|
||
"Scikit-learn provides simple and efficient tools for data mining and
|
||
data analysis.")
|
||
(properties `((python2-variant . ,(delay python2-scikit-learn))))
|
||
(license license:bsd-3)))
|
||
|
||
;; scikit-learn 0.22 and later only supports Python 3, so we stick with
|
||
;; an older version here.
|
||
(define-public python2-scikit-learn
|
||
(let ((base (package-with-python2 (strip-python2-variant python-scikit-learn))))
|
||
(package
|
||
(inherit base)
|
||
(version "0.20.4")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/scikit-learn/scikit-learn")
|
||
(commit version)))
|
||
(file-name (git-file-name "python-scikit-learn" version))
|
||
(sha256
|
||
(base32
|
||
"08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))
|
||
(inputs
|
||
`(("openblas" ,openblas)))
|
||
(native-inputs
|
||
`(("python2-pytest" ,python2-pytest)
|
||
("python2-pandas" ,python2-pandas) ;for tests
|
||
("python2-cython" ,python2-cython)))
|
||
(propagated-inputs
|
||
`(("python2-numpy" ,python2-numpy)
|
||
("python2-scipy" ,python2-scipy)
|
||
("python2-joblib" ,python2-joblib))))))
|
||
|
||
(define-public python-threadpoolctl
|
||
(package
|
||
(name "python-threadpoolctl")
|
||
(version "2.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "threadpoolctl" version))
|
||
(sha256
|
||
(base32
|
||
"0szsxcm2fbxrn83iynn42bnvrdh7mfsmkhfn8pdn7swblfb7rifx"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
|
||
(when tests?
|
||
(add-installed-pythonpath inputs outputs)
|
||
(invoke "pytest"))
|
||
#t)))))
|
||
(native-inputs
|
||
`(("python-pytest" ,python-pytest)))
|
||
(home-page "https://github.com/joblib/threadpoolctl")
|
||
(synopsis "Python helpers for common threading libraries")
|
||
(description "Thread-pool Controls provides Python helpers to limit the
|
||
number of threads used in the threadpool-backed of common native libraries used
|
||
for scientific computing and data science (e.g. BLAS and OpenMP).")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-pynndescent
|
||
(package
|
||
(name "python-pynndescent")
|
||
(version "0.5.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pynndescent" version))
|
||
(sha256
|
||
(base32 "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr"))))
|
||
(build-system python-build-system)
|
||
(native-inputs
|
||
`(("python-nose" ,python-nose)))
|
||
(propagated-inputs
|
||
`(("python-joblib" ,python-joblib)
|
||
("python-llvmlite" ,python-llvmlite)
|
||
("python-numba" ,python-numba)
|
||
("python-scikit-learn" ,python-scikit-learn)
|
||
("python-scipy" ,python-scipy)))
|
||
(home-page "https://github.com/lmcinnes/pynndescent")
|
||
(synopsis "Nearest neighbor descent for approximate nearest neighbors")
|
||
(description
|
||
"PyNNDescent provides a Python implementation of Nearest Neighbor Descent
|
||
for k-neighbor-graph construction and approximate nearest neighbor search.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public python-opentsne
|
||
(package
|
||
(name "python-opentsne")
|
||
(version "0.5.2")
|
||
(source
|
||
(origin
|
||
;; No tests in the PyPI tarball.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pavlin-policar/openTSNE")
|
||
(commit (string-append "v" version))))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(sha256
|
||
(base32 "1hl42wmafydk4fxdx05l180k3canmqw8h9r20fsqq2aq440b09gh"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
;; Benchmarks require the 'macosko2015' data files.
|
||
(add-after 'unpack 'delete-benchmark
|
||
(lambda _
|
||
(delete-file-recursively "benchmarks")
|
||
#t))
|
||
;; Numba needs a writable dir to cache functions.
|
||
(add-before 'check 'set-numba-cache-dir
|
||
(lambda _
|
||
(setenv "NUMBA_CACHE_DIR" "/tmp")
|
||
#t)))))
|
||
(native-inputs
|
||
`(("python-cython" ,python-cython)))
|
||
(inputs
|
||
`(("fftw" ,fftw)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-pynndescent" ,python-pynndescent)
|
||
("python-scikit-learn" ,python-scikit-learn)
|
||
("python-scipy" ,python-scipy)))
|
||
(home-page "https://github.com/pavlin-policar/openTSNE")
|
||
(synopsis "Extensible, parallel implementations of t-SNE")
|
||
(description
|
||
"This is a modular Python implementation of t-Distributed Stochastic
|
||
Neighbor Embedding (t-SNE), a popular dimensionality-reduction algorithm for
|
||
visualizing high-dimensional data sets.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-scikit-rebate
|
||
(package
|
||
(name "python-scikit-rebate")
|
||
(version "0.6")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "skrebate" version))
|
||
(sha256
|
||
(base32
|
||
"1h7qs9gjxpzqabzhb8rmpv3jpmi5iq41kqdibg48299h94iikiw7"))))
|
||
(build-system python-build-system)
|
||
;; Pandas is only needed to run the tests.
