5447 lines
222 KiB
Scheme
5447 lines
222 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2016, 2020-2023 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, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net>
|
||
;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
|
||
;;; Copyright © 2022, 2023 Nicolas Graves <ngraves@ngraves.fr>
|
||
;;; Copyright © 2022 Kiran Shila <me@kiranshila.com>
|
||
;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe>
|
||
;;; Copyright © 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de>
|
||
;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
|
||
;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
|
||
;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
|
||
;;; Copyright © 2024 David Pflug <david@pflug.io>
|
||
;;; Copyright © 2024 Timothee Mathieu <timothee.mathieu@inria.fr>
|
||
;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.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 gexp)
|
||
#: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 pyproject)
|
||
#:use-module (guix build-system python)
|
||
#:use-module (guix build-system r)
|
||
#:use-module (guix build-system trivial)
|
||
#:use-module (guix git-download)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages adns)
|
||
#:use-module (gnu packages algebra)
|
||
#:use-module (gnu packages assembly)
|
||
#: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 bdw-gc)
|
||
#:use-module (gnu packages c)
|
||
#: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 documentation)
|
||
#:use-module (gnu packages freedesktop)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages gettext)
|
||
#:use-module (gnu packages gl)
|
||
#:use-module (gnu packages glib)
|
||
#:use-module (gnu packages graphviz)
|
||
#:use-module (gnu packages gstreamer)
|
||
#:use-module (gnu packages guile)
|
||
#:use-module (gnu packages haskell-xyz)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages image-processing)
|
||
#:use-module (gnu packages imagemagick)
|
||
#:use-module (gnu packages jupyter)
|
||
#: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 opencl)
|
||
#: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 pulseaudio)
|
||
#: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 rdf)
|
||
#:use-module (gnu packages regex)
|
||
#: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 time)
|
||
#:use-module (gnu packages tls)
|
||
#:use-module (gnu packages vulkan)
|
||
#:use-module (gnu packages video)
|
||
#:use-module (gnu packages web)
|
||
#:use-module (gnu packages xml)
|
||
#:use-module (gnu packages xdisorg)
|
||
#:use-module (gnu packages xorg)
|
||
#:use-module (ice-9 match))
|
||
|
||
(define-public fasttext
|
||
(package
|
||
(name "fasttext")
|
||
(version "0.9.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/facebookresearch/fastText")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "07cz2ghfq6amcljaxpdr5chbd64ph513y8zqmibfx2xwfp74xkhn"))))
|
||
(build-system cmake-build-system)
|
||
;; Tests require downloading of test data.
|
||
(arguments (list #:tests? #false))
|
||
(home-page "https://github.com/facebookresearch/fastText")
|
||
(synopsis "Library for fast text representation and classification")
|
||
(description "fastText is a library for efficient learning of word
|
||
representations and sentence classification.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-fasttext
|
||
(package
|
||
(inherit fasttext)
|
||
(name "python-fasttext")
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy python-scipy))
|
||
(inputs (list fasttext))
|
||
(native-inputs (list pybind11))))
|
||
|
||
(define-public python-funsor
|
||
(package
|
||
(name "python-funsor")
|
||
(version "0.4.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "funsor" version))
|
||
(sha256
|
||
(base32 "0cgysij0dix0fikyz2x4f8jvaskm5s5a04s07chzaz2dw1fpxdq8"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-makefun python-multipledispatch
|
||
python-numpy python-opt-einsum
|
||
python-typing-extensions))
|
||
(native-inputs (list python-black
|
||
python-flake8
|
||
python-isort
|
||
python-nbsphinx
|
||
python-pandas
|
||
python-pillow
|
||
python-pyro-api
|
||
python-pytest
|
||
python-pytest-xdist
|
||
python-requests
|
||
python-scipy
|
||
python-sphinx
|
||
python-sphinx-gallery
|
||
python-sphinx-rtd-theme
|
||
python-torchvision))
|
||
(home-page "https://github.com/pyro-ppl/funsor")
|
||
(synopsis "Tensor-like library for functions and distributions")
|
||
(description
|
||
"This package provides a tensor-like library for functions and
|
||
distributions.")
|
||
(license license:asl2.0)))
|
||
|
||
(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)
|
||
(add-after 'build 'build-lib
|
||
(lambda _
|
||
(invoke "make" "lib")))
|
||
(replace 'install ; no ‘install’ target
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin/"))
|
||
(lib (string-append out "/lib/"))
|
||
(inc (string-append out "/include/libsvm")))
|
||
(mkdir-p bin)
|
||
(for-each (lambda (file)
|
||
(copy-file file (string-append bin file)))
|
||
'("svm-train"
|
||
"svm-predict"
|
||
"svm-scale"))
|
||
(mkdir-p lib)
|
||
(install-file "libsvm.so.2" lib)
|
||
(mkdir-p inc)
|
||
(install-file "svm.h" inc)))))))
|
||
(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
|
||
(list python))
|
||
(synopsis "Python bindings of libSVM")))
|
||
|
||
(define-public python-ml-collections
|
||
(package
|
||
(name "python-ml-collections")
|
||
(version "0.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "ml_collections" version))
|
||
(sha256
|
||
(base32 "1k38psfzqsqnl99fl578bd07zdmvfkja61r3sgjs2fj3xircrvrz"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
;; TODO: we can't seem to run the config_flags tests, because
|
||
;; the installed Python files conflict with those from the
|
||
;; source directory, resulting in constants to be defined more
|
||
;; than once.
|
||
(invoke "pytest" "ml_collections/config_dict/tests"
|
||
;; This one fails because we're testing the __main__
|
||
;; class, not config_dict_test.
|
||
"-k" "not testJSONConversionBestEffort")))))))
|
||
(propagated-inputs
|
||
(list python-absl-py python-contextlib2 python-pyyaml python-six))
|
||
(native-inputs (list python-mock python-pytest))
|
||
(home-page "https://github.com/google/ml_collections")
|
||
(synopsis "Python collections designed for Machine Learning usecases")
|
||
(description
|
||
"ML Collections is a library of Python collections designed for Machine
|
||
Learning usecases.")
|
||
(license license:asl2.0)))
|
||
|
||
(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
|
||
"07kdsngvr4n1qxpqzv1nlay7g41d6jzjppa8vzmrg220s8ing87z"))))
|
||
(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.*$")
|
||
"label_higher_order_test\n"))
|
||
|
||
;; These Python unittests are broken as there is no gato.
|
||
;; See https://sourceforge.net/p/ghmm/support-requests/3/
|
||
(substitute* "ghmmwrapper/ghmmunittests.py"
|
||
(("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
|
||
line indent)
|
||
(string-append indent
|
||
"@unittest.skip(\"Disabled by Guix\")\n"
|
||
line))))))))
|
||
(inputs
|
||
`(("python" ,python-2) ; only Python 2 is supported
|
||
("libxml2" ,libxml2)))
|
||
(native-inputs
|
||
(list pkg-config
|
||
dejagnu
|
||
swig
|
||
autoconf
|
||
automake
|
||
libtool))
|
||
(home-page "http://ghmm.org")
|
||
(synopsis "Hidden Markov Model library")
|
||
(description
|
||
"The General Hidden Markov Model library (GHMM) is a C library with
|
||
additional Python bindings implementing a wide range of types of @dfn{Hidden
|
||
Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
|
||
training, HMM clustering, HMM mixtures.")
|
||
(license license:lgpl2.0+))))
|
||
|
||
(define-public guile-aiscm
|
||
(package
|
||
(name "guile-aiscm")
|
||
(version "0.25.2")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/wedesoft/aiscm")
|
||
(commit "v0.25.2")))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1sagpxwrqxkn5b9zqzd07c9r7swmw45q672pa8fy6s71iw6a0x77"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
#:make-flags
|
||
#~(list (string-append "GUILE_CACHE=" #$output "/lib/guile/3.0/site-ccache")
|
||
(string-append "GUILE_EXT=" #$output "/lib/guile/3.0/extensions")
|
||
(string-append "GUILE_SITE=" #$output "/share/guile/site/3.0"))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'build-reproducibly
|
||
(lambda _
|
||
(substitute* "doc/Makefile.am"
|
||
(("\\$\\(DATE\\)") "1970-01-01"))))
|
||
(add-after 'unpack 'find-clearsilver
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(substitute* "configure.ac"
|
||
(("/usr/local/include/ClearSilver")
|
||
(string-append (assoc-ref inputs "clearsilver")
|
||
"/include/ClearSilver")))
|
||
(substitute* "aiscm/Makefile.am"
|
||
(("-lneo_utl" m)
|
||
(string-append m " -lstreamhtmlparser")))
|
||
(setenv "C_INCLUDE_PATH"
|
||
(string-append (assoc-ref inputs "clearsilver")
|
||
"/include/ClearSilver:"
|
||
(or (getenv "C_INCLUDE_PATH") "")))))
|
||
(add-after 'unpack 'use-llvm-config
|
||
(lambda _
|
||
(substitute* "m4/ax_llvmc.m4"
|
||
(("llvm-config-11") "llvm-config")
|
||
;; For some reason this library is not on the link list.
|
||
(("(LLVM_LIBS=\"\\$\\(\\$ac_llvm_config_path --libs \\$1\\))\"" _ m)
|
||
(string-append m " -lLLVMMCJIT\"")))
|
||
|
||
;; Because of this message:
|
||
;; symbol lookup error: ./.libs/libguile-aiscm-core.so: undefined symbol: LLVMInitializeX86TargetInfo
|
||
;; This probably needs to differ when building on architectures
|
||
;; other than x86_64.
|
||
(substitute* "aiscm/Makefile.am"
|
||
(("LLVM_LIBS\\)") "LLVM_LIBS) \
|
||
-lLLVMX86AsmParser -lLLVMX86CodeGen -lLLVMX86Desc -lLLVMX86Info"))))
|
||
;; This test fails because our version of tensorflow is too old
|
||
;; to provide tf-string-length.
|
||
(add-after 'unpack 'disable-broken-test
|
||
(lambda _
|
||
(substitute* "tests/test_tensorflow.scm"
|
||
(("\\(test-eqv \"determine string length" m)
|
||
(string-append "#;" m)))))
|
||
;; Use Clang instead of GCC.
|
||
(add-before 'configure 'prepare-build-environment
|
||
(lambda _
|
||
(setenv "AR" "llvm-ar")
|
||
(setenv "NM" "llvm-nm")
|
||
(setenv "CC" "clang")
|
||
(setenv "CXX" "clang++"))))))
|
||
(inputs
|
||
(list clearsilver
|
||
ffmpeg-4
|
||
freeglut
|
||
guile-3.0
|
||
imagemagick
|
||
libgc
|
||
libjpeg-turbo
|
||
libomp
|
||
libxi
|
||
libxmu
|
||
libxpm
|
||
libxt
|
||
libxv
|
||
mesa
|
||
mjpegtools
|
||
pandoc
|
||
pulseaudio
|
||
tensorflow))
|
||
(native-inputs
|
||
(list clang-13
|
||
llvm-13
|
||
pkg-config
|
||
protobuf-c-for-aiscm
|
||
autoconf
|
||
automake
|
||
gettext-minimal
|
||
libtool
|
||
which))
|
||
(home-page "https://wedesoft.github.io/aiscm/")
|
||
(synopsis "Guile extension for numerical arrays and tensors")
|
||
(description "AIscm is a Guile extension for numerical arrays and tensors.
|
||
Performance is achieved by using the LLVM JIT compiler.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public guile-aiscm-next
|
||
(deprecated-package "guile-aiscm-next" guile-aiscm))
|
||
|
||
(define-public llama-cpp
|
||
(let ((commit "03bf161eb6dea6400ee49c6dc6b69bdcfa9fd3fc")
|
||
(revision "1"))
|
||
(package
|
||
(name "llama-cpp")
|
||
(version (git-version "0.0.0" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/ggerganov/llama.cpp")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1ag1jash84hasz10h0piw72a8ginm8kzvhihbzzljz96gq2kjm88"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:modules '((ice-9 textual-ports)
|
||
(guix build utils)
|
||
((guix build python-build-system) #:prefix python:)
|
||
(guix build cmake-build-system))
|
||
#:imported-modules `(,@%cmake-build-system-modules
|
||
(guix build python-build-system))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-before 'install 'install-python-scripts
|
||
(lambda _
|
||
(let ((bin (string-append #$output "/bin/")))
|
||
(define (make-script script)
|
||
(let ((suffix (if (string-suffix? ".py" script) "" ".py")))
|
||
(call-with-input-file
|
||
(string-append "../source/" script suffix)
|
||
(lambda (input)
|
||
(call-with-output-file (string-append bin script)
|
||
(lambda (output)
|
||
(format output "#!~a/bin/python3\n~a"
|
||
#$(this-package-input "python")
|
||
(get-string-all input))))))
|
||
(chmod (string-append bin script) #o555)))
|
||
(mkdir-p bin)
|
||
(make-script "convert-hf-to-gguf")
|
||
(make-script "convert-llama-ggml-to-gguf")
|
||
(make-script "convert-lora-to-ggml")
|
||
(make-script "convert-persimmon-to-gguf")
|
||
(make-script "convert"))))
|
||
(add-after 'install-python-scripts 'wrap-python-scripts
|
||
(assoc-ref python:%standard-phases 'wrap))
|
||
(replace 'install
|
||
(lambda _
|
||
(copy-file "bin/main" (string-append #$output "/bin/llama")))))))
|
||
(inputs (list python))
|
||
(propagated-inputs
|
||
(list python-numpy python-pytorch python-sentencepiece))
|
||
(home-page "https://github.com/ggerganov/llama.cpp")
|
||
(synopsis "Port of Facebook's LLaMA model in C/C++")
|
||
(description "This package provides a port to Facebook's LLaMA collection
|
||
of foundation language models. It requires models parameters to be downloaded
|
||
independently to be able to run a LLaMA model.")
|
||
(license license:expat))))
|
||
|
||
(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"
|
||
"CFLAGS=-fcommon")))
|
||
(inputs
|
||
(list perl))
|
||
(home-page "https://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 -fcommon")
|
||
|
||
;; 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 -fcommon"))
|
||
;; 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
|
||
(list 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 openmm
|
||
(package
|
||
(name "openmm")
|
||
(version "8.1.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/openmm/openmm")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"064vv6zaci30pj38z5lwfqscxssm67jqxkz30hcya9vm4ng831d5"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:configure-flags
|
||
'(list "-DOPENMM_BUILD_SHARED_LIB=TRUE"
|
||
"-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=TRUE"
|
||
"-DOPENMM_BUILD_PYTHON_WRAPPERS=TRUE"
|
||
"-DOPENMM_BUILD_CUDA_LIB=FALSE")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-python-build-system
|
||
(lambda _
|
||
(substitute* "wrappers/python/CMakeLists.txt"
|
||
(("install --root=\\\\\\$ENV\\{DESTDIR\\}/")
|
||
(string-append "install --prefix=" #$output
|
||
" --root=/ --single-version-externally-managed")))))
|
||
(add-after 'install 'install-python
|
||
(lambda _
|
||
(invoke "make" "PythonInstall"))))))
|
||
(inputs
|
||
(list python-wrapper))
|
||
(propagated-inputs
|
||
(list python-numpy))
|
||
(native-inputs
|
||
(list doxygen gfortran opencl-headers python-cython swig))
|
||
(home-page "https://github.com/openmm/openmm/")
|
||
(synopsis "Toolkit for molecular simulation")
|
||
(description
|
||
"OpenMM is a toolkit for molecular simulation. It can be used either as
|
||
a stand-alone application for running simulations, or as a library you call
|
||
from your own code.")
