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guix-mirrors/gnu/packages/machine-learning.scm
Nicolas Graves 14e0bca6dd
gnu: Add python-ml-dtypes. 
* gnu/packages/machine-learning.scm (python-ml-dtypes): New variable.

Change-Id: I127edac9317d6380d22c41b6c6d578e183ab6b9f
Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-09-20 13:13:33 +02:00

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015-2025 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2020-2024 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 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 © 2020-2025 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim@guixotic.coop>
;;; Copyright © 2022-2025 Nicolas Graves <ngraves@ngraves.fr>
;;; Copyright © 2022 Kiran Shila <me@kiranshila.com>
;;; Copyright © 2022 Wiktor Zelazny <wzelazny@vurv.cz>
;;; 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 © 2024-2025 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>
;;; Copyright © 2024, 2025 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2024 Andy Tai <atai@atai.org>
;;; Copyright © 2025 Lapearldot <lapearldot@disroot.org>
;;; Copyright © 2025 Cayetano Santos <csantosb@inventati.org>
;;;
;;; 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 download)
#:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix svn-download)
#:use-module (guix utils)
#:use-module (guix build-system cargo)
#:use-module (guix build-system cmake)
#:use-module (guix build-system copy)
#: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 (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 bdw-gc)
#:use-module (gnu packages boost)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages c)
#:use-module (gnu packages calendar)
#:use-module (gnu packages check)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpp)
#:use-module (gnu packages cran)
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages digest)
#: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 libedit)
#:use-module (gnu packages libevent)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages logging)
#: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 pretty-print)
#: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 qt)
#:use-module (gnu packages rdf)
#:use-module (gnu packages regex)
#:use-module (gnu packages rocm)
#:use-module (gnu packages rpc)
#:use-module (gnu packages sdl)
#:use-module (gnu packages serialization)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
#:use-module (gnu packages textutils)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages valgrind)
#:use-module (gnu packages version-control)
#:use-module (gnu packages video)
#:use-module (gnu packages vulkan)
#:use-module (gnu packages web)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (ice-9 match))
(define-public dlpack
(package
(name "dlpack")
(version "1.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dmlc/dlpack")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0vlp8gcf7s3snalj6xmvgqxxn96fki6gw9hzph30gmgdbaz730j6"))))
(build-system cmake-build-system)
(arguments (list #:tests? #f)) ;No tests.
(home-page "https://dmlc.github.io/dlpack/latest/")
(synopsis "In memory tensor structure")
(description
"DLPack is an in-memory tensor structure for sharing tensors among
frameworks.")
(license license:asl2.0)))
(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-autograd-gamma
(package
(name "python-autograd-gamma")
(version "0.5.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "autograd-gamma" version))
(sha256
(base32 "1i699a9m5ndnj8cwzjjf2agb77aawhzrzxfbmn5zrkxridxvnypj"))))
(build-system pyproject-build-system)
(native-inputs
(list python-setuptools
python-wheel))
(propagated-inputs
(list python-autograd
python-scipy))
(home-page "https://github.com/CamDavidsonPilon/autograd-gamma")
(synopsis
"Autograd-compatible approximations to the gamma family of functions")
(description
"This package provides Autograd-compatible approximations to the gamma
family of functions.")
(license license:expat)))
(define-public python-faster-whisper
(package
(name "python-faster-whisper")
(version "1.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/SYSTRAN/faster-whisper")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0wmc9aszpnbr60l5v97np0rc3zsz4pldjald7kmnr668rhpakzcj"))))
(build-system pyproject-build-system)
;; XXX: Currently tests requires model download, which we'd rather avoid
;; in Guix unless we're sure about the FOSS weights. To test in source :
;; guix shell -D python-faster-whisper -- pytest
(arguments (list #:tests? #f))
(propagated-inputs (list (list onnxruntime "python")
python-av
python-ctranslate2
python-huggingface-hub
python-tokenizers
python-tqdm))
(native-inputs (list python-numpy
python-pytest
python-setuptools-next))
(home-page "https://github.com/SYSTRAN/faster-whisper")
(synopsis "Whisper transcription reimplementation")
(description
"This package provides a reimplementation of OpenAI's Whisper model using
CTranslate2, which is a inference engine for transformer models.")
(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 python-setuptools python-wheel))))
(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)
(arguments
(list
;; tests: 7636 passed, 3859 skipped, 2 deselected, 69 xfailed, 2 xpassed
#:test-flags
'(list "-k"
(string-append
;; Disable flaky test
"not test_integrate_variable[x23-i]"
;; XXX This test fails because the length of arguments
;; is longer than the length of inputs.
" and not test_function_of_numeric_array"))))
(propagated-inputs (list python-makefun python-multipledispatch
python-numpy python-opt-einsum
python-typing-extensions))
(native-inputs (list python-pandas
python-pillow
python-pyro-api
python-pytest
python-requests
python-scipy
python-setuptools-next
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 14 years old.
(let ((commit "1783cbf6239a597c4d29f694e227e22b8d4f4bf6")
(revision "2"))
(package
(name "fann")
(version (git-version "2.2.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/libfann/fann")
(commit commit)))
(modules '((guix build utils)))
(snippet #~(delete-file-recursively "lib/googletest"))
(file-name (git-file-name name version))
(sha256
(base32
"0jlcxl0czlr3982mak3935mb08i2f368f0jsxca91ppgfd596ldr"))))
(build-system cmake-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'remove-googletest
(lambda _
(substitute* "CMakeLists.txt"
(("ADD_SUBDIRECTORY\\( lib/googletest \\)")
""))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(with-directory-excursion "tests"
(invoke "./fann_tests"))))))))
(native-inputs (list googletest))
(home-page "https://leenissen.dk/")
(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 "336")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/cjlin1/libsvm/")
(commit (string-append "v" version))))
(sha256
(base32 "03ns6frhfdcyl661ws1yqbzsa6m8wrmba544vlacghry2kg88hn2"))))
(build-system gnu-build-system)
(arguments
(list
#: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 _
(for-each (lambda (file)
(install-file file
(string-append #$output "/bin")))
'("svm-train" "svm-predict" "svm-scale"))
(install-file "libsvm.so.4"
(string-append #$output "/lib"))
(symlink (string-append #$output "/lib/libsvm.so.4")
(string-append #$output "/lib/libsvm.so"))
(install-file "svm.h"
(string-append #$output "/include/"
#$name)))))))
(native-inputs (list python-minimal-wrapper))
(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-gpy
(package
(name "python-gpy")
(version "1.13.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "GPy" version))
(sha256
(base32 "083rl8nr4nmmr1pzn0g8gsc4wi9dnhj3jjhkwsssadm5vns5d0m3"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'compatibility
(lambda _
;; This file uses Python 2 statements
(delete-file "GPy/testing/mpi_test__.py")
(substitute* "setup.py"
(("scipy>=1.3.0,<1.12.0")
"scipy>=1.3.0,<=1.13.0"))
;; Use numpy.exp because scipy.ext no longer exists
(substitute* "GPy/kern/src/sde_standard_periodic.py"
(("sp\\.exp") "np.exp"))
(substitute* "GPy/kern/src/sde_stationary.py"
(("sp\\.poly1d") "np.poly1d")
(("sp\\.roots") "np.roots")))))))
(native-inputs
(list python-cython
python-matplotlib
python-pods
python-pytest
python-setuptools
python-wheel))
(propagated-inputs
(list python-numpy
python-paramz
python-scipy
python-six))
(home-page "https://sheffieldml.github.io/GPy/")
(synopsis "The Gaussian Process Toolbox")
(description
"@command{GPy} is a Gaussian Process (GP) framework written in
Python, from the Sheffield machine learning group. GPy implements a range of
machine learning algorithms based on GPs.")
(license license:bsd-3)))
(define-public python-libsvm
(package
(inherit libsvm)
(name "python-libsvm")
(build-system pyproject-build-system)
(arguments
(list
#:tests? #f ;no "check" target
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'chdir
(lambda _
(chdir "python"))))))
(native-inputs (list python-setuptools python-wheel))
(propagated-inputs (list libsvm python-scipy))
(synopsis "Python bindings of libSVM")))
(define-public python-mcfit
;; PyPI variant fails during compile-bytecode phase: "IndentationError:
;; expected an indented block after function definition on line 10
;; (mkfit.py, line 15)".
;; GitHub provides no release tags, use the latest commit from the master
;; branch.
;; See: <https://github.com/eelregit/mcfit/issues/5>.
(let ((commit "be3a5cf9c474e16875126adcd35ba785fb781ebb")
(revision "0"))
(package
(name "python-mcfit")
(version (git-version "0.0.22" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/eelregit/mcfit")
(commit commit)))
(sha256
(base32 "120ybwhrqpn9a9q96m6l8pw8a7cdz705vzqn3s87wnffa8nslbsi"))))
(build-system pyproject-build-system)
(native-inputs
(list python-pytest
python-setuptools
python-wheel))
(propagated-inputs
(list python-mpmath
python-numpy
python-scipy))
(home-page "https://github.com/eelregit/mcfit")
(synopsis "Multiplicatively convolutional fast integral transforms")
(description
"This package provides multiplicatively convolutional fast integral
transforms.")
(license license:gpl3+))))
(define-public python-ml-collections
(package
(name "python-ml-collections")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/google/ml_collections")
(commit (string-append "v" version))))
(sha256
(base32 "1f3rwbgnnvgh2jgnkwxfjdw18yly41hlx9fy56h0x36zyy8p0j21"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags '(list "--pyargs" "ml_collections/config_dict/tests")))
(propagated-inputs
(list python-absl-py python-pyyaml))
(native-inputs (list python-pylint
python-pytest
python-pytest-xdist
python-flit-core))
(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 python-ml-dtypes
(package
(name "python-ml-dtypes")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jax-ml/ml_dtypes")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1yv90f28c9w34430xjwvn1lzxdylvp1zi6b02cx7crla6qkvrzn5"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'use-eigen-package
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "setup.py"
(("third_party/eigen")
(search-input-directory inputs "include/eigen3")))))
(add-after 'install 'symlink-lib
(lambda* (#:key inputs outputs #:allow-other-keys)
(for-each
(lambda (file)
(symlink file
(string-append #$output "/lib/ml_dtypes.so")))
(find-files (site-packages inputs outputs) "\\.so$")))))))
(inputs (list eigen-for-python-ml-dtypes))
(propagated-inputs (list python-numpy))
(native-inputs (list pybind11
python-absl-py
python-pytest
python-setuptools
python-wheel))
(home-page "https://github.com/jax-ml/ml_dtypes")
(synopsis "NumPy dtype extensions used in machine learning")
(description
"This package is a stand-alone implementation of several
NumPy @code{dtype} extensions used in machine learning libraries, including:
@itemize
@item @code{bfloat16}: an alternative to the standard @code{float16} format
@item @code{float8_*}: several experimental 8-bit floating point
representations including:
@itemize
@item @code{float8_e4m3b11fnuz}
@item @code{float8_e4m3fn}
@item @code{float8_e4m3fnuz}
@item @code{float8_e5m2}
@item @code{float8_e5m2fnuz}
@end itemize
@item @code{int4} and @code{uint4}: low precision integer types.
@end itemize
")
(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 (,@%default-gnu-imported-modules
(guix build python-build-system))
#:modules ((guix build python-build-system)
,@%default-gnu-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.*$")
"label_higher_order_test\n"))
;; These Python unittests are broken as there is no gato.
;; See https://sourceforge.net/p/ghmm/support-requests/3/
(substitute* "ghmmwrapper/ghmmunittests.py"
(("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
line indent)
(string-append indent
"@unittest.skip(\"Disabled by Guix\")\n"
line))))))))
(inputs
`(("python" ,python-2) ; only Python 2 is supported
("libxml2" ,libxml2)))
(native-inputs
(list pkg-config
dejagnu
swig
autoconf
automake
libtool))
(home-page "http://ghmm.org")
(synopsis "Hidden Markov Model library")
(description
"The General Hidden Markov Model library (GHMM) is a C library with
additional Python bindings implementing a wide range of types of @dfn{Hidden
Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
training, HMM clustering, HMM mixtures.")
(license license:lgpl2.0+))))
(define-public llama-cpp
(let ((tag "b6101"))
(package
(name "llama-cpp")
(version (string-append "0.0.0-" tag))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ggml-org/llama.cpp")
(commit tag)))
(file-name (git-file-name name tag))
(sha256
(base32 "0yz97dk19pxqck9l83wvlwzf1i78wrc55hrk9ynraqybdz7yqjdc"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
#~(list #$(string-append "-DGGML_BUILD_NUMBER=" tag)
"-DBUILD_SHARED_LIBS=ON"
"-DGGML_VULKAN=ON"
"-DLLAMA_CURL=ON"
"-DGGML_BLAS=ON"
"-DGGML_BLAS_VENDOR=OpenBLAS"
(string-append "-DBLAS_INCLUDE_DIRS="
#$(this-package-input "openblas")
"/include")
(string-append "-DBLAS_LIBRARIES="
#$(this-package-input "openblas")
"/lib/libopenblas.so")
"-DGGML_NATIVE=OFF" ;no '-march=native'
"-DGGML_FMA=OFF" ;and no '-mfma', etc.
"-DGGML_AVX2=OFF"
"-DGGML_AVX512=OFF"
"-DGGML_AVX512_VBMI=OFF"
"-DGGML_AVX512_VNNI=OFF")
#: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-after 'unpack 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* (format #f "~a~a"
"ggml/src/ggml-vulkan/vulkan-shaders/"
"vulkan-shaders-gen.cpp")
(("\"/bin/sh\"")
(string-append "\"" (search-input-file inputs "/bin/sh")
"\"")))))
(add-after 'unpack 'fix-tests
(lambda _
;; test-thread-safety downloads ML model from network,
;; cannot run in Guix build environment
(substitute* '("tests/CMakeLists.txt")
(("llama_build_and_test\\(test-thread-safety.cpp.*")
"")
;; error while handling argument "-m": expected value for
;; argument
(("llama_build_and_test\\(test-arg-parser.cpp.*")
""))
;; test-eval-callback downloads ML model from network, cannot
;; run in Guix build environment
(substitute* '("examples/eval-callback/CMakeLists.txt")
(("COMMAND llama-eval-callback")
"COMMAND true llama-eval-callback"))
;; Help it find the test files it needs
(substitute* "tests/test-chat.cpp"
(("\"\\.\\./\"") "\"../source/\""))))
(add-after 'install 'wrap-python-scripts
(assoc-ref python:%standard-phases 'wrap))
(add-after 'install 'remove-tests
(lambda* (#:key outputs #:allow-other-keys)
(for-each delete-file (find-files
(string-append (assoc-ref outputs "out")
"/bin")
"^test-")))))))
(inputs
(list curl glslang python-gguf python-minimal openblas spirv-headers
spirv-tools vulkan-headers vulkan-loader))
(native-inputs
(list bash-minimal pkg-config shaderc))
(propagated-inputs
(list python-numpy python-pytorch python-sentencepiece))
(properties '((tunable? . #true))) ;use AVX512, FMA, etc. when available
(home-page "https://github.com/ggml-org/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 whisper-cpp
(package
(name "whisper-cpp")
(version "1.7.6")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ggml-org/whisper.cpp")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0gn64jw4pr4vfnn2hll7yd98r8yhaqg97hhg5z22vq4j423436kn"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
#~(list "-DWHISPER_STANDALONE=TRUE"
"-DWHISPER_SDL2=TRUE"
"-DWHISPER_BUILD_TESTS=TRUE"
; "-DWHISPER_FFMPEG=TRUE" ; TODO
"-DBUILD_SHARED_LIBS=ON"
"-DGGML_BLAS=ON"
"-DGGML_BLAS_VENDOR=OpenBLAS"
(string-append "-DBLAS_INCLUDE_DIRS="
#$(this-package-input "openblas")
"/include")
(string-append "-DBLAS_LIBRARIES="
#$(this-package-input "openblas")
"/lib/libopenblas.so")
"-DGGML_NATIVE=OFF" ;no '-march=native'
"-DGGML_FMA=OFF" ;and no '-mfma', etc.