|
||
(native-inputs
|
||
`(("python-pandas" ,python-pandas)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-scipy" ,python-scipy)
|
||
("python-scikit-learn" ,python-scikit-learn)
|
||
("python-joblib" ,python-joblib)))
|
||
(home-page "https://epistasislab.github.io/scikit-rebate/")
|
||
(synopsis "Relief-based feature selection algorithms for Python")
|
||
(description "Scikit-rebate is a scikit-learn-compatible Python
|
||
implementation of ReBATE, a suite of Relief-based feature selection algorithms
|
||
for Machine Learning. These algorithms excel at identifying features that are
|
||
predictive of the outcome in supervised learning problems, and are especially
|
||
good at identifying feature interactions that are normally overlooked by
|
||
standard feature selection algorithms.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-cmaes
|
||
(package
|
||
(name "python-cmaes")
|
||
(version "0.8.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ;no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/CyberAgent/cmaes")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32 "1jyckaifir528dz6m95nvky8hvqmz5gz6dlp65baahhbca0danzb"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system python-build-system)
|
||
(native-inputs
|
||
`(("python-setuptools" ,python-setuptools) ;build fails without this
|
||
("python-wheel" ,python-wheel)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)))
|
||
(home-page "https://github.com/CyberAgent/cmaes")
|
||
(synopsis "CMA-ES implementation for Python")
|
||
(description "This package provides provides an implementation of the
|
||
Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
|
||
(license license:expat)))
|
||
|
||
(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 git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Microsoft/LightGBM")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32
|
||
"0jlvyn7k81dzrh9ij3zw576wbgiwmmr26rzpdxjn1dbpc3njpvzi"))
|
||
(file-name (git-file-name name version))))
|
||
(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 _
|
||
(with-directory-excursion "../source"
|
||
(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 git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/JohnLangford/vowpal_wabbit")
|
||
(commit version)))
|
||
(sha256
|
||
(base32
|
||
"04bwzk6ifgnz3fmzid8b7avxf9n5pnx9xcjm61nkjng1vv0bpj8x"))
|
||
(file-name (git-file-name name version))))
|
||
(inputs
|
||
`(("boost" ,boost)
|
||
("zlib" ,zlib)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "--with-boost="
|
||
(assoc-ref %build-inputs "boost")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'make-files-writable
|
||
(lambda _
|
||
(for-each make-file-writable (find-files "." ".*")) #t))
|
||
(add-after 'install 'install-more-headers
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(for-each
|
||
(lambda (file)
|
||
(install-file file (string-append
|
||
(assoc-ref outputs "out")
|
||
"/include/vowpalwabbit")))
|
||
(find-files "vowpalwabbit" "\\.h$"))
|
||
#t)))))
|
||
(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)))
|
||
|
||
(define-public python-hyperopt
|
||
(package
|
||
(name "python-hyperopt")
|
||
(version "0.2.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "hyperopt" version))
|
||
(sha256
|
||
(base32 "1k4ma8ci0bxghw7g4ms944zak1pi83yv2d6bxd7fcslm1zalfq5w"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
|
||
(when tests?
|
||
(add-installed-pythonpath inputs outputs)
|
||
(invoke "python" "-m" "pytest" "--ignore"
|
||
;; Needs python-pyspark.
|
||
"hyperopt/tests/test_spark.py"
|
||
;; Needs both python-scikit-learn and python-lightgbm.
|
||
"--ignore" "hyperopt/tests/test_atpe_basic.py"
|
||
;; The tests below need python-lightgbm.
|
||
"-k" (string-append "not test_branin"
|
||
" and not test_distractor"
|
||
" and not test_q1lognormal"
|
||
" and not test_quadratic1"
|
||
" and not test_twoarms"))))))))
|
||
(propagated-inputs
|
||
`(("python-cloudpickle" ,python-cloudpickle)
|
||
("python-future" ,python-future)
|
||
("python-networkx" ,python-networkx)
|
||
("python-numpy" ,python-numpy)
|
||
("python-scipy" ,python-scipy)
|
||
("python-six" ,python-six)
|
||
("python-tqdm" ,python-tqdm)))
|
||
(native-inputs
|
||
`(("python-black" ,python-black)
|
||
("python-ipython" ,python-ipython)
|
||
("python-ipyparallel" ,python-ipyparallel)
|
||
("python-nose" ,python-nose)
|
||
("python-pymongo" ,python-pymongo)
|
||
("python-pytest" ,python-pytest)))
|
||
(home-page "https://hyperopt.github.io/hyperopt/")
|
||
(synopsis "Library for hyperparameter optimization")
|
||
(description "Hyperopt is a Python library for serial and parallel
|
||
optimization over awkward search spaces, which may include real-valued,
|
||
discrete, and conditional dimensions.")
|
||
(license license:bsd-3)))
|
||
|
||
;; There have been no proper releases yet.
