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-rw-r--r--gnu/packages/machine-learning.scm825
1 files changed, 477 insertions, 348 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 1a17c73eea..aac5b81a06 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -15,7 +15,7 @@
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
-;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
@@ -35,6 +35,7 @@
(define-module (gnu packages machine-learning)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix gexp)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix download)
@@ -53,6 +54,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages bdw-gc)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cmake)
@@ -61,10 +63,16 @@
#:use-module (gnu packages databases)
#:use-module (gnu packages dejagnu)
#: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 libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
@@ -77,6 +85,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
+ #:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
@@ -90,6 +99,7 @@
#:use-module (gnu packages sqlite)
#:use-module (gnu packages swig)
#:use-module (gnu packages tls)
+ #:use-module (gnu packages video)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ -141,20 +151,28 @@ sparsely connected networks.")
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
- #:phases (modify-phases %standard-phases
- (delete 'configure)
- (replace
- 'install ; no ‘install’ target
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin/")))
- (mkdir-p bin)
- (for-each (lambda (file)
- (copy-file file (string-append bin file)))
- '("svm-train"
- "svm-predict"
- "svm-scale")))
- #t)))))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'build 'build-lib
+ (lambda _
+ (invoke "make" "lib")))
+ (replace 'install ; no ‘install’ target
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/"))
+ (lib (string-append out "/lib/"))
+ (inc (string-append out "/include/libsvm")))
+ (mkdir-p bin)
+ (for-each (lambda (file)
+ (copy-file file (string-append bin file)))
+ '("svm-train"
+ "svm-predict"
+ "svm-scale"))
+ (mkdir-p lib)
+ (install-file "libsvm.so.2" lib)
+ (mkdir-p inc)
+ (install-file "svm.h" inc)))))))
(home-page "https://www.csie.ntu.edu.tw/~cjlin/libsvm/")
(synopsis "Library for Support Vector Machines")
(description
@@ -193,7 +211,7 @@ classification.")
(string-append site "libsvm.so.2")))
#t)))))
(inputs
- `(("python" ,python)))
+ (list python))
(synopsis "Python bindings of libSVM")))
(define-public ghmm
@@ -222,20 +240,7 @@ classification.")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-dir
- (lambda _ (chdir "ghmm") #t))
- (delete 'check)
- (add-after 'install 'check
- (assoc-ref %standard-phases 'check))
- (add-before 'check 'fix-PYTHONPATH
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((python-version (python-version
- (assoc-ref inputs "python"))))
- (setenv "PYTHONPATH"
- (string-append (getenv "PYTHONPATH")
- ":" (assoc-ref outputs "out")
- "/lib/python" python-version
- "/site-packages")))
- #t))
+ (lambda _ (chdir "ghmm")))
(add-after 'enter-dir 'fix-runpath
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "ghmmwrapper/setup.py"
@@ -246,8 +251,7 @@ classification.")
line
"\"-Wl,-rpath="
(assoc-ref outputs "out")
- "/lib\", ")))
- #t))
+ "/lib\", ")))))
(add-after 'enter-dir 'disable-broken-tests
(lambda _
(substitute* "tests/Makefile.am"
@@ -267,18 +271,17 @@ classification.")
line indent)
(string-append indent
"@unittest.skip(\"Disabled by Guix\")\n"
- line)))
- #t)))))
+ line))))))))
(inputs
`(("python" ,python-2) ; only Python 2 is supported
("libxml2" ,libxml2)))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("dejagnu" ,dejagnu)
- ("swig" ,swig)
- ("autoconf" ,autoconf)
- ("automake" ,automake)
- ("libtool" ,libtool)))
+ (list pkg-config
+ dejagnu
+ swig
+ autoconf
+ automake
+ libtool))
(home-page "http://ghmm.org")
(synopsis "Hidden Markov Model library")
(description
@@ -288,6 +291,149 @@ Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
training, HMM clustering, HMM mixtures.")