"-DGGML_AVX2=OFF"
"-DGGML_AVX512=OFF"
"-DGGML_AVX512_VBMI=OFF"
"-DGGML_AVX512_VNNI=OFF"
"-DGGML_VULKAN=ON")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "ggml/src/ggml-vulkan/vulkan-shaders/vulkan-shaders-gen.cpp"
(("\"/bin/sh\"")
(string-append "\"" (search-input-file inputs "/bin/sh") "\"")))))
#$@(if (not (target-64bit?))
'((add-after 'unpack 'skip-failing-tests
(lambda _
;; 32-bit system
;; large model does not fit in RAM in 32-bit system,
;; disable large model test
(substitute* "tests/CMakeLists.txt"
(("LABELS \"large\"")
"DISABLED true")))))
'())
(add-after 'unpack 'skip-failing-vad-tests
(lambda _
(substitute* "tests/CMakeLists.txt"
;; error: failed to read audio data as wav (Unknown error)
(("\\$\\{VAD_TEST\\} PROPERTIES LABELS \"unit\"")
"${VAD_TEST} PROPERTIES DISABLED true")
;; error: failed to read audio data as wav (Unknown error)
(("\\$\\{VAD_TARGET\\} PROPERTIES LABELS \"base;en\"")
"${VAD_TEST} PROPERTIES DISABLED true")))))))
(native-inputs
(list pkg-config shaderc))
(inputs
(list openblas sdl2 git spirv-headers spirv-tools
vulkan-headers vulkan-loader))
(synopsis "OpenAI's Whisper model in C/C++")
(description
"This package is a high-performance inference of OpenAI's
Whisper automatic speech recognition (ASR) model, implemented in plain C/C++
without dependencies, with
@itemize
@item AVX intrinsics support for x86 architectures
@item VSX intrinsics support for POWER architectures
@item Mixed F16 / F32 precision
@item 4-bit and 5-bit integer quantization support
@item Zero memory allocations at runtime
@item Support for CPU-only inference
@item Efficient GPU support for NVIDIA
@item OpenVINO Support
@item C-style API
@end itemize")
(properties '((tunable? . #true))) ;use AVX512, FMA, etc. when available
(home-page "https://github.com/ggml-org/whisper.cpp/")
(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
(list
#:configure-flags
#~(list "--enable-blast"
(string-append "CFLAGS=-fcommon -g -O2"
" -Wno-error=implicit-function-declaration"))))
(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 "8.3.1")
(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
"0pcy1f6r4h6z0b75gx4lcnkf7yr8342w2dch7jml1ycmzpqkxvfx"))))
(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 "5449a5b479908f40f56cf911f11e0a7e156d207f")
(revision "2"))
(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
"0sfn6cm8qqsv1g80wc6pimldr0q11vfqik0hcynp8dfrkmvzhj8n"))))
(properties `((upstream-name . "RcppML")))
(build-system r-build-system)
(propagated-inputs (list r-matrix r-rcpp))
(native-inputs (list r-knitr r-testthat))
(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 "1.8.4")
(source (origin
(method url-fetch)
(uri (string-append "https://www.openfst.org/twiki/pub/FST/"
"FstDownload/openfst-" version ".tar.gz"))
(sha256
(base32
"05l057mx1cmbm2jm99mrg75qgz4ca5r78n002mkpxl4j7mpvpsx8"))))
(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)))
(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"))
(patches
(search-patches "openfst-for-vosk-fix-unique-ptr.patch"))))
(arguments
'(#:configure-flags
'("--enable-shared" "--enable-far" "--enable-ngram-fsts"
"--enable-lookahead-fsts" "--with-pic" "--disable-bin")))))
(define-public sentencepiece
(package
(name "sentencepiece")
(version "0.2.1")
(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 "1yzsaam3kk9fqzxfc3nm2pskwq1bdgkrijmcmzmg5x0338rn0hmb"))))
(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)
(native-inputs (list python-setuptools python-wheel))
(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 "0.3.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "persim" version))
(sha256
(base32 "03d4kgakpgj54c3pl9dkqrkbmj6w13gmczkds5jagf3n85c1hgg1"))))
(build-system pyproject-build-system)
(native-inputs
(list python-pytest python-setuptools-next))
(propagated-inputs
(list python-deprecated
python-hopcroftkarp
python-joblib
python-matplotlib
python-numpy
python-scikit-learn
python-scipy))
(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-pot
(package
(name "python-pot")
(version "0.9.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pot" version))
(sha256
(base32 "0hk0dmjgnpwka0a7gyzrcq155wzlvzcrsav3qaizyg0wymzywi4n"))
(snippet '(delete-file "ot/lp/emd_wrap.cpp"))))
(build-system pyproject-build-system)
(propagated-inputs
(list python-autograd
python-numpy
python-pytorch
python-pytorch-geometric
python-pymanopt
python-scikit-learn
python-scipy))
(native-inputs (list python-cython
python-setuptools
python-wheel))
(home-page "https://github.com/PythonOT/POT")
(synopsis "Python Optimal Transport Library")
(description "This Python library provides several solvers for
optimization problems related to Optimal Transport for signal, image
processing and machine learning.")
(license license:expat)))
(define-public python-pymanopt
(package
(name "python-pymanopt")
(version "2.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pymanopt" version))
(sha256
(base32 "1nm1yz5hbj1valqq23r8c1g9rhfdndfswlqv6xrnvc3f8fd95167"))))
(build-system pyproject-build-system)
(arguments
(list
;; Tests require jax and tensorflow, which are optional.
#:tests? #false
#:phases
'(modify-phases %standard-phases
;; This is probably a bad idea. We don't have scipy 1.13 just yet.
(add-after 'unpack 'relax-requirements
(lambda _
(substitute* "pyproject.toml"
((",!=1.12\\.\\*") "")))))))
(propagated-inputs (list python-numpy python-scipy))
(native-inputs (list python-autograd
python-flake8
python-flake8-bugbear
python-isort
python-matplotlib
python-pytest
python-pytest-cov
python-setuptools
python-setuptools-scm
python-wheel))
(home-page "https://pymanopt.org/")
(synopsis "Toolbox for optimization on Riemannian manifolds")
(description
"This package is a toolbox for optimization on Riemannian manifolds with
support for automatic differentiation.")
(license license:bsd-3)))
(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
python-setuptools
python-wheel))
(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 python-setuptools python-wheel))
(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-safetensors
(package
(name "python-safetensors")
(version "0.4.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "safetensors" version))
(sha256
(base32 "1hhiwy67jarm70l0k26fs1cjhzkgzrh79q14bklj2yp0qi8gr19g"))
(modules '((guix build utils)
(ice-9 ftw)))
(snippet
#~(begin ;Only keep bindings.
(for-each
(lambda (file)
(unless (member file '("." ".." "bindings" "PKG-INFO"))
(delete-file-recursively file)))
(scandir "."))
(for-each
(lambda (file)
(unless (member file '("." ".."))
(rename-file (string-append "bindings/python/" file)
file)))
(scandir "bindings/python"))
(substitute* "Cargo.toml"
(("^path = .*") ""))))))
(build-system cargo-build-system)
(arguments
(list
#:install-source? #f
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'install-rust-library
(lambda _
(copy-file "target/release/libsafetensors_rust.so"
"py_src/safetensors/_safetensors_rust.so")))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "PYTHONPATH" (string-append (getcwd) "/py_src"))
(invoke "python3"
"-m" "pytest"
"-n" "auto"
"--dist=loadfile"
"-s" "-v" "./tests/"
;; Missing jax and tensorflow dependency
"--ignore=./tests/test_flax_comparison.py"
"--ignore=./tests/test_tf_comparison.py"))))
(add-after 'install 'install-python
(lambda _
(let* ((pversion #$(version-major+minor
(package-version python)))
(lib (string-append #$output "/lib/python" pversion
"/site-packages/"))
(info (string-append lib "safetensors-"
#$(package-version this-package)
".dist-info")))
(mkdir-p info)
(copy-file "PKG-INFO" (string-append info "/METADATA"))
(copy-recursively
"py_src/safetensors"
(string-append lib "safetensors"))))))))
(inputs
(cargo-inputs 'python-safetensors))
(native-inputs
(list python-h5py
python-minimal
python-numpy
python-pytest
python-pytest-xdist
python-pytorch))
(home-page "https://huggingface.co/docs/safetensors")
(synopsis "Simple and safe way to store and distribute tensors")
(description
"This package provides a fast (zero-copy) and safe (dedicated) format for
storing tensors safely.")
(license license:asl2.0)))
(define-public python-sentencepiece
(package
(inherit sentencepiece)
(name "python-sentencepiece")
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "python"))))))
(native-inputs
(list pkg-config protobuf python-pytest python-setuptools-next))
(propagated-inputs (list sentencepiece))
(synopsis "SentencePiece python wrapper")
(description "This package provides a Python wrapper for the SentencePiece
unsupervised text tokenizer.")))
(define-public python-sentence-transformers
(package
(name "python-sentence-transformers")
(version "5.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/UKPLab/sentence-transformers/")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1jkj77q25b21nxrdszvlw127jnx1m7x8czldiq2mfyj76yjk0ymj"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #f)) ;network access is required
(propagated-inputs (list python-huggingface-hub
python-numpy
python-pillow
python-pytorch
python-typing-extensions
python-scikit-learn
python-scipy
python-tqdm
python-transformers))
(native-inputs (list python-pytest python-setuptools python-wheel))
(home-page "https://www.SBERT.net")
(synopsis "Multilingual text embeddings")
(description "This framework provides an easy method to compute dense
vector representations for sentences, paragraphs, and images. The models are
based on transformer networks like BERT / RoBERTa / XLM-RoBERTa and achieve
state-of-the-art performance in various tasks. Text is embedded in vector
space such that similar text are closer and can efficiently be found using
cosine similarity.
This package provides easy access to pretrained models for more than 100
languages, fine-tuned for various use-cases.
Further, this framework allows an easy fine-tuning of custom embeddings
models, to achieve maximal performance on your specific task.")
(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 python-setuptools python-wheel))
(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 python-setuptools python-wheel))
(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 "3.6.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "spacy" version))
(sha256
(base32
"0ri1cz62kswawsa4hflh0ah8f63mnnqah0sbd5hmabdf0s3sj8v3"))))
(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-2
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 python-wheel))
(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 onnx
(package
(name "onnx")
(version "1.17.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/onnx/onnx")
(commit (string-append "v" version))))
(sha256
(base32
"1i6bh4z2xzz1maykr0xmrwfybm6i3g38vnx7hsls8hr58rdr30zn"))
(file-name (git-file-name name version))
(patches (search-patches
"onnx-shared-libraries.patch"
"onnx-skip-model-downloads.patch"))
(modules '((guix build utils)))
(snippet '(delete-file-recursively "third_party"))))
(build-system pyproject-build-system)
(arguments
(list
;; python-nbval depends transitively on Rust.
#:tests?
(->bool (member (or (%current-target-system)
(%current-system))
(package-transitive-supported-systems python-nbval)))
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'pass-cmake-arguments
(lambda* (#:key outputs tests? #:allow-other-keys)
;; For derived package use
(substitute* "CMakeLists.txt"
(("set\\(ONNX_ROOT.*") "")
(("\\$\\{ROOT_DIR\\}(/tools.*)" _ rest)
(string-append "${PROJECT_SOURCE_DIR}" rest)))
;; Pass options to the CMake-based build process.
(define out
(assoc-ref outputs "out"))
(define args
;; Copy arguments from 'cmake-build-system', plus ask
;; for shared libraries.
(list "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
(string-append "-DCMAKE_INSTALL_PREFIX=" out)
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
(string-append "-DCMAKE_INSTALL_RPATH=" out
"/lib")
"-DCMAKE_VERBOSE_MAKEFILE=ON"
(string-append "-DONNX_BUILD_TESTS="
(if tests? "ON" "OFF"))
"-DBUILD_SHARED_LIBS=ON"
"-DONNX_USE_PROTOBUF_SHARED_LIBS=ON"
(string-append
"-DONNX_ROOT=" #$(package-source this-package))))
;; 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
(append
(list cmake-minimal
googletest
pybind11
python-coverage
python-fb-re2
python-parameterized
python-pytest
python-pytest-runner
python-setuptools
python-wheel)
(filter
(lambda (pkg)
(member (or (%current-target-system)
(%current-system))
(package-transitive-supported-systems pkg)))
(list python-nbval))))
(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 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: 0.3.x is *more* recent than 1.5.0.
(version "0.3.19")
(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
"1mx3hsl42na6fr05nh2x3j9kxm56cpfmwk6lwl2cfq9zs3gv929w"))
(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 pyproject-build-system)
(arguments
;; reuse build system tweaks
(substitute-keyword-arguments (package-arguments onnx)
((#:phases phases)
#~(modify-phases #$phases
(add-after 'pass-cmake-arguments
'pass-onnx-optimizer-cmake-arguments
(lambda _
(setenv
"CMAKE_ARGS"
(string-append
(getenv "CMAKE_ARGS")
" -DONNX_OPT_USE_SYSTEM_PROTOBUF=ON"
" -DCMAKE_CXX_FLAGS=\"-DONNX_ML=1 -DONNX_NAMESPACE=onnx\""))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(if tests?