|
||
(define-public kaldi
|
||
(let ((commit "d4791c0f3fc1a09c042dac365e120899ee2ad21e")
|
||
(revision "2"))
|
||
(package
|
||
(name "kaldi")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/kaldi-asr/kaldi")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"07k80my6f19mhrkwbzhjsnpf9871wmrwkl0ym468i830w67qyjrz"))))
|
||
(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 "cb227ef43b66a9835c14eb0ad39e08ee03c210ad")
|
||
(revision "2"))
|
||
(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")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1i6ffwiavxx07ri0lxix6s8q0r31x7i4xxvhys5jxkixf5q34w8g"))))
|
||
(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" "-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")))
|
||
(substitute* "Makefile"
|
||
(("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
|
||
(("\\$\\(error Cannot find") "#"))
|
||
#t))
|
||
(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
|
||
;; This is the tip of the py3 branch
|
||
(let ((commit "f68cab490be7eb0da2af1475fbc16655f50a60cb")
|
||
(revision "2"))
|
||
(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")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"17lh1368vkg8ngrcbn2phvigzlmalrqg6djx2gg61qq1a0nj87dm"))))
|
||
(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"
|
||
;; See https://github.com/alumae/kaldi-gstreamer-server/issues/232
|
||
(substitute* "master_server.py"
|
||
(("\\.replace\\('\\\\.*") ")"))
|
||
|
||
;; This is a Python 2 file
|
||
(delete-file "decoder_test.py")
|
||
(delete-file "test-buffer.py")
|
||
|
||
(for-each (lambda (file)
|
||
(apply invoke
|
||
`("python"
|
||
"-m" "compileall"
|
||
"-f" ; force rebuild
|
||
,file)))
|
||
(find-files "." "\\.py$")))
|
||
#t))
|
||
(replace 'install
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin"))
|
||
(share (string-append out "/share/kaldi-gstreamer-server/")))
|
||
;; Install Python files
|
||
(with-directory-excursion "kaldigstserver"
|
||
(for-each (cut install-file <> share)
|
||
(find-files "." ".*")))
|
||
|
||
;; Install sample configuration files
|
||
(for-each (cut install-file <> share)
|
||
(find-files "." "\\.yaml"))
|
||
|
||
;; Install executables
|
||
(mkdir-p bin)
|
||
(let* ((server (string-append bin "/kaldi-gst-server"))
|
||
(client (string-append bin "/kaldi-gst-client"))
|
||
(worker (string-append bin "/kaldi-gst-worker"))
|
||
(PYTHONPATH (getenv "GUIX_PYTHONPATH"))
|
||
(GST_PLUGIN_PATH (string-append
|
||
(assoc-ref inputs "gst-kaldi-nnet2-online")
|
||
"/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
|
||
(wrap (lambda (wrapper what)
|
||
(with-output-to-file wrapper
|
||
(lambda _
|
||
(format #t
|
||
"#!~a
|
||
export GUIX_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)
|
||
("python" ,python-wrapper)
|
||
("python-pygobject" ,python-pygobject)
|
||
("python-pyyaml" ,python-pyyaml)
|
||
("python-tornado" ,python-tornado-6)))
|
||
(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))))
|
||
|
||
;; 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")
|
||
(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)
|
||
((guix build python-build-system)
|
||
#:select (python-version)))
|
||
#:imported-modules (,@%cmake-build-system-modules
|
||
(guix build python-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 >.*") ""))
|
||
|
||
;; Fix the build with python-3.8, taken from rejected upstream patch:
|
||
;; https://github.com/tensorflow/tensorflow/issues/34197
|
||
(substitute* (find-files "tensorflow/python" ".*\\.cc$")
|
||
(("(nullptr,)(\\ +/. tp_print)" _ _ tp_print)
|
||
(string-append "NULL, " tp_print)))))
|
||
(add-after 'python3.7-compatibility 'chdir
|
||
(lambda _ (chdir "tensorflow/contrib/cmake")))
|
||
(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\\}")
|
||
(search-input-file inputs "/lib/libsqlite3.so"))
|
||
(("sqlite_copy_headers_to_destination") "")
|
||
|
||
;; PNG
|
||
(("include\\(png\\)") "")
|
||
(("\\$\\{png_STATIC_LIBRARIES\\}")
|
||
(search-input-file inputs "/lib/libpng16.so"))
|
||
(("png_copy_headers_to_destination") "")
|
||
|
||
;; JPEG
|
||
(("include\\(jpeg\\)") "")
|
||
(("\\$\\{jpeg_STATIC_LIBRARIES\\}")
|
||
(search-input-file inputs "/lib/libjpeg.so"))
|
||
(("jpeg_copy_headers_to_destination") "")
|
||
|
||
;; GIF
|
||
(("include\\(gif\\)") "")
|
||
(("\\$\\{gif_STATIC_LIBRARIES\\}")
|
||
(search-input-file inputs "/lib/libgif.so"))
|
||
(("gif_copy_headers_to_destination") "")
|
||
|
||
;; lmdb
|
||
(("include\\(lmdb\\)") "")
|
||
(("\\$\\{lmdb_STATIC_LIBRARIES\\}")
|
||
(search-input-file inputs "/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/")))
|
||
(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"
|
||
;; 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")
|
||
(search-input-directory inputs "/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 ${target_compile_flags} \
|
||
INSTALL_RPATH_USE_LINK_PATH TRUE \
|
||
INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))))
|
||
(add-after 'build 'build-pip-package
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(setenv "LDFLAGS"
|
||
(string-append "-Wl,-rpath="
|
||
(assoc-ref outputs "out") "/lib"))
|
||
(invoke "make" "tf_python_build_pip_package")))
|
||
(add-after 'build-pip-package 'install-python
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(wheel (car (find-files "../build/tf_python/dist/" "\\.whl$")))
|
||
(python-version (python-version
|
||
(assoc-ref inputs "python"))))
|
||
(invoke "python" "-m" "pip" "install" wheel
|
||
(string-append "--prefix=" out))
|
||
|
||
;; XXX: broken RUNPATH, see fix-python-build phase.