(license license:lgpl2.0+))))
+(define-public guile-aiscm
+ (package
+ (name "guile-aiscm")
+ (version "0.23.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/wedesoft/aiscm")
+ (commit "c78b91edb7c17c6fbf3b294452f44e91d75e3c67")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "09rdbcr8dinzijyx9h940ann91yjlbg0fangx365llhvy354n840"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:make-flags
+ #~(list (string-append "GUILE_CACHE=" #$output "/lib/guile/3.0/site-ccache")
+ (string-append "GUILE_EXT=" #$output "/lib/guile/3.0/extensions")
+ (string-append "GUILE_SITE=" #$output "/share/guile/site/3.0"))
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'build-reproducibly
+ (lambda _
+ (substitute* "doc/Makefile.am"
+ (("\\$\\(DATE\\)") "1970-01-01"))))
+ (add-after 'unpack 'use-llvm-config
+ (lambda _
+ (substitute* "m4/ax_llvmc.m4"
+ (("llvm-config-13") "llvm-config")
+ ;; For some reason this library is not on the link list.
+ (("(LLVM_LIBS=\"\\$\\(\\$ac_llvm_config_path --libs \\$1\\))\"" _ m)
+ (string-append m " -lLLVMMCJIT\"")))
+
+ ;; Because of this message:
+ ;; symbol lookup error: ./.libs/libguile-aiscm-core.so: undefined symbol: LLVMInitializeX86TargetInfo
+ ;; This probably needs to differ when building on architectures
+ ;; other than x86_64p
+ (substitute* "aiscm/Makefile.am"
+ (("LLVM_LIBS\\)") "LLVM_LIBS) \
+-lLLVMX86AsmParser -lLLVMX86CodeGen -lLLVMX86Desc -lLLVMX86Info"))))
+ ;; Use Clang instead of GCC.
+ (add-before 'configure 'prepare-build-environment
+ (lambda _
+ (setenv "AR" "llvm-ar")
+ (setenv "NM" "llvm-nm")
+ (setenv "CC" "clang")
+ (setenv "CXX" "clang++"))))))
+ (inputs
+ (list ffmpeg
+ freeglut
+ guile-3.0
+ imagemagick
+ libjpeg-turbo
+ libomp
+ libxi
+ libxmu
+ libxpm
+ libxt
+ libxv
+ mesa
+ mjpegtools
+ pandoc
+ pulseaudio))
+ (native-inputs
+ (list clang-13
+ llvm-13
+ pkg-config
+ autoconf
+ automake
+ gettext-minimal
+ libtool
+ which))
+ (home-page "https://wedesoft.github.io/aiscm/")
+ (synopsis "Guile extension for numerical arrays and tensors")
+ (description "AIscm is a Guile extension for numerical arrays and tensors.
+Performance is achieved by using the LLVM JIT compiler.")
+ (license license:gpl3+)))
+
+(define-public guile-aiscm-next
+ (let ((commit "b17ed538c303badc419a7c358d91f266d2a8c354")
+ (revision "1"))
+ (package
+ (inherit guile-aiscm)
+ (name "guile-aiscm-next")
+ (version (git-version "0.23.1" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/wedesoft/aiscm")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0px7r7lfskbp1prdrfrcvrsc4wjrk3ahkigsw4pqvny6zs7jnvc0"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments guile-aiscm)
+ ((#:configure-flags flags '())
+ #~(list (string-append "OPENCV_CFLAGS=-I" #$(this-package-input "opencv")
+ "/include/opencv4")
+ (let ((modules
+ (list "aruco" "barcode" "bgsegm" "bioinspired"
+ "calib3d" "ccalib" "core" "datasets" "dnn"
+ "dnn_objdetect" "dnn_superres" "dpm" "face"
+ "features2d" "flann" "freetype" "fuzzy" "hdf"
+ "hfs" "highgui" "img_hash" "imgcodecs" "imgproc"
+ "intensity_transform" "line_descriptor" "mcc"
+ "ml" "objdetect" "optflow" "phase_unwrapping"
+ "photo" "plot" "quality" "rapid" "reg" "rgbd"
+ "saliency" "shape" "stereo" "stitching"
+ "structured_light" "superres" "surface_matching"
+ "text" "tracking" "video" "videoio" "videostab"
+ "wechat_qrcode" "ximgproc" "xobjdetect" "xphoto")))
+ (format #false "OPENCV_LIBS=~{-lopencv_~a~^ ~}" modules))))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-after 'unpack 'find-clearsilver
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "configure.ac"
+ (("/usr/local/include/ClearSilver")
+ (string-append (assoc-ref inputs "clearsilver")
+ "/include/ClearSilver")))
+ (substitute* "aiscm/Makefile.am"
+ (("-lneo_utl" m)
+ (string-append m " -lstreamhtmlparser")))
+ (setenv "C_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "clearsilver")
+ "/include/ClearSilver:"
+ (or (getenv "C_INCLUDE_PATH") "")))))
+ ;; This test fails because our version of tensorflow is too old
+ ;; to provide tf-string-length.