(invoke "pytest" "-vv" "-k"
;; These tests fail with upstream ONNX:
;; https://github.com/onnx/optimizer/issues/138
(string-append
"not test_fuse_matmul"
" and not test_fuse_consecutive"
" and not test_fuse_transpose")))))))))
(native-inputs
(append
(list cmake-minimal
python-pytest
python-setuptools-next)
(filter
(lambda (pkg)
(member (or (%current-target-system)
(%current-system))
(package-transitive-supported-systems pkg)))
(list python-nbval))))
(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 onnxruntime
(package
(name "onnxruntime")
(version "1.22.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/microsoft/onnxruntime")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0z2s79l4wdilssw9lmj319ypyyqi2y0dx0fpwr2yhq8bax3ci50n"))))
(build-system cmake-build-system)
(arguments
(list
#:modules '((guix build cmake-build-system)
(guix build utils)
((guix build pyproject-build-system) #:prefix py:))
#:imported-modules (append %cmake-build-system-modules
%pyproject-build-system-modules)
#:configure-flags
#~(list "-Donnxruntime_BUILD_UNIT_TESTS=OFF"
"-Donnxruntime_BUILD_SHARED_LIB=ON"
"-Donnxruntime_ENABLE_LTO=ON"
"-Donnxruntime_ENABLE_PYTHON=ON"
"-Donnxruntime_USE_FULL_PROTOBUF=OFF"
;; XXX: Fixes build with gcc@14.
"-DCMAKE_CXX_FLAGS=-Wl,-z,noexecstack")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "cmake")))
(add-after 'unpack 'relax-dependencies
(lambda _
(with-output-to-file "cmake/external/eigen.cmake"
(lambda _
(display "find_package(Eigen3 REQUIRED)\n")))
(substitute* "cmake/external/abseil-cpp.cmake"
(("20240722")
(car (string-split #$(package-version
(this-package-input "abseil-cpp"))
#\.))))))
(add-after 'install 'build-python
(lambda _
(invoke "python3" "../setup.py" "bdist_wheel")))
(add-after 'build-python 'install-python
(lambda* (#:key inputs #:allow-other-keys)
((assoc-ref py:%standard-phases 'install)
#:inputs inputs
#:outputs `(("out" . ,#$output:python)))))
(add-after 'install-python 'add-install-to-pythonpath
(lambda* (#:key inputs #:allow-other-keys)
((assoc-ref py:%standard-phases 'add-install-to-pythonpath)
#:inputs inputs
#:outputs `(("out" . ,#$output:python)))))
(delete 'check)
(add-after 'add-install-to-pythonpath 'check
(lambda* (#:key tests? #:allow-other-keys)
(with-directory-excursion "../onnxruntime/test/python"
((assoc-ref py:%standard-phases 'check)
#:tests? tests?
#:test-flags
`(;; XXX: NotImplementedError
"--ignore-glob=quantization/*"
;; XXX: These tests require transformer models or have
;; import issues.
"--ignore=transformers/test_generation.py"
"--ignore=transformers/test_gpt2_benchmark.py"
"--ignore=transformers/test_gpt2_to_onnx.py"
"--ignore=transformers/test_optimizer_huggingface_bert.py"
"--ignore=transformers/test_parity_huggingface_gpt_attention.py"
"--ignore=transformers/test_shape_infer_helper.py"
;; XXX: onnxscript ModuleNotFound
"--ignore=transformers/test_gelu_fusions.py"
"--ignore=transformers/test_gemma3_vision.py"
;; XXX: Other failing tests.
"-k" ,(string-append
"not test_gelu_is_fused_by_default"
" and not test_inverse"))))))
(add-after 'check 'python-sanity-check
(lambda* (#:key tests? inputs #:allow-other-keys)
((assoc-ref py:%standard-phases 'sanity-check)
#:inputs `(("sanity-check.py" . ,#$(default-sanity-check.py))
,@inputs)
#:outputs `(("out" . ,#$output:python))))))))
(outputs (list "out" "python"))
(inputs
(list abseil-cpp
boost
cpuinfo
dlpack
c++-gsl
date
eigen-for-onnxruntime
flatbuffers-23.5
googletest
nlohmann-json
onnx
protobuf
pybind11
re2-next
safeint
zlib))
(native-inputs
(list pkg-config
python-einops
python-wrapper
python-numpy
python-parameterized
python-psutil
python-pytest
python-pytorch
python-sentencepiece
python-setuptools-next))
(propagated-inputs
(list python-coloredlogs
python-flatbuffers
python-protobuf
python-sympy))
(home-page "https://github.com/microsoft/onnxruntime")
(synopsis "Cross-platform, high performance scoring engine for ML models")
(description
"ONNX Runtime is a performance-focused complete scoring engine
for Open Neural Network Exchange (ONNX) models, with an open
extensible architecture to continually address the latest developments
in AI and Deep Learning. ONNX Runtime stays up to date with the ONNX
standard with complete implementation of all ONNX operators, and
supports all ONNX releases (1.2+) with both future and backwards
compatibility.")
(license license:expat)))
(define-public gemmlowp
(let ((commit "16e8662c34917be0065110bfcd9cc27d30f52fdf")
(version "0.1")
(revision "2"))
(package
(name "gemmlowp")
(version (git-version version revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/google/gemmlowp")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "02xmrv921al94nihiqrvi8inlq6qc07j0zll3f9qi8322r31x83v"))))
(arguments
(list
#:configure-flags
#~(list #$@(match (%current-system)
((or "x86_64-linux" "i686-linux")
'("-DCMAKE_CXX_FLAGS=-msse2"))
(_ '()))
"-DBUILD_SHARED_LIBS=ON")
#:phases
#~(modify-phases %standard-phases
;; This directory contains the CMakeLists.txt.
(add-after 'unpack 'chdir
(lambda _
(chdir "contrib")))
;; There is no install target
(replace 'install
(lambda _
(let ((lib (string-append #$output "/lib/")))
(install-file "../build/libeight_bit_int_gemm.so" lib)
(for-each
(lambda (dir)
(let ((target (string-append #$output
"/include/gemmlowp/" dir)))
(for-each (lambda (h)
(install-file h target))
(find-files (string-append "../" dir)
"\\.h$"))))
'("meta" "profiling" "public" "fixedpoint"
"eight_bit_int_gemm" "internal"))))))))
(build-system cmake-build-system)
(home-page "https://github.com/google/gemmlowp")
(synopsis "Small self-contained low-precision GEMM library")
(description
"This is a small self-contained low-precision @dfn{general matrix
multiplication} (GEMM) library. It is not a full linear algebra library.
Low-precision means that the input and output matrix entries are integers on
at most 8 bits. To avoid overflow, results are internally accumulated on more
than 8 bits, and at the end only some significant 8 bits are kept.")
(license license:asl2.0))))
(define-public dlib
(package
(name "dlib")
(version "19.24.6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/davisking/dlib.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "11j86nxkj78v8xdx2s80mfplq4j0rs0y0iidqgma12b2pdk3p486"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file-recursively "dlib/external")))))
(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 _
;; XXX: This causes a rebuild--however, trying to run the tests
;; without rebuilding causes a lot of errors.
;; Also, the official way is to rebuild.
(mkdir "../source/dlib/test/build")
(with-directory-excursion "../source/dlib/test/build"
(invoke "cmake" "-DBUILD_SHARED_LIBS=ON" "..")
(invoke "cmake" "--build" "." "--config" "Release")
(invoke "./dtest" "--runall")))))))
(native-inputs
(list pkg-config
;; For tests.
libnsl))
(inputs
`(("ffmpeg" ,ffmpeg)
("giflib" ,giflib)
("libjpeg" ,libjpeg-turbo)
("libjxl" ,libjxl-0.10)
("libpng" ,libpng)
("libwebp" ,libwebp)
("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 "1.6.1")
(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 "08z1b58n31grfvl42wi6rdwrfhrdhnzkkxhg19iag3zkvkcvxqjl"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "--numprocesses" (number->string (parallel-job-count))
"-m" "not network"
"-k" (string-join
;; This test tries to access the internet.
(list "not test_load_boston_alternative"
;; XXX: 35 failed with various reasons, 36871 (!)
;; passed; invistigate if we need care about that.
"test_check_pandas_sparse_invalid"
"test_ard_accuracy_on_easy_problem"
"test_check_inplace_ensure_writeable"
"test_covariance"
"test_estimators"
"test_ledoit_wolf"
"test_mcd"
"test_mcd_issue1127"
"test_mcd_support_covariance_is_zero"
"test_oas"
"test_shrunk_covariance"
"test_toy_ard_object")
" and not "))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'remove-notice-rgx
(lambda _
;; FIXME: This line contains regexps and breaks toml parser.
(substitute* "pyproject.toml"
(("notice-rgx.*") ""))))
(add-before 'build 'configure
(lambda _
(setenv "SKLEARN_BUILD_PARALLEL"
(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 gfortran
meson-python
python-cython-3
python-pandas
python-pytest
python-pytest-xdist))
(propagated-inputs
(list python-joblib
python-numpy
python-scipy
python-threadpoolctl))
(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" (string-append "not test_build"
;; The error message format has changed,
;; but the behavior itself is still the
;; same.
" and not test_parameter_validation"
;; exceptions must be derived from Warning,
;; not <class 'NoneType'>
" and not test_seuclidean"))
#: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
python-setuptools python-wheel))
(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))
(native-inputs (list python-setuptools python-wheel))
(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 "8.1.12")
(source (origin
(method url-fetch)
(uri (pypi-uri "thinc" version))
(sha256
(base32
"0lx37vl84y2jcsfn9sphdzbjny2jjyfb85llrrvz0xmig5f2rlcx"))))
(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-cymem
python-murmurhash
python-numpy
python-packaging
python-preshed
python-pydantic-2
python-setuptools
python-srsly
python-wasabi))
(native-inputs (list python-cython python-mock python-pytest
python-setuptools python-wheel))
(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-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
python-setuptools
python-wheel))
(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 "0.5.13")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pynndescent" version))
(sha256
(base32 "1yq0k15964klz7135gpa7rcpixywzs4zxmcp8p4fw7haxv058hnp"))))
(build-system pyproject-build-system)
(native-inputs (list python-pytest python-setuptools python-wheel))
(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 "1.0.2")
(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 "1jn15h8b53z6ah47y51y8y4m0mk20xr6l2kd27ffr0hxswbifmkv"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
;; Benchmarks require the 'macosko2015' data files.
(add-after 'unpack 'delete-benchmark
(lambda _
(delete-file-recursively "benchmarks")))
(add-before 'check 'preparations
(lambda _
;; Numba needs a writable dir to cache functions.
(setenv "NUMBA_CACHE_DIR" "/tmp")
;; Rebuild extensions to run tests.
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs (list python-cython-3 python-pytest python-setuptools
python-wheel))
(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)))
;; XXX: Potentially it is an abandonware, no releases or any updates since
;; 2021, consider to remove when become incompatible with propagated inputs.
(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 pyproject-build-system)
;; There are no tests on PyPI, tests in git repo require an old release of
;; python-scikit-learn
(arguments '(#:tests? #f))
(native-inputs
(list python-setuptools-next))
(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 "2.7.1")
;; 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
"073w45azq496x4bhrh8mdywcrg3gk33n13w1pqh1kiykw826ld9b"))))
(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"
;; These need datasets, which needs jax, so it could only live in
;; the guix-science channel.
"--ignore-glob=tests/datalab/**"
;; Tries to download datasets from the internet at runtime.
"--ignore=tests/test_dataset.py"
;; Test requiring not packaged dataset.
"--ignore=tests/spurious_correlation/test_correlation_visualizer.py"
"--ignore=tests/spurious_correlation/test_spurious_correlation.py")
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'remove-datasets
(lambda _
(delete-file "tests/datalab/conftest.py"))))))
(propagated-inputs
(list python-numpy
python-pandas
python-scikit-learn
python-termcolor
python-tqdm))
(native-inputs
(list ;; python-dataset ; https://github.com/huggingface/datasets
python-pytest
python-pytorch
python-setuptools
python-torchvision
python-typing-extensions
python-wheel))
(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 python-setuptools python-wheel))))
(define-public python-cma
(package
(name "python-cma")
(version "4.2.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "cma" version))
(sha256
(base32
"17wv4r80av3cpr3dqad7jf7bwnjahk4bgagqlkqxjp8zfmg60s0q"))))
(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" "cma.test")))))))
(native-inputs (list python-pytest python-setuptools-next))
(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 "0.11.1")
(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 "1xh7cwcz38g7qk9y4668bxv4qc33wwv6q0gkql6d0dzwv59s0q5v"))
(file-name (git-file-name name version))))
(build-system pyproject-build-system)
(native-inputs (list python-pytest python-setuptools python-wheel))
(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
(package
(name "python-autograd")
(version "1.8.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/HIPS/autograd")
(commit (string-append "v" version))))
(sha256
(base32 "054pkhzz0h9p1jzva8774wb9dj7rvax4rcpr8ava971kbimdr2lk"))
(file-name (git-file-name name version))))
(build-system pyproject-build-system)
(native-inputs
(list python-hatchling
python-pytest
python-pytest-cov
python-pytest-xdist))
(propagated-inputs
(list python-future
python-numpy))
(home-page "https://github.com/HIPS/autograd")
(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 python-torchdiffeq
;; There are neither releases nor tags.
(let ((commit "a88aac53cae738addee44251288ce5be9a018af3")
(revision "0"))
(package
(name "python-torchdiffeq")
(version (git-version "0.2.5" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/rtqichen/torchdiffeq")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0c2zqbdxqvd5abfpk0im6rcy1ij39xvrmixc6l9znb6bhcxk2jra"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
'(list "-k" "not test_seminorm" "tests/run_all.py")))
(propagated-inputs (list python-numpy python-scipy python-pytorch))
(native-inputs (list python-pytest python-setuptools))
(home-page "https://github.com/rtqichen/torchdiffeq")
(synopsis "ODE solvers and adjoint sensitivity analysis in PyTorch")
(description
"This tool provides ordinary differential equation solvers implemented
in PyTorch. Backpropagation through ODE solutions is supported using the
adjoint method for constant memory cost.")