|
||
(delete-file
|
||
(string-append
|
||
out "/lib/python" python-version
|
||
"/site-packages/tensorflow/contrib/"
|
||
"seq2seq/python/ops/lib_beam_search_ops.so"))))))))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("protobuf:native" ,protobuf-3.6) ; protoc
|
||
("protobuf:src" ,(package-source protobuf-3.6))
|
||
("eigen:src" ,(package-source eigen-for-tensorflow))
|
||
;; install_pip_packages.sh wants setuptools 39.1.0 specifically.
|
||
("python-setuptools" ,python-setuptools-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")
|
||
(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")
|
||
(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-3.6)
|
||
("python-six" ,python-six)
|
||
("python-termcolo" ,python-termcolor)
|
||
("python-wheel" ,python-wheel)))
|
||
(inputs
|
||
`(("c-ares" ,c-ares)
|
||
("eigen" ,eigen-for-tensorflow)
|
||
("gemmlowp" ,gemmlowp-for-tensorflow)
|
||
("lmdb" ,lmdb)
|
||
("libjpeg" ,libjpeg-turbo)
|
||
("libpng" ,libpng)
|
||
("giflib" ,giflib)
|
||
("grpc" ,grpc-1.16.1 "static")
|
||
("grpc:bin" ,grpc-1.16.1)
|
||
("jsoncpp" ,jsoncpp-for-tensorflow)
|
||
("snappy" ,snappy)
|
||
("sqlite" ,sqlite)
|
||
("protobuf" ,protobuf-3.6)
|
||
("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 tensorflow-lite
|
||
(package
|
||
(name "tensorflow-lite")
|
||
(version "2.5.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tensorflow/tensorflow")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1jdw2i1rq06zqd6aabh7bbm0avsg4pygnfmd7gviv0blhih9054l"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:tests? #false ; no "check" target
|
||
#:build-type "Release"
|
||
#:configure-flags
|
||
(list
|
||
"-DTFLITE_ENABLE_GPU=OFF"
|
||
"-DTFLITE_ENABLE_RUY=OFF"
|
||
|
||
;; TODO: The build system attempts to build xnnpack from source. We
|
||
;; would like to use our xnnpack package here, but this requires more
|
||
;; work.
|
||
"-DTFLITE_ENABLE_XNNPACK=OFF"
|
||
|
||
;; Pretend we've already fetched abseil. We won't actually build it
|
||
;; but use the existing package.
|
||
"-Dabseil-cpp_POPULATED=TRUE"
|
||
|
||
;; Don't fetch the sources. We have already built flatbuffers.
|
||
"-Dflatbuffers_POPULATED=TRUE"
|
||
|
||
"-DFFT2D_SOURCE_DIR=/tmp/fft2d"
|
||
"-Dneon2sse_SOURCE_DIR=/tmp/neon2sse"
|
||
"-Dneon2sse_BINARY_DIR=/tmp/neon2sse-bin"
|
||
"-DFARMHASH_SOURCE_DIR=/tmp/farmhash"
|
||
"-Dgemmlowp_SOURCE_DIR=/tmp/gemmlowp"
|
||
(string-append "-DRUY_SOURCE_DIR="
|
||
(assoc-ref %build-inputs "ruy-src")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "tensorflow/lite")))
|
||
(add-after 'chdir 'copy-sources
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; Use external cmake finders instead of these stubs that won't
|
||
;; find anything but the bundled sources.
|
||
(delete-file "tools/cmake/modules/Findabsl.cmake")
|
||
(delete-file "tools/cmake/modules/Findeigen.cmake")
|
||
|
||
(substitute* "CMakeLists.txt"
|
||
(("find_package\\(eigen REQUIRED")
|
||
"find_package(eigen REQUIRED NAMES Eigen3"))
|
||
(substitute* "tools/cmake/modules/Findflatbuffers.cmake"
|
||
(("get_target_property.*")
|
||
(format #false "set(FLATBUFFERS_INCLUDE_DIRS ~a/include)\n"
|
||
(assoc-ref inputs "flatbuffers"))))
|
||
|
||
;; Don't fetch source code; we already have everything we need.
|
||
(substitute* '("tools/cmake/modules/fft2d.cmake"
|
||
"tools/cmake/modules/ruy.cmake"
|
||
"tools/cmake/modules/farmhash.cmake"
|
||
"tools/cmake/modules/neon2sse.cmake"
|
||
"tools/cmake/modules/gemmlowp.cmake")
|
||
(("OverridableFetchContent_Populate.*") ""))
|
||
|
||
(mkdir-p "/tmp/farmhash")
|
||
(with-directory-excursion "/tmp/farmhash"
|
||
(invoke "tar" "--strip-components=1"
|
||
"-xf" (assoc-ref inputs "farmhash-src")))
|
||
|
||
(mkdir-p "/tmp/fft2d")
|
||
(with-directory-excursion "/tmp/fft2d"
|
||
(invoke "tar" "--strip-components=1"
|
||
"-xf" (assoc-ref inputs "fft2d-src")))
|
||
|
||
(copy-recursively (assoc-ref inputs "neon2sse-src")
|
||
"/tmp/neon2sse/")
|
||
(copy-recursively (assoc-ref inputs "gemmlowp-src")
|
||
"/tmp/gemmlowp/")))
|
||
(add-after 'copy-sources 'prepare-shared-library-build
|
||
(lambda _ (chdir "c")))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib"))
|
||
(headers (string-append out "/include/tensorflow/lite")))
|
||
(install-file "../build/libtensorflowlite_c.so" lib)
|
||
(with-directory-excursion ".."