+ (add-after 'unpack 'disable-broken-test
+ (lambda _
+ (substitute* "tests/test_tensorflow.scm"
+ (("\\(test-eqv \"determine string length" m)
+ (string-append "#;" m)))))))))
+ (inputs
+ (modify-inputs (package-inputs guile-aiscm)
+ (append clearsilver opencv tensorflow libgc)))
+ (native-inputs
+ (modify-inputs (package-native-inputs guile-aiscm)
+ (append protobuf-c))))))
+
(define-public mcl
(package
(name "mcl")
@@ -303,9 +449,10 @@ training, HMM clustering, HMM mixtures.")
"15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
(build-system gnu-build-system)
(arguments
- `(#:configure-flags (list "--enable-blast")))
+ `(#:configure-flags (list "--enable-blast"
+ "CFLAGS=-fcommon")))
(inputs
- `(("perl" ,perl)))
+ (list perl))
(home-page "http://micans.org/mcl/")
(synopsis "Clustering algorithm for graphs")
(description
@@ -341,7 +488,7 @@ networks) based on simulation of (stochastic) flow in graphs.")
(substitute* "setup.ml"
(("LDFLAGS=-fPIC")
(string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))
- (("-std=c89") "-std=gnu99")
+ (("-std=c89") "-std=gnu99 -fcommon")
;; This is a mutable string, which is no longer supported. Use
;; a byte buffer instead.
@@ -354,14 +501,14 @@ networks) based on simulation of (stochastic) flow in graphs.")
((" s;")
" s);"))
(substitute* "myocamlbuild.ml"
- (("std=c89") "std=gnu99"))
+ (("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
- `(("ocamlbuild" ,ocamlbuild)))
+ (list ocamlbuild))
(home-page "https://github.com/fhcrc/mcl")
(synopsis "OCaml wrappers around MCL")
(description
@@ -391,16 +538,18 @@ algorithm.")
(assoc-ref %build-inputs "boost")))
#:phases
(modify-phases %standard-phases
- (add-before
- 'configure 'set-CXXFLAGS
- (lambda _
- (setenv "CXXFLAGS" "-fpermissive ")
- #t)))))
+ (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
- `(("boost" ,boost)
- ("gsl" ,gsl)
- ("libxml2" ,libxml2)
- ("zlib" ,zlib)))
+ (list boost gsl libxml2 zlib))
(native-inputs
`(("gfortran" ,gfortran)
("gfortran:lib" ,gfortran "lib")))
@@ -570,8 +719,7 @@ optimizing, and searching weighted finite-state transducers (FSTs).")
("lzo" ,lzo)
("zlib" ,zlib)))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("rxcpp" ,rxcpp)))
+ (list pkg-config rxcpp))
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(supported-systems '("x86_64-linux"))
@@ -648,22 +796,18 @@ in terms of new algorithms.")