|
||
;; See https://github.com/openmm/openmm/issues/4278#issuecomment-1772982471
|
||
(license license:expat)))
|
||
|
||
(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"))
|
||
(file-name (string-append name "-" 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-after 'unpack 'fix-compatibility-errors
|
||
(lambda _
|
||
(substitute* "src/library/IAM2WayImportance.h"
|
||
(("= std::make_pair.*")
|
||
"= std::minmax(varID1, varID2);"))
|
||
(substitute* "src/library/DataFrame.h"
|
||
(("isFirst\\?.*")
|
||
"if (isFirst) { isFirst = false; } else { os << par.delimiter; }\n"))))
|
||
(add-before 'configure 'set-CXXFLAGS
|
||
(lambda _ (setenv "CXXFLAGS" "-fpermissive "))))))
|
||
(inputs
|
||
(list boost gsl libxml2 zlib))
|
||
(native-inputs
|
||
(list gfortran-7 (list gfortran-7 "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 r-rcppml/devel
|
||
(let ((commit "e685b3bd7909d3ae74c98f85f81bc0bb679bce23")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-rcppml-devel")
|
||
(version (git-version "0.5.6" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/zdebruine/RcppML")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"18ykh9s9h3x79az7qm3pg48iqm0nmkh2wkppc9wx0lq7kjfqm67a"))))
|
||
(properties `((upstream-name . "RcppML")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-matrix r-rcpp))
|
||
(native-inputs (list r-knitr))
|
||
(home-page "https://github.com/zdebruine/RcppML")
|
||
(synopsis "Rcpp machine learning Library")
|
||
(description
|
||
"This package provides fast machine learning algorithms including
|
||
matrix factorization and divisive clustering for large sparse and dense
|
||
matrices.")
|
||
(license license:gpl3+))))
|
||
|
||
(define-public openfst
|
||
(package
|
||
(name "openfst")
|
||
(version "1.8.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.openfst.org/twiki/pub/FST/"
|
||
"FstDownload/openfst-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0hlbdmjjf1jgsvi3d2hwni5lz3l9a5bzj6ijpbawa8a7cbrpp66y"))))
|
||
(build-system gnu-build-system)
|
||
(arguments '(#:configure-flags '("--enable-ngram-fsts")))
|
||
(home-page "https://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)))
|
||
|
||
;; This is a temporary addition to bypass upstream issues with the kaldi
|
||
;; package.
|
||
(define-public openfst-1.7.3
|
||
(package (inherit openfst)
|
||
(version "1.7.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.openfst.org/twiki/pub/FST/"
|
||
"FstDownload/openfst-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"038a60w7y8qnbxmcrsim9rafz9mihsny8xv50jpzlr7rl166pp5q"))))
|
||
(arguments '(#:configure-flags '("--enable-ngram-fsts" "CXXFLAGS=-std=c++14")
|
||
#:make-flags '("CXXFLAGS=-std=c++14")))))
|
||
|
||
(define openfst-for-vosk
|
||
(package
|
||
(inherit openfst)
|
||
(version "1.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.openfst.org/twiki/pub/FST/"
|
||
"FstDownload/openfst-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0h2lfhhihg63b804hrcljnkggijbjmp84i5g8q735wb09y9z2c4p"))))
|
||
(arguments
|
||
'(#:configure-flags
|
||
'("--enable-shared" "--enable-far" "--enable-ngram-fsts"
|
||
"--enable-lookahead-fsts" "--with-pic" "--disable-bin")))))
|
||
|
||
(define-public sentencepiece
|
||
(package
|
||
(name "sentencepiece")
|
||
(version "0.1.97")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/google/sentencepiece")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1kzfkp2pk0vabyw3wmkh16h11chzq63mzc20ddhsag5fp6s91ajg"))))
|
||
(build-system cmake-build-system)
|
||
(arguments (list #:tests? #f)) ;no tests
|
||
(native-inputs (list gperftools))
|
||
(home-page "https://github.com/google/sentencepiece")
|
||
(synopsis "Unsupervised tokenizer for Neural Network-based text generation")
|
||
(description
|
||
"SentencePiece is an unsupervised text tokenizer and detokenizer mainly
|
||
for Neural Network-based text generation systems where the vocabulary size is
|
||
predetermined prior to the neural model training. SentencePiece implements
|
||
subword units---e.g., byte-pair-encoding (BPE) and unigram language
|
||
model---with the extension of direct training from raw sentences.
|
||
SentencePiece allows us to make a purely end-to-end system that does not
|
||
depend on language-specific pre- or post-processing.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-hopcroftkarp
|
||
;; This commit fixes a broken import, but has not been released to PyPI.
|
||
(let ((commit "2846e1dd3265d95d2bddb0cf4190b830cbb4efe6")
|
||
(revision "1"))
|
||
(package
|
||
(name "python-hopcroftkarp")
|
||
(version (git-version "1.2.5" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/sofiatolaosebikan/hopcroftkarp")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "018ilrp41fcclmb5lsml3aijwbmhbq3m7wy65hr1fryj0avic8fr"))))
|
||
(build-system pyproject-build-system)
|
||
(home-page "https://github.com/sofiatolaosebikan/hopcroftkarp")
|
||
(synopsis "Implementation of the Hopcroft-Karp algorithm")
|
||
(description
|
||
"This package implements the Hopcroft-Karp algorithm, producing a maximum
|
||
cardinality matching from a bipartite graph.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public python-persim
|
||
(package
|
||
(name "python-persim")
|
||
(version "0.3.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "persim" version))
|
||
(sha256
|
||
(base32 "0q8wfakx8q4h3ryvw8cba0v6z7xn9139qkrzs3mi1ggyzacnx9d7"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-deprecated
|
||
python-hopcroftkarp
|
||
python-joblib
|
||
python-matplotlib
|
||
python-numpy
|
||
python-scikit-learn
|
||
python-scipy))
|
||
(native-inputs (list python-pytest python-pytest-cov))
|
||
(home-page "https://persim.scikit-tda.org")
|
||
(synopsis "Tools for analyzing persistence diagrams in Python")
|
||
(description
|
||
"This package includes a variety of tools used to analyze persistence diagrams.
|
||
It currently houses implementations of
|
||
@itemize
|
||
@item Persistence images
|
||
@item Persistence landscapes
|
||
@item Bottleneck distance
|
||
@item Modified Gromov–Hausdorff distance
|
||
@item Sliced Wasserstein kernel
|
||
@item Heat kernel
|
||
@item Diagram plotting
|
||
@end itemize
|
||
")
|
||
(license license:expat))) ; MIT License
|
||
|
||
(define-public python-ripser
|
||
(package
|
||
(name "python-ripser")
|
||
(version "0.6.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "ripser" version))
|
||
(sha256
|
||
(base32 "1575nwsn6b29z7w1mjk23ri83bxq2b4ld979hpgm174642a3x6vs"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy python-persim python-scikit-learn
|
||
python-scipy))
|
||
(native-inputs (list python-cython python-pytest))
|
||
(home-page "https://ripser.scikit-tda.org")
|
||
(synopsis "Persistent homology library for Python")
|
||
(description
|
||
"This package implements a variety of persistent homology algorithms. It
|
||
provides an interface for
|
||
@itemize
|
||
@item computing persistence cohomology of sparse and dense data sets
|
||
@item visualizing persistence diagrams
|
||
@item computing lowerstar filtrations on images
|
||
@item computing representative cochains
|
||
@end itemize
|
||
")
|
||
(license license:expat))) ; MIT License
|
||
|
||
(define-public python-sacrebleu
|
||
(package
|
||
(name "python-sacrebleu")
|
||
(version "2.3.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mjpost/sacrebleu")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1al4qf9wsq5l453qqb6clims62ns0s07wb9rfbf4hbpr1f2iv7zv"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; These all need internet access.
|
||
'(list "-k" "not test_api_get_source \
|
||
and not test_api_get_reference \
|
||
and not test_maybe_download \
|
||
and not test_process_to_text \
|
||
and not test_get_files_and_fieldnames \
|
||
and not test_source_and_references \
|
||
and not test_wmt22_references")
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
;; Needed for tests.
|
||
(add-before 'check 'set-HOME
|
||
(lambda _ (setenv "HOME" "/tmp"))))))
|
||
(propagated-inputs (list python-colorama
|
||
python-lxml
|
||
python-numpy
|
||
python-portalocker
|
||
python-regex
|
||
python-tabulate))
|
||
(native-inputs (list python-pytest))
|
||
(home-page "https://github.com/mjpost/sacrebleu")
|
||
(synopsis
|
||
"Compute shareable, comparable, and reproducible BLEU, chrF, and TER scores")
|
||
(description
|
||
"This is a package for hassle-free computation of shareable, comparable,
|
||
and reproducible BLEU, chrF, and TER scores for natural language processing.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-sentencepiece
|
||
(package
|
||
(name "python-sentencepiece")
|
||
(version "0.1.97")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "sentencepiece" version))
|
||
(sha256
|
||
(base32 "0v0z9ryl66432zajp099bcbnwkkldzlpjvgnjv9bq2vi19g300f9"))))
|
||
(build-system python-build-system)
|
||
(native-inputs (list pkg-config))
|
||
(propagated-inputs (list sentencepiece))
|
||
(home-page "https://github.com/google/sentencepiece")
|
||
(synopsis "SentencePiece python wrapper")
|
||
(description "This package provides a Python wrapper for the SentencePiece
|
||
unsupervised text tokenizer.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-spacy-legacy
|
||
(package
|
||
(name "python-spacy-legacy")
|
||
(version "3.0.12")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "spacy-legacy" version))
|
||
(sha256
|
||
(base32
|
||
"0x57aw1qgjrzgapsv1cwymqlck2anqm1bisvryhpq7bfkc66wzdk"))))
|
||
(build-system pyproject-build-system)
|
||
;; This package depends on spacy, which depends on this package.
|
||
(arguments (list #:tests? #false))
|
||
(native-inputs (list python-pytest))
|
||
(home-page "https://spacy.io")
|
||
(synopsis "Legacy registered functions for spaCy backwards compatibility")
|
||
(description
|
||
"This package contains legacy registered functions for spaCy backwards
|
||
compatibility.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-spacy-loggers
|
||
(package
|
||
(name "python-spacy-loggers")
|
||
(version "1.0.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "spacy-loggers" version))
|
||
(sha256
|
||
(base32
|
||
"0a5zjfxd0mci7pwda24ihg55whalpmjby4bvpgar2013f6zq7yg6"))))
|
||
(build-system pyproject-build-system)
|
||
;; This package depends on spacy, which depends on this package.
|
||
(arguments (list #:tests? #false))
|
||
(native-inputs (list python-pytest))
|
||
(home-page "https://github.com/explosion/spacy-loggers")
|
||
(synopsis "Logging utilities for SpaCy")
|
||
(description "This package provides logging utilities for the SpaCy
|
||
natural language processing framework.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-spacy
|
||
(package
|
||
(name "python-spacy")
|
||
(version "3.5.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "spacy" version))
|
||
(sha256
|
||
(base32
|
||
"13141hc966d8nxbnlwj01vhndgq0rq4nmii3qkb3hrap45kiv5rm"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "-k"
|
||
(string-append
|
||
;; We don't do that around here.
|
||
"not test_download_compatibility"
|
||
;; This needs to download a model.
|
||
" and not test_validate_compatibility_table"
|
||
;; This tries to run the application with typer, which fails
|
||
;; with an unspecified error, possibly because the build
|
||
;; container doesn't have /bin/sh.
|
||
" and not test_project_assets"))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'build 'build-ext
|
||
(lambda _
|
||
(invoke "python" "setup.py" "build_ext" "--inplace"
|
||
"-j" (number->string (parallel-job-count))))))))
|
||
(propagated-inputs (list python-catalogue
|
||
python-cymem
|
||
python-jinja2
|
||
python-langcodes
|
||
python-murmurhash
|
||
python-numpy
|
||
python-packaging
|
||
python-pathy
|
||
python-preshed
|
||
python-pydantic
|
||
python-requests
|
||
python-setuptools
|
||
python-smart-open
|
||
python-spacy-legacy
|
||
python-spacy-loggers
|
||
python-srsly
|
||
python-thinc
|
||
python-tqdm
|
||
python-typer
|
||
python-typing-extensions
|
||
python-wasabi))
|
||
(native-inputs
|
||
(list python-cython python-pytest python-mock))
|
||
(home-page "https://spacy.io")
|
||
(synopsis "Natural Language Processing (NLP) in Python")
|
||
(description
|
||
"SpaCy is a library for advanced Natural Language Processing in Python
|
||
and Cython. It comes with pretrained pipelines and currently supports
|
||
tokenization and training for 70+ languages. It features state-of-the-art
|
||
speed and neural network models for tagging, parsing, named entity
|
||
recognition, text classification and more, multi-task learning with pretrained
|
||
transformers like BERT, as well as a production-ready training system and easy
|
||
model packaging, deployment and workflow management.")
|
||
(license license:expat)))
|
||
|
||
(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
|
||
(list pkg-config 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 "1.12.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/onnx/onnx")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32
|
||
"1g9f1hviksbn7gi6fnd0dsm7nf0w3yia0mjj33d9mggklrl0db6x"))
|
||
(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-after 'unpack 'relax-requirements
|
||
(lambda _
|
||
;; Does this difference really matter?
|
||
(substitute* "requirements.txt"
|
||
(("3.20.1") "3.20.2"))))
|
||
(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
|
||
(list cmake
|
||
googletest
|
||
pybind11
|
||
python-coverage
|
||
python-nbval
|
||
python-pytest
|
||
python-pytest-runner))
|
||
(inputs
|
||
(list protobuf))
|
||
(propagated-inputs
|
||
(list python-numpy python-protobuf python-six python-tabulate
|
||
python-typing-extensions))
|
||
(home-page "https://onnx.ai/")
|
||
(synopsis "Open Neural Network Exchange")
|
||
(description
|
||
"@acronym{ONNX, Open Neural Network Exchange} is a format for AI models,
|
||
both deep learning and traditional @acronym{ML, machine learning}. It defines
|
||
an extensible computation graph model, as well as definitions of built-in
|
||
operators and standard data types.")
|
||
(license license:expat)))
|
||
|
||
(define-public onnx-for-torch2
|
||
(package
|
||
(inherit onnx)
|
||
(name "onnx")
|
||
(version "1.13.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/onnx/onnx")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32
|
||
"16967dbq2j40diqd0s37r19llsab8q8vbxkg1ppgy0p9fpdhfhyp"))
|
||
(file-name (git-file-name name version))
|
||
(patches (search-patches "onnx-1.13.1-use-system-googletest.patch"
|
||
"onnx-shared-libraries.patch"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
(delete-file-recursively "third_party")
|
||
(substitute* "onnx/backend/test/runner/__init__.py"
|
||
(("urlretrieve\\(.*") "raise unittest.SkipTest('Skipping download')\n"))))))
|
||
(arguments
|
||
;; reuse build system tweaks
|
||
(substitute-keyword-arguments (package-arguments onnx)
|
||
((#:phases phases)
|
||
#~(modify-phases #$phases
|
||
(delete 'relax-requirements)))))))
|
||
|
||
(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
|
||
;; reuse build system tweaks
|
||
(substitute-keyword-arguments (package-arguments onnx)
|
||
((#:phases phases)
|
||
#~(modify-phases #$phases
|
||
(delete 'relax-requirements)))))
|
||
(native-inputs
|
||
(list cmake python-pytest python-pytest-runner python-nbval
|
||
python-coverage))
|
||
(inputs
|
||
(list onnx protobuf pybind11))
|
||
(propagated-inputs
|
||
(list 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 onnx-optimizer-for-torch2
|
||
(package
|
||
(inherit onnx-optimizer)
|
||
(inputs
|
||
(modify-inputs (package-inputs onnx-optimizer)
|
||
(replace "onnx" onnx-for-torch2)))))
|
||
|
||
(define-public rxcpp
|
||
(package
|
||
(name "rxcpp")
|
||
(version "4.1.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/ReactiveX/RxCpp")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32 "1blyjjw6szd74pckdc15ham9i48xf0vwwz5nhl9vyjfq8z7w3piy"))
|
||
(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
|
||
(list catch-framework))
|
||
(home-page "https://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 "08e4bb339e34017a0835269d4a37c4ea04d15a69")
|
||
(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
|
||
"1q8f3w5slxd8fbn31hpm00y6wyp7gm71rzr27cmcff4b3px4ca6k"))))
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list ,@(match (%current-system)
|
||
((or "x86_64-linux" "i686-linux")
|
||
'("-DCMAKE_CXX_FLAGS=-msse2"))
|
||
(_ '()))
|
||
"-DBUILD_SHARED_LIBS=ON")
|
||
#: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
|
||
(list 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
|
||
(list pkg-config
|
||
;; For tests.