(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-setuptools ; For pkg_resources.
python-six
python-tqdm))
(native-inputs
(list python-black
python-nose
python-pymongo
python-pytest
python-wheel))
(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 "1.13.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "deepxde" version))
(sha256
(base32
"11fm9c717pf2j5kb7skvy1nshdqz76m783ndxsd3q3lr5lkqg087"))))
(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
python-setuptools-scm python-wheel))
(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 "01aadd7c19372e3eacadec88caabd86162f33d69")
(revision "2"))
(package
(name "kaldi")
(version (git-version "0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/kaldi-asr/kaldi")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"08l31g256wl81fsrm1dvi0d2rq2vk5zq7ihbbiw7hp51iwg2miif"))
(patches
(search-patches "kaldi-openblas-0.3.29-compatibility.patch"
"kaldi-ignore-failing-test.patch"))))
(build-system gnu-build-system)
(arguments
(list
#:test-target "test"
#:configure-flags
(let ((fst (this-package-input "openfst")))
#~(list "--use-cuda=no"
"--shared"
(string-append "--openblas-root="
#$(this-package-input "openblas"))
(string-append "--fst-root=" #$fst)
(string-append "--fst-version=" #$(package-version fst))))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "src")))
(replace 'configure
(lambda* (#:key build system inputs configure-flags
#:allow-other-keys)
(when (not (or (string-prefix? "x86_64" system)
(string-prefix? "i686" system)))
(substitute* "makefiles/linux_openblas.mk"
(("-msse -msse2") "")))
(substitute* "makefiles/default_rules.mk"
(("/bin/bash") (which "bash")))
(substitute* "Makefile"
(("ext_depend: check_portaudio")
"ext_depend:"))
(substitute* '("online/Makefile"
"onlinebin/Makefile"
"gst-plugin/Makefile")
(("../../tools/portaudio/install")
(assoc-ref inputs "portaudio")))
(substitute* "matrix/Makefile" ;temporary test bypass
(("matrix-lib-test sparse-matrix-test") ""))
;; This `configure' script doesn't support variables passed as
;; arguments, nor does it support "prefix".
(substitute* "configure"
(("check_for_slow_expf;") "")
;; This affects the RPATH and also serves as the installation
;; directory.
(("KALDILIBDIR=`pwd`/lib")
(string-append "KALDILIBDIR=" #$output "/lib")))
(mkdir-p #$output) ; must exist
(setenv "CONFIG_SHELL" (which "bash"))
(apply invoke "./configure" configure-flags)))
(add-after 'build 'build-ext-and-gstreamer-plugin
(lambda _
(invoke "make" "-C" "online" "depend")
(invoke "make" "-C" "online")
(invoke "make" "-C" "onlinebin" "depend")
(invoke "make" "-C" "onlinebin")
(invoke "make" "-C" "gst-plugin" "depend")
(invoke "make" "-C" "gst-plugin")))
;; TODO: also install the executables.
(replace 'install
(lambda _
(let* ((inc (string-append #$output "/include"))
(lib (string-append #$output "/lib")))
(mkdir-p lib)
;; The build phase installed symlinks to the actual
;; libraries. Install the actual targets.
(for-each (lambda (file)
(let ((target (readlink file)))
(delete-file file)
(install-file target lib)))
(find-files lib "\\.so"))
;; Install headers
(for-each (lambda (file)
(let ((target-dir (string-append inc "/" (dirname file))))
(install-file file target-dir)))
(find-files "." "\\.h"))
(install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
(string-append lib "/gstreamer-1.0"))))))))
(inputs
(list alsa-lib
`(,gfortran "lib")
glib
gstreamer
jack-1
openblas
openfst
portaudio
python))
(native-inputs
(list `(,glib "bin") ; glib-genmarshal
grep
sed
pkg-config
which))
(home-page "https://kaldi-asr.org/")
(synopsis "Speech recognition toolkit")
(description "Kaldi is an extensible toolkit for speech recognition
written in C++.")
(license license:asl2.0))))
(define kaldi-for-vosk
;; Commit of branch "vosk"
(let* ((commit "bc5baf14231660bd50b7d05788865b4ac6c34481")
(revision "1")
(openfst openfst-for-vosk))
(package
(inherit kaldi)
(name "kaldi")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/alphacep/kaldi")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1y3d6918srr7cn5r72v5wvbdwz9p9j2bjw1x78sfis2r2k60lllw"))
(patches
(search-patches "kaldi-openblas-0.3.29-compatibility.patch"))))
(inputs
(list alsa-lib
glib
gstreamer
jack-2
openblas
openfst
portaudio
python))
(arguments
(list
#:test-target "test"
#:make-flags '(list "online2" "lm" "rnnlm")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "src")))
(replace 'configure
(lambda _
(let ((portaudio #$(this-package-input "portaudio"))
(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$OPENBLASLIBDIR -lopenblas "
"-L" openblas "/lib -lopenblas")))
(mkdir-p #$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 #$output "/lib")))
;; The build phase installed symlinks to the actual
;; libraries. Install the actual targets.
(for-each (lambda (file)
(let ((target (readlink file)))
(delete-file file)
(install-file target lib)))
(find-files lib "\\.so"))
;; Install headers
(for-each (lambda (file)
(let ((target-dir (string-append inc "/" (dirname file))))
(install-file file target-dir)))
(find-files "." "\\.h")))))))))))
(define-public gst-kaldi-nnet2-online
(let ((commit "7888ae562a65bd7e406783ce2c33535bc66a30ef")
(revision "3"))
(package
(name "gst-kaldi-nnet2-online")
(version (git-version "0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/alumae/gst-kaldi-nnet2-online")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0xp59a6lmx1y24i8bkmxcm27lhm5x5m6y41670yjzhamcbnx8jcr"))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #f ; there are none
#:make-flags
(let ((kaldi (this-package-input "kaldi"))
(bash (this-package-native-input "bash")))
#~(list (string-append "SHELL=" #$bash "/bin/bash")
(string-append "KALDI_ROOT=" #$(package-source kaldi))
(string-append "KALDILIBDIR=" #$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 ((fst-version #$(package-version
(this-package-input "openfst"))))
(setenv "CXXFLAGS"
(string-append
"-fPIC -DOPENFST_VER="
(string-join (string-split fst-version #\.) "0")))
(setenv "CPLUS_INCLUDE_PATH"
(string-join
(append (map (lambda (dir)
(search-input-directory inputs dir))
'("/include/glib-2.0"
"/lib/glib-2.0/include"
"/include/gstreamer-1.0"))
(list (getenv "CPLUS_INCLUDE_PATH")))
":")))
(substitute* "Makefile"
(("include \\$\\(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 _
(install-file
"libgstkaldinnet2onlinedecoder.so"
(string-append #$output "/lib/gstreamer-1.0")))))))
(inputs
(list glib gstreamer jansson openfst kaldi))
(native-inputs
(list bash `(,glib "bin") 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"))
;; XXX: Tests are broken beyond repair and are mingled in the
;; source directory. Remove them to avoid installing them.
;; See https://github.com/nicolas-graves/kaldi-gstreamer-server
;; for a fork that tries to repair them, to no avail.
(snippet #~(for-each delete-file
'("kaldigstserver/test-buffer.py"
"kaldigstserver/decoder_test.py"
"kaldigstserver/decoder2_test.py")))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
#:modules ((guix build utils)
(guix build gnu-build-system)
(srfi srfi-26))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda _
;; Migrate to Glib.MainLoop.
(substitute* (find-files "kaldigstserver" "\\.py")
(("GObject\\.threads_init\\(\\)") "")
(("GObject") "GLib"))
;; 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\\('\\\\.*") ")"))
(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"))
(wrap (lambda (wrapper what)
(with-output-to-file wrapper
(lambda _
(format #t "#!~a
export GUIX_PYTHONPATH=~a
export GI_TYPELIB_PATH=~a:${GI_TYPELIB_PATH}
export GST_PLUGIN_SYSTEM_PATH=~a:${GST_PLUGIN_SYSTEM_PATH}
exec ~a ~a~a \"$@\"~%"
(which "bash")
(getenv "GUIX_PYTHONPATH")
(getenv "GI_TYPELIB_PATH")
(getenv "GST_PLUGIN_SYSTEM_PATH")
(which "python") share what)))
(chmod wrapper #o555))))
(for-each wrap
(list server client worker)
(list "master_server.py"
"client.py"
"worker.py")))))))))
(inputs
(list gstreamer
gst-kaldi-nnet2-online
gst-plugins-base
gst-plugins-good
kaldi
python-wrapper
python-pygobject
python-pyyaml
python-tornado-6))
(home-page "https://github.com/alumae/kaldi-gstreamer-server")
(synopsis "Real-time full-duplex speech recognition server")
(description "This is a real-time full-duplex speech recognition server,
based on the Kaldi toolkit and the GStreamer framework and implemented in
Python.")
(license license:bsd-2))))
(define-public tensorflow-lite
(package
(name "tensorflow-lite")
(version "2.13.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tensorflow/tensorflow")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"09mfskmpvpbq919wibnw3bnhi1y3hkx3qrzm72gdr0gsivn1yb3w"))
(patches (search-patches "tensorflow-lite-unbundle.patch"))))
(build-system cmake-build-system)
(arguments
(list
#:build-type "Release"
#:modules '((ice-9 match)
(guix build utils)
(guix build cmake-build-system))
#:configure-flags
#~(list
;; "-DTFLITE_KERNEL_TEST=ON" ; TODO: build tests
;; so cmake can be used to find this from other packages
"-DTFLITE_ENABLE_INSTALL=ON"
;; Use Guix's own packages as dependencies.
"-DCMAKE_FIND_PACKAGE_PREFER_CONFIG=ON"
"-DTFLITE_ENABLE_GPU=ON"
"-DTFLITE_ENABLE_RUY=ON"
"-DTFLITE_ENABLE_XNNPACK=ON"
;; TODO: turn on Farmhash
;;"-DSYSTEM_FARMHASH=ON"
(string-append "-Dabsl_DIR=" #$(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")
"/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=" #$(this-package-input "ruy")
"/lib/cmake/ruy")
;; Don't fetch the sources. We have these already
"-Dgemmlowp_POPULATED=TRUE"
"-Degl_headers_POPULATED=TRUE"
"-Dfp16_headers_POPULATED=TRUE"
"-Dopencl_headers_POPULATED=TRUE"
"-Dopengl_headers_POPULATED=TRUE"
"-Dvulkan_headers_POPULATED=TRUE"
"-Dgoogletest_POPULATED=TRUE"
"-Dgoogle_benchmark_POPULATED=TRUE"
"-Dnsync_POPULATED=TRUE"
"-Dre2_POPULATED=TRUE"
"-Dxnnpack_POPULATED=TRUE"
"-DFFT2D_SOURCE_DIR=/tmp/fft2d"
"-DFARMHASH_SOURCE_DIR=/tmp/farmhash"
(string-append "-Dgemmlowp_ROOT=" #$(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 'copy-sources 'opencl-fix
(lambda _ (substitute* "delegates/gpu/cl/opencl_wrapper.h"
(("cl_ndrange_kernel_command_properties_khr")
"cl_command_properties_khr"))))
(add-after 'opencl-fix 'absl-fix
(lambda _ (substitute* '(
"delegates/gpu/cl/cl_operation.h"
"delegates/gpu/common/task/qcom_thin_filter_desc.cc"
"delegates/gpu/common/tasks/special/thin_pointwise_fuser.cc")
(("#include <vector>")
"#include <vector>\n\n#include \"absl/strings/str_cat.h\"\n"))))
(add-after 'opencl-fix 'stdint-fix
(lambda _ (substitute* "kernels/internal/spectrogram.cc"
(("#include <math.h>")
"#include <math.h>\n#include <cstdint>\n"))))
(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)
("cpuinfo" ,cpuinfo)
("eigen" ,eigen)
("fp16" ,fp16)
("flatbuffers" ,flatbuffers-23.1)
("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)
("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
(list
#:configure-flags #~(list "-DGOOGLE_TEST=ON")))
(native-inputs
(list googletest 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 dmlc-core-next
;; Apache Tvm needs the latest code from git commits in May 2024 or later.
(let ((commit "13341857549852a9a86b1894b5ba84c6276ab381")
(revision "1"))
(package
(inherit dmlc-core)
(name "dmlc-core")
(version (git-version "0.5" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dmlc/dmlc-core")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1hj6h103lal3cm5mnry9lrm3d7aij89rxv46yv6y49vzd5hbnfbd")))))))
(define-public xgboost
(package
(name "xgboost")
(version "1.7.6")
(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 "16fbm5y3hn6ccflmbdlmn7krrdq7c0az3mxd8j1d23s9ky8niw05"))))
(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
#:tests? #f ; all tests require network access
#: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 #$(package-version xgboost))))
(mkdir-p (string-append xgbdir "/lib"))
(symlink libxgboost (string-append xgbdir "/lib"
"/libxgboost.so"))))))))
(native-inputs
(list python-pandas python-pytest python-scikit-learn python-setuptools
python-wheel))
(inputs
(list xgboost))
(propagated-inputs
(list python-numpy python-scipy))
(synopsis "Python interface for the XGBoost library")))
(define-public python-iml
(package
(name "python-iml")
(version "0.6.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "iml" version))
(sha256
(base32
"1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
(build-system pyproject-build-system)
(propagated-inputs
(list python-ipython python-numpy python-pandas python-scipy))
(native-inputs
(list python-nose python-setuptools-next))
(home-page "https://github.com/interpretable-ml/iml")
(synopsis "Interpretable Machine Learning (iML) package")
(description "Interpretable ML (iML) is a set of data type objects,
visualizations, and interfaces that can be used by any method designed to
explain the predictions of machine learning models (or really the output of
any function). It currently contains the interface and IO code from the Shap
project, and it will potentially also do the same for the Lime project.")
(license license:expat)))
(define-public gloo
(let ((version "0.0.0") ; no proper version tag
(commit "c7b7b022c124d9643957d9bd55f57ac59fce8fa2")
(revision "3"))
(package
(name "gloo")
(version (git-version version revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/facebookincubator/gloo")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0xsp2m2if3g85l0c3cx9l0j3kz36j3kbmz9mai6kchdhrs13r7d5"))))
(build-system cmake-build-system)
(native-inputs
(list googletest))
(inputs
(append (list openssl-1.1)
(if (supported-package? rdma-core)
(list rdma-core)
'())))
(arguments
(list #:configure-flags #~'("-DBUILD_SHARED_LIBS=ON"
"-DBUILD_TEST=1"
"-DCMAKE_CXX_STANDARD=17"
#$@(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")
(supported-systems %64bit-supported-systems)
(license license:bsd-3))))
(define-public python-tensorly
(package
(name "python-tensorly")
(version "0.9.0")
(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
"01xdkhzwq7s18pp6433d4dhyblmlhjs87acagxh73vfsqyknb9h3"))))
(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
python-setuptools python-wheel))
(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 "0.5.9")
(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 "0pkniia9lccdbshwl4sh2iria7dny13qk0flkk67msb777sm5bmn"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; XXX: this one fails with unusually large deviation from the expected
;; result.
'(list "-k" "not test_umap_update_large")
#: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 python-setuptools python-wheel))
(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)))
;; Requires AVX2 on x86_64-linux.
(define-public nnpack
(let ((version "0.0")
(commit "70a77f485e8b934224f3a79efd8edcd84cd377b8")
(revision "2"))
(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
"0c4pw926279s3rlx7mg4l4vhnfy6dh374n6w7zqhcn0bxpym1hv1"))
(patches (search-patches "nnpack-system-libraries.patch"))))
(build-system cmake-build-system)
;; XXX: The test suite runs but it's very expensive. On x86_64-linux, it
;; requires AVX2 instructions.
(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
`(,python
,@(if (target-x86-64?) (list python-peachpy) '())
,python-six))
;; Supported for Linux.