(invoke "make" "install"
"-C" ".setuptools-cmake-build"))))))
(native-inputs
- `(("cmake" ,cmake)
- ("googletest" ,googletest)
- ("pybind11" ,pybind11)
- ("python-coverage" ,python-coverage)
- ("python-nbval" ,python-nbval)
- ("python-pytest" ,python-pytest)
- ("python-pytest-runner" ,python-pytest-runner)))
+ (list cmake
+ googletest
+ pybind11
+ python-coverage
+ python-nbval
+ python-pytest
+ python-pytest-runner))
(inputs
- `(("protobuf" ,protobuf)))
+ (list protobuf))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-protobuf" ,python-protobuf)
- ("python-six" ,python-six)
- ("python-tabulate" ,python-tabulate)
- ("python-typing-extensions"
- ,python-typing-extensions)))
+ (list python-numpy python-protobuf python-six python-tabulate
+ python-typing-extensions))
(home-page "https://onnx.ai/")
(synopsis "Open Neural Network Exchange")
(description
@@ -700,17 +844,12 @@ standard data types.")
(build-system python-build-system)
(arguments (package-arguments onnx)) ;reuse build system tweaks
(native-inputs
- `(("cmake" ,cmake)
- ("python-pytest" ,python-pytest)
- ("python-pytest-runner" ,python-pytest-runner)
- ("python-nbval" ,python-nbval)
- ("python-coverage" ,python-coverage)))
+ (list cmake python-pytest python-pytest-runner python-nbval
+ python-coverage))
(inputs
- `(("onnx" ,onnx)
- ("protobuf" ,protobuf)
- ("pybind11" ,pybind11)))
+ (list onnx protobuf pybind11))
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(synopsis "Library to optimize ONNX models")
(description
"This package provides a C++ and Python library for performing arbitrary
@@ -749,7 +888,7 @@ with a single function call.")
(lambda _
(invoke "ctest"))))))
(native-inputs
- `(("catch" ,catch-framework)))
+ (list catch-framework))
(home-page "http://reactivex.io/")
(synopsis "Reactive Extensions for C++")
(description
@@ -854,7 +993,7 @@ than 8 bits, and at the end only some significant 8 bits are kept.")
'("meta" "profiling" "public" "fixedpoint"
"eight_bit_int_gemm" "internal")))))))))
(native-inputs
- `(("unzip" ,unzip)))
+ (list unzip))
(properties '((hidden? . #t))))))
(define-public dlib
@@ -917,9 +1056,9 @@ than 8 bits, and at the end only some significant 8 bits are kept.")
(invoke "./dtest" "--runall"))
#t))))))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ;; For tests.
- ("libnsl" ,libnsl)))
+ (list pkg-config
+ ;; For tests.
+ libnsl))
(inputs
`(("giflib" ,giflib)
("lapack" ,lapack)
@@ -941,7 +1080,7 @@ computing environments.")
(define-public python-scikit-learn
(package
(name "python-scikit-learn")
- (version "0.24.2")
+ (version "1.0.2")
(source
(origin
(method git-fetch)
@@ -951,7 +1090,7 @@ computing environments.")
(file-name (git-file-name name version))
(sha256
(base32
- "0hm92biqwwc87bqnr56lwa5bz77lr7k9q21rdwksnfzq3vsdp2nm"))))
+ "1rli53544vlsnmx4v4xcb8fdqcy5n3zksl4plwp76gsmrppb2lig"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -959,32 +1098,24 @@ computing environments.")
(add-after 'build 'build-ext
(lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))
(replace 'check
- (lambda _
- ;; Restrict OpenBLAS threads to prevent segfaults while testing!
- (setenv "OPENBLAS_NUM_THREADS" "1")
+ (lambda* (#:key tests? #: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")
+ ;; Some tests require write access to $HOME.
+ (setenv "HOME" "/tmp")
- (invoke "pytest" "sklearn" "-m" "not network")))
- (add-before 'reset-gzip-timestamps 'make-files-writable
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Make sure .gz files are writable so that the
- ;; 'reset-gzip-timestamps' phase can do its work.
- (let ((out (assoc-ref outputs "out")))
- (for-each make-file-writable
- (find-files out "\\.gz$"))))))))
+ (invoke "pytest" "sklearn" "-m" "not network"
+ ;; This test tries to access the internet.