|
||
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 "1.3.2")
|
||
(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
|
||
"1hr024vcilbjwlwn32ppadri0ypnzjmkfxhkkw8gih0qjvcvjbs7"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "-m" "not network"
|
||
"-k" (string-append
|
||
;; This test tries to access the internet.
|
||
"not test_load_boston_alternative"
|
||
;; DID NOT RAISE <class 'ValueError'>
|
||
" and not test_singular_matrix"))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-before 'build 'configure
|
||
(lambda _
|
||
(setenv "SKLEARN_BUILD_PARALLEL"
|
||
(number->string (parallel-job-count)))))
|
||
(add-after 'build 'build-ext
|
||
(lambda _ (invoke "python" "setup.py" "build_ext" "--inplace"
|
||
"-j" (number->string (parallel-job-count)))))
|
||
(replace 'check
|
||
(lambda* (#:key tests? test-flags #:allow-other-keys)
|
||
(when tests?
|
||
;; Restrict OpenBLAS threads to prevent segfaults while testing!
|
||
(setenv "OPENBLAS_NUM_THREADS" "1")
|
||
|
||
;; Some tests require write access to $HOME.
|
||
(setenv "HOME" "/tmp")
|
||
|
||
;; Step out of the source directory to avoid interference;
|
||
;; we want to run the installed code with extensions etc.
|
||
(with-directory-excursion "/tmp"
|
||
(apply invoke "pytest" "--pyargs" "sklearn"
|
||
test-flags))))))))
|
||
(inputs (list openblas))
|
||
(native-inputs
|
||
(list python-cython-0.29.35
|
||
python-pandas
|
||
python-pytest
|
||
python-pytest-xdist))
|
||
(propagated-inputs
|
||
(list python-numpy python-threadpoolctl python-scipy 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.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-scikit-learn-extra
|
||
;; This commit fixes an incompatibility with newer versions of scikit-learn
|
||
(let ((commit "0f95d8dda4c69f9de4fb002366041adcb1302f3b")
|
||
(revision "1"))
|
||
(package
|
||
(name "python-scikit-learn-extra")
|
||
(version (git-version "0.3.0" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/scikit-learn-contrib/scikit-learn-extra")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0a248sff1psfwzmngj465gzyisq20d83nzpwpq2cspxhih51m6j9"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; ignore tests that require network
|
||
'(list "--pyargs" "sklearn_extra"
|
||
"-k" "not test_build")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'build 'build-ext
|
||
(lambda _
|
||
(invoke "python" "setup.py" "build_ext"
|
||
"--inplace")))
|
||
(replace 'check
|
||
(lambda* (#:key tests? test-flags #:allow-other-keys)
|
||
(when tests?
|
||
;; Restrict OpenBLAS threads to prevent segfaults while testing!
|
||
(setenv "OPENBLAS_NUM_THREADS" "1")
|
||
|
||
;; Some tests require write access to $HOME.
|
||
(setenv "HOME" "/tmp")
|
||
|
||
;; Step out of the source directory to avoid interference;
|
||
;; we want to run the installed code with extensions etc.
|
||
(with-directory-excursion "/tmp"
|
||
(apply invoke "pytest" "-vv" test-flags))))))))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-packaging))
|
||
(native-inputs (list python-pytest python-pytest-cov python-cython))
|
||
(home-page "https://github.com/scikit-learn-contrib/scikit-learn-extra")
|
||
(synopsis "Set of tools for scikit-learn")
|
||
(description
|
||
"This package provides a Python module for machine learning that extends
|
||
scikit-learn. It includes algorithms that are useful but do not satisfy the
|
||
scikit-learn inclusion criteria, for instance due to their novelty or lower
|
||
citation number.")
|
||
(license license:bsd-3))))
|
||
|
||
(define-public python-mord
|
||
(package
|
||
(name "python-mord")
|
||
(version "0.7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "mord" version))
|
||
(sha256
|
||
(base32 "1cvv9b9w69v0inq0zgcw0vmkiq3zn9q9r6clkynpzjik9rrh405n"))))
|
||
(build-system pyproject-build-system)
|
||
;; v0.7 does not provide any test cases
|
||
;; v0.6 relies on deprecated scikit-learn functionality
|
||
(arguments `(#:tests? #f))
|
||
(inputs (list python-numpy python-scipy python-scikit-learn))
|
||
(home-page "https://pypi.org/project/mord/")
|
||
(synopsis "Ordinal regression models for scikit-learn")
|
||
(description
|
||
"This package provides a collection of ordinal regression models for
|
||
machine learning in Python. They are intended to be used with scikit-learn
|
||
and are compatible with its API.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-thinc
|
||
(package
|
||
(name "python-thinc")
|
||
(version "8.1.10")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "thinc" version))
|
||
(sha256
|
||
(base32
|
||
"14drmwa2sh8fqszv1fm2jl4lky1j5yrbkjv89bl49q07vbblhjkc"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
'(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-ext
|
||
(lambda _
|
||
(invoke "python" "setup.py" "build_ext" "--inplace"
|
||
"-j" (number->string (parallel-job-count))))))))
|
||
(propagated-inputs (list python-blis-for-thinc
|
||
python-catalogue
|
||
python-confection
|
||
python-contextvars
|
||
python-cymem
|
||
python-dataclasses
|
||
python-murmurhash
|
||
python-numpy
|
||
python-packaging
|
||
python-preshed
|
||
python-pydantic
|
||
python-srsly
|
||
python-typing-extensions
|
||
python-wasabi))
|
||
(native-inputs (list python-cython python-mock python-pytest))
|
||
(home-page "https://github.com/explosion/thinc")
|
||
(synopsis "Functional take on deep learning")
|
||
(description
|
||
"This package provides a functional take on deep learning, compatible
|
||
with your favorite libraries.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-threadpoolctl
|
||
(package
|
||
(name "python-threadpoolctl")
|
||
(version "3.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "threadpoolctl" version))
|
||
(sha256
|
||
(base32
|
||
"100k76nmajf408lbn5ipis1gilklcs6sbqyqy3hhlh54zanbldd3"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs
|
||
(list python-flit-core 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-imbalanced-learn
|
||
(package
|
||
(name "python-imbalanced-learn")
|
||
(version "0.11.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "imbalanced-learn" version))
|
||
(sha256
|
||
(base32 "1p4gdgc8nsq0vjmw4y4d2bp9g0m1c23d0zgrzs90pnz6b24ax0km"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags '(list "-k"
|
||
;; Although we cannot satify the Tensorflow and Keras requirements
|
||
;; (python-keras >= 2.4.3 and tensorflow >= 2.4.3), all tests
|
||
;; besides these pass.
|
||
"not balanced_batch_generator and not BalancedBatchGenerator")
|
||
#:phases '(modify-phases %standard-phases
|
||
(add-after 'unpack 'unbreak-tests
|
||
(lambda _
|
||
;; Some tests require a home directory
|
||
(setenv "HOME"
|
||
(getcwd)))))))
|
||
(propagated-inputs (list python-joblib python-numpy python-scikit-learn
|
||
python-scipy python-threadpoolctl))
|
||
(native-inputs (list python-black
|
||
python-flake8
|
||
python-keras
|
||
python-mypy
|
||
python-numpydoc
|
||
python-pandas
|
||
python-pytest
|
||
python-pytest-cov
|
||
tensorflow))
|
||
(home-page "https://github.com/scikit-learn-contrib/imbalanced-learn")
|
||
(synopsis "Toolbox for imbalanced dataset in machine learning")
|
||
(description
|
||
"This is a Python package offering a number of re-sampling
|
||
techniques commonly used in datasets showing strong between-class imbalance.
|
||
It is compatible with @code{scikit-learn}.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-hdbscan
|
||
(package
|
||
(name "python-hdbscan")
|
||
(version "0.8.33")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "hdbscan" version))
|
||
(sha256
|
||
(base32 "03gr70ys1zrnp15pxzhichvrdj5bj88p6p5k0wj8vx251rgvryjp"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-before 'check 'build-extensions
|
||
(lambda _
|
||
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
||
(propagated-inputs (list python-joblib
|
||
python-numpy
|
||
python-scikit-learn
|
||
python-scipy))
|
||
(native-inputs (list python-cython
|
||
python-nose
|
||
python-pytest
|
||
python-pandas
|
||
python-networkx))
|
||
(home-page "https://github.com/scikit-learn-contrib/hdbscan")
|
||
(synopsis "High performance implementation of HDBSCAN clustering")
|
||
(description "HDBSCAN - Hierarchical Density-Based Spatial Clustering of
|
||
Applications with Noise. Performs DBSCAN over varying epsilon values and
|
||
integrates the result to find a clustering that gives the best stability over
|
||
epsilon. This allows HDBSCAN to find clusters of varying densities (unlike
|
||
DBSCAN), and be more robust to parameter selection. HDBSCAN is ideal for
|
||
exploratory data analysis; it's a fast and robust algorithm that you can trust
|
||
to return meaningful clusters (if there are any).")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-pynndescent
|
||
(package
|
||
(name "python-pynndescent")
|
||
(version "0.5.11")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pynndescent" version))
|
||
(sha256
|
||
(base32 "0l5dpdsk5vg7rpay81bncp04119hnl5z7zxjv63jrnm9spcwwi3g"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs (list python-pytest))
|
||
(propagated-inputs
|
||
(list python-importlib-metadata
|
||
python-joblib
|
||
python-llvmlite
|
||
python-numba
|
||
python-scikit-learn
|
||
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 "1.0.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ; no tests in PyPI release
|
||
(uri (git-reference
|
||
(url "https://github.com/pavlin-policar/openTSNE")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0xjp0l4rxk1s685skbx50m3m9hwlj78w74qwgswnkmkk6f7c8dsi"))))
|
||
(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")))
|
||
(add-after 'unpack 'skip-test
|
||
(lambda _ ;; TODO: figure out why this test fails.
|
||
(substitute* "tests/test_correctness.py"
|
||
(("def test_iris\\(self\\)") "def _test_iris(self)"))))
|
||
;; Numba needs a writable dir to cache functions.
|
||
(add-before 'check 'set-numba-cache-dir
|
||
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
|
||
(native-inputs (list python-cython))
|
||
(inputs (list fftw))
|
||
(propagated-inputs
|
||
(list python-numpy python-pynndescent python-scikit-learn
|
||
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 "0.62")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "skrebate" version))
|
||
(sha256
|
||
(base32
|
||
"0n55ghvnv7rxqa5agq6a4892ad0ghha165b0g4ghwr9gqm6ss3dj"))))
|
||
(build-system python-build-system)
|
||
(arguments '(#:tests? #f)) ;no tests on PyPI and no tags in repo
|
||
(propagated-inputs
|
||
(list python-numpy python-scipy python-scikit-learn 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-cleanlab
|
||
(package
|
||
(name "python-cleanlab")
|
||
(version "2.2.0")
|
||
;; The version on pypi does not come with tests.
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/cleanlab/cleanlab")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"00dqhxpwg781skknw943ynll2s44g4j125dx8aapk1d5d71sbzqy"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; This test fails because the newer version of scikit learn returns one
|
||
;; more classification result than expected. This should be harmless.
|
||
'(list "-k" "not test_aux_inputs"
|
||
;; Requires Tensorflow
|
||
"--ignore=tests/test_frameworks.py"
|
||
;; Tries to download datasets from the internet at runtime.
|
||
"--ignore=tests/test_dataset.py")))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-pandas
|
||
python-scikit-learn
|
||
python-termcolor
|
||
python-tqdm))
|
||
(native-inputs
|
||
(list python-pytest
|
||
python-pytest-lazy-fixture
|
||
python-pytorch
|
||
python-torchvision))
|
||
(home-page "https://cleanlab.ai")
|
||
(synopsis "Automatically find and fix dataset issues")
|
||
(description
|
||
"cleanlab automatically finds and fixes errors in any ML dataset. This
|
||
data-centric AI package facilitates machine learning with messy, real-world
|
||
data by providing clean labels during training.")
|
||
(license license:agpl3+)))
|
||
|
||
(define-public python-cleanlab-1
|
||
(package
|
||
(inherit python-cleanlab)
|
||
(name "python-cleanlab")
|
||
(version "1.0.1")
|
||
;; The version on pypi does not come with tests.
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/cleanlab/cleanlab")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"03kw2agnhadmrq9zvrlvvlc2c37dpflga5nhmsaag8scw223gqyp"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments (list))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-tqdm))
|
||
(native-inputs
|
||
(list python-pytest))))
|
||
|
||
(define-public python-cma
|
||
(package
|
||
(name "python-cma")
|
||
(version "3.3.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "cma" version))
|
||
(sha256
|
||
(base32
|
||
"1v31b2vnnr4v6ack7zfmw7zb47vbzjr9nyvx2lbfhyjf7zhbhj5p"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
(list #:phases #~(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(invoke "python" "-m" "cma.test")))))))
|
||
(propagated-inputs (list python-numpy))
|
||
(home-page "https://github.com/CMA-ES/pycma")
|
||
(synopsis "Python implementation of CMA-ES")
|
||
(description "This package provides a Python implementation of the
|
||
@acronym{CMA-ES, Covariance Matrix Adaptation Evolution Strategy} algorithm
|
||
and a few related numerical optimization tools.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-cmaes
|
||
(package
|
||
(name "python-cmaes")
|
||
(version "0.9.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ;no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/CyberAgentAILab/cmaes")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32 "1f3143w8ii6i93bdh65iazrq1lryccd805ndnqww5l8h7qnnzpkm"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs (list python-hypothesis))
|
||
(propagated-inputs (list python-numpy))
|
||
(home-page "https://github.com/CyberAgentAILab/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 "c6d81ce7eede6db801d4e9a92b27ec5d409d0eab")
|
||
(revision "0")
|
||
(version (git-version "1.5" 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
|
||
"04kljgydng42xlg044h6nbzxpban1ivd6jzb8ydkngfq88ppipfk"))
|
||
(file-name (git-file-name name version))))
|
||
(version version)
|
||
(build-system pyproject-build-system)
|
||
(native-inputs
|
||
(list python-nose python-pytest))
|
||
(propagated-inputs
|
||
(list python-future python-numpy))
|
||
(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 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
|
||
(list python-pytest python-nose))
|
||
(inputs
|
||
(list openmpi))
|
||
(propagated-inputs
|
||
(list python-numpy 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
|
||
(list boost 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 python-hyperopt
|
||
(package
|
||
(name "python-hyperopt")
|
||
(version "0.2.7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "hyperopt" version))
|
||
(sha256
|
||
(base32 "0jd1ghmm423kbhjvd6pxq92y5vkz25390687fcnd7fshh3jrmy0v"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(invoke "python" "-m" "pytest"
|
||
;; Needs python-pyspark.
|
||
"--ignore" "hyperopt/tests/integration/test_spark.py"
|
||
;; Needs both python-scikit-learn and python-lightgbm.
|
||
"--ignore" "hyperopt/tests/unit/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"
|
||
;; XXX Type error with this version of scipy
|
||
" and not test_distribution_rvs"))))))))
|
||
(propagated-inputs
|
||
(list python-cloudpickle
|
||
python-future
|
||
python-py4j
|
||
python-networkx
|
||
python-numpy
|
||
python-scipy
|
||
python-six
|
||
python-tqdm))
|
||
(native-inputs
|
||
(list python-black
|
||
python-nose
|
||
python-pymongo
|
||
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)))
|
||
|
||
(define-public python-deepxde
|
||
(package
|
||
(name "python-deepxde")
|
||
(version "1.10.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "DeepXDE" version))
|
||
(sha256
|
||
(base32
|
||
"1lgn4sa9bnmhsccddb9vjz7nsvdnccxqkvv7xssxmfb413dpg1mz"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:tests? #f ; there are no tests
|
||
#:phases #~(modify-phases %standard-phases
|
||
(add-before 'sanity-check 'writable-home
|
||
;; sanity-check writes ~/.deepxde/config.json to set
|
||
;; the default backend.