|
||
(for-each
|
||
(lambda (file)
|
||
(let ((target-dir (string-append headers "/" (dirname file))))
|
||
(install-file file target-dir)))
|
||
(find-files "." "\\.h$")))))))))
|
||
(inputs
|
||
`(("abseil-cpp" ,abseil-cpp)
|
||
("eigen" ,eigen-for-tensorflow-lite)
|
||
("flatbuffers" ,flatbuffers)
|
||
("python" ,python)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("gemmlowp-src"
|
||
;; The commit hash is taken from
|
||
;; "tensorflow/lite/tools/cmake/modules/gemmlowp.cmake".
|
||
,(let ((commit "fda83bdc38b118cc6b56753bd540caa49e570745"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/google/gemmlowp")
|
||
(commit commit)))
|
||
(file-name (git-file-name "gemmlowp" (string-take commit 8)))
|
||
(sha256
|
||
(base32
|
||
"1sbp8kmr2azwlvfbzryy1frxi99jhsh1nc93bdbxdf8zdgpv0kxl")))))
|
||
("neon2sse-src"
|
||
,(let ((commit "a1652fd5253afbf3e39357b012974f93511f6108"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/intel/ARM_NEON_2_x86_SSE")
|
||
(commit commit)))
|
||
(file-name (git-file-name "neon2sse" (string-take commit 8)))
|
||
(sha256
|
||
(base32
|
||
"1q8gkxag9wlnwdwad2pclsrkwzrdjy94hyrkayrsvxyj7szb5y8i")))))
|
||
("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 (git-file-name "farmhash" (string-take commit 8)))
|
||
(sha256
|
||
(base32
|
||
"185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
|
||
("fft2d-src"
|
||
,(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://storage.googleapis.com/"
|
||
"mirror.tensorflow.org/"
|
||
"www.kurims.kyoto-u.ac.jp/~ooura/fft2d.tgz"))
|
||
(file-name "fft2d.tar.gz")
|
||
(sha256
|
||
(base32
|
||
"1jfflzi74fag9z4qmgwvp90aif4dpbr1657izmxlgvf4hy8fk9xd"))))
|
||
("ruy-src"
|
||
,(let ((commit "9c56af3fce210a8a103eda19bd6f47c08a9e3d90"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/google/ruy")
|
||
(commit commit)
|
||
(recursive? #true)))
|
||
(file-name (git-file-name "ruy" (string-take commit 8)))
|
||
(sha256
|
||
(base32
|
||
"1cfd5gk6kaj8kbl3h98gx1ap8czd59y6p8qq8nr28fklpyzf5cis")))))))
|
||
(home-page "https://tensorflow.org")
|
||
(synopsis "Machine learning framework")
|
||
(description
|
||
"TensorFlow is a flexible platform for building and training machine
|
||
learning models. This package provides the \"lite\" variant for mobile
|
||
devices.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public dmlc-core
|
||
(package
|
||
(name "dmlc-core")
|
||
(version "0.5")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/dmlc/dmlc-core")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1x4ad1jhn84fywlk031fmv1kxyiscclmrqn9hhj8gz0mh7z9vcrh"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list "-DGOOGLE_TEST=ON")))
|
||
(native-inputs
|
||
`(("googletest" ,googletest)
|
||
("python" ,python-wrapper)))
|
||
(home-page "https://github.com/dmlc/dmlc-core")
|
||
(synopsis "Common bricks library for machine learning")
|
||
(description
|
||
"DMLC-Core is the backbone library to support all DMLC projects,
|
||
offers the bricks to build efficient and scalable distributed machine
|
||
learning libraries.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public xgboost
|
||
(package
|
||
(name "xgboost")
|
||
(version "1.4.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/dmlc/xgboost")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(patches (search-patches "xgboost-use-system-dmlc-core.patch"))
|
||
(sha256
|
||
(base32 "00liz816ahk9zj3jv3m2fqwlf6xxfbgvpmpl72iklx32vl192w5d"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags (list "-DGOOGLE_TEST=ON")))
|
||
(native-inputs
|
||
`(("googletest" ,googletest)
|
||
("python" ,python-wrapper)))
|
||
(inputs
|
||
`(("dmlc-core" ,dmlc-core)))
|
||
(home-page "https://xgboost.ai/")
|
||
(synopsis "Gradient boosting (GBDT, GBRT or GBM) library")
|
||
(description
|
||
"XGBoost is an optimized distributed gradient boosting library designed
|
||
to be highly efficient, flexible and portable. It implements machine learning
|
||
algorithms under the Gradient Boosting framework. XGBoost provides a parallel
|
||
tree boosting (also known as GBDT, GBM) that solve many data science problems
|
||
in a fast and accurate way.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-xgboost
|
||
(package
|
||
(inherit xgboost)
|
||
(name "python-xgboost")
|
||
(source (package-source xgboost))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'preparations
|
||
(lambda _
|
||
;; Move python-package content to parent directory to silence
|
||
;; some warnings about files not being found if we chdir.
|
||
(rename-file "python-package/xgboost" "xgboost")
|
||
(rename-file "python-package/README.rst" "README.rst")
|
||
(rename-file "python-package/setup.cfg" "setup.cfg")
|
||
(rename-file "python-package/setup.py" "setup.py")
|
||
;; Skip rebuilding libxgboost.so.