(supported-systems '("x86_64-linux" "armhf-linux" "aarch64-linux"))
(license license:bsd-2))))
(define-public qnnpack
(let ((commit "7d2a4e9931a82adc3814275b6219a03e24e36b4c")
(revision "0"))
(package
(name "qnnpack")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pytorch/qnnpack")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1dgzriiaz9arsrfwhx42y4l74wbzn6xvdmllfb66v4pmvi5gpxc5"))
(modules '((guix build utils)))
(snippet
'(delete-file-recursively "deps"))))
(build-system cmake-build-system)
(arguments
(list
;; The shared library build fails with linker errors, so we build the
;; static library with -fPIC as in the bundled PyTorch version.
#:configure-flags
''("-DQNNPACK_LIBRARY_TYPE=static"
"-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-cmake
(lambda _
(substitute* "CMakeLists.txt"
(("IF.*SOURCE_DIR.*")
"IF(FALSE)\n")
(("IF\\(NOT TARGET.*")
"IF(FALSE)\n")
(("TARGET_LINK_LIBRARIES.*(fxdiv|psimd|fp16)\\).*")
"")
(("(TARGET_LINK_LIBRARIES.*) fp16 (.*)" _ before after)
(string-append before " " after))))))))
(inputs (list clog cpuinfo fp16 fxdiv psimd pthreadpool))
(native-inputs (list googletest googlebenchmark))
(home-page "https://github.com/pytorch/qnnpack")
(synopsis "Quantized Neural Network PACKage")
(description "QNNPACK is a library for low-precision neural network
inference. It contains the implementation of common neural network operators
on quantized 8-bit tensors.")
(supported-systems
'("armhf-linux" "aarch64-linux" "i686-linux" "x86_64-linux"))
(license license:bsd-3))))
(define-public xnnpack
;; There's currently no tag on this repo.
(let ((version "0.0")
(commit "51a0103656eff6fc9bfd39a4597923c4b542c883")
(revision "4"))
(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
"0j4smj8yaxw6r14caqn0dgb8j8mnsq34zp8ixxn11zmgbab306ly"))
(modules '((guix build utils)
(ice-9 ftw)
(ice-9 textual-ports)
(srfi srfi-26)))
(snippet
'(begin
(when (directory-exists? "bench/models")
(delete-file-recursively "bench/models"))
;; Remove autogenerated files, which contain the string
;; "Auto-generated file"
(for-each
(lambda (dir)
(for-each
(lambda (name)
(let ((path (string-append dir "/" name)))
(when (call-with-input-file path
(lambda (port)
(string-contains
(get-string-all port)
"Auto-generated file")))
(delete-file path))))
(or (scandir dir (negate (cut member <> '("." ".." "simd"))))
'())))
(cons*
"test" "bench" "src/enums" "src/xnnpack" "gen" "cmake/gen"
(filter file-exists?
(map (cut string-append "src/" <> "/gen")
(scandir "src")))))))))
(build-system cmake-build-system)
(arguments
(list
#:build-type "Release" ;; Debugging symbols require a lot of disk space
#:configure-flags
#~(list "-DXNNPACK_USE_SYSTEM_LIBS=YES"
"-DBUILD_SHARED_LIBS=ON"
"-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
"-DXNNPACK_LIBRARY_TYPE=shared"
"-DXNNPACK_BUILD_BENCHMARKS=FALSE"
;; Tests fail to build with -DXNNPACK_LIBRARY_TYPE=shared:
;; https://github.com/google/XNNPACK/issues/6285
"-DXNNPACK_BUILD_TESTS=OFF")
#:tests? #f
#:modules '((ice-9 ftw)
(guix build cmake-build-system)
(guix build utils))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-cmake
(lambda _
(substitute* "CMakeLists.txt"
(("TARGET_INCLUDE_DIRECTORIES\\((pthreadpool|cpuinfo).*") "")
(("AMD64") "x86_64"))))
(add-after 'patch-source-shebangs 'generate-files
(lambda _
;; This script just calls two other scripts.
(delete-file "scripts/generate-tests-and-benchmarks.sh")
;; The bash scripts run all jobs at once and then wait, so we
;; convert them to Makefiles.
(for-each
(lambda (name)
(define counter 0) ; For the targets
(define target-deps "")
(when (and (string-prefix? "generate" name)
(string-suffix? ".sh" name))
(let ((file (string-append "scripts/" name)))
(substitute* file
;; Turn the commands into targets. Avoid comments and
;; lines starting with - (rest of multilines).
(("\
^[[:space:]]*([^ #-].*/.*(\\.sh|\\.py|-o |--output)[^&]*).*$"
_ command)
(begin
(set! counter (+ counter 1))
(string-append "\ntarget" (number->string counter)
":" target-deps
"\n\t" command)))
;; Remove trailing '&' characters.
(("&?[[:space:]]*$") "\n")
(("[[:space:]]*wait[[:space:]]*") "")
;; The commands after this line depend on the
;; previous commands in the file.
(("JIT requires assembly files to be generated first.*" all)
(begin
(set! target-deps
(string-append
target-deps " target"
(string-join
(map number->string (iota counter 1)) " target")))
all)))
(display (string-append "Running " name "\n"))
(apply invoke "make" "-s" "-f" file "-j"
(number->string (parallel-job-count))
(map
(lambda (i)
(string-append "target" (number->string i)))
(iota counter 1))))))
(scandir "scripts"))
;; These need to run after the above scripts
(display "Remaining files\n")
(invoke "python3" "tools/update-microkernels.py")
(invoke "python3" "tools/generate-lut-norm-test.py"
"--spec" "test/u8-lut32norm.yaml"
"--output" "test/u8-lut32norm.cc")
;; Check existence to avoid doubling the phase for r-torch.
(when (file-exists? "test/qd8-f16-qb4w-gemm-minmax.yaml")
(invoke "python3" "tools/generate-gemm-test.py"
"--spec" "test/qd8-f16-qb4w-gemm-minmax.yaml"
"--output-test" "test/qd8-f16-qb4w-gemm-minmax.cc"))
(when (file-exists? "test/qd8-f32-qb4w-gemm-minmax.yaml")
(invoke "python3" "tools/generate-gemm-test.py"
"--spec" "test/qd8-f32-qb4w-gemm-minmax.yaml"
"--output-test" "test/qd8-f32-qb4w-gemm-minmax.cc")))))))
(inputs
(list clog
cpuinfo
pthreadpool
googletest
googlebenchmark
fxdiv
fp16
psimd))
(native-inputs
(append (if (target-riscv64?)
;; Required by "#include <riscv_vector.h>"
(list gcc-14)
(list))
(list python-pyyaml python-wrapper)))
(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.")
(supported-systems
'("armhf-linux" "aarch64-linux" "riscv64-linux"
"i686-linux" "x86_64-linux"))
(license license:bsd-3))))
(define-public xnnpack-for-r-torch
(let ((version "0.0")
(commit "51a987591a6fc9f0fc0707077f53d763ac132cbf")
(revision "2"))
(package
(inherit xnnpack)
(version (git-version version revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference (url (package-home-page xnnpack)) (commit commit)))
(file-name (git-file-name (package-name xnnpack) version))
(sha256
(base32
"1rzby82xq8d0rl1d148yz88jh9cpsw5c8b2yw7yg39mi7qmr55rm"))
(modules '((guix build utils)
(ice-9 ftw)
(ice-9 textual-ports)
(srfi srfi-26)))
(snippet
'(begin
;; Remove autogenerated files
(for-each
(lambda (dir)
(let ((gendir (string-append "src/" dir "/gen")))
(when (file-exists? gendir)
(delete-file-recursively gendir)
;; Needed for the scripts generating the files
(mkdir gendir))))
(scandir "src" (negate (cut member <> '("." "..")))))
(delete-file-recursively "google3")
(delete-file "cmake/microkernels.cmake")
;; Additional autogenerated files which contain the string
;; "Auto-generated file"
(for-each
(lambda (dir)
(for-each
(lambda (name)
(let ((path (string-append dir "/" name)))
(when (call-with-input-file path
(lambda (port)
(string-contains
(get-string-all port)
"Auto-generated file")))
(delete-file path))))
(scandir dir (negate (cut member <> '("." ".."))))))
'("test" "bench" "eval" "models" "src/enums" "src/xnnpack"))))))
(arguments
(substitute-keyword-arguments (package-arguments xnnpack)
((#:phases phases)
#~(modify-phases #$phases
(replace 'generate-files
(lambda _
(for-each
(lambda (name)
(when (and (string-prefix? "generate" name)
(string-suffix? ".sh" name)
(not (equal? "generate-amalgamation.sh" name)))
(display (string-append name "\n"))
(invoke "bash" (string-append "scripts/" name))))
(scandir "scripts"))
;; These need to run after the above scripts
(display "Remaining files\n")
(invoke "python3" "tools/update-microkernels.py")
(substitute* "tools/amalgamate-microkernels.py"
(("BUILD") "BUILD.bazel"))
(invoke "bash" "scripts/generate-amalgamation.sh"))))))))))
;; Warning: This package requires AVX2 or AVX-512 instructions.
(define-public fbgemm
(package
(name "fbgemm")
(version "1.2.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pytorch/fbgemm")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0fjs7179iq5hy6nl4nyswnmk90fz87zsg14p7i5bk2vbd2vrq8a3"))
(patches (search-patches "fbgemm-use-system-libraries.patch"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
''("-DFBGEMM_LIBRARY_TYPE=shared")
;; Tests require AVX2 or AVX-512 instructions
#:tests? #f))
(inputs (list asmjit cpuinfo))
(native-inputs (list pkg-config python googletest))
(home-page "https://github.com/pytorch/fbgemm")
(synopsis "Facebook GEneral Matrix Multiplication")
(description "Low-precision, high-performance matrix-matrix
multiplications and convolution library for server-side inference.")
(supported-systems '("x86_64-linux"))
(license license:bsd-3)))
(define-public tensorpipe
(let ((commit "bb1473a4b38b18268e8693044afdb8635bc8351b")
(revision "0"))
(package
(name "tensorpipe")
(version (git-version "0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pytorch/tensorpipe")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0sbpkd69rzybw2j89sjkf4s0j8vkk96d51bsps28894989a75j6v"))
(modules '((guix build utils)))
(snippet
'(delete-file-recursively "third_party"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
''("-DBUILD_SHARED_LIBS=ON")
;; There are no tests
#:tests? #f))
(inputs (list libuv))
(native-inputs (list googletest pkg-config pybind11 libnop))
(home-page "https://github.com/pytorch/tensorpipe")
(synopsis "Tensor-aware point-to-point communication primitive for
machine learning")
(description "TensorPipe provides a tensor-aware channel to transfer
rich objects from one process to another while using the fastest transport for
the tensors contained therein.")
(license license:bsd-3))))
(define-public tvm
;; Include a bug fix post 0.19 release.
(let ((commit "d3a2ed68a42f8b51d8ab1533b62e837b9ea74b8e")
(revision "1"))
(package
(name "tvm")
(version (git-version "0.20.dev0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/apache/tvm")
(commit commit)))
(patches (search-patches "tvm_fix_cpptest_build.patch"))
(file-name (git-file-name name version))
(sha256
(base32 "0ng52i0aydljnlrkyg069838c8b311fynhy5976w74smma2m7v72"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
#~(list "-DUSE_OPENCL=ON"
"-DUSE_VULKAN=ON"
"-DUSE_OPENCL_ENABLE_HOST_PTR=ON"
"-DINSTALL_DEV=ON"
"-DUSE_GTEST=ON"
"-DHIDE_PRIVATE_SYMBOLS=ON" ;per upstream build instructions
"-DUSE_LLVM=llvm-config\\ --ignore-libllvm\\ --link-static"
;; per upstream build instructions
(string-append "-DDLPACK_PATH="
(assoc-ref %build-inputs "dlpack") "/include")
(string-append "-DDMLC_PATH="
(assoc-ref %build-inputs "dmlc-core")
"/include")
(string-append "-DRANG_PATH="
(assoc-ref %build-inputs "rang") "/include"))
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key source tests? #:allow-other-keys)
(when tests?
(begin
(invoke "make" "-j"
(number->string (parallel-job-count)) "cpptest")
;; Disable below the actual run of the tests because
;; several fail due to platform variations (for example,
;; fp16 tests fail because not supported on CPUs).
;;
;; (chdir "..")
;; (invoke (which "bash")
;; (string-append source
;; "/tests/scripts/task_cpp_unittest.sh"))
)))))))
(inputs (list dmlc-core-next
dlpack
libedit
libxml2
llvm-19
opencl-clhpp
opencl-headers
rang
mesa
mesa-opencl
spirv-headers
spirv-tools
vulkan-headers ;TODO; now not building due to missing vta-hw
vulkan-loader
zlib
zstd))
(native-inputs (list bash-minimal
gcc-14
googletest
(module-ref (resolve-interface '(gnu packages debug))
'libbacktrace)
pkg-config
python
python-cython))
(home-page "https://tvm.apache.org/")
(synopsis
"Machine learning compiler framework for CPUs, GPUs and accelerators")
(description
"Apache TVM is a compiler stack for deep learning systems. It is
designed to close the gap between the productivity-focused deep learning
frameworks, and the performance- and efficiency-focused hardware backends.
TVM works with deep learning frameworks to provide end to end compilation to
different backends")
(license license:asl2.0))))
(define-public foxi
(let
((commit "c278588e34e535f0bb8f00df3880d26928038cad")
(revision "0"))
(package
(name "foxi")
(version (git-version "1.4.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/houseroad/foxi")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0q3ssm5hmmvwfwx87mnnajbavzgpahybw6rpn8ysr9r095dwgq5a"))
(patches (search-patches "foxi-fix-build.patch"))))
(build-system cmake-build-system)
(arguments
(list
;; No tests
#:tests? #f))
(home-page "https://github.com/houseroad/foxi")
(synopsis "ONNXIFI with Facebook Extension")
(description "ONNX Interface for Framework Integration is a cross-platform
API for loading and executing ONNX graphs on optimized backends. This package
contains facebook extensions and is used by PyTorch.")
(license license:expat))))
(define-public ideep-pytorch
(package
(name "ideep-pytorch")
(version "3.3.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/intel/ideep")
(commit (string-append "pytorch-rls-v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0y6r938qryi3bnf15rp0fbilsfimdcgmvsa0ygwrn3zifw6386rb"))))
(build-system copy-build-system)
(arguments
(list
#:install-plan
''(("include" "include"))))
(home-page "https://github.com/intel/ideep")
(synopsis "Ideep headers for internal use by PyTorch")
(description "This library is used internally as header-only library by
PyTorch.")