|
||
(lambda _
|
||
(setenv "HOME" "/tmp"))))))
|
||
;; DeepXDE supported backends are TensorFlow (v1 and v2), PyTorch, JAX and
|
||
;; PaddlePaddle. We test with PyTorch because we have it up to date.
|
||
(native-inputs (list python-pytorch python-setuptools-scm))
|
||
(propagated-inputs (list python-matplotlib python-numpy
|
||
python-scikit-learn python-scikit-optimize
|
||
python-scipy))
|
||
(home-page "https://deepxde.readthedocs.io/en/latest/")
|
||
(synopsis "Library for scientific machine learning")
|
||
(description "DeepXDE is a library for scientific machine learning and
|
||
physics-informed learning. It includes implementations for the PINN
|
||
(physics-informed neural networks), DeepONet (deep operator network) and
|
||
MFNN (multifidelity neural network) algorithms.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public python-jaxtyping
|
||
(package
|
||
(name "python-jaxtyping")
|
||
(version "0.2.21")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "jaxtyping" version))
|
||
(sha256
|
||
(base32
|
||
"19qmsnbn4wv2jl99lpn622qs49mrfxmx8s9pr5y8izzgdjq1fvii"))))
|
||
(build-system pyproject-build-system)
|
||
;; Tests require JAX, but JAX can't be packaged because it uses the Bazel
|
||
;; build system.
|
||
(arguments (list #:tests? #f))
|
||
(native-inputs (list python-hatchling))
|
||
(propagated-inputs (list python-numpy python-typeguard
|
||
python-typing-extensions))
|
||
(home-page "https://github.com/google/jaxtyping")
|
||
(synopsis
|
||
"Type annotations and runtime checking for JAX arrays and others")
|
||
(description "@code{jaxtyping} provides type annotations and runtime
|
||
checking for shape and dtype of JAX arrays, PyTorch, NumPy, TensorFlow, and
|
||
PyTrees.")
|
||
(license license:expat)))
|
||
|
||
;; There have been no proper releases yet.
|
||
(define-public kaldi
|
||
(let ((commit "be22248e3a166d9ec52c78dac945f471e7c3a8aa")
|
||
(revision "1")
|
||
(openfst openfst-1.7.3)) ;; Temporary bypass for upstream issues
|
||
(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
|
||
"1wkxz3p0h68mxbg41i1wygir2r4rraxbb4672xkkvvs85r6c8r8i"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:test-target "test"
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "src")))
|
||
(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")))
|
||
(substitute* "matrix/Makefile" ;temporary test bypass
|
||
(("matrix-lib-test sparse-matrix-test") ""))
|
||
|
||
;; 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")))
|
||
;; 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"))))))))
|
||
(inputs
|
||
(list alsa-lib
|
||
`(,gfortran "lib")
|
||
glib
|
||
gstreamer
|
||
jack-1
|
||
openblas
|
||
openfst
|
||
portaudio
|
||
python))
|
||
(native-inputs
|
||
(list `(,glib "bin") ; glib-genmarshal
|
||
grep
|
||
sed
|
||
pkg-config
|
||
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 kaldi-for-vosk
|
||
(let* ((commit "a25f216f5ce4eec5e45a6ab7651e20c9840a05cd")
|
||
(revision "0")
|
||
(openfst openfst-for-vosk))
|
||
(package
|
||
(inherit kaldi)
|
||
(name "kaldi")
|
||
(version (git-version "0" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/alphacep/kaldi")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "16w90za8narkfi590cxj4p7vc1f5sdxc927g5hk6kh4l3mf6iisl"))))
|
||
(inputs
|
||
(list alsa-lib
|
||
lapack ;compared to base kaldi, replacing `(,gfortran "lib")
|
||
glib
|
||
gstreamer
|
||
jack-2
|
||
openblas
|
||
openfst
|
||
portaudio
|
||
python))
|
||
(arguments
|
||
(list
|
||
#:test-target "test"
|
||
#:make-flags '(list "online2" "lm" "rnnlm")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "src")))
|
||
(replace 'configure
|
||
(lambda _
|
||
(let ((portaudio #$(this-package-input "portaudio"))
|
||
(lapack #$(this-package-input "lapack"))
|
||
(openfst #$(this-package-input "openfst"))
|
||
(openblas #$(this-package-input "openblas")))
|
||
#$@(if (target-x86?)
|
||
'()
|
||
#~((substitute* "makefiles/linux_openblas.mk"
|
||
(("-msse -msse2") ""))))
|
||
(substitute* "makefiles/default_rules.mk"
|
||
(("/bin/bash") (which "bash")))
|
||
(substitute* "Makefile"
|
||
(("ext_depend: check_portaudio")
|
||
"ext_depend:"))
|
||
(substitute* '("online/Makefile"
|
||
"onlinebin/Makefile"
|
||
"gst-plugin/Makefile")
|
||
(("../../tools/portaudio/install")
|
||
portaudio))
|
||
(substitute* "matrix/Makefile" ;temporary test bypass
|
||
(("matrix-lib-test sparse-matrix-test") ""))
|
||
(substitute* "cudamatrix/Makefile"
|
||
((" cu-array-test") ""))
|
||
|
||
;; This `configure' script doesn't support variables passed as
|
||
;; arguments, nor does it support "prefix".
|
||
(substitute* "configure"
|
||
(("check_for_slow_expf;") "")
|
||
;; This affects the RPATH and also serves as the installation
|
||
;; directory.
|
||
(("KALDILIBDIR=`pwd`/lib")
|
||
(string-append "KALDILIBDIR=" #$output "/lib"))
|
||
(("OPENBLASROOT=\\\"\\$\\(rel2abs ..\\/tools\\/OpenBLAS\\/install\\)\\\"")
|
||
(string-append "OPENBLASROOT=\"" openblas "\""))
|
||
(("-L\\$OPENBLASLIBDIR -l:libopenblas.a -l:libblas.a -l:liblapack.a -l:libf2c.a")
|
||
(string-append "-L$OPENBLASLIBDIR -lopenblas "
|
||
"-L" lapack "/lib -lblas -llapack")))
|
||
(mkdir-p #$output) ; must exist
|
||
(setenv "CONFIG_SHELL" (which "bash"))
|
||
(setenv "OPENFST_VER" #$(package-version openfst))
|
||
(invoke "./configure"
|
||
"--use-cuda=no"
|
||
"--mathlib=OPENBLAS_CLAPACK"
|
||
"--shared"
|
||
(string-append "--fst-root=" openfst)))))
|
||
(add-after 'configure 'optimize-build
|
||
(lambda _ (substitute* "kaldi.mk" ((" -O1") " -O3"))))
|
||
(replace 'install
|
||
(lambda _
|
||
(let ((inc (string-append #$output "/include"))
|
||
(lib (string-append #$output "/lib")))
|
||
;; The build phase installed symlinks to the actual
|
||
;; libraries. Install the actual targets.
|
||
(for-each (lambda (file)
|
||
(let ((target (readlink file)))
|
||
(delete-file file)
|
||
(install-file target lib)))
|
||
(find-files lib "\\.so"))
|
||
;; Install headers
|
||
(for-each (lambda (file)
|
||
(let ((target-dir (string-append inc "/" (dirname file))))
|
||
(install-file file target-dir)))
|
||
(find-files "." "\\.h")))))))))))
|
||
|
||
(define-public gst-kaldi-nnet2-online
|
||
(let ((commit "7888ae562a65bd7e406783ce2c33535bc66a30ef")
|
||
(revision "3"))
|
||
(package
|
||
(name "gst-kaldi-nnet2-online")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/alumae/gst-kaldi-nnet2-online")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0xp59a6lmx1y24i8bkmxcm27lhm5x5m6y41670yjzhamcbnx8jcr"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
#:tests? #f ; there are none
|
||
#:make-flags
|
||
'(list (string-append "SHELL="
|
||
(assoc-ref %build-inputs "bash") "/bin/bash")
|
||
(string-append "KALDI_ROOT="
|
||
(assoc-ref %build-inputs "kaldi-src"))
|
||
(string-append "KALDILIBDIR="
|
||
(assoc-ref %build-inputs "kaldi") "/lib")
|
||
"KALDI_FLAVOR=dynamic")
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "src")))
|
||
(replace 'configure
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((glib (assoc-ref inputs "glib")))
|
||
(setenv "CXXFLAGS" "-fPIC")
|
||
(setenv "CPLUS_INCLUDE_PATH"
|
||
(string-append glib "/include/glib-2.0:"
|
||
glib "/lib/glib-2.0/include:"
|
||
(assoc-ref inputs "gstreamer")
|
||
"/include/gstreamer-1.0:"
|
||
(getenv "CPLUS_INCLUDE_PATH"))))
|
||
(substitute* "Makefile"
|
||
(("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
|
||
(("\\$\\(error Cannot find") "#"))))
|
||
(add-before 'build 'build-depend
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "depend" make-flags)))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib/gstreamer-1.0")))
|
||
(install-file "libgstkaldinnet2onlinedecoder.so" lib)))))))
|
||
(inputs
|
||
(list glib gstreamer jansson openfst-1.7.3 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 "f79e204d751a5964918001822e4520fa2acfd246")
|
||
(revision "3"))
|
||
(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
|
||
"1iijq8jmgdxr7961inal1ggs496ymxradm51m4sqx8vl983x14y8"))))
|
||
(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$")))))
|
||
(replace 'install
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin"))
|
||
(share (string-append out "/share/kaldi-gstreamer-server/")))
|
||
;; Install Python files
|
||
(with-directory-excursion "kaldigstserver"
|
||
(for-each (cut install-file <> share)
|
||
(find-files "." ".*")))
|
||
|
||
;; Install sample configuration files
|
||
(for-each (cut install-file <> share)
|
||
(find-files "." "\\.yaml"))
|
||
|
||
;; Install executables
|
||
(mkdir-p bin)
|
||
(let* ((server (string-append bin "/kaldi-gst-server"))
|
||
(client (string-append bin "/kaldi-gst-client"))
|
||
(worker (string-append bin "/kaldi-gst-worker"))
|
||
(PYTHONPATH (getenv "GUIX_PYTHONPATH"))
|
||
(GST_PLUGIN_PATH (string-append
|
||
(assoc-ref inputs "gst-kaldi-nnet2-online")
|
||
"/lib/gstreamer-1.0:${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")))))))))
|
||
(inputs
|
||
(list gst-kaldi-nnet2-online
|
||
python-wrapper
|
||
python-pygobject
|
||
python-pyyaml
|
||
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"))
|
||
(patches
|
||
(search-patches "tensorflow-c-api-fix.patch"))))
|
||
(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")))
|
||
(add-after 'unpack 'python3.10-compatibility
|
||
(lambda _
|
||
;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
|
||
(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)))
|
||
|
||
;; Many collections classes have been moved to collections.abc
|
||
(substitute* '("tensorflow/python/framework/ops.py"
|
||
"tensorflow/python/ops/clip_ops.py"
|
||
"tensorflow/python/ops/data_flow_ops.py"
|
||
"tensorflow/python/ops/gradients_impl.py"
|
||
"tensorflow/python/training/input.py"
|
||
"tensorflow/python/training/checkpointable/data_structures.py"
|
||
"tensorflow/python/util/nest.py"
|
||
"tensorflow/python/util/protobuf/compare.py")
|
||
(("collections.Mapping") "collections.abc.Mapping")
|
||
(("collections.Sequence") "collections.abc.Sequence"))
|
||
(substitute* "tensorflow/python/feature_column/feature_column.py"
|
||
(("collections.Iterator") "collections.abc.Iterator"))
|
||
(substitute* "tensorflow/python/ops/sparse_ops.py"
|
||
(("collections.Iterable") "collections.abc.Iterable"))
|
||
(substitute* "tensorflow/python/keras/callbacks.py"
|
||
(("from collections import Iterable")
|
||
"from collections.abc import Iterable"))
|
||
(substitute* "tensorflow/python/ops/variable_scope.py"
|
||
(("collections_lib.Sequence") "collections_lib.abc.Sequence"))
|
||
|
||
;; XXX: it is not clear if this is a good idea, but the build
|
||
;; system tries to overwrite the __or__ and __ror__ methods of
|
||
;; the Tensor class.
|
||
(substitute* "tensorflow/python/framework/ops.py"
|
||
(("if not isinstance\\(existing, type\\(object.__lt__\\)\\)" m)
|
||
(string-append m
|
||
" and not isinstance(existing, type(object.__or__))")))
|
||
|
||
;; Fix the build with numpy >= 1.19.
|
||
;; Suggested in https://github.com/tensorflow/tensorflow/issues/41086#issuecomment-656833081
|
||
(substitute* "tensorflow/python/lib/core/bfloat16.cc"
|
||
(("void BinaryUFunc\\(char\\*\\* args, npy_intp\\* dimensions, npy_intp\\* steps,")
|
||
"void BinaryUFunc(char** args, npy_intp const* dimensions, npy_intp const* steps,")
|
||
(("void CompareUFunc\\(char\\*\\* args, npy_intp\\* dimensions, npy_intp\\* steps,")
|
||
"void CompareUFunc(char** args, npy_intp const* dimensions, npy_intp const* steps,"))
|
||
|
||
;; ...and for numpy >= 1.23
|
||
(substitute* "tensorflow/python/framework/tensor_util.py"
|
||
(("np.asscalar\\(x\\[0\\]\\)") "x[0].item()")
|
||
(("np.asscalar\\(x\\)") "x.item()")
|
||
(("np.asscalar\\(v\\)") "np.ndarray.item(v)")
|
||
(("return np.asscalar") "return np.ndarray.item"))
|
||
(substitute* "tensorflow/python/kernel_tests/cwise_ops_test.py"
|
||
(("np.asscalar\\(np.random.rand\\(1\\) \\* 100.\\)")
|
||
"(np.random.rand(1) * 100.).item()"))
|
||
(substitute* '("tensorflow/python/framework/fast_tensor_util.pyx"
|
||
"tensorflow/python/estimator/canned/linear_testing_utils.py")
|
||
(("np.asscalar") "np.ndarray.item"))))
|
||
(add-after 'python3.10-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")))
|
||
(add-after 'configure 'unpack-third-party-sources
|
||
(lambda* (#:key inputs outputs #: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"))
|
||
|
||
;; https://github.com/google/farmhash/issues/24
|
||
(substitute* "../build/farmhash/src/farmhash/src/farmhash.cc"
|
||
(("using namespace std;") "")
|
||
(("make_pair") "std::make_pair")
|
||
(("pair<") "std::pair<"))
|
||
|
||
(rename-file "../build/cub/src/cub/cub-1.8.0/"
|
||
"../build/cub/src/cub/cub/")
|
||
|
||
(setenv "LDFLAGS"
|
||
(string-append "-Wl,-rpath="
|
||
(assoc-ref outputs "out") "/lib"))))
|
||
(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")
|
||
(copy-recursively (assoc-ref inputs "eigen:src") "eigen-src")
|
||
|
||
;; distutils.sysconfig is deprecated and prints a deprecation
|
||
;; warning that breaks the generated CXX_INCLUDES line.
|
||
(substitute* "tensorflow/contrib/cmake/tf_python.cmake"
|
||
(("import distutils.sysconfig; print\\(distutils.sysconfig.get_python_inc\\(\\)\\)")
|
||
"import sysconfig; print(sysconfig.get_path('include'))"))
|
||
|
||
(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 'unpack 'patch-cmake-file-to-install-c-headers
|
||
(lambda _
|
||
(substitute* "tensorflow/contrib/cmake/tf_c.cmake"
|
||
(("if\\(tensorflow_BUILD_PYTHON_BINDINGS" m)
|
||
(string-append
|
||
"install(DIRECTORY ${tensorflow_source_dir}/tensorflow/c/ \
|
||
DESTINATION include/tensorflow/c FILES_MATCHING PATTERN \"*.h\")\n" m)))))
|
||
(add-after 'build 'build-c-bindings
|
||
(lambda* (#:key outputs parallel-build? #:allow-other-keys)
|
||
(invoke "make" "-j" (if parallel-build?