|
||
(substitute* "setup.py"
|
||
(("ext_modules=\\[CMakeExtension\\('libxgboost'\\)\\],") "")
|
||
(("'install_lib': InstallLib,") ""))))
|
||
(add-after 'install 'install-version-and-libxgboost
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(pylib (string-append out "/lib/python"
|
||
,(version-major+minor
|
||
(package-version python))
|
||
"/site-packages"))
|
||
(xgbdir (string-append pylib "/xgboost"))
|
||
(version-file (string-append xgbdir "/VERSION"))
|
||
(libxgboost (string-append (assoc-ref inputs "xgboost")
|
||
"/lib/libxgboost.so")))
|
||
(with-output-to-file version-file
|
||
(lambda ()
|
||
(display ,(package-version xgboost))))
|
||
(mkdir-p (string-append xgbdir "/lib"))
|
||
(symlink libxgboost (string-append xgbdir "/lib"
|
||
"/libxgboost.so")))))
|
||
(replace 'check
|
||
;; Python-specific tests are located in tests/python.
|
||
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
|
||
(when tests?
|
||
(add-installed-pythonpath inputs outputs)
|
||
(invoke "pytest" "tests/python"
|
||
;; FIXME: CLI tests fail with PermissionError.
|
||
"--ignore" "tests/python/test_cli.py" "-k"
|
||
(string-append
|
||
"not test_cli_regression_demo"
|
||
;; The tests below open a network connection.
|
||
" and not test_model_compatibility"
|
||
" and not test_get_group"
|
||
" and not test_cv_no_shuffle"
|
||
" and not test_cv"
|
||
" and not test_training"
|
||
;; FIXME: May pass in the next version.
|
||
" and not test_pandas"
|
||
;; "'['./runexp.sh']' returned non-zero exit status 1"
|
||
" and not test_cli_binary_classification"))))))))
|
||
(native-inputs
|
||
`(("python-pandas" ,python-pandas)
|
||
("python-pytest" ,python-pytest)
|
||
("python-scikit-learn" ,python-scikit-learn)))
|
||
(inputs
|
||
`(("xgboost" ,xgboost)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-scipy" ,python-scipy)))
|
||
(synopsis "Python interface for the XGBoost library")))
|
||
|
||
(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)
|
||
("numpy" ,python-numpy)
|
||
("pandas" ,python-pandas)
|
||
("scipy" ,python-scipy)))
|
||
(native-inputs
|
||
`(("nose" ,python-nose)))
|
||
(home-page "https://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))
|
||
(patches (search-patches "python-keras-integration-test.patch"))
|
||
(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")
|
||
;; Backport https://github.com/keras-team/keras/pull/12479.
|
||
(substitute* "tests/keras/engine/test_topology.py"
|
||
(("np.ones\\(\\(3, 2\\)\\)")
|
||
"1."))
|
||
(invoke "python" "-m" "pytest"
|
||
;; The following test fail only in the build container;
|
||
;; skip it.
|
||
"-k" "not test_selu"))))))
|
||
(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 gloo
|
||
(let ((version "0.0.0") ; no proper version tag
|
||
(commit "c22a5cfba94edf8ea4f53a174d38aa0c629d070f")
|
||
(revision "1"))
|
||
(package
|
||
(name "gloo")
|
||
(version (git-version version revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/facebookincubator/gloo")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1crmqgybzkgkpbmcx16912gsl5qsj49swa0ikx6mhqgph0chrh11"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("googletest" ,googletest)))
|
||
(inputs
|
||
`(("openssl" ,openssl)))
|
||
(arguments
|
||
`(#:configure-flags '("-DBUILD_TEST=1")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(invoke "make" "gloo_test")))))))
|
||
(synopsis "Collective communications library")
|
||
(description
|
||
"Gloo is a collective communications library. It comes with a
|
||
number of collective algorithms useful for machine learning applications.
|
||
These include a barrier, broadcast, and allreduce.")
|
||
(home-page "https://github.com/facebookincubator/gloo")
|
||
(license license:bsd-3))))
|
||
|
||
(define-public python-umap-learn
|
||
(package
|
||
(name "python-umap-learn")
|
||
(version "0.3.10")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "umap-learn" version))
|
||
(sha256
|
||
(base32
|
||
"02ada2yy6km6zgk2836kg1c97yrcpalvan34p8c57446finnpki1"))))
|
||
(build-system python-build-system)
|
||
(native-inputs
|
||
`(("python-joblib" ,python-joblib)
|
||
("python-nose" ,python-nose)))
|
||
(propagated-inputs
|
||
`(("python-numba" ,python-numba)
|
||
("python-numpy" ,python-numpy)
|
||
("python-scikit-learn" ,python-scikit-learn)
|
||
("python-scipy" ,python-scipy)))
|
||
(home-page "https://github.com/lmcinnes/umap")
|
||
(synopsis
|
||
"Uniform Manifold Approximation and Projection")
|
||
(description
|
||
"Uniform Manifold Approximation and Projection is a dimension reduction
|
||
technique that can be used for visualisation similarly to t-SNE, but also for
|
||
general non-linear dimension reduction.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public nnpack
|
||
(let ((version "0.0")
|
||
(commit "c07e3a0400713d546e0dea2d5466dd22ea389c73")
|
||
(revision "1"))
|
||
(package
|
||
(name "nnpack")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/Maratyszcza/NNPACK")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0s0kk3a35w3yzf0q447p72350sbsh4qhg6vm3y2djbj4xpg7jc8v"))
|
||
(patches (search-patches "nnpack-system-libraries.patch"))))
|
||
(build-system cmake-build-system)
|
||
;; XXX: The test suite runs but it's very expensive, and on x86_64 CPUs
|
||
;; that lack the right ISA extensions, tests fail with:
|
||
;;
|
||
;; Expected equality of these values:
|
||
;; nnp_status_success
|
||
;; Which is: 0
|
||
;; status
|
||
;; Which is: 51
|
||
;;
|
||
;; where 51 is 'nnp_status_unsupported_hardware'.