(license license:expat)))
(define-public ideep-pytorch-for-r-torch
(package
(inherit ideep-pytorch)
(version "2.7.3-1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/intel/ideep")
(commit (string-append "pytorch-rls-v" version))))
(file-name (git-file-name (package-name ideep-pytorch) version))
(sha256
(base32
"0hdpkhcjry22fjx2zg2r48v7f4ljrclzj0li2pgk76kvyblfbyvm"))))))
(define %python-pytorch-version "2.8.0")
(define %python-pytorch-src
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pytorch/pytorch")
(commit (string-append "v" %python-pytorch-version))))
(file-name (git-file-name "python-pytorch" %python-pytorch-version))
(sha256
(base32
"0am8mx0mq3hqsk1g99a04a4fdf865g93568qr1f247pl11r2jldl"))
(patches (search-patches "python-pytorch-system-libraries.patch"
"python-pytorch-runpath.patch"
"python-pytorch-without-kineto.patch"
;; Some autogeneration scripts depend on the
;; compile PyTorch library. Therefore, we create
;; dummy versions which are regenerated later.
"python-pytorch-fix-codegen.patch"))
(modules '((guix build utils)))
(snippet
'(begin
;; Bundled or unused code
(for-each
(lambda (dir)
(when (file-exists? dir)
(delete-file-recursively dir)))
'("android"
"aten/src/ATen/native/cuda/cutlass_extensions"
"aten/src/ATen/native/quantized/cpu/qnnpack"
"caffe2/mobile/contrib/libopencl-stub"
"caffe2/mobile/contrib/libvulkan-stub"
"third_party"))
;; Autogenerated files
(for-each
delete-file
'("aten/src/ATen/nnapi/nnapi_wrapper.cpp"
"aten/src/ATen/nnapi/nnapi_wrapper.h"
;; These files contain just lists of floating point values and
;; might be as well hand-written.
;; "test/cpp/api/init_baseline.h"
;; "test/cpp/api/optim_baseline.h"
"test/mobile/test_upgrader_bytecode_table_example.cpp"
"torch/csrc/jit/mobile/upgrader_mobile.cpp"
"torch/csrc/jit/runtime/decomposition_registry_util.cpp"
"torch/csrc/jit/runtime/serialized_shape_function_registry.cpp"
"torch/csrc/jit/tensorexpr/external_functions_codegen.cpp"
"torch/csrc/jit/serialization/mobile_bytecode_generated.h"))
(delete-file-recursively ".github")
(for-each
(lambda (dir)
(for-each
delete-file
(find-files dir "\\.cu$")))
'("aten/src/ATen/native/transformers/cuda/flash_attn"
"aten/src/ATen/native/transformers/cuda/mem_eff_attention"
"aten/src/ATen/native/transformers/hip/flash_attn"))))))
(define-public qnnpack-pytorch
(package
(inherit qnnpack)
(name "qnnpack-pytorch")
(version (string-append "pytorch-" %python-pytorch-version))
(source
(origin
(inherit %python-pytorch-src)
(patches '())
(modules '((guix build utils)
(srfi srfi-26)
(ice-9 ftw)))
(snippet
'(begin
(rename-file "aten/src/ATen/native/quantized/cpu/qnnpack"
"../qnnpack")
(let ((outdir (getcwd)))
(chdir "..")
(rename-file outdir "dummy")
(rename-file "qnnpack" outdir)
(chdir outdir)
(delete-file-recursively "deps"))))))
(arguments
(substitute-keyword-arguments (package-arguments qnnpack)
((#:phases phases #~%standard-phases)
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-cmake
(lambda _
(substitute* "CMakeLists.txt"
(("project\\(.*" orig)
(apply
string-append
orig "\n"
(map (lambda (name)
(string-append
"option(" name " \"\" ON)\n"))
'("USE_SYSTEM_CPUINFO" "USE_SYSTEM_FP16" "USE_SYSTEM_FXDIV"
"USE_SYSTEM_PSIMD" "USE_SYSTEM_PTHREADPOOL"))))
(("if.*SOURCE_DIR.*")
"if(FALSE)\n")
(("if\\(NOT TARGET (clog|gtest|benchmark).*")
"if(FALSE)\n")
(("target_link_libraries.*(fxdiv|psimd|fp16)\\).*")
"")
(("(target_link_libraries.*) fp16 (.*)" _ before after)
(string-append before " " after)))))
(add-after 'unpack 'fix-cstring-include
(lambda _
(substitute* "include/pack_block_sparse.h"
(("#include.*<vector>.*" orig)
(string-append orig "\n#include <cstring>\n")))))
(add-after 'install 'install-missing-headers
(lambda _
(for-each
(lambda (name)
(install-file (string-append "../source/include/" name)
(string-append #$output "/include")))
'("pack_block_sparse.h"
"pytorch_qnnpack.h"
"qnnpack_func.h"))
(copy-recursively
"../source/src/qnnpack"
(string-append #$output "/include/qnnpack"))))))
;; Some tests occasionally fail on i686 due to floating point rounding.
((#:tests? _ #t)
(not (string-prefix? "i686" (or (%current-target-system)
(%current-system)))))))))
;; Please also update python-torchvision when updating this package.
(define-public python-pytorch
(package
(name "python-pytorch")
(version %python-pytorch-version)
(source %python-pytorch-src)
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'cmake-patches
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "cmake/Dependencies.cmake"
(("#POCKETFFT_INCLUDE_DIR")
(string-append
#$(this-package-native-input "pocketfft-cpp") "/include"))
(("#FP16_INCLUDE_DIR")
(string-append
#$(this-package-input "fp16") "/include"))
(("#CONCURRENTQUEUE_INCLUDE_DIR")
(search-input-directory inputs "include/concurrentqueue"))
;; Disable opentelemetry
((".*(add_library|target_include_directories).*opentelemetry.*")
""))
(substitute* "torch/CMakeLists.txt"
((".*opentelemetry.*") ""))
;; Fix Python install directory
(substitute* "caffe2/CMakeLists.txt"
(("\\$\\{Python_SITELIB\\}")
(site-packages inputs outputs)))
;; Ensure httplib::httplib is defined when used.
(substitute* "cmake/Caffe2Config.cmake.in"
(("include *\\(.*Caffe2Targets\\.cmake.*\\)" all)
(string-append "find_package(httplib REQUIRED)\n" all)))))
;; This entry point is broken, because it refers to a module that is
;; (intentionally) not installed
;; (https://github.com/pytorch/pytorch/pull/134729), which causes
;; the 'sanity-check phase to fail.
(add-after 'unpack 'remove-fr-trace-script
(lambda _
(substitute* "setup.py"
(("entry_points\\[\"console_scripts\"\\]\\.append\\(") "("))))
(add-before 'build 'use-system-libraries
(lambda _
(for-each
(lambda (file)
;; Check whether the files exist for the
;; python-pytorch-for-r-torch package
(when (file-exists? file)
(substitute* file
(("\"miniz\\.h\"") "<miniz/miniz.h>")
(("<miniz\\.h>") "<miniz/miniz.h>"))))
'("caffe2/serialize/crc.cc"
"caffe2/serialize/inline_container.cc"
"torch/csrc/inductor/aoti_package/model_package_loader.cpp"))
;; Fix moodycamel/concurrentqueue includes for system package
(substitute* '("c10/util/Semaphore.h"
"c10/test/util/Semaphore_test.cpp")
(("<moodycamel/concurrentqueue\\.h>") "<concurrentqueue.h>")
(("<moodycamel/lightweightsemaphore\\.h>") "<lightweightsemaphore.h>"))
(substitute* "aten/src/ATen/native/vulkan/api/Allocator.h"
(("<include/vk_mem_alloc.h>")
"<vk_mem_alloc.h>"))
;; Fix missing <algorithm> header for std::for_each in Vulkan API
(substitute* "aten/src/ATen/native/vulkan/api/QueryPool.cpp"
(("#include <utility>" all)
(string-append all "\n#include <algorithm>")))
;; For Vulkan
(substitute* "CMakeLists.txt"
(("append_cxx_flag.*-Werror=(return-type|range-loop-construct).*") ""))
(substitute*
(cons*
"torch/csrc/Module.cpp"
(map
(lambda (name)
(string-append
"torch/utils/benchmark/utils/valgrind_wrapper/"
name))
'("compat_bindings.cpp" "timer_callgrind_template.cpp")))
(("<callgrind.h>") "<valgrind/callgrind.h>"))
(setenv "USE_VULKAN" "1")
;; 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")
;; For oneDNN
(setenv "USE_MKLDNN" "1")
;; Only works with CUPTI
(setenv "USE_KINETO" "0")
;; Prevent CMake error by disabling explicitely
(setenv "USE_ITT" "0")
;; Disable on unsupported systems
(if #$(not (member
(or (%current-target-system)
(%current-system))
(package-transitive-supported-systems qnnpack)))
(setenv "USE_QNNPACK" "0"))
(substitute* '("requirements.txt" "setup.py")
(("sympy>=1\\.13\\.3")
"sympy>=1.13.1"))))
(add-after 'use-system-libraries 'skip-nccl-call
(lambda _
;; Comment-out `checkout_nccl()` invokation in build_pytorch().
(substitute* "tools/build_pytorch_libs.py"
(("^[[:blank:]]*checkout_nccl\\(\\)" all)
(string-append "# " all "\n pass")))))
;; PyTorch is still built with AVX2 and AVX-512 support selected at
;; runtime, but these dependencies require it (nnpack only for
;; x86_64).
(add-before 'build 'disable-avx-dependencies
(lambda _
(setenv "USE_FBGEMM" "0")
(if #$(not
(member (or (%current-target-system)
(%current-system))
'("armhf-linux" "aarch64-linux")))
(setenv "USE_NNPACK" "0"))))
(add-after 'use-system-libraries 'set-max-jobs
(lambda _
(setenv "MAX_JOBS" (number->string (parallel-job-count)))))
(add-after 'set-max-jobs 'codegen1
(lambda _
(with-directory-excursion "torch/csrc/jit/tensorexpr"
(setenv "PYTHONPATH" "../../../..")
(invoke "python3" "codegen_external.py")
(setenv "PYTHONPATH" #f))
(invoke "python3" "aten/src/ATen/nnapi/codegen.py")
(invoke "bash" "tools/gen_flatbuffers.sh")
;; Generate dummy files as the generation depends on the compiled
;; library. They are regenerated later.
(setenv "PYTHONPATH" ".")
(invoke "python3"
"torchgen/operator_versions/gen_mobile_upgraders.py"
"dummy")
(setenv "PYTHONPATH" #f)
(invoke "python3"
"torchgen/shape_functions/gen_jit_shape_functions.py"
"dummy")
(invoke "python3"
"torchgen/decompositions/gen_jit_decompositions.py"
"dummy")))
;; Properly generate autogenerated files ...
(add-after 'install 'codegen2
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(invoke "python3"
"torchgen/operator_versions/gen_mobile_upgraders.py")
(invoke "python3"
"torchgen/shape_functions/gen_jit_shape_functions.py")
(invoke "python3"
"torchgen/decompositions/gen_jit_decompositions.py")))
;; ... rebuild their dependencies ...
(add-after 'codegen2 'build2
(lambda _
(invoke "python3" "setup.py" "build")))
;; ... and install again.
(add-after 'build2 'install2
(lambda _
(invoke "python3" "setup.py" "install" (string-append "--prefix=" #$output)
"--no-compile" "--single-version-externally-managed" "--root=/")
(invoke "python" "-m" "compileall"
"--invalidation-mode=unchecked-hash" #$output)))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
;; Run the test suite following the instructions in
;; 'CONTRIBUTING.md'. Unfortunately this doesn't work, unless
;; you set PYTHONPATH or GUIX_PYTHONPATH, but this is done in
;; the codegen2 phase already.
(when tests?
(invoke "python3" "test/run_test.py" "--core"))))
(add-after 'install2 '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)$")))))
(add-after 'install2 'remove-caffe2-onnx-scripts
(lambda _
(let ((bin (string-append #$output "/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 #$output "^entry_points\\.txt$")
(("^convert-.*" all)
(string-append "# " all "\n")))))))
;; Even only the core tests take a very long time to run.
#:tests? #f))
(native-inputs
(list cmake-minimal
doxygen
ideep-pytorch
ninja
nlohmann-json
pocketfft-cpp
python-expecttest
python-pytest-flakefinder
python-pytest-rerunfailures-13
python-pytest-shard
python-pytest-xdist
python-hypothesis
python-types-dataclasses
shaderc
valgrind/pinned))
(inputs
(append
(list asmjit
brotli ; for cpp-httplib
clog
concurrentqueue
cpp-httplib
eigen
flatbuffers
fmt
fp16
fxdiv
gemmlowp
gloo
googletest
googlebenchmark
libuv
miniz-for-pytorch
oneapi-dnnl
openblas
openmpi
openssl ; for cpp-httplib
pthreadpool
protobuf
pybind11
;; qnnpack
qnnpack-pytorch
rdma-core
sleef
tensorpipe
vulkan-headers
vulkan-loader
vulkan-memory-allocator
xnnpack
zlib ; for cpp-httplib
zstd)
;; nnpack requires AVX2 for x86_64-linux
(if (equal? (or (%current-target-system)
(%current-system))
'("aarch64-linux"))
(list nnpack)
'())))
(propagated-inputs
(append
(list cpuinfo
onnx ;propagated for its Python modules
onnx-optimizer
python-astunparse
python-click
python-filelock
python-fsspec
python-future
python-jinja2
python-networkx
python-numpy
python-opt-einsum
python-optree
python-packaging
python-psutil
python-pyyaml
python-requests
python-sympy
python-typing-extensions)))
(home-page "https://pytorch.org/")
(synopsis "Python library for tensor computation and deep neural networks")
;; TODO: Support other 64-bit systems.
(supported-systems '("x86_64-linux" "aarch64-linux"))
(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-torchaudio
(package
(name "python-torchaudio")
(version %python-pytorch-version)
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pytorch/audio")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0snrn6bhc7hcfzs5y4h61dl4dmwxymkf46dygjq6c09nc1jvmxj8"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list
;; XXX: Those packages require additional inputs.
"--ignore=\
test/torchaudio_unittest/prototype/hifi_gan/hifi_gan_cpu_test.py"
"--ignore=\
test/torchaudio_unittest/prototype/hifi_gan/hifi_gan_gpu_test.py"
"--ignore=test/torchaudio_unittest/kaldi_io_test.py"
"--ignore=test/torchaudio_unittest/test_load_save_torchcodec.py"
"--ignore-glob=test/torchaudio_unittest/backend/dispatcher/ffmpeg"
;; XXX: We don't really want to run those tests.
"--ignore-glob=test/torchaudio_unittest/example"
;; XXX: Integration tests require additional data / models.
"--ignore-glob=test/integration_tests"
;; XXX: Those tests are very costly.