|
||
(number->string (parallel-job-count))
|
||
"1")
|
||
"tf_c")))
|
||
(add-after 'install 'build-pip-package
|
||
(lambda* (#:key outputs parallel-build? #:allow-other-keys)
|
||
(invoke "make" "-j" (if parallel-build?
|
||
(number->string (parallel-job-count))
|
||
"1")
|
||
"tf_python_build_pip_package")))
|
||
(add-after 'build-pip-package 'install-python
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(wheel (car (find-files "../build/tf_python/dist/" "\\.whl$")))
|
||
(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
|
||
(list python-absl-py
|
||
python-astor
|
||
python-gast
|
||
python-grpcio
|
||
python-numpy
|
||
python-protobuf-3.6
|
||
python-six
|
||
python-termcolor
|
||
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 "2.13.1")
|
||
(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
|
||
"09mfskmpvpbq919wibnw3bnhi1y3hkx3qrzm72gdr0gsivn1yb3w"))
|
||
(patches (search-patches "tensorflow-lite-unbundle.patch"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:tests? #false ;tests are not building now
|
||
#:build-type "Release"
|
||
#:modules '((ice-9 match)
|
||
(guix build utils)
|
||
(guix build cmake-build-system))
|
||
#:configure-flags
|
||
#~(list
|
||
;; "-DTFLITE_KERNEL_TEST=ON" ; TODO: build tests
|
||
;; so cmake can be used to find this from other packages
|
||
"-DTFLITE_ENABLE_INSTALL=ON"
|
||
|
||
;; Use Guix's own packages as dependencies.
|
||
"-DCMAKE_FIND_PACKAGE_PREFER_CONFIG=ON"
|
||
|
||
"-DTFLITE_ENABLE_GPU=ON"
|
||
"-DTFLITE_ENABLE_RUY=ON"
|
||
|
||
;; TODO: turn on Farmhash
|
||
;;"-DSYSTEM_FARMHASH=ON"
|
||
(string-append "-Dabsl_DIR=" #$(this-package-input "abseil-cpp")
|
||
"/lib/cmake/absl")
|
||
(string-append "-DEigen3_DIR=" #$(this-package-input "eigen")
|
||
"/share/eigen3/cmake")
|
||
(string-append "-DFlatBuffers_DIR="
|
||
#$(this-package-input "flatbuffers-shared")
|
||
"/lib/cmake/flatbuffers")
|
||
(string-append "-DNEON_2_SSE_DIR=" #$(this-package-input "neon2sse")
|
||
"/lib/cmake/NEON_2_SSE")
|
||
(string-append "-Dcpuinfo_DIR=" #$(this-package-input "cpuinfo")
|
||
"/share/cpuinfo")
|
||
(string-append "-Druy_DIR=" #$(this-package-input "ruy")
|
||
"/lib/cmake/ruy")
|
||
|
||
;; 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"
|
||
|
||
;; Don't fetch the sources. We have these already
|
||
"-Dgemmlowp_POPULATED=TRUE"
|
||
"-Degl_headers_POPULATED=TRUE"
|
||
"-Dfp16_headers_POPULATED=TRUE"
|
||
"-Dopencl_headers_POPULATED=TRUE"
|
||
"-Dopengl_headers_POPULATED=TRUE"
|
||
"-Dvulkan_headers_POPULATED=TRUE"
|
||
"-Dgoogletest_POPULATED=TRUE"
|
||
"-Dgoogle_benchmark_POPULATED=TRUE"
|
||
"-Dnsync_POPULATED=TRUE"
|
||
"-Dre2_POPULATED=TRUE"
|
||
|
||
"-DFFT2D_SOURCE_DIR=/tmp/fft2d"
|
||
"-DFARMHASH_SOURCE_DIR=/tmp/farmhash"
|
||
(string-append "-Dgemmlowp_ROOT=" #$(this-package-input "gemmlowp")))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "tensorflow/lite")))
|
||
(add-after 'chdir 'copy-sources
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; TODO: properly use Guix's pthreaqdpool. We are not using
|
||
;; pthreadpool because we are not enabling xnnpack
|
||
(substitute* "CMakeLists.txt"
|
||
(("if\\(NOT DEFINED PTHREADPOOL_SOURCE_DIR\\)")
|
||
"if(false)"))
|
||
(substitute* "CMakeLists.txt"
|
||
(("if\\(NOT TARGET pthreadpool\\)")
|
||
"if(false)"))
|
||
|
||
;; Don't fetch source code; we already have everything we need.
|
||
(substitute* '("tools/cmake/modules/fft2d.cmake"
|
||
"tools/cmake/modules/farmhash.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")))))
|
||
(add-after 'build 'build-shared-library
|
||
(lambda* (#:key configure-flags #:allow-other-keys)
|
||
(mkdir-p "c")
|
||
(with-directory-excursion "c"
|
||
(apply invoke "cmake" (append configure-flags (list "../../lite/c")))
|
||
(invoke "cmake" "--build" "." "-j" (number->string
|
||
(parallel-job-count))))))
|
||
(add-after 'build-shared-library 'build-benchmark-model
|
||
(lambda _
|
||
(invoke "cmake" "--build" "." "--target" "benchmark_model"
|
||
"-j" (number->string (parallel-job-count)))))
|
||
|
||
(add-after 'install 'install-extra
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib"))
|
||
(bin (string-append out "/bin")))
|
||
(install-file "../build/c/libtensorflowlite_c.so" lib)
|
||
(install-file "../build/tools/benchmark/benchmark_model" bin))))
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(invoke "ctest" "-L" "plain")))))))
|
||
(inputs
|
||
`(("abseil-cpp" ,abseil-cpp-20200923.3)
|
||
("cpuinfo" ,cpuinfo)
|
||
("eigen" ,eigen)
|
||
("fp16" ,fp16)
|
||
("flatbuffers-shared" ,flatbuffers-next-shared)
|
||
("gemmlowp" ,gemmlowp)
|
||
("mesa-headers" ,mesa-headers)
|
||
("neon2sse" ,neon2sse)
|
||
("nsync" ,nsync)
|
||
("opencl-clhpp" ,opencl-clhpp)
|
||
("opencl-headers" ,opencl-headers)
|
||
("opencl-icd-loader" ,opencl-icd-loader)
|
||
("pthreadpool" ,pthreadpool)
|
||
("python" ,python)
|
||
("ruy" ,ruy)
|
||
("re2" ,re2)
|
||
;;("xnnpack" ,xnnpack) ; TODO: use Guix's copy of xnnpack
|
||
("vulkan-headers" ,vulkan-headers)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("googletest" ,googletest)
|
||
("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/github.com/petewarden/"
|
||
"OouraFFT/archive/v1.0.tar.gz"))
|
||
(file-name "fft2d.tar.gz")
|
||
(sha256
|
||
(base32
|
||
"1jfflzi74fag9z4qmgwvp90aif4dpbr1657izmxlgvf4hy8fk9xd"))))))
|
||
(home-page "https://www.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 "1.5.2")
|
||
(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 "0qx04y7cz8z7qv6bk9q7d7ba9b7xzj53l83l2x9ykdwhzacc3dn0"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags (list "-DGOOGLE_TEST=ON")))
|
||
(native-inputs
|
||
`(("googletest" ,googletest)
|
||
("python" ,python-wrapper)))
|
||
(inputs
|
||
(list 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 pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "tests/python"
|
||
;; FIXME: CLI tests fail with PermissionError.
|
||
"--ignore" "tests/python/test_cli.py"
|
||
"-k"
|
||
(string-append
|
||
"not test_cli_regression_demo"
|
||
;; These tests use the Boston dataset that has been
|
||
;; removed from scipy.
|
||
" and not test_sklearn_demo"
|
||
" and not test_sklearn_parallel_demo"
|
||
" and not test_predict_shape"
|
||
" and not test_num_parallel_tree"
|
||
" and not test_boston_housing_regression"
|
||
" and not test_boston_housing_rf_regression"
|
||
" and not test_parameter_tuning"
|
||
" and not test_regression_with_custom_objective"
|
||
" and not test_RFECV"
|
||
;; Pandas incompatibility? Says:
|
||
;; '_CalibratedClassifier' object has no attribute
|
||
;; 'base_estimator'
|
||
" and not test_pandas_input"
|
||
;; Accuracy problems?
|
||
" and not test_exact"
|
||
" and not test_approx"
|
||
" and not test_hist"
|
||
;; 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"
|
||
;; "'['./runexp.sh']' returned non-zero exit status 1"
|
||
" and not test_cli_binary_classification"))
|
||
#: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,") ""))
|
||
;; Remove bad dataset. This has been removed in scipy.
|
||
(substitute* "tests/python/testing.py"
|
||
(("TestDataset\\('boston', get_boston, 'reg:squarederror', 'rmse'\\),")
|
||
"")
|
||
(("datasets.load_boston")
|
||
"datasets.load_digits"))))
|
||
(add-after 'install 'install-version-and-libxgboost
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let* ((pylib (string-append #$output "/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"))))))))
|
||
(native-inputs
|
||
(list python-pandas python-pytest python-scikit-learn))
|
||
(inputs
|
||
(list xgboost))
|
||
(propagated-inputs
|
||
(list python-numpy 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
|
||
(list python-ipython python-numpy python-pandas python-scipy))
|
||
(native-inputs
|
||
(list 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
|
||
(list python-h5py python-numpy))
|
||
(native-inputs
|
||
(list python-pytest python-pytest-cov python-pytest-pep8
|
||
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
|
||
(list python-numpy python-six))
|
||
(native-inputs
|
||
(list python-pandas
|
||
python-pillow
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-pytest-xdist
|
||
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 "2.3.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "Keras" version))
|
||
(sha256
|
||
(base32
|
||
"1k68xd8n2y9ldijggjc8nn4d6d1axw0p98gfb0fmm8h641vl679j"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(substitute* '("keras/callbacks/callbacks.py"
|
||
"keras/engine/training_utils.py"
|
||
"keras/engine/training.py"
|
||
"keras/engine/training_generator.py"
|
||
"keras/utils/generic_utils.py")
|
||
(("from collections import Iterable")
|
||
"from collections.abc import Iterable")
|
||
(("collections.Container")
|
||
"collections.abc.Container")
|
||
(("collections.Mapping")
|
||
"collections.abc.Mapping")
|
||
(("collections.Sequence")
|
||
"collections.abc.Sequence")))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'tf-compatibility
|
||
(lambda _
|
||
(substitute* "keras/backend/tensorflow_backend.py"
|
||
(("^get_graph = .*")
|
||
"get_graph = tf.get_default_graph")
|
||
(("tf.compat.v1.nn.fused_batch_norm")
|
||
"tf.nn.fused_batch_norm")
|
||
;; categorical_crossentropy does not support axis
|
||
(("from_logits=from_logits, axis=axis")
|
||
"from_logits=from_logits")
|
||
;; dropout accepts a level number, not a named rate argument.
|
||
(("dropout\\(x, rate=level,")
|
||
"dropout(x, level,")
|
||
(("return x.shape.rank")
|
||
"return len(x.shape)"))))
|
||
(add-after 'unpack 'hdf5-compatibility
|
||
(lambda _
|
||
;; The truth value of an array with more than one element is ambiguous.
|
||
(substitute* "tests/keras/utils/io_utils_test.py"
|
||
((" *assert .* == \\[b'(asd|efg).*") ""))
|
||
(substitute* "tests/test_model_saving.py"
|
||
(("h5py.File\\('does not matter',")
|
||
"h5py.File('does not matter', 'w',"))
|
||
(substitute* "keras/utils/io_utils.py"
|
||
(("h5py.File\\('in-memory-h5py', driver='core', backing_store=False\\)")
|
||
"h5py.File('in-memory-h5py', 'w', driver='core', backing_store=False)")
|
||
(("h5file.fid.get_file_image")
|
||
"h5file.id.get_file_image"))
|
||
(substitute* "keras/engine/saving.py"
|
||
(("\\.decode\\('utf-?8'\\)") ""))))
|
||
(add-after 'unpack 'delete-unavailable-backends
|
||
(lambda _
|
||
(delete-file "keras/backend/theano_backend.py")
|
||
(delete-file "keras/backend/cntk_backend.py")))
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
;; 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")
|
||
(invoke "python" "-m" "pytest" "tests"
|
||
"-p" "no:pep8"
|
||
;; FIXME: python-build-system lacks PARALLEL-TESTS?
|
||
"-n" (number->string (parallel-job-count))
|
||
;; This one uses the theano backend that we don't have.
|
||
"--ignore=tests/test_api.py"
|
||
"--ignore=tests/keras/backend/backend_test.py"
|
||
;; Our Tensorflow version does not have the coder ops library.
|
||
"--ignore=tests/keras/callbacks/callbacks_test.py"
|
||
;; ...nor do we have tensorboard
|
||
"--ignore=tests/keras/callbacks/tensorboard_test.py"
|
||
"-k"
|
||
(string-append
|
||
;; See https://github.com/keras-team/keras/pull/7033
|
||
"not test_TimeDistributed_learning_phase "
|
||
;; XXX fails because no closure is provided
|
||
"and not test_func_dump_and_load_backwards_compat "
|
||
;; XXX real bug? These are all tests that fail due to
|
||
;; shape mismatch, e.g. "got logits shape [12,3] and
|
||
;; labels shape [9]"
|
||
"and not test_model_with_crossentropy_losses_channels_first "
|
||
"and not test_masking_correctness_output_size_not_equal_to_first_state_size "
|
||
"and not test_convolutional_recurrent "
|
||
"and not test_axis "
|
||
|
||
;; XXX fails because of 3/15 values have unexpected differences.
|
||
"and not test_masking_correctness_output_not_equal_to_first_state "
|
||
;; XXX fails because of a difference of about 0.1
|
||
"and not test_sample_weighted "
|
||
;; XXX fails because of a difference of about 0.3
|
||
"and not test_scalar_weighted "
|
||
;; XXX fails because of a difference of about 0.2
|
||
"and not test_unweighted "
|
||
|
||
;; XXX I cannot reproduce this in an interactive
|
||
;; Python session, because l2_norm works just fine.
|
||
"and not test_weighted " ;TestCosineSimilarity
|
||
"and not test_config " ;TestCosineSimilarity
|
||
|
||
;; The following test fails only in the build
|
||
;; container; skip it.
|
||
"and not test_selu "
|
||
;; The following test was found flaky and removed in
|
||
;; recent versions.
|
||
"and not test_stateful_metrics"))))))))
|
||
(propagated-inputs
|
||
(list python-h5py
|
||
python-keras-applications
|
||
python-keras-preprocessing
|
||
python-numpy
|
||
python-pydot
|
||
python-pyyaml
|
||
python-scipy
|
||
python-six
|
||
tensorflow
|
||
graphviz))
|
||
(native-inputs
|
||
(list python-flaky
|
||
python-markdown
|
||
python-pandas
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-pytest-pep8
|
||
python-pytest-timeout
|
||
python-pytest-xdist
|
||
python-pyux
|
||
python-sphinx
|
||
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
|
||
(list googletest))
|
||
(inputs
|
||
(append (list openssl-1.1)
|
||
(if (supported-package? rdma-core)
|
||
(list rdma-core)
|
||
'())))
|
||
(arguments
|
||
(list #:configure-flags #~'("-DBUILD_SHARED_LIBS=ON"
|
||
"-DBUILD_TEST=1"
|
||
#$@(if (this-package-input "rdma-core")
|
||
#~("-DUSE_IBVERBS=ON")
|
||
#~()))
|
||
#: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-tensorly
|
||
(package
|
||
(name "python-tensorly")
|
||
(version "0.8.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tensorly/tensorly")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"184mvs1gwycsh2f8jgdyc3jyhiylbn4xw2srpjd264dz2l9ms2l7"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list
|
||
;; These tests fail due to missing example, documentation, or tutorial files.
|
||
"--ignore=doc/sphinx_ext/sphinx_gallery/tests/test_gen_rst.py"
|
||
;; XXX There is no "get_marker" method.