|
||
(arguments '(#:tests? #f))
|
||
(synopsis "Acceleration package for neural network computations")
|
||
(description
|
||
"NNPACK is an acceleration package for neural network computations.
|
||
NNPACK aims to provide high-performance implementations of convnet layers for
|
||
multi-core CPUs.
|
||
|
||
NNPACK is not intended to be directly used by machine learning researchers;
|
||
instead it provides low-level performance primitives leveraged in leading deep
|
||
learning frameworks, such as PyTorch, Caffe2, MXNet, tiny-dnn, Caffe, Torch,
|
||
and Darknet.")
|
||
(inputs
|
||
`(("cpuinfo" ,cpuinfo)
|
||
("fp16" ,fp16)
|
||
("fxdiv" ,fxdiv)
|
||
("psimd" ,psimd)
|
||
("pthreadpool" ,pthreadpool)
|
||
("googletest" ,googletest)))
|
||
(native-inputs
|
||
`(("python" ,python)
|
||
("python-peachpy" ,python-peachpy)
|
||
("python-six" ,python-six)))
|
||
(license license:bsd-2))))
|
||
|
||
(define-public xnnpack
|
||
;; There's currently no tag on this repo.
|
||
(let ((version "0.0")
|
||
(commit "bbe88243aba847f6a3dd86defec0fea4a0e415a1")
|
||
(revision "1"))
|
||
(package
|
||
(name "xnnpack")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/google/XNNPACK") ;fork of QNNPACK
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"19j605x1l2h95mjhcj90zwjh1153pdgmqggl35ya5w0wll628iiz"))
|
||
(patches (search-patches "xnnpack-system-libraries.patch"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#:configure-flags '("-DXNNPACK_USE_SYSTEM_LIBS=YES"
|
||
"-DBUILD_SHARED_LIBS=ON"
|
||
"-DXNNPACK_LIBRARY_TYPE=shared"
|
||
"-DXNNPACK_BUILD_TESTS=FALSE" ;FIXME: see below
|
||
"-DXNNPACK_BUILD_BENCHMARKS=FALSE")
|
||
|
||
;; FIXME: Building tests leads to a CMake error:
|
||
;;
|
||
;; ADD_LIBRARY cannot create target "all_microkernels" because
|
||
;; another target with the same name already exists.
|
||
#:tests? #f))
|
||
(inputs
|
||
`(("cpuinfo" ,cpuinfo)
|
||
("pthreadpool" ,pthreadpool)
|
||
("googletest" ,googletest)
|
||
("googlebenchmark" ,googlebenchmark)
|
||
("fxdiv" ,fxdiv)
|
||
("fp16" ,fp16)
|
||
("psimd" ,psimd)))
|
||
(synopsis "Optimized floating-point neural network inference operators")
|
||
(description
|
||
"XNNPACK is a highly optimized library of floating-point neural network
|
||
inference operators for ARM, WebAssembly, and x86 platforms. XNNPACK is not
|
||
intended for direct use by deep learning practitioners and researchers;
|
||
instead it provides low-level performance primitives for accelerating
|
||
high-level machine learning frameworks, such as TensorFlow Lite,
|
||
TensorFlow.js, PyTorch, and MediaPipe.")
|
||
(license license:bsd-3))))
|
||
|
||
(define-public python-pytorch
|
||
(package
|
||
(name "python-pytorch")
|
||
(version "1.9.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pytorch/pytorch")
|
||
(commit (string-append "v" version))
|
||
(recursive? #t)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0cznsh68hwk5761gv7iijb4g6jgjpvs3bbixwpzzmkbkbn2q96c1"))
|
||
(patches (search-patches "python-pytorch-system-libraries.patch"
|
||
"python-pytorch-runpath.patch"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; XXX: Let's be clear: this package is a bundling fest. We
|
||
;; delete as much as we can, but there's still a lot left.
|
||
(for-each (lambda (directory)
|
||
(delete-file-recursively
|
||
(string-append "third_party/" directory)))
|
||
'("benchmark" "cpuinfo" "eigen"
|
||
|
||
;; FIXME: QNNPACK (of which XNNPACK is a fork)
|
||
;; needs these.
|
||
;; "FP16" "FXdiv" "gemmlowp" "psimd"
|
||
|
||
"gloo" "googletest" "ios-cmake" "NNPACK"
|
||
"onnx" "protobuf" "pthreadpool"
|
||
"pybind11" "python-enum" "python-peachpy"
|
||
"python-six" "tbb" "XNNPACK" "zstd"))
|
||
|
||
;; Adjust references to the onnx-optimizer headers.