"--ignore-glob=test/torchaudio_unittest/functional"
"--ignore-glob=test/torchaudio_unittest/models"
"--ignore=test/torchaudio_unittest/models/models_test.py"
"--ignore=test/torchaudio_unittest/transforms/autograd_cpu_test.py"
"-k" (string-append "not test_torchscript_fails" ; requires BUILD_SOX=1
;; XXX: Unmatching harmless warning message.
" and not test_unknown_subtype_warning"))
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(setenv "BUILD_SOX" "0")
(setenv "USE_FFMPEG" "0")
(substitute* "tools/setup_helpers/extension.py"
(("^( *)\"-DCMAKE_VERBOSE_MAKEFILE=ON\"," all blank)
(string-append
blank "f\"-DCMAKE_INSTALL_RPATH="
(site-packages inputs
`(("out" .
,(assoc-ref inputs "python-pytorch"))))
"/torch/lib;"
(site-packages inputs outputs) "/torchaudio/lib\",\n"
blank "\"-DCMAKE_BUILD_WITH_INSTALL_RPATH=ON\",\n"
all))))))))
(native-inputs
(list cmake
ninja
oneapi-dnnl
python-expecttest
python-parameterized
python-pytest
python-scipy
python-setuptools
python-wheel
sox))
(inputs (package-inputs python-pytorch))
(propagated-inputs (list python-soundfile python-pytorch))
(home-page "https://pytorch.org/audio")
(synopsis
"Data manipulation and transformation for audio signal processing")
(description
"This package provides a machine learning library of popular datasets,
model architectures, and common transformations to apply @code{python-pytorch}
in the audio domain.")
(license license:bsd-2)))
;; This package variant includes the dependencies requiring at least AVX2 or
;; AVX-512.
(define-public python-pytorch-avx
(package/inherit python-pytorch
(name "python-pytorch-avx")
(inputs
(modify-inputs (package-inputs python-pytorch)
(append fbgemm nnpack)))
(arguments
(substitute-keyword-arguments (package-arguments python-pytorch)
((#:phases phases)
#~(modify-phases #$phases
(delete 'disable-avx-dependencies)))))
(supported-systems '("x86_64-linux"))))
(define %python-pytorch-for-r-torch-version "2.0.1")
(define %python-pytorch-for-r-torch-src
(origin
(inherit %python-pytorch-src)
(uri (git-reference
(url "https://github.com/pytorch/pytorch")
(commit (string-append "v" %python-pytorch-for-r-torch-version))))
(file-name (git-file-name "python-pytorch"
%python-pytorch-for-r-torch-version))
(sha256
(base32
"0iirrn687i7sfv0p0i7dn89x3rf13a7l8y1y5h190h51yjxpxqxa"))
(patches (search-patches
"python-pytorch-for-r-torch-system-libraries.patch"
"python-pytorch-runpath.patch"
"python-pytorch-without-kineto.patch"
;; Some autogeneration scripts depend on the
;; compile PyTorch library. Therefore, we create
;; dummy versions which are regenerated later.
"python-pytorch-for-r-torch-fix-codegen.patch"))))
(define-public qnnpack-pytorch-for-r-torch
(package
(inherit qnnpack-pytorch)
(version (string-append "pytorch-" %python-pytorch-for-r-torch-version))
(source
(origin
(inherit %python-pytorch-for-r-torch-src)
(patches '())
(modules '((guix build utils)
(srfi srfi-26)
(ice-9 ftw)))
(snippet
(origin-snippet (package-source qnnpack-pytorch)))))))
;; Keep in sync with r-torch
(define-public python-pytorch-for-r-torch
(package
(inherit python-pytorch)
(name "python-pytorch")
(version %python-pytorch-for-r-torch-version)
(source %python-pytorch-for-r-torch-src)
(arguments
(substitute-keyword-arguments (package-arguments python-pytorch)
((#:phases phases)
#~(modify-phases #$phases
;; See https://github.com/pytorch/pytorch/issues/61244
(add-after 'unpack 'fix-aten-vec
(lambda _
(substitute*
'("aten/src/ATen/cpu/vec/vec512/vec512_bfloat16.h"
"aten/src/ATen/cpu/vec/vec256/vec256_bfloat16.h")
(("map\\(const __") "map(__"))))))))
(native-inputs
(modify-inputs (package-native-inputs python-pytorch)
(replace "ideep-pytorch" ideep-pytorch-for-r-torch)))
(inputs
(modify-inputs (package-inputs python-pytorch)
(prepend foxi)
(prepend qnnpack)
(replace "qnnpack-pytorch" qnnpack-pytorch-for-r-torch)
(replace "oneapi-dnnl" oneapi-dnnl-for-r-torch)
(replace "xnnpack" xnnpack-for-r-torch)))
(propagated-inputs
(modify-inputs (package-propagated-inputs python-pytorch)
(append python-filelock
python-jinja2
python-networkx
python-opt-einsum
python-sympy)))))
(define-public python-pytorch-geometric
(let ((commit "85cf9fc12b1138c1f2adbed8a761356c3f4197e7")
(revision "0"))
(package
(name "python-pytorch-geometric")
(version (git-version "2.6.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pyg-team/pytorch_geometric/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"104v3w9yv7akyxpyd8aq85mw1mncql8mvr1p1b34ph09csqh68hq"))))
(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"
;; Requires the nonfree MKL on CPU.
"--ignore=test/nn/models/test_graph_unet.py"
"-k" (string-append
;; Permissions error
"not test_packaging"
;; Unknown multiprocessing failure
" and not test_data_share_memory"
;; 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"
;; Failed when switched to python@3.11
;; typing module internals
" and not test_type_repr"))
#: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
'("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
python-xxhash))
(native-inputs
(list openssl
python-flit-core-next
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 "0.5.70")
(source (origin
(method url-fetch)
(uri (pypi-uri "lightning_cloud" version))
(sha256
(base32
"11xx7w7ypyf6bzwz7pbdakap68a1lnsv3icis8wm8magkfglash2"))))
(arguments (list #:tests? #f)) ; no tests in PyPI archive.
(build-system pyproject-build-system)
(propagated-inputs (list python-boto3
python-click
python-fastapi
python-multipart
python-protobuf
python-pyjwt
python-requests
python-rich
python-six
python-urllib3
python-uvicorn
python-websocket-client))
(native-inputs (list python-setuptools python-wheel))
(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 "0.14.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "lightning_utilities" version))
(sha256
(base32
"1xg9cngdz9dsxwcpcmzf28q306i15hw58h54allhb41q4wzziqip"))))
(build-system pyproject-build-system)
(native-inputs
(list python-coverage
python-setuptools
python-wheel))
(propagated-inputs
(list python-importlib-metadata
python-packaging
python-typing-extensions))
(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 "0.8.0")
(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
"066sal7hzpk9gsb6pk61sa9x01ckjbjb2mc8c69nc7aghqqrpqjs"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "-k" (string-append
;; 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"
;; This test fails with PyTorch 2.7.0 due to stricter
;; torch.load weights_only behavior.
" and not test_exp_sets_with_diffent_lengths")
"tests")))
(native-inputs
(list python-flask
python-pytest
python-flask-compress
python-parameterized
python-scikit-learn
python-setuptools))
(propagated-inputs
(list python-matplotlib
python-numpy
python-pytorch
python-tqdm))
(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 "4.2.1")
(source
(origin
;; There is no tests data in PyPI archive.
(method git-fetch)
(uri (git-reference
(url "https://github.com/magmax/python-readchar/")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"16ypci664l54ka6ickwkpaa2id14h9h00y7z24z0bv0szld4mrxg"))))
(build-system pyproject-build-system)
(native-inputs
(list python-pytest
python-pytest-cov
python-setuptools-next))
(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
(let ((commit "1617f70428a791b2d81c392d6a0b8a078d8e7fb1")
(revision "0"))
(package
(name "python-pytorch-lightning")
(version (git-version "2.5.2" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Lightning-AI/pytorch-lightning")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1i11n4094a8ysb7cj1lww23nh0mk3d9licw9c9pgzws2m0qy70yd"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; The tests train a model. They are much too expensive for our
;; purposes, so we only run the core tests.
'(list "-m" "not cloud and not tpu"
"tests/tests_pytorch/core"
"-k"
(string-append
;; Some multiprocessing complaint.
"not test_result_reduce_ddp"
;; FutureWarning is raised.
" and not test_result_collection_restoration"
;; These need tensorboard
" and not test_property_logger"
" and not test_property_loggers"))
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'patch-version-detection
(lambda _
;; We do have pytorch 2.4.0, but the version comparison fails.
(substitute* "src/lightning/fabric/utilities/imports.py"
(("_TORCH_GREATER_EQUAL_2_4 =.*")
"_TORCH_GREATER_EQUAL_2_4 = 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
python-fsspec
python-inquirer
python-jsonargparse
python-lightning-cloud
python-lightning-utilities
python-numpy
python-packaging
python-pytorch
python-pyyaml
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
python-setuptools-next))
(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 "1.4.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Lightning-AI/torchmetrics")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0371kx2fpp46rlhzkafa7397kp1lirgykpzk9g12kxsqypb67v1l"))))
(build-system pyproject-build-system)
(arguments
(list
;; Tests require many additional dependencies
#:tests? #f))
(propagated-inputs
(list python-numpy python-packaging python-pytorch
python-typing-extensions
python-lightning-utilities))
(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/torchmetrics")
(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 "0.23.0")
(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
"1d09xwblldgzmzfdlrsyx6mgv939z4yi1hqanm9yx63cs2mr7w85"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file-recursively "android")
(delete-file-recursively "ios")))))
(build-system pyproject-build-system)
(arguments
(list
;; The test suite is expensive and there is no easy way to subset it.
#:tests? #f
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'setenv
(lambda _
(let ((jpegdir #$(this-package-input "libjpeg-turbo")))
(setenv "TORCHVISION_INCLUDE"
(string-append jpegdir "/include/"))
(setenv "TORCHVISION_LIBRARY"
(string-append jpegdir "/lib/"))))))))
(inputs
(list ffmpeg
libpng
libjpeg-turbo))
(propagated-inputs
(list python-numpy
python-typing-extensions
python-requests
python-pillow
python-pillow-simd
python-pytorch))
(native-inputs
(list pybind11
python-pytest
python-setuptools
python-wheel
which))
(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
;; Latest release is nine years old.
(let ((commit "fbd434a5b5562c88b91a95e6476e11dbb7735436")
(revision "0"))
(package
(name "python-torchfile")
(version (git-version "0.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bshillingford/python-torchfile/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1f03ks5n3i3cdh16wx5ysxsxh0ai9vpf0k5pdx759vf31f4niz36"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python3" "tests.py")))))))
(propagated-inputs
(list python-numpy python-setuptools-next))
(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-geomloss
(package
(name "python-geomloss")
(version "0.2.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "geomloss" version))
(sha256
(base32 "1szsjpcwjlvqiiws120fwn581a6hs8gm9si8c75v40ahbh44f729"))))
(build-system pyproject-build-system)
;; There are no automated tests.
(arguments (list #:tests? #false))
(propagated-inputs (list python-numpy python-pytorch))
(native-inputs (list python-setuptools python-wheel))
(home-page "https://www.kernel-operations.io/geomloss/")
(synopsis
"Geometric loss functions between point clouds, images and volumes")
(description
"The GeomLoss library provides efficient GPU implementations for:
@itemize
@item Kernel norms (also known as Maximum Mean Discrepancies).
@item Hausdorff divergences, which are positive definite generalizations of
the Chamfer-ICP loss and are analogous to log-likelihoods of Gaussian Mixture
Models.
@item Debiased Sinkhorn divergences, which are affordable yet positive and
definite approximations of Optimal Transport (Wasserstein) distances.
@end itemize")
(license license:expat)))
(define-public python-tokenizers
(package
(name "python-tokenizers")
(version "0.19.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tokenizers" version))
(sha256
(base32 "1qw8mjp0q9w7j1raq1rvcbfw38000kbqpwscf9mvxzfh1rlfcngf"))
(modules '((guix build utils)
(ice-9 ftw)))
(snippet
#~(begin ;; Only keeping bindings.
(for-each (lambda (file)
(unless (member file '("." ".." "bindings" "PKG-INFO"))
(delete-file-recursively file)))
(scandir "."))
(for-each (lambda (file)
(unless (member file '("." ".."))
(rename-file (string-append "bindings/python/" file) file)))
(scandir "bindings/python"))
(delete-file-recursively ".cargo")
(substitute* "Cargo.toml"
(("^path = .*")
(format #f "version = ~s~%" #$version)))))))
(build-system cargo-build-system)
(arguments
(list
#:install-source? #f
#:cargo-test-flags ''("--no-default-features")
#:imported-modules `(,@%cargo-build-system-modules
,@%pyproject-build-system-modules)
#:modules '((guix build cargo-build-system)
((guix build pyproject-build-system) #:prefix py:)
(guix build utils))
#:phases
#~(modify-phases %standard-phases
(add-after 'check 'python-check
(lambda _
(copy-file "target/release/libtokenizers.so"
"py_src/tokenizers/tokenizers.so")
(invoke "python3"
"-c" (format #f
"import sys; sys.path.append(\"~a/py_src\")"
(getcwd))
"-m" "pytest"
"-s" "-v" "./tests/")))
(add-after 'install 'install-python
(lambda _
(let* ((pversion #$(version-major+minor (package-version python)))
(lib (string-append #$output "/lib/python" pversion
"/site-packages/"))
(info (string-append lib "tokenizers-"
#$(package-version this-package)
".dist-info")))
(mkdir-p info)
(copy-file "PKG-INFO" (string-append info "/METADATA"))
(copy-recursively
"py_src/tokenizers"
(string-append lib "tokenizers"))))))))
(native-inputs
(list pkg-config python-minimal python-pytest))
(inputs
(cons oniguruma (cargo-inputs 'python-tokenizers)))
(home-page "https://huggingface.co/docs/tokenizers")
(synopsis "Implementation of various popular tokenizers")
(description
"This package provides an implementation of today’s most used tokenizers,
with a focus on performance and versatility.")
(license license:asl2.0)))
(define-public python-transformers
(package
(name "python-transformers")
(version "4.44.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "transformers" version))
(sha256
(base32 "09h84wqqk2bgi4vr9d1m3dsliard99l53n96wic405gfjb61gain"))))
(build-system pyproject-build-system)
(arguments
;; Missing inputs.
(list #:test-flags
'(list "--ignore=tests/test_modeling_tf_common.py"
"--ignore=tests/test_configuration_common.py"
"--ignore=tests/test_pipeline_mixin.py"
"--ignore=tests/test_sequence_feature_extraction_common.py")))
;; The imported package contains ~60 more inputs, but they don't seem
;; necessary to build a minimal version of the package.