|
||
"--ignore=doc/sphinx_ext/sphinx_gallery/tests/test_gen_gallery.py"
|
||
"-k"
|
||
(string-append
|
||
;; tutorials/plot_parse.py is not included
|
||
"not test_jupyter_notebook"
|
||
;; nor is examples/plot_quantum.py
|
||
" and not test_file_is_generated"))))
|
||
(propagated-inputs (list python-jsmin python-numpy python-scipy))
|
||
(native-inputs (list python-pytest python-pytest-cov python-sphinx))
|
||
(home-page "https://github.com/tensorly/tensorly")
|
||
(synopsis "Tensor learning in Python")
|
||
(description
|
||
"This is a Python library that aims at making tensor learning simple and
|
||
accessible. It allows performing tensor decomposition, tensor learning and
|
||
tensor algebra easily. Its backend system allows seamlessly perform
|
||
computation with NumPy, PyTorch, JAX, MXNet, TensorFlow or CuPy and run
|
||
methodxs at scale on CPU or GPU.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-umap-learn
|
||
(package
|
||
(name "python-umap-learn")
|
||
(version "0.5.5")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ;no tests in pypi release
|
||
(uri (git-reference
|
||
(url "https://github.com/lmcinnes/umap")
|
||
(commit (string-append "release-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0ijyiaqycynwj1383cxp519c765gjbg1f6fjwbvqj1gims710w3d"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
;; Numba needs a writable dir to cache functions.
|
||
(add-before 'check 'set-numba-cache-dir
|
||
(lambda _
|
||
(setenv "NUMBA_CACHE_DIR" "/tmp"))))))
|
||
(native-inputs (list python-pytest))
|
||
(propagated-inputs
|
||
(list python-numba
|
||
python-numpy
|
||
python-pynndescent
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-tqdm))
|
||
(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 visualization 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
|
||
(list cpuinfo
|
||
fp16
|
||
fxdiv
|
||
psimd
|
||
pthreadpool
|
||
googletest))
|
||
(native-inputs
|
||
(list python python-peachpy python-six))
|
||
(license license:bsd-2))))
|
||
|
||
(define-public xnnpack
|
||
;; There's currently no tag on this repo.
|
||
(let ((version "0.0")
|
||
(commit "ae108ef49aa5623b896fc93d4298c49d1750d9ba")
|
||
(revision "2"))
|
||
(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
|
||
"0q68q2jxiiiblx45q4337k13ppgh5vqjwrwznchcnpb8hawjj3zl"))
|
||
(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
|
||
(list cpuinfo
|
||
pthreadpool
|
||
googletest
|
||
googlebenchmark
|
||
fxdiv
|
||
fp16
|
||
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 xnnpack-for-torch2
|
||
;; There's currently no tag on this repo.
|
||
(let ((version "0.0")
|
||
(commit "51a987591a6fc9f0fc0707077f53d763ac132cbf")
|
||
(revision "3"))
|
||
(package
|
||
(inherit xnnpack)
|
||
(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
|
||
"1rzby82xq8d0rl1d148yz88jh9cpsw5c8b2yw7yg39mi7qmr55rm"))
|
||
(patches (search-patches "xnnpack-for-torch2-system-libraries.patch"))))
|
||
(arguments
|
||
(list
|
||
#:tests? #false
|
||
#:configure-flags '(list "-DXNNPACK_USE_SYSTEM_LIBS=YES"
|
||
"-DBUILD_SHARED_LIBS=ON"
|
||
"-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
|
||
"-DXNNPACK_LIBRARY_TYPE=shared"
|
||
"-DXNNPACK_BUILD_TESTS=FALSE" ;FIXME: see below
|
||
"-DXNNPACK_BUILD_BENCHMARKS=FALSE"))))))
|
||
|
||
;; Please also update python-torchvision when updating this package.
|
||
(define-public python-pytorch
|
||
(package
|
||
(name "python-pytorch")
|
||
(version "1.13.1")
|
||
(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
|
||
"17yxjzwp4zp75fz7czgz9acijzw7dpyqcza50v8y1x7hfg2gw369"))
|
||
(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"))
|
||
(substitute* "functorch/CMakeLists.txt"
|
||
(("\\$\\{_rpath_portable_origin\\}/../torch/lib")
|
||
"$ORIGIN/../torch/lib"))))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
'(#:phases (modify-phases %standard-phases
|
||
(add-before 'build 'use-system-libraries
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Tell 'setup.py' to let 'CMakeLists.txt' know that we
|
||
;; want to use "system libraries" instead of the bundled
|
||
;; ones.
|
||
(setenv "USE_SYSTEM_LIBS" "1")
|
||
|
||
(substitute* "cmake/Dependencies.cmake"
|
||
(("if\\(USE_SYSTEM_BIND11\\)")
|
||
"if(TRUE)"))
|
||
|
||
;; XXX: Disable that for simplicity for now.
|
||
(setenv "USE_FBGEMM" "0")))
|
||
(add-before 'build 'make-things-writable
|
||
(lambda _
|
||
;; The 'build_caffe2' function in
|
||
;; 'tools/build_pytorch_libs.py', called from the
|
||
;; top-level 'setup.py', needs write access to this
|
||
;; directory.
|
||
(for-each make-file-writable
|
||
(find-files "caffe2/proto" "."
|
||
#:directories? #t))))
|
||
(replace 'check
|
||
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
|
||
;; Run the test suite following the instructions in
|
||
;; 'CONTRIBUTING.md'. XXX: Unfortunately this doesn't
|
||
;; work, unless you set GUIX_PYTHONPATH presumably.
|
||
(when tests?
|
||
(add-installed-pythonpath inputs outputs)
|
||
(invoke "python" "test/run_test.py"))))
|
||
(add-after 'install 'remove-test-executables
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
;; Remove test executables, but keep other executables
|
||
;; such as 'torch_shm_manager' and and .so files such as
|
||
;; 'libtorch_global_deps.so'.
|
||
(let ((python-site (site-packages inputs outputs)))
|
||
(for-each delete-file
|
||
(find-files python-site
|
||
"(^test_cpp_rpc|_test)$")))))
|
||
(add-after 'install 'remove-caffe2-onnx-scripts
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin")))
|
||
;; Remove 'convert-caffe2-to-onnx' and
|
||
;; 'convert-onnx-to-caffe2': they seem to be
|
||
;; deprecated and they cause a failure of the
|
||
;; 'sanity-check' phase:
|
||
;;
|
||
;; ImportError: cannot import name 'metanet_pb2' from partially initialized module 'caffe2.proto' (most likely due to a circular import)
|
||
(for-each delete-file
|
||
(find-files bin "^convert-.*caffe2"))
|
||
|
||
(substitute* (find-files out "^entry_points\\.txt$")
|
||
(("^convert-.*" all)
|
||
(string-append "# " all "\n")))))))
|
||
|
||
;; XXX: Tests attempt to download data such as
|
||
;; <https://raw.githubusercontent.com/pytorch/test-infra/master/stats/slow-tests.json>.
|
||
;; We're also missing some Python modules, such as expecttest.
|
||
#:tests? #f))
|
||
(native-inputs
|
||
(list cmake ninja))
|
||
(inputs
|
||
(list eigen
|
||
;; ("fmt" ,fmt)
|
||
fp16
|
||
gemmlowp
|
||
googletest
|
||
googlebenchmark
|
||
gloo
|
||
nnpack
|
||
openblas
|
||
openmpi
|
||
pthreadpool
|
||
protobuf
|
||
pybind11
|
||
sleef
|
||
xnnpack
|
||
zstd))
|
||
(propagated-inputs
|
||
(list python-astunparse
|
||
python-click
|
||
python-numpy
|
||
python-pyyaml
|
||
python-cffi
|
||
python-typing-extensions
|
||
python-future
|
||
python-six
|
||
python-requests
|
||
onnx ;propagated for its Python modules
|
||
onnx-optimizer
|
||
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-pytorch-for-r-torch
|
||
(package
|
||
(inherit python-pytorch)
|
||
(name "python-pytorch")
|
||
(version "2.0.1")
|
||
(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
|
||
"14m7v54zyd2qg2xk9mqdpbf4ps7091mdzinzh4vq9p5k4bpznj65"))
|
||
(patches (search-patches "python-pytorch2-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"))
|
||
(substitute* "caffe2/CMakeLists.txt"
|
||
(("target_link_libraries\\(\\$\\{test_name\\}_\\$\\{CPU_CAPABILITY\\} c10 sleef gtest_main\\)")
|
||
"target_link_libraries(${test_name}_${CPU_CAPABILITY} c10 sleef gtest gtest_main)"))
|
||
(substitute* "functorch/CMakeLists.txt"
|
||
(("\\$\\{_rpath_portable_origin\\}/../torch/lib")
|
||
"$ORIGIN/../torch/lib"))))))
|
||
(inputs
|
||
(modify-inputs (package-inputs python-pytorch)
|
||
(replace "xnnpack" xnnpack-for-torch2)))
|
||
(propagated-inputs
|
||
(modify-inputs (package-propagated-inputs python-pytorch)
|
||
(append python-filelock
|
||
python-jinja2
|
||
python-networkx
|
||
python-opt-einsum
|
||
python-sympy)
|
||
(replace "onnx" onnx-for-torch2)
|
||
(replace "onnx-optimizer" onnx-optimizer-for-torch2)))))
|
||
|
||
(define-public python-pytorch-geometric
|
||
(package
|
||
(name "python-pytorch-geometric")
|
||
(version "2.4.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pyg-team/pytorch_geometric/")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0hrs579asjsph16hyb4ablkbgfwd5j9y5s6ny7ahn3qrbkl2ji1g"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; Hangs with AttributeError: 'NoneType' object has no attribute 'rpc_async'
|
||
'(list "--ignore=test/distributed/test_rpc.py"
|
||
;; A message passing jinja template is missing
|
||
"--ignore=test/nn/conv/test_message_passing.py"
|
||
"--ignore=test/nn/test_sequential.py"
|
||
"--ignore=test/nn/models/test_basic_gnn.py"
|
||
;; These all fail with a size mismatch error such as
|
||
;; RuntimeError: shape '[-1, 2, 1, 1]' is invalid for input of size 3
|
||
"--ignore=test/explain/algorithm/test_captum_explainer.py"
|
||
"-k" (string-append
|
||
;; Permissions error
|
||
"not test_packaging"
|
||
;; This can fail due to accuracy problems
|
||
" and not test_gdc"
|
||
;; These refuse to be run on CPU and really want a GPU
|
||
" and not test_add_random_walk_pe"
|
||
" and not test_asap"
|
||
" and not test_two_hop"))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'delete-top-level-directories
|
||
(lambda _
|
||
;; The presence of these directories confuses the pyproject build
|
||
;; system.
|
||
(for-each delete-file-recursively
|
||
'("conda" "docker" "graphgym")))))))
|
||
(propagated-inputs
|
||
(list onnx
|
||
python-captum
|
||
python-graphviz
|
||
python-h5py
|
||
python-jinja2
|
||
python-matplotlib
|
||
python-networkx
|
||
python-numba
|
||
python-numpy
|
||
python-opt-einsum
|
||
python-pandas
|
||
python-protobuf
|
||
python-psutil
|
||
python-pyparsing
|
||
python-pytorch-lightning
|
||
python-rdflib
|
||
python-requests
|
||
python-scikit-image
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-statsmodels
|
||
python-sympy
|
||
python-tabulate
|
||
python-torchmetrics
|
||
python-tqdm))
|
||
(native-inputs
|
||
(list python-flit-core
|
||
python-pytest
|
||
python-pytest-cov))
|
||
(home-page "https://pyg.org")
|
||
(synopsis "Graph Neural Network library for PyTorch")
|
||
(description
|
||
"PyG is a library built upon PyTorch to easily write and train Graph
|
||
Neural Networks for a wide range of applications related to structured data.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-lightning-cloud
|
||
(package
|
||
(name "python-lightning-cloud")
|
||
(version "0.5.34")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "lightning_cloud" version))
|
||
(sha256
|
||
(base32
|
||
"0mqrhq3s23mn8n4i0q791pshn3dgplp0h9ny0pmmp798q0798dzs"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-click
|
||
python-fastapi-for-pytorch-lightning
|
||
python-multipart
|
||
python-pyjwt
|
||
python-requests
|
||
python-rich
|
||
python-six
|
||
python-urllib3
|
||
python-uvicorn
|
||
python-websocket-client))
|
||
(home-page "https://lightning.ai")
|
||
(synopsis "Lightning Cloud command line client")
|
||
(description "This package provides a command line interface for Lightning
|
||
AI services.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-lightning-utilities
|
||
(package
|
||
(name "python-lightning-utilities")
|
||
(version "0.8.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "lightning-utilities" version))
|
||
(sha256
|
||
(base32
|
||
"084pn8fizxrcn1699jb8x2jsg4wcx01l65bwxpgnq0kzqp3rapcf"))))
|
||
(build-system python-build-system)
|
||
(propagated-inputs (list python-importlib-metadata python-packaging
|
||
python-typing-extensions))
|
||
(native-inputs (list python-coverage))
|
||
(home-page "https://github.com/Lightning-AI/utilities")
|
||
(synopsis "PyTorch Lightning sample project")
|
||
(description "This package provides common Python utilities and GitHub
|
||
Actions for the Lightning suite of libraries.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-captum
|
||
(package
|
||
(name "python-captum")
|
||
(version "0.7.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pytorch/captum")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0bgfwnlsi50hbmknn7qljiy93fi6ggwz3k7yk9kj7s37mhzaylym"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "-k"
|
||
;; These two tests (out of more than 1000 tests) fail because of
|
||
;; accuracy problems.
|
||
"not test_softmax_classification_batch_multi_target\
|
||
and not test_softmax_classification_batch_zero_baseline")))
|
||
(propagated-inputs
|
||
(list python-matplotlib python-numpy python-pytorch python-tqdm))
|
||
(native-inputs (list jupyter
|
||
python-annoy
|
||
python-black
|
||
python-flake8
|
||
python-flask
|
||
python-flask-compress
|
||
python-ipython
|
||
python-ipywidgets
|
||
python-mypy
|
||
python-parameterized
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-scikit-learn))
|
||
(home-page "https://captum.ai")
|
||
(synopsis "Model interpretability for PyTorch")
|
||
(description "Captum is a model interpretability and understanding library
|
||
for PyTorch. Captum contains general purpose implementations of integrated
|
||
gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models.
|
||
It has quick integration for models built with domain-specific libraries such
|
||
as torchvision, torchtext, and others.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-readchar
|
||
(package
|
||
(name "python-readchar")
|
||
(version "4.0.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "readchar" version))
|
||
(sha256
|
||
(base32
|
||
"09n8vl2jjbnbnrzfvkynijrnwrqvc91bb2267zg8r261sz15d908"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
;; This one file requires the msvcrt module, which we don't have.
|
||
(add-after 'unpack 'delete-windows-file
|
||
(lambda _
|
||
(delete-file "readchar/_win_read.py"))))))
|
||
(propagated-inputs (list python-setuptools))
|
||
(home-page "https://github.com/magmax/python-readchar")
|
||
(synopsis "Library to easily read single chars and key strokes")
|
||
(description "This package provides a Python library to easily read single
|
||
characters and key strokes.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-inquirer
|
||
(package
|
||
(name "python-inquirer")
|
||
(version "3.1.3")
|
||
;; Pypi has no tests.