+ "-k" "not test_load_boston_alternative")))))))
(inputs
- `(("openblas" ,openblas)))
+ (list openblas))
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-pandas" ,python-pandas) ;for tests
- ("python-cython" ,python-cython)))
+ (list python-pytest python-pandas ;for tests
+ python-cython))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-threadpoolctl" ,python-threadpoolctl)
- ("python-scipy" ,python-scipy)
- ("python-joblib" ,python-joblib)))
+ (list python-numpy python-threadpoolctl python-scipy python-joblib))
(home-page "https://scikit-learn.org/")
(synopsis "Machine Learning in Python")
(description
@@ -1009,16 +1140,35 @@ data analysis.")
(sha256
(base32
"08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-ext
+ (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))
+ (replace 'check
+ (lambda* (#:key tests? #: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")
+
+ (invoke "pytest" "sklearn" "-m" "not network"
+ "-k"
+ (string-append
+ ;; This test tries to access the internet.
+ "not test_load_boston_alternative"
+ ;; This test fails for unknown reasons
+ " and not test_rank_deficient_design"))))))))
(inputs
- `(("openblas" ,openblas)))
+ (list openblas))
(native-inputs
- `(("python2-pytest" ,python2-pytest)
- ("python2-pandas" ,python2-pandas) ;for tests
- ("python2-cython" ,python2-cython)))
+ (list python2-pytest python2-pandas ;for tests
+ python2-cython))
(propagated-inputs
- `(("python2-numpy" ,python2-numpy)
- ("python2-scipy" ,python2-scipy)
- ("python2-joblib" ,python2-joblib))))))
+ (list python2-numpy python2-scipy python2-joblib)))))
(define-public python-threadpoolctl
(package
@@ -1042,7 +1192,7 @@ data analysis.")
(invoke "pytest"))
#t)))))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list 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
@@ -1053,22 +1203,27 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
(define-public python-pynndescent
(package
(name "python-pynndescent")
- (version "0.5.2")
+ (version "0.5.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pynndescent" version))
(sha256
- (base32 "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr"))))
+ (base32 "10pqqqc3jkpw03cyzy04slxmpgyhqnlgbyk0c1cv7kqr5d0zhzbs"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "-m" "pytest" "--pyargs" "pynndescent")))))))
(native-inputs
- `(("python-nose" ,python-nose)))
+ (list python-pytest))
(propagated-inputs
- `(("python-joblib" ,python-joblib)
- ("python-llvmlite" ,python-llvmlite)
- ("python-numba" ,python-numba)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)))
+ (list 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
@@ -1079,17 +1234,16 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
(define-public python-opentsne
(package
(name "python-opentsne")
- (version "0.5.2")
+ (version "0.6.1")
(source
(origin
- ;; No tests in the PyPI tarball.
- (method git-fetch)
+ (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 (string-append name "-" version "-checkout"))
+ (file-name (git-file-name name version))
(sha256
- (base32 "1hl42wmafydk4fxdx05l180k3canmqw8h9r20fsqq2aq440b09gh"))))
+ (base32 "124nid27lfq1ipfjd2gkynqcmb4khisjb4r05jv42ckfkk4dbsxs"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -1097,22 +1251,22 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
;; Benchmarks require the 'macosko2015' data files.
(add-after 'unpack 'delete-benchmark
(lambda _
- (delete-file-recursively "benchmarks")
- #t))
+ (delete-file-recursively "benchmarks")))
+ (add-after 'unpack 'skip-test
+ (lambda _ ;; TODO: figure out why this test fails.
+ (substitute* "tests/test_correctness.py"
+ (("def test_iris\\(self\\)") "def _test_iris(self)"))))
;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir
(lambda _
- (setenv "NUMBA_CACHE_DIR" "/tmp")
- #t)))))
+ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
(inputs
- `(("fftw" ,fftw)))
+ (list fftw))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-pynndescent" ,python-pynndescent)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)))
+ (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
@@ -1124,22 +1278,17 @@ visualizing high-dimensional data sets.")