|
||
(substitute* "caffe2/onnx/backend.cc"
|
||
(("onnx/optimizer/")
|
||
"onnxoptimizer/"))))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
'(#:phases (modify-phases %standard-phases
|
||
(add-before 'build 'use-system-libraries
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Tell 'setup.py' to let 'CMakeLists.txt' know that we
|
||
;; want to use "system libraries" instead of the bundled
|
||
;; ones.
|
||
(setenv "USE_SYSTEM_LIBS" "1")
|
||
|
||
;; XXX: Disable that for simplicity for now.
|
||
(setenv "USE_FBGEMM" "0")))
|
||
(add-before 'build 'make-things-writable
|
||
(lambda _
|
||
;; The 'build_caffe2' function in
|
||
;; 'tools/build_pytorch_libs.py', called from the
|
||
;; top-level 'setup.py', needs write access to this
|
||
;; directory.
|
||
(for-each make-file-writable
|
||
(find-files "caffe2/proto" "."
|
||
#:directories? #t))))
|
||
(replace 'check
|
||
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
|
||
;; Run the test suite following the instructions in
|
||
;; 'CONTRIBUTING.md'. XXX: Unfortunately this doesn't
|
||
;; work, unless you set PYTHONPATH presumably.
|
||
(when tests?
|
||
(let ((python-site (site-packages inputs outputs)))
|
||
(setenv "PYTHONPATH"
|
||
(string-append python-site ":"
|
||
(getenv "PYTHONPATH")))
|
||
(invoke "python" "test/run_test.py")))))
|
||
(add-after 'install 'remove-test-executables
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
;; Remove test executables, but keep other executables
|
||
;; such as 'torch_shm_manager' and and .so files such as
|
||
;; 'libtorch_global_deps.so'.
|
||
(let ((python-site (site-packages inputs outputs)))
|
||
(for-each delete-file
|
||
(find-files python-site
|
||
"(^test_cpp_rpc|_test)$"))))))
|
||
|
||
;; XXX: Tests attempt to download data such as
|
||
;; <https://raw.githubusercontent.com/pytorch/test-infra/master/stats/slow-tests.json>.
|
||
#:tests? #f))
|
||
(native-inputs
|
||
`(("cmake" ,cmake)
|
||
("ninja" ,ninja)))
|
||
(inputs
|
||
`(("eigen" ,eigen)
|
||
;; ("fmt" ,fmt)
|
||
("fp16" ,fp16)
|
||
("gemmlowp" ,gemmlowp)
|
||
("googletest" ,googletest)
|
||
("googlebenchmark" ,googlebenchmark)
|
||
("gloo" ,gloo)
|
||
("nnpack" ,nnpack)
|
||
("openblas" ,openblas)
|
||
("openmpi" ,openmpi)
|
||
("pthreadpool" ,pthreadpool)
|
||
("protobuf" ,protobuf)
|
||
("pybind11" ,pybind11)
|
||
("sleef" ,sleef)
|
||
("xnnpack" ,xnnpack)
|
||
("zstd" ,zstd)))
|
||
(propagated-inputs
|
||
`(("python-astunparse" ,python-astunparse)
|
||
("python-numpy" ,python-numpy)
|
||
("python-pyyaml" ,python-pyyaml)
|
||
("python-cffi" ,python-cffi)
|
||
("python-typing-extensions" ,python-typing-extensions)
|
||
("python-future" ,python-future)
|
||
("python-six" ,python-six)
|
||
("python-requests" ,python-requests)
|
||
("onnx" ,onnx) ;propagated for its Python modules
|
||
("onnx-optimizer" ,onnx-optimizer)
|
||
("cpuinfo" ,cpuinfo)))
|
||
(home-page "https://pytorch.org/")
|
||
(synopsis "Python library for tensor computation and deep neural networks")
|
||
(description
|
||
"PyTorch is a Python package that provides two high-level features:
|
||
|
||
@itemize
|
||
@item tensor computation (like NumPy) with strong GPU acceleration;
|
||
@item deep neural networks (DNNs) built on a tape-based autograd system.
|
||
@end itemize
|
||
|
||
You can reuse Python packages such as NumPy, SciPy, and Cython to extend
|
||
PyTorch when needed.
|
||
|
||
Note: currently this package does not provide GPU support.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-hmmlearn
|
||
(package
|
||
(name "python-hmmlearn")
|
||
(version "0.2.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "hmmlearn" version))
|
||
(sha256
|
||
(base32
|
||
"1my0j3rzp17438idr32ssh0j969a98yjblx5igx5kgiiigr9qa1a"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
|
||
(when tests?
|
||
(add-installed-pythonpath inputs outputs)
|
||
(with-directory-excursion (string-append (assoc-ref outputs "out") "/lib")
|
||
(invoke "python" "-m" "pytest"))))))))
|
||
(propagated-inputs
|
||
`(("python-cython" ,python-cython)
|
||
("python-numpy" ,python-numpy)
|
||
("python-scikit-learn" ,python-scikit-learn)
|
||
("python-scipy" ,python-scipy)
|
||
("python-setuptools-scm" ,python-setuptools-scm)))
|
||
(native-inputs
|
||
`(("python-pytest" ,python-pytest)))
|
||
(home-page "https://github.com/hmmlearn/hmmlearn")
|
||
(synopsis "Hidden Markov Models with scikit-learn like API")
|
||
(description
|
||
"Hmmlearn is a set of algorithms for unsupervised learning and inference
|
||
of Hidden Markov Models.")
|
||
(license license:bsd-3)))
|