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/magmax/python-inquirer")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0kp6a0535n9ra5sk8bmb5qvhrv0fbn1zawydi0fkb7104jqcfrzc"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs
|
||
(list python-blessed python-editor python-readchar))
|
||
(native-inputs
|
||
(list python-poetry-core python-pexpect python-pytest))
|
||
(home-page "https://github.com/magmax/python-inquirer")
|
||
(synopsis "Collection of common interactive command line user interfaces")
|
||
(description
|
||
"Inquirer should ease the process of asking end user questions, parsing,
|
||
validating answers, managing hierarchical prompts and providing error
|
||
feedback.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-pytorch-lightning
|
||
(package
|
||
(name "python-pytorch-lightning")
|
||
(version "2.0.2")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Lightning-AI/lightning")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1w4lajiql4y5nnhqf6i5wii1mrwnhp5f4bzbwdzb5zz0d0lysb1i"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "-m" "not cloud and not tpu" "tests/tests_pytorch"
|
||
;; we don't have onnxruntime
|
||
"--ignore=tests/tests_pytorch/models/test_onnx.py"
|
||
|
||
;; We don't have tensorboard, so we skip all those tests that
|
||
;; require it for logging.
|
||
"--ignore=tests/tests_pytorch/checkpointing/test_model_checkpoint.py"
|
||
"--ignore=tests/tests_pytorch/loggers/test_all.py"
|
||
"--ignore=tests/tests_pytorch/loggers/test_logger.py"
|
||
"--ignore=tests/tests_pytorch/loggers/test_tensorboard.py"
|
||
"--ignore=tests/tests_pytorch/models/test_cpu.py"
|
||
"--ignore=tests/tests_pytorch/models/test_hparams.py"
|
||
"--ignore=tests/tests_pytorch/models/test_restore.py"
|
||
"--ignore=tests/tests_pytorch/profilers/test_profiler.py"
|
||
"--ignore=tests/tests_pytorch/trainer/flags/test_fast_dev_run.py"
|
||
"--ignore=tests/tests_pytorch/trainer/logging_/test_eval_loop_logging.py"
|
||
"--ignore=tests/tests_pytorch/trainer/logging_/test_train_loop_logging.py"
|
||
"--ignore=tests/tests_pytorch/trainer/properties/test_loggers.py"
|
||
"--ignore=tests/tests_pytorch/trainer/properties/test_log_dir.py"
|
||
"--ignore=tests/tests_pytorch/trainer/test_trainer.py"
|
||
|
||
;; This needs internet access
|
||
"--ignore=tests/tests_pytorch/helpers/test_models.py"
|
||
"--ignore=tests/tests_pytorch/helpers/test_datasets.py"
|
||
"--ignore=tests/tests_pytorch/helpers/datasets.py"
|
||
|
||
;; We have no legacy checkpoints
|
||
"--ignore=tests/tests_pytorch/checkpointing/test_legacy_checkpoints.py"
|
||
|
||
;; TypeError: _FlakyPlugin._make_test_flaky() got an unexpected keyword argument 'reruns'
|
||
"--ignore=tests/tests_pytorch/models/test_amp.py"
|
||
"--ignore=tests/tests_pytorch/profilers/test_profiler.py"
|
||
|
||
"--ignore=tests/tests_pytorch/graveyard/test_legacy_import_unpickler.py"
|
||
|
||
"-k"
|
||
(string-append
|
||
;; We don't have tensorboard
|
||
"not test_property_logger"
|
||
" and not test_cli_logger_shorthand"
|
||
;; Something wrong with Flaky
|
||
" and not test_servable_module_validator_with_trainer"))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-version-detection
|
||
(lambda _
|
||
;; We do have pytorch 1.13.1, but the version comparison fails.
|
||
(substitute* "src/lightning/fabric/utilities/imports.py"
|
||
(("_TORCH_GREATER_EQUAL_1_13 =.*")
|
||
"_TORCH_GREATER_EQUAL_1_13 = True\n"))))
|
||
(add-before 'build 'pre-build
|
||
(lambda _ (setenv "PACKAGE_NAME" "lightning")))
|
||
(add-after 'install 'pre-build-pytorch
|
||
(lambda _
|
||
;; pyproject-build-system only tolerates unicycles.
|
||
(for-each delete-file (find-files "dist" "\\.whl"))
|
||
(setenv "PACKAGE_NAME" "pytorch")))
|
||
(add-after 'pre-build-pytorch 'build-pytorch
|
||
(assoc-ref %standard-phases 'build))
|
||
(add-after 'build-pytorch 'install-pytorch
|
||
(assoc-ref %standard-phases 'install))
|
||
(add-before 'check 'pre-check
|
||
(lambda _
|
||
;; We don't have Tensorboard
|
||
(substitute* "tests/tests_pytorch/test_cli.py"
|
||
((" TensorBoardLogger\\(\".\"\\)") "")))))))
|
||
(propagated-inputs
|
||
(list python-arrow
|
||
python-beautifulsoup4
|
||
python-croniter
|
||
python-dateutils
|
||
python-deepdiff
|
||
python-fastapi-for-pytorch-lightning
|
||
python-fsspec
|
||
python-inquirer
|
||
python-jsonargparse
|
||
python-lightning-cloud
|
||
python-lightning-utilities
|
||
python-numpy
|
||
python-packaging
|
||
python-pytorch
|
||
python-pyyaml
|
||
python-starsessions-for-pytorch-lightning
|
||
python-torchmetrics
|
||
python-torchvision
|
||
python-tqdm
|
||
python-traitlets
|
||
python-typing-extensions))
|
||
(native-inputs
|
||
(list python-aiohttp
|
||
python-cloudpickle
|
||
python-coverage
|
||
python-flaky
|
||
python-pympler
|
||
python-pytest
|
||
python-psutil
|
||
python-requests-mock
|
||
python-scikit-learn))
|
||
(home-page "https://lightning.ai/")
|
||
(synopsis "Deep learning framework to train, deploy, and ship AI products")
|
||
(description
|
||
"PyTorch Lightning is just organized PyTorch; Lightning disentangles
|
||
PyTorch code to decouple the science from the engineering.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-torchmetrics
|
||
(package
|
||
(name "python-torchmetrics")
|
||
(version "0.11.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "torchmetrics" version))
|
||
(sha256
|
||
(base32
|
||
"150lcy6c20n42rwxl4d3m1b8s4js9ddds5wh3685vmjdnha5mr0z"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs
|
||
(list python-numpy python-packaging python-pytorch
|
||
python-typing-extensions))
|
||
(native-inputs
|
||
(list python-cloudpickle
|
||
python-coverage
|
||
python-fire
|
||
python-mir-eval
|
||
python-mypy
|
||
python-pandas
|
||
python-psutil
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-pytest-doctestplus
|
||
python-pytest-rerunfailures
|
||
python-pytest-timeout
|
||
python-requests
|
||
python-scikit-image
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-types-protobuf
|
||
python-types-setuptools))
|
||
(home-page "https://github.com/Lightning-AI/metrics")
|
||
(synopsis "Machine learning metrics for PyTorch applications")
|
||
(description "TorchMetrics is a collection of 100+ PyTorch metrics
|
||
implementations and an easy-to-use API to create custom metrics. It offers:
|
||
|
||
@itemize
|
||
@item A standardized interface to increase reproducibility
|
||
@item Reduces boilerplate
|
||
@item Automatic accumulation over batches
|
||
@item Metrics optimized for distributed-training
|
||
@item Automatic synchronization between multiple devices
|
||
@end itemize
|
||
")
|
||
(license license:asl2.0)))
|
||
|
||
;; Keep this in sync with python-pytorch
|
||
(define-public python-torchvision
|
||
(package
|
||
(name "python-torchvision")
|
||
(version "0.15.2")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pytorch/vision")
|
||
(commit (string-append "v" version))
|
||
(recursive? #t)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1cq2s13vkgg9rljjbrm4g33yxq7q5zqp7f4xm5cq624gvs0wxmi8"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:tests? #false)) ;the test suite is expensive and there is no easy
|
||
;way to subset it.
|
||
(inputs
|
||
(list libpng
|
||
libjpeg-turbo))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-typing-extensions
|
||
python-requests
|
||
python-pillow
|
||
python-pillow-simd
|
||
python-pytorch))
|
||
(native-inputs
|
||
(list which python-pytest))
|
||
(home-page "https://pytorch.org/vision/stable/index.html")
|
||
(synopsis "Datasets, transforms and models specific to computer vision")
|
||
(description
|
||
"The torchvision package consists of popular datasets, model architectures,
|
||
and common image transformations for computer vision.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-torchfile
|
||
(package
|
||
(name "python-torchfile")
|
||
(version "0.1.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "torchfile" version))
|
||
(sha256
|
||
(base32
|
||
"0vhklj6krl9r0kdynb4kcpwp8y1ihl2zw96byallay3k9c9zwgd5"))))
|
||
(build-system python-build-system)
|
||
(arguments '(#:tests? #false)) ;there are no tests
|
||
(propagated-inputs
|
||
(list python-numpy))
|
||
(home-page "https://github.com/bshillingford/python-torchfile")
|
||
(synopsis "Torch7 binary serialized file parser")
|
||
(description "This package enables you to deserialize Lua torch-serialized objects from
|
||
Python.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-hmmlearn
|
||
(package
|
||
(name "python-hmmlearn")
|
||
(version "0.2.8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "hmmlearn" version))
|
||
(sha256
|
||
(base32
|
||
"1yd5l9ra37mks41mn5bigav7xpb161a9yqlcnz4ir076vkik2sb9"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(with-directory-excursion (string-append #$output "/lib")
|
||
(invoke "python" "-m" "pytest"))))))))
|
||
(propagated-inputs
|
||
(list pybind11
|
||
python-numpy
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-setuptools-scm))
|
||
(native-inputs
|
||
(list 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)))
|
||
|
||
;; Keep this in sync with the r-torch package.
|
||
(define-public liblantern
|
||
;; There has been no release or tagged commit for r-torch 0.12.0. The
|
||
;; selected commit corresponds to the 0.12.0 release.
|
||
(let ((commit "4d83bd087be581f7db321c27f55897ff021d2537")
|
||
(revision "1"))
|
||
(package
|
||
(name "liblantern")
|
||
(version (git-version "0.11.0" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mlverse/torch")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1xxc6vr7sr2mg0va0hc2fs4f6v5b78mx43dp2shzzbcgw90mgpvk"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:tests? #false ;no test target
|
||
#:phases
|
||
(let ((python-version (version-major+minor (package-version python))))
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "src/lantern")))
|
||
(add-after 'chdir 'do-not-download-binaries
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(substitute* "CMakeLists.txt"
|
||
(("find_package\\(Torch.*") "set(TORCH_CXX_FLAGS \"-ltorch\")\n")
|
||
(("retrieve_lib\\(.*") ""))
|
||
(let ((site-packages (string-append "/lib/python"
|
||
#$python-version
|
||
"/site-packages")))
|
||
(setenv "LIBRARY_PATH"
|
||
(string-append
|
||
(search-input-directory
|
||
inputs (string-append site-packages "/torch/lib"))
|
||
":" (or (getenv "LIBRARY_PATH") "")))
|
||
(setenv "CPLUS_INCLUDE_PATH"
|
||
(string-append
|
||
(search-input-directory
|
||
inputs (string-append
|
||
site-packages "/torch/include/torch/csrc/api/include/"))
|
||
":"
|
||
(search-input-directory
|
||
inputs (string-append site-packages "/torch/include/"))
|
||
":"
|
||
(or (getenv "CPLUS_INCLUDE_PATH") "")))
|
||
(setenv "C_INCLUDE_PATH"
|
||
(string-append
|
||
(search-input-directory
|
||
inputs (string-append site-packages "/torch/include/"))
|
||
":"
|
||
(or (getenv "C_INCLUDE_PATH") ""))))))
|
||
(replace 'install
|
||
(lambda _
|
||
(install-file
|
||
"../build/liblantern.so"
|
||
(string-append #$output "/lib"))
|
||
(copy-recursively
|
||
"../lantern/include"
|
||
(string-append #$output "/include"))))))))
|
||
(inputs (list python-pytorch-for-r-torch))
|
||
(home-page "https://github.com/mlverse/torch/")
|
||
(synopsis "C API to libtorch")
|
||
(description
|
||
"Lantern provides a C API to the libtorch machine learning library.")
|
||
(license license:expat))))
|
||
|
||
(define-public python-lap
|
||
(package
|
||
(name "python-lap")
|
||
(version "0.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "lap" version))
|
||
(sha256
|
||
(base32
|
||
"0fqfxpq4jg9h4wxjw540gjmvfg1ccc1nssk7i9njg7qfdybxknn4"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'build
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(invoke "python" "setup.py" "build"
|
||
"--cpu-baseline=sse2")))
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
;; The tests must be run from elsewhere.
|
||
(mkdir-p "/tmp/test")
|
||
(copy-recursively "lap/tests" "/tmp/test")
|
||
(with-directory-excursion "/tmp/test"
|
||
(invoke "pytest" "-vv"))))))))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-scipy))
|
||
(native-inputs
|
||
(list python-cython python-pytest))
|
||
(home-page "https://github.com/gatagat/lap")
|
||
(synopsis "Linear Assignment Problem solver (LAPJV/LAPMOD)")
|
||
(description "Lap is a linear assignment problem solver using Jonker-Volgenant
|
||
algorithm for dense (LAPJV) or sparse (LAPMOD) matrices.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public python-visdom
|
||
(package
|
||
(name "python-visdom")
|
||
(version "0.1.8.9")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "visdom" version))
|
||
(sha256
|
||
(base32
|
||
"09kiczx2i5asqsv214fz7sx8wlyldgbqvxwrd0alhjn24cvx4fn7"))))
|
||
(build-system python-build-system)
|
||
(propagated-inputs
|
||
(list python-jsonpatch
|
||
python-numpy
|
||
python-pillow
|
||
python-pyzmq
|
||
python-requests
|
||
python-scipy
|
||
python-six
|
||
python-torchfile
|
||
python-tornado
|
||
python-websocket-client))
|
||
(home-page "https://github.com/fossasia/visdom")
|
||
(synopsis "Visualizations of live, rich data for Torch and Numpy")
|
||
(description
|
||
"This package provides a tool for visualizing live, rich data for Torch
|
||
and Numpy.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-pyro-api
|
||
(package
|
||
(name "python-pyro-api")
|
||
(version "0.1.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pyro-api" version))
|
||
(sha256
|
||
(base32
|
||
"086r2h6x9i5d9ayl1x65lx6p84rlydzsn8xingxc588ab3ch1fd1"))))
|
||
(build-system python-build-system)
|
||
(arguments '(#:tests? #false)) ;requires pyro
|
||
(native-inputs
|
||
(list python-flake8
|
||
python-ipython
|
||
python-pytest
|
||
python-sphinx
|
||
python-sphinx-rtd-theme))
|
||
(home-page "https://github.com/pyro-ppl/pyro-api")
|
||
(synopsis "Generic API for dispatch to Pyro backends")
|
||
(description "This package provides a generic API for dispatch to Pyro backends.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-pyro-ppl
|
||
(package
|
||
(name "python-pyro-ppl")
|
||
(version "1.8.6")
|
||
;; The sources on pypi don't include tests.