(define-public python-scikit-rebate
(package
(name "python-scikit-rebate")
- (version "0.6")
+ (version "0.62")
(source (origin
(method url-fetch)
(uri (pypi-uri "skrebate" version))
(sha256
(base32
- "1h7qs9gjxpzqabzhb8rmpv3jpmi5iq41kqdibg48299h94iikiw7"))))
+ "0n55ghvnv7rxqa5agq6a4892ad0ghha165b0g4ghwr9gqm6ss3dj"))))
(build-system python-build-system)
- ;; Pandas is only needed to run the tests.
- (native-inputs
- `(("python-pandas" ,python-pandas)))
+ (arguments '(#:tests? #f)) ;no tests on PyPI and no tags in repo
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-joblib" ,python-joblib)))
+ (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
@@ -1165,10 +1314,10 @@ standard feature selection algorithms.")
(file-name (git-file-name name version))))
(build-system python-build-system)
(native-inputs
- `(("python-setuptools" ,python-setuptools) ;build fails without this
- ("python-wheel" ,python-wheel)))
+ (list python-setuptools ;build fails without this
+ python-wheel))
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(home-page "https://github.com/CyberAgent/cmaes")
(synopsis "CMA-ES implementation for Python")
(description "This package provides provides an implementation of the
@@ -1194,11 +1343,9 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
(version version)
(build-system python-build-system)
(native-inputs
- `(("python-nose" ,python-nose)
- ("python-pytest" ,python-pytest)))
+ (list python-nose python-pytest))
(propagated-inputs
- `(("python-future" ,python-future)
- ("python-numpy" ,python-numpy)))
+ (list python-future python-numpy))
(arguments
`(#:phases (modify-phases %standard-phases
(replace 'check
@@ -1232,13 +1379,11 @@ main intended application of Autograd is gradient-based optimization.")
"0jlvyn7k81dzrh9ij3zw576wbgiwmmr26rzpdxjn1dbpc3njpvzi"))
(file-name (git-file-name name version))))
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-nose" ,python-nose)))
+ (list python-pytest python-nose))
(inputs
- `(("openmpi" ,openmpi)))
+ (list openmpi))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)))
+ (list python-numpy python-scipy))
(arguments
`(#:configure-flags
'("-DUSE_MPI=ON")
@@ -1279,8 +1424,7 @@ the following advantages:
"04bwzk6ifgnz3fmzid8b7avxf9n5pnx9xcjm61nkjng1vv0bpj8x"))
(file-name (git-file-name name version))))
(inputs
- `(("boost" ,boost)
- ("zlib" ,zlib)))
+ (list boost zlib))
(arguments
`(#:configure-flags
(list (string-append "--with-boost="
@@ -1323,17 +1467,14 @@ interactive learning.")
`(#:tests? #f ; some test files are missing
#:python ,python-2)) ; only Python 2.7 is supported
(propagated-inputs
- `(("python2-numpy" ,python2-numpy)
- ("python2-scipy" ,python2-scipy)
- ("python2-matplotlib" ,python2-matplotlib)
- ("python2-pandas" ,python2-pandas)
- ("python2-scikit-learn" ,python2-scikit-learn)
- ("python2-pysnptools" ,python2-pysnptools)))
+ (list python2-numpy
+ python2-scipy
+ python2-matplotlib
+ python2-pandas
+ python2-scikit-learn
+ python2-pysnptools))
(native-inputs
- `(("unzip" ,unzip)
- ("python2-cython" ,python2-cython)
- ("python2-mock" ,python2-mock)
- ("python2-nose" ,python2-nose)))
+ (list unzip python2-cython python2-mock python2-nose))
(home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
(synopsis "Perform genome-wide association studies on large data sets")
(description
@@ -1372,20 +1513,20 @@ association studies (GWAS) on extremely large data sets.")