(propagated-inputs
(list python-filelock
python-huggingface-hub
python-numpy
python-pytorch
python-pyyaml
python-regex
python-requests
python-safetensors
python-tokenizers
python-tqdm))
(native-inputs
(list python-parameterized
python-pytest python-setuptools python-wheel))
(home-page "https://github.com/huggingface/transformers")
(synopsis "Machine Learning for PyTorch and TensorFlow")
(description
"This package provides easy download of thousands of pretrained models to
perform tasks on different modalities such as text, vision, and audio.
These models can be applied on:
@itemize
@item Text, for tasks like text classification, information extraction,
question answering, summarization, translation, and text generation, in over
100 languages.
@item Images, for tasks like image classification, object detection, and
segmentation.
@item Audio, for tasks like speech recognition and audio classification.
@end itemize
Transformer models can also perform tasks on several modalities combined, such
as table question answering, optical character recognition, information
extraction from scanned documents, video classification, and visual question
answering.
This package provides APIs to quickly download and use those pretrained models
on a given text, fine-tune them on your own datasets and then share them with
the community. At the same time, each Python module defining an architecture
is fully standalone and can be modified to enable quick research experiments.
Transformers is backed by the three most popular deep learning libraries —
Jax, PyTorch and TensorFlow — with a seamless integration between them.")
(license license:asl2.0)))
(define-public ctranslate2
(package
(name "ctranslate2")
(version "4.6.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/OpenNMT/CTranslate2")
(commit (string-append "v" version))))
(file-name (git-file-name "CTranslate2" version))
(sha256 (base32 "0sngxjq5rmrgjabgxfazdnhfn3wpfi62n226f4k47cx1xjjkllcd"))
(patches (search-patches "ctranslate2-local-build.patch"))))
(build-system cmake-build-system)
(arguments
(list
;; XXX: mkl and openblas seem incompatible.
#:configure-flags `(list "-DBUILD_TESTS=ON"
"-DWITH_ACCELERATE=OFF"
"-DWITH_RUY=OFF"
"-DWITH_DNNL=ON"
"-DWITH_CUDA=OFF"
"-DWITH_CUDNN=OFF"
"-DWITH_MKL=OFF"
"-DWITH_OPENBLAS=ON")
#:modules '((guix build cmake-build-system)
((guix build gnu-build-system) #:prefix gnu:)
(guix build utils))
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:rest args)
(apply (assoc-ref gnu:%standard-phases 'check)
#:test-target "ctranslate2_test" args))))))
(native-inputs (list libomp
cxxopts
spdlog
googletest
cpu-features
oneapi-dnnl
openblas))
(home-page "https://opennmt.net/CTranslate2/")
(synopsis "Fast inference engine for Transformer models")
(description "CTranslate2 is a C++ and Python library for efficient
inference with Transformer models.
The project implements a custom runtime that applies many performance
optimization techniques such as weights quantization, layers fusion, batch
reordering, etc., to accelerate and reduce the memory usage of Transformer
models on CPU and GPU.")
(license license:expat)))
(define-public python-ctranslate2
(package/inherit ctranslate2
(name "python-ctranslate2")
(build-system pyproject-build-system)
(arguments
(list
;; XXX: tests require the eole python project.
#:tests? #f
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'cd-to-build-dir
(lambda _
(chdir "python"))))))
(native-inputs (list ctranslate2
python-setuptools
python-wheel
pybind11-2.10
python-pyyaml
python-numpy))))
(define-public python-hmmlearn
(package
(name "python-hmmlearn")
(version "0.3.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "hmmlearn" version))
(sha256
(base32
"1v24rkqjjf67w2rys25qxa3vk30bf23m7zn1ilihqzi5qp25sg0x"))))
(properties
'((updater-extra-native-inputs . ("pybind11" "python-setuptools-scm"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; _flapack.error: (liwork>=max(1,10*n)||liwork==-1) failed for 10th
;; keyword liwork: dsyevr:liwork=1
#~(list "-k" (string-join
(list "not test_fit_mcgrory_titterington1d"
"test_common_initialization"
"test_initialization")
" and not "))
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'set-core-count
(lambda _
;; "Could not find the number of physical cores", so we tell it
;; how many cores to use.
(setenv "LOKY_MAX_CPU_COUNT" "1")))
(add-before 'check 'build-extensions
(lambda _
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(propagated-inputs
(list python-numpy python-scikit-learn python-scipy))
(native-inputs
(list pybind11
python-pytest
python-setuptools
python-setuptools-scm
python-wheel
util-linux)) ;for lscpu
(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
(package
(name "liblantern")
(version "0.13.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mlverse/torch")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1yy5xpn9mi5qm7k4w7040d6frpixm9ifs46v1cn9b6bpc1qs1a02"))))
(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 "0.5.12")
(source (origin
(method url-fetch)
(uri (pypi-uri "lap" version))
(sha256
(base32
"1za4mf5nd7vzwd24sy2mfxrk8mnwq7d8rv6h96yh8v5flx7422sp"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags #~(list "-v" #$output)
#:phases
#~(modify-phases %standard-phases
(add-after 'check 'check-cleanup
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(for-each
delete-file-recursively
(find-files #$output
(lambda (file stat)
(or (member (basename file)
'("tests" ".pytest_cache"))))
#:directories? #t))))))))
(propagated-inputs
(list python-numpy))
(native-inputs
(list python-cython python-pytest python-setuptools python-wheel))
(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 "0.2.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "visdom" version))
(sha256
(base32 "0x05faxh45bh1zz8afjhzjy49jrqv4dkhaw1ainhajl1r39i3ac4"))))
(build-system pyproject-build-system)
(arguments (list #:tests? #f)) ;tests require launching the server
(native-inputs
(list python-setuptools-next))
(propagated-inputs
(list python-jsonpatch
python-networkx
python-numpy
python-pillow
python-requests
python-scipy
python-six
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 git-fetch)
(uri (git-reference
(url "https://github.com/pyro-ppl/pyro-api")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "17x7niagx43cajqq67dxmssr7q94db6axyg154y7vqdxzp25hf7g"))))
(build-system pyproject-build-system)
(arguments '(#:tests? #false)) ;requires pyro
(native-inputs
(list python-flake8
python-ipython
python-pytest
python-setuptools
python-sphinx
python-sphinx-rtd-theme
python-wheel))
(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 "1.9.1")
;; 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 "0q87d0frgzn1ljnpbyxmj582yfn6zy3m960m3ab826h4rpzybxhf"))))
(build-system pyproject-build-system)
(arguments
;; Tests take too long.
;; XXX: Maybe select the most important test modules.
(list #:tests? #f))
(propagated-inputs
(list python-numpy
python-opt-einsum
python-pyro-api
python-pytorch
python-tqdm))
(native-inputs (list python-setuptools python-wheel))
(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 "0.6")
(source (origin
(method url-fetch)
(uri (pypi-uri "linear_operator" version))
(sha256
(base32
"0m56f3zrm8xh1bpwh4g7jfc79rf4j94g6zmz663b58pig4w6dqm9"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-jaxtyping
python-mpmath
python-pytorch
python-scipy))
(native-inputs (list python-pytest
python-setuptools
python-setuptools-scm
python-typeguard
python-wheel))
(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 "1.14")
(source (origin
(method url-fetch)
(uri (pypi-uri "gpytorch" version))
(sha256
(base32
"13cs6dx8qa5j4ygji9w5xbmaqc68ihqyzz33fyyf9qa6d8gc2b03"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags
#~(list "-k" (string-append
;; test_deprecated_methods fails with an AssertionError.
"not test_deprecated_methods"
;; This test is flaky: Expects gradients of 0 exactly,
;; can get negligible ones (e-10 to e-16).
" and not test_optimization_optimal_error")
;; Ignore lenghty tests of little relevance.
"--ignore=test/examples/")))
(propagated-inputs (list python-jaxtyping
python-linear-operator
python-mpmath
python-scikit-learn
python-scipy))
(native-inputs (list python-nbval
python-pytest
python-setuptools
python-setuptools-scm
python-wheel))
(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 python-botorch
(package
(name "python-botorch")
(version "0.15.1")
(source (origin
(method git-fetch) ;no tests in PyPI
(uri (git-reference
(url "https://github.com/pytorch/botorch")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1c6p5h5gypiyj59820q2w3k7rx715r3vxxcr5mnwdjbhi4l2q47a"))))
(build-system pyproject-build-system)
(arguments
;; 7 failed, 1502 passed, 1 skipped, 1 deselected, 807 warnings
(list #:test-flags #~(list "-k"
(string-append
"not test_all_cases_covered"
" and not test_input_constructors"
" and not test_gen"
" and not test_mock"
" and not test_evaluation"))
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'pretend-version
;; The version string is usually derived via setuptools-scm,
;; but without the git metadata available, the version string
;; is set to '0.0.0'.
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
#$(package-version this-package)))))))
(propagated-inputs (list python-gpytorch
python-linear-operator
python-multipledispatch
python-pyre-extensions
python-pyro-ppl
python-pytorch
python-scipy
python-threadpoolctl
python-typing-extensions))
(native-inputs (list python-pytest
python-setuptools
python-setuptools-scm
python-wheel))
(home-page "https://botorch.org")
(synopsis "Bayesian Optimization in PyTorch")
(description
"BoTorch is a library for Bayesian Optimization built on PyTorch.")
(license license:expat)))
(define-public vosk-api
(let* ((openfst openfst-for-vosk)
(kaldi kaldi-for-vosk))
(package
(name "vosk-api")
(version "0.3.50")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/alphacep/vosk-api")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0rm7c1n9iv4y9q6a860rqiy2bdawxjhbfd993lms1ly86vwyai8k"))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #f
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "src")))
(replace 'configure
(lambda _
(let* ((openfst #$(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 "))
(("-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$"))))))))
(inputs (list kaldi openfst openblas))
(home-page "https://alphacephei.com/vosk/")
(synopsis "Speech recognition toolkit based on @code{kaldi}")
(description "This package provides a speech recognition toolkit based
on @code{kaldi}. It supports more than 20 languages and dialects - English,
Indian English, German, French, Spanish, Portuguese, Chinese, Russian,
Turkish, Vietnamese, Italian, Dutch, Catalan, Arabic, Greek, Farsi, Filipino,
Ukrainian, Kazakh, Swedish, Japanese, Esperanto, Hindi, Czech, Polish. The
program works offline, even on lightweight devices. Portable per-language
models are about 50Mb each, and there are much bigger and precise models
available.
Vosk API provides a streaming API allowing to use it @emph{on-the-fly} and
bindings for different programming languages. It allows quick reconfiguration
of vocabulary for better accuracy, and supports speaker identification beside
simple speech recognition.")
(license license:asl2.0))))
(define-public python-vosk
(package
(inherit vosk-api)
(name "python-vosk")
(build-system pyproject-build-system)
(propagated-inputs
(list python-cffi python-requests python-tqdm python-srt python-websockets))
(inputs (list vosk-api))
(native-inputs
(list python-setuptools python-wheel))
(arguments
(list
#:tests? #f ;; TODO There are tests but not run through Makefile.
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'config
(lambda _
(chdir "python")
(setenv "VOSK_SOURCE" #$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=["
"'" #$vosk-api "/lib'"
"],\n\t"
"libraries=['vosk', 'python3.11'],\n\t"
"include_dirs=["
"'" #$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 "03ce043a6d569a5bb9a715be6a8e45d8ba0930fd")
(revision "2"))
(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 "0ksnlpy2jcldxamq7bsbcgxgafcmgxkbjccd4fwmmn0y814kkz9k"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "package/python"))))))
(native-inputs (list python-setuptools python-wheel))
(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 python-wheel))
(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 "3.5.3")
(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 "1m2d7qlbfk86rmvmpvx2k3rc2k0l9hf9qpa54jl44670ls9n8i7w"))
(modules '((guix build utils)
(ice-9 rdelim)))
;; Copyright date used by code generation script
(snippet
'(for-each
(lambda (file)
(with-atomic-file-replacement
file
(lambda (in out)
(let loop ((line (read-line in 'concat)))
(if (string-contains line "Copyright")
(display line out)
(loop (read-line in 'concat)))))))
'("include/oneapi/dnnl/dnnl_debug.h"
"src/common/dnnl_debug_autogenerated.cpp"
"tests/benchdnn/dnnl_debug_autogenerated.cpp"
"tests/benchdnn/dnnl_debug.hpp")))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
`(list
,@(if (target-riscv64?)
(list #:configure-flags '("-DDNNL_CPU_RUNTIME=SEQ"))
'())
;; Used in PyTorch
"-DDNNL_EXPERIMENTAL_UKERNEL=ON")
#:phases
'(modify-phases %standard-phases
(add-after 'configure 'codegen
(lambda _
(with-directory-excursion "../source"
(invoke "castxml" "--castxml-cc-gnu-c" "clang"
"--castxml-output=1" "-DDNNL_EXPERIMENTAL_SPARSE"
"-Iinclude" "-I../build/include"
"include/oneapi/dnnl/dnnl_types.h" "-o" "types.xml")
(invoke "python3" "scripts/generate_dnnl_debug.py" "types.xml")
;; Modifies include/oneapi/dnnl/dnnl.hpp
(invoke "python3" "scripts/generate_format_tags.py")))))))
(native-inputs (list castxml clang-17 python))
(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.")
(supported-systems %64bit-supported-systems)
(license license:asl2.0)))
(define-public oneapi-dnnl-for-r-torch
(package
(inherit oneapi-dnnl)
(version "2.7.3")
(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 (package-name oneapi-dnnl) version))
(sha256
(base32 "1zyw5rd8x346bb7gac9a7x3saviw3zvp6aqz2z1l9sv163vmjfz6"))))))
(define-public python-gguf
(package
(name "python-gguf")
(version "0.17.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ggml-org/llama.cpp")
(commit (string-append "gguf-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0lrvj0ahhyj5paxfzk0brps2m8j7fy47n7k4v4xjg9xqqq6wqc2y"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "gguf-py"))))))
(propagated-inputs (list python-numpy python-pyyaml python-pyside-6
python-sentencepiece python-tqdm))
(native-inputs (list python-poetry-core python-pytest))
(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)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'create-tests-module
(lambda _
(with-output-to-file "tests/__init__.py"
(lambda _ (display ""))))))))
(propagated-inputs (list python-cloudpickle python-farama-notifications
python-importlib-metadata python-numpy
python-typing-extensions))
(native-inputs
(list python-pytest python-scipy python-setuptools python-wheel))
(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)))
;; This will build dlib in the process of building python-dlib--and that
;; seems to be intended by upstream. Well, at least it probably optimizes
;; better that way.
(define-public python-dlib
(package
(inherit dlib)
(name "python-dlib")
(build-system pyproject-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'subst
(lambda _
(substitute* "tools/python/CMakeLists.txt"
(("add_subdirectory[(][.][.]/[.][.]/dlib/external/pybind11 pybind11_build[)]")
"find_package(pybind11 CONFIG)")))))))
(native-inputs (list python-setuptools python-wheel cmake-minimal perl pkg-config pybind11))))
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