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pyro-ppl/pyro")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0n1vsih99pvswcaygdxkc6kq6r48ny130z6ca8pp3281396r2ykw"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "-vv" "--stage=unit"
|
||
;; This tests features that are only implemented when non-free
|
||
;; software is available (Intel MKL or CUDA).
|
||
"--ignore=tests/distributions/test_spanning_tree.py"
|
||
"--ignore=tests/infer/mcmc/test_mcmc_api.py"
|
||
;; This test fails sometimes.
|
||
"--ignore=tests/optim/test_optim.py"
|
||
;; Four test_gamma_elbo tests fail with bad values for unknown
|
||
;; reasons.
|
||
"--ignore=tests/distributions/test_rejector.py"
|
||
;; This looks like a test system failure. All of these fail
|
||
;; because x is an array of functions, not an array of numbers.
|
||
"-k" "not test_sample")))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-opt-einsum
|
||
python-pyro-api
|
||
python-pytorch
|
||
python-tqdm))
|
||
(native-inputs
|
||
(list ninja
|
||
jupyter
|
||
python-black
|
||
python-flake8
|
||
python-graphviz
|
||
python-isort
|
||
python-lap
|
||
python-matplotlib
|
||
python-mypy
|
||
python-nbformat
|
||
python-nbsphinx
|
||
python-nbstripout
|
||
python-nbval
|
||
python-pandas
|
||
python-pillow
|
||
python-pypandoc
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-pytest-xdist
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-seaborn
|
||
python-sphinx
|
||
python-sphinx-rtd-theme
|
||
python-torchvision
|
||
python-visdom
|
||
python-wget
|
||
python-yapf))
|
||
(home-page "https://pyro.ai")
|
||
(synopsis "Python library for probabilistic modeling and inference")
|
||
(description
|
||
"This package provides a Python library for probabilistic modeling and
|
||
inference.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-linear-operator
|
||
(package
|
||
(name "python-linear-operator")
|
||
(version "0.5.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "linear_operator" version))
|
||
(sha256
|
||
(base32
|
||
"03drb4hn9nn8jrqd9vbalihhahgpdm956hbs05bix7svradhknaw"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-jaxtyping
|
||
python-pytorch
|
||
python-scipy
|
||
python-typeguard))
|
||
(native-inputs (list python-flake8
|
||
python-flake8-print
|
||
python-pytest
|
||
python-setuptools-scm
|
||
python-twine))
|
||
(home-page "https://github.com/cornellius-gp/linear_operator/")
|
||
(synopsis "Linear operator implementation")
|
||
(description "LinearOperator is a PyTorch package for abstracting away the
|
||
linear algebra routines needed for structured matrices (or operators).")
|
||
(license license:expat)))
|
||
|
||
(define-public python-gpytorch
|
||
(package
|
||
(name "python-gpytorch")
|
||
(version "1.11")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "gpytorch" version))
|
||
(sha256
|
||
(base32
|
||
"0q17bml53vixk3cwj3p893809927hz81fprwsmxpxqv5i4mvgyvj"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:test-flags
|
||
;; The error message in test_t_matmul_matrix suggests the error may
|
||
;; be due to a bug in gpytorch. test_deprecated_methods fails with
|
||
;; an AssertionError.
|
||
#~(list "-k" (string-append "not test_deprecated_methods"
|
||
" and not test_t_matmul_matrix"))))
|
||
(propagated-inputs (list python-linear-operator python-scikit-learn))
|
||
(native-inputs (list python-coverage
|
||
python-flake8
|
||
python-flake8-print
|
||
python-nbval
|
||
python-pytest
|
||
python-twine))
|
||
(home-page "https://gpytorch.ai")
|
||
(synopsis "Implementation of Gaussian Processes in PyTorch")
|
||
(description
|
||
"GPyTorch is a Gaussian process library implemented using PyTorch.")
|
||
(license license:expat)))
|
||
|
||
(define-public vosk-api
|
||
(let* ((openfst openfst-for-vosk)
|
||
(kaldi kaldi-for-vosk))
|
||
(package
|
||
(name "vosk-api")
|
||
(version "0.3.43")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/alphacep/vosk-api")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0xmp8i140c2hd3rj9dap8a2rnsvzb1k9hnqm12xzbaxrw73rkc29"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
#:tests? #f
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "src")))
|
||
(replace 'configure
|
||
(lambda _
|
||
(let* ((lapack #$(this-package-input "lapack"))
|
||
(openfst #$(this-package-input "openfst"))
|
||
(openblas #$(this-package-input "openblas"))
|
||
(kaldi #$(this-package-input "kaldi")))
|
||
(substitute* "./Makefile"
|
||
(("USE_SHARED\\?=0")
|
||
"USE_SHARED?=1")
|
||
(("-DFST_NO_DYNAMIC_LINKING")
|
||
"")
|
||
(("-lopenblas -llapack -lblas -lf2c")
|
||
(string-append
|
||
"-L" openblas "/lib " "-lopenblas "
|
||
"-L" lapack "/lib " "-llapack -lblas "))
|
||
(("-lfst -lfstngram")
|
||
(string-append
|
||
"-L" openfst "/lib " "-lfst -lfstngram "))
|
||
(("\\$\\(HOME\\)\\/travis\\/kaldi")
|
||
(string-append kaldi "/include"))
|
||
(("\\$\\(KALDI_ROOT\\)\\/tools\\/openfst")
|
||
openfst)
|
||
(("\\$\\(KALDI_ROOT\\)\\/tools\\/OpenBLAS\\/install")
|
||
openblas)
|
||
(("\\$\\(KALDI_ROOT\\)\\/libs")
|
||
(string-append kaldi "/lib"))))))
|
||
(replace 'install
|
||
(lambda _
|
||
(let* ((lib (string-append #$output "/lib"))
|
||
(src (string-append #$output "/src")))
|
||
(mkdir-p lib)
|
||
(mkdir-p src)
|
||
(install-file "libvosk.so" lib)
|
||
(for-each
|
||
(lambda (x) (install-file x src))
|
||
(find-files "." "\\.h$"))))))))
|
||
(inputs (list kaldi openfst lapack openblas))
|
||
(home-page "https://alphacephei.com/vosk")
|
||
(synopsis "Speech recognition toolkit based on @code{kaldi}")
|
||
(description "\
|
||
This package provides a speech recognition toolkit based on @code{kaldi}. It
|
||
supports more than 20 languages and dialects - English, Indian English,
|
||
German, French, Spanish, Portuguese, Chinese, Russian, Turkish, Vietnamese,
|
||
Italian, Dutch, Catalan, Arabic, Greek, Farsi, Filipino, Ukrainian, Kazakh,
|
||
Swedish, Japanese, Esperanto, Hindi, Czech, Polish. The program works offline,
|
||
even on lightweight devices. Portable per-language models are about 50Mb each,
|
||
and there are much bigger and precise models available.
|
||
|
||
Vosk API provides a streaming API allowing to use it `on-the-fly' and bindings
|
||
for different programming languages. It allows quick reconfiguration of
|
||
vocabulary for better accuracy, and supports speaker identification beside
|
||
simple speech recognition.")
|
||
(license license:asl2.0))))
|
||
|
||
(define-public python-vosk
|
||
(package
|
||
(inherit vosk-api)
|
||
(name "python-vosk")
|
||
(build-system python-build-system)
|
||
(propagated-inputs
|
||
(list python-cffi python-requests python-tqdm python-srt python-websockets))
|
||
(inputs (list vosk-api))
|
||
(arguments
|
||
(list
|
||
#:tests? #f ;; TODO There are tests but not run through Makefile.
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'config
|
||
(lambda _
|
||
(chdir "python")
|
||
(setenv "VOSK_SOURCE" #$vosk-api)))
|
||
(add-before 'build 'from-abi-to-api
|
||
(lambda _
|
||
(substitute* "vosk_builder.py"
|
||
(("ffibuilder\\.set_source\\(\"vosk.vosk_cffi\", None\\)")
|
||
(string-append
|
||
"ffibuilder.set_source(\"vosk.vosk_cffi\", "
|
||
"r\"\"\"\n#include<vosk_api.h>\n#include<Python.h>\"\"\",\n\t"
|
||
"library_dirs=["
|
||
"'" #$vosk-api "/lib'"
|
||
"],\n\t"
|
||
"libraries=['vosk', 'python3.10'],\n\t"
|
||
"include_dirs=["
|
||
"'" #$vosk-api "/src'" "])")))
|
||
(substitute* "vosk/__init__.py"
|
||
(("_c = open_dll\\(\\)")
|
||
"")
|
||
(("_ffi")
|
||
"ffi")
|
||
(("from \\.vosk_cffi import ffi as ffi")
|
||
"from .vosk_cffi import ffi, lib")
|
||
(("_c\\.")
|
||
"lib.")))))))))
|
||
|
||
(define-public nerd-dictation
|
||
(let* ((commit "0eb44b7fd0927d69c92de5566e5807ed2c2e20b7")
|
||
(revision "1"))
|
||
(package
|
||
(name "nerd-dictation")
|
||
(version (git-version "0" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/ideasman42/nerd-dictation")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0frdpswv6w3cwj3c7wd5w8gj3s1hvpdwd48qhfhfxf7imahz9bqf"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
'(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _ (chdir "package/python"))))))
|
||
(propagated-inputs (list python-vosk))
|
||
(home-page "https://github.com/ideasman42/nerd-dictation")
|
||
(synopsis "Offline speech-to-text for desktop Linux")
|
||
(description "\
|
||
This package provides simple access speech to text for using in
|
||
Linux without being tied to a desktop environment, using the @code{vosk-api}.
|
||
The user configuration lets you manipulate text using Python string
|
||
operations. It has zero overhead, as this relies on manual activation and
|
||
there are no background processes. Dictation is accessed manually with
|
||
@code{nerd-dictation begin} and @code{nerd-dictation end} commands.")
|
||
(license license:gpl2+))))
|
||
|
||
(define (nerd-dictation-gexp input-name output-name bash nerd-dictation)
|
||
(with-imported-modules '((guix build utils))
|
||
#~(begin
|
||
(use-modules (guix build utils))
|
||
|
||
(let* ((exe (string-append #$output "/bin/nerd-dictation"))
|
||
(nerd-dictation-exe
|
||
#$(file-append nerd-dictation "/bin/nerd-dictation")))
|
||
(mkdir-p (dirname exe))
|
||
(call-with-output-file exe
|
||
(lambda (port)
|
||
(format port "#!~a
|
||
if [ \"$1\" = begin ]
|
||
then
|
||
exec ~a $@ --input=~a --simulate-input-tool=~a
|
||
else
|
||
exec ~a $@
|
||
fi"
|
||
#$(file-append bash "/bin/bash")
|
||
nerd-dictation-exe
|
||
#$input-name
|
||
#$output-name
|
||
nerd-dictation-exe)))
|
||
(chmod exe #o555)))))
|
||
|
||
(define-public nerd-dictation/xdotool
|
||
(package
|
||
(inherit nerd-dictation)
|
||
(name "nerd-dictation-xdotool")
|
||
(build-system trivial-build-system)
|
||
(arguments
|
||
(list #:builder
|
||
(nerd-dictation-gexp "PAREC" "XDOTOOL"
|
||
(this-package-input "bash-minimal")
|
||
(this-package-input "nerd-dictation"))))
|
||
(inputs (list bash-minimal nerd-dictation))
|
||
(propagated-inputs (list pulseaudio xdotool))))
|
||
|
||
(define-public nerd-dictation/sox-xdotool
|
||
(package
|
||
(inherit nerd-dictation/xdotool)
|
||
(name "nerd-dictation-sox-xdotool")
|
||
(arguments
|
||
(list #:builder
|
||
(nerd-dictation-gexp "SOX" "XDOTOOL"
|
||
(this-package-input "bash-minimal")
|
||
(this-package-input "nerd-dictation"))))
|
||
(propagated-inputs (list sox xdotool))))
|
||
|
||
(define-public nerd-dictation/sox-ydotool
|
||
(package
|
||
(inherit nerd-dictation/xdotool)
|
||
(name "nerd-dictation-sox-ydotool")
|
||
(arguments
|
||
(list #:builder
|
||
(nerd-dictation-gexp "SOX" "YDOTOOL"
|
||
(this-package-input "bash-minimal")
|
||
(this-package-input "nerd-dictation"))))
|
||
(propagated-inputs (list sox ydotool))))
|
||
|
||
(define-public nerd-dictation/sox-wtype
|
||
(package
|
||
(inherit nerd-dictation/xdotool)
|
||
(name "nerd-dictation-sox-wtype")
|
||
(arguments
|
||
(list #:builder
|
||
(nerd-dictation-gexp "SOX" "WTYPE"
|
||
(this-package-input "bash-minimal")
|
||
(this-package-input "nerd-dictation"))))
|
||
(propagated-inputs (list sox wtype))))
|
||
|
||
(define-public python-brian2
|
||
(package
|
||
(name "python-brian2")
|
||
(version "2.5.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "Brian2" version))
|
||
(sha256
|
||
(base32
|
||
"1g48hzn3cdsvfjgz64s3kvh5d5287ggjxdyacb7wh2n5nd5iqlf7"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(setenv "HOME" "/tmp")
|
||
;; Must be run in a different directory, otherwise compiled
|
||
;; modules are not found.
|
||
(with-directory-excursion "/tmp"
|
||
;; Invoking brian2.test() is preferred to running pytest.
|
||
(invoke "python" "-c"
|
||
"import brian2, sys; sys.exit(0 if brian2.test() else 1)"))))))))
|
||
(propagated-inputs (list python-cython ; Required by codegen.
|
||
python-jinja2
|
||
python-numpy
|
||
python-py-cpuinfo
|
||
python-pyparsing
|
||
;; Required by codegen.
|
||
python-setuptools
|
||
python-sympy))
|
||
(native-inputs (list python-pytest python-pytest-xdist))
|
||
(home-page "https://briansimulator.org/")
|
||
(synopsis "Clock-driven simulator for spiking neural networks")
|
||
(description
|
||
"Brian is a simulator for spiking neural networks written in Python. It
|
||
is therefore designed to be easy to learn and use, highly flexible and
|
||
easily extensible.")
|
||
(license license:cecill)))
|
||
|
||
(define-public python-brian2tools
|
||
(package
|
||
(name "python-brian2tools")
|
||
(version "0.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "brian2tools" version))
|
||
(sha256
|
||
(base32
|
||
"0fn028mfy3qlzjkadd0wr5d7rcplijd5jphln414xifvvsb9jcc2"))))
|
||
(build-system python-build-system)
|
||
;; Both pypi tarball and git repo lack test files.
|
||
(arguments (list #:tests? #f))
|
||
(propagated-inputs (list python-brian2
|
||
python-libneuroml
|
||
python-markdown-strings
|
||
python-matplotlib
|
||
python-pylems
|
||
python-setuptools
|
||
python-setuptools-scm))
|
||
(native-inputs (list python-pytest))
|
||
(home-page "https://github.com/brian-team/brian2tools")
|
||
(synopsis "Tools for the Brian 2 simulator")
|
||
(description "Visualization and NeuroML import/export tools for the
|
||
Brian 2 simulator.")
|
||
(license license:cecill)))
|
||
|
||
(define-public oneapi-dnnl
|
||
(package
|
||
(name "oneapi-dnnl")
|
||
(version "3.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/oneapi-src/oneDNN")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1jgmb5kl0bf4a2zfn94zlb117672r9lvvkkmwl86ihlyr1mpr3d0"))))
|
||
(build-system cmake-build-system)
|
||
(arguments (if (target-riscv64?)
|
||
(list #:configure-flags #~'("-DDNNL_CPU_RUNTIME=SEQ"))
|
||
'()))
|
||
(home-page "https://github.com/oneapi-src/oneDNN")
|
||
(synopsis "Deep Neural Network Library")
|
||
(description
|
||
"OneAPI Deep Neural Network Library (oneDNN) is a cross-platform
|
||
performance library of basic building blocks for deep learning applications.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-gguf
|
||
(package
|
||
(name "python-gguf")
|
||
(version "0.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "gguf" version))
|
||
(sha256
|
||
(base32 "0rbyc2h3kpqnrvbyjvv8a69l577jv55a31l12jnw21m1lamjxqmj"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:tests? #false))
|
||
(inputs (list poetry python-pytest))
|
||
(propagated-inputs (list python-numpy))
|
||
(home-page "https://ggml.ai")
|
||
(synopsis "Read and write ML models in GGUF for GGML")
|
||
(description "A Python library for reading and writing GGUF & GGML format ML models.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-gymnasium
|
||
(package
|
||
(name "python-gymnasium")
|
||
(version "0.29.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "gymnasium" version))
|
||
(sha256
|
||
(base32 "1cab4wsnlsxn2z90qmymv8ppmsq8yq2amiqwid3r0xfbxx92flqs"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-cloudpickle python-farama-notifications
|
||
python-importlib-metadata python-numpy
|
||
python-typing-extensions))
|
||
(native-inputs (list python-pytest python-scipy))
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'create-tests-module
|
||
(lambda _
|
||
(with-output-to-file "tests/__init__.py"
|
||
(lambda _ (display ""))))))))
|
||
(home-page "https://gymnasium.farama.org/")
|
||
(synopsis
|
||
"Standard API for reinforcement learning and a set of reference environments")
|
||
(description
|
||
"This package provides a standard API for reinforcement learning and a
|
||
diverse set of reference environments (formerly Gym).")
|
||
(license license:expat)))
|