" and not test_quadratic1"
" and not test_twoarms"))))))))
(propagated-inputs
- `(("python-cloudpickle" ,python-cloudpickle)
- ("python-future" ,python-future)
- ("python-networkx" ,python-networkx)
- ("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)
- ("python-six" ,python-six)
- ("python-tqdm" ,python-tqdm)))
+ (list python-cloudpickle
+ python-future
+ python-networkx
+ python-numpy
+ python-scipy
+ python-six
+ python-tqdm))
(native-inputs
- `(("python-black" ,python-black)
- ("python-ipython" ,python-ipython)
- ("python-ipyparallel" ,python-ipyparallel)
- ("python-nose" ,python-nose)
- ("python-pymongo" ,python-pymongo)
- ("python-pytest" ,python-pytest)))
+ (list python-black
+ python-ipython
+ python-ipyparallel
+ python-nose
+ python-pymongo
+ python-pytest))
(home-page "https://hyperopt.github.io/hyperopt/")
(synopsis "Library for hyperparameter optimization")
(description "Hyperopt is a Python library for serial and parallel
@@ -1484,21 +1625,21 @@ discrete, and conditional dimensions.")
(string-append lib "/gstreamer-1.0"))
#t))))))
(inputs
- `(("alsa-lib" ,alsa-lib)
- ("gfortran" ,gfortran "lib")
- ("glib" ,glib)
- ("gstreamer" ,gstreamer)
- ("jack" ,jack-1)
- ("openblas" ,openblas)
- ("openfst" ,openfst)
- ("portaudio" ,portaudio)
- ("python" ,python)))
+ (list alsa-lib
+ `(,gfortran "lib")
+ glib
+ gstreamer
+ jack-1
+ openblas
+ openfst
+ portaudio
+ python))
(native-inputs
- `(("glib" ,glib "bin") ; glib-genmarshal
- ("grep" ,grep)
- ("sed" ,sed)
- ("pkg-config" ,pkg-config)
- ("which" ,which)))
+ (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
@@ -1558,11 +1699,7 @@ written in C++.")
(install-file "libgstkaldinnet2onlinedecoder.so" lib)
#t))))))
(inputs
- `(("glib" ,glib)
- ("gstreamer" ,gstreamer)
- ("jansson" ,jansson)
- ("openfst" ,openfst)
- ("kaldi" ,kaldi)))
+ (list glib gstreamer jansson openfst kaldi))
(native-inputs
`(("bash" ,bash)
("glib:bin" ,glib "bin") ; glib-genmarshal
@@ -1642,7 +1779,7 @@ automatically.")
(let* ((server (string-append bin "/kaldi-gst-server"))
(client (string-append bin "/kaldi-gst-client"))
(worker (string-append bin "/kaldi-gst-worker"))
- (PYTHONPATH (getenv "PYTHONPATH"))
+ (PYTHONPATH (getenv "GUIX_PYTHONPATH"))
(GST_PLUGIN_PATH (string-append
(assoc-ref inputs "gst-kaldi-nnet2-online")
"/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
@@ -1651,7 +1788,7 @@ automatically.")
(lambda _
(format #t
"#!~a
-export PYTHONPATH=~a
+export GUIX_PYTHONPATH=~a
export GST_PLUGIN_PATH=~a
exec ~a ~a/~a \"$@\"~%"
(which "bash") PYTHONPATH GST_PLUGIN_PATH
@@ -1695,7 +1832,9 @@ Python.")
(file-name (string-append "tensorflow-" version "-checkout"))
(sha256
(base32
- "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
+ "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))
+ (patches
+ (search-patches "tensorflow-c-api-fix.patch"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; no "check" target
@@ -1755,9 +1894,9 @@ Python.")
;; SOURCE_DATE_EPOCH is respected, which we set to some time in
;; 1980.
(lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
- ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
- (add-after 'unpack 'python3.7-compatibility
+ (add-after 'unpack 'python3.9-compatibility
(lambda _
+ ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
(substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
"tensorflow/python/lib/core/ndarray_tensor.cc"
"tensorflow/python/lib/core/py_func.cc")
@@ -1775,9 +1914,17 @@ Python.")
;; https://github.com/tensorflow/tensorflow/issues/34197
(substitute* (find-files "tensorflow/python" ".*\\.cc$")
(("(nullptr,)(\\ +/. tp_print)" _ _ tp_print)
- (string-append "NULL, " tp_print)))))
- (add-after 'python3.7-compatibility 'chdir
- (lambda _ (chdir "tensorflow/contrib/cmake") #t))
+ (string-append "NULL, " tp_print)))
+
+ ;; Fix the build with numpy >= 1.19.
+ ;; Suggested in https://github.com/tensorflow/tensorflow/issues/41086#issuecomment-656833081
+ (substitute* "tensorflow/python/lib/core/bfloat16.cc"
+ (("void BinaryUFunc\\(char\\*\\* args, npy_intp\\* dimensions, npy_intp\\* steps,")
+ "void BinaryUFunc(char** args, npy_intp const* dimensions, npy_intp const* steps,")
+ (("void CompareUFunc\\(char\\*\\* args, npy_intp\\* dimensions, npy_intp\\* steps,")
+ "void CompareUFunc(char** args, npy_intp const* dimensions, npy_intp const* steps,"))))
+ (add-after 'python3.9-compatibility 'chdir
+ (lambda _ (chdir "tensorflow/contrib/cmake")))
(add-after 'chdir 'disable-downloads
(lambda* (#:key inputs #:allow-other-keys)
(substitute* (find-files "external" "\\.cmake$")
@@ -1792,36 +1939,31 @@ Python.")
;; Sqlite
(("include\\(sqlite\\)") "")
(("\\$\\{sqlite_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "sqlite")
- "/lib/libsqlite3.so"))
+ (search-input-file inputs "/lib/libsqlite3.so"))
(("sqlite_copy_headers_to_destination") "")
;; PNG
(("include\\(png\\)") "")
(("\\$\\{png_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "libpng")
- "/lib/libpng16.so"))
+ (search-input-file inputs "/lib/libpng16.so"))
(("png_copy_headers_to_destination") "")
;; JPEG
(("include\\(jpeg\\)") "")
(("\\$\\{jpeg_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "libjpeg")
- "/lib/libjpeg.so"))
+ (search-input-file inputs "/lib/libjpeg.so"))
(("jpeg_copy_headers_to_destination") "")
;; GIF
(("include\\(gif\\)") "")
(("\\$\\{gif_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "giflib")
- "/lib/libgif.so"))
+ (search-input-file inputs "/lib/libgif.so"))
(("gif_copy_headers_to_destination") "")
;; lmdb
(("include\\(lmdb\\)") "")
(("\\$\\{lmdb_STATIC_LIBRARIES\\}")
- (string-append (assoc-ref inputs "lmdb")
- "/lib/liblmdb.so"))
+ (search-input-file inputs "/lib/liblmdb.so"))
(("lmdb_copy_headers_to_destination") "")
;; Protobuf
@@ -1875,7 +2017,7 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
;; This directory is a dependency of many targets.
(mkdir-p "protobuf")))
(add-after 'configure 'unpack-third-party-sources
- (lambda* (#:key inputs #:allow-other-keys)
+ (lambda* (#:key inputs outputs #:allow-other-keys)
;; This is needed to configure bundled packages properly.
(setenv "CONFIG_SHELL" (which "bash"))
(for-each
@@ -1913,20 +2055,20 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
"re2"))
(rename-file "../build/cub/src/cub/cub-1.8.0/"
- "../build/cub/src/cub/cub/")))
+ "../build/cub/src/cub/cub/")
+
+ (setenv "LDFLAGS"
+ (string-append "-Wl,-rpath="
+ (assoc-ref outputs "out") "/lib"))))
(add-after 'unpack 'fix-python-build
(lambda* (#:key inputs outputs #:allow-other-keys)
(mkdir-p "protobuf-src")
(invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
"-C" "protobuf-src" "--strip-components=1")
(mkdir-p "eigen-src")
- (invoke "tar" "xf" (assoc-ref inputs "eigen:src")
- "-C" "eigen-src" "--strip-components=1")
+ (copy-recursively (assoc-ref inputs "eigen:src") "eigen-src")
(substitute* "tensorflow/contrib/cmake/tf_python.cmake"
- ;; Ensure that all Python dependencies can be found at build time.
- (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
- (string-append m ":" (getenv "PYTHONPATH")))
;; Take protobuf source files from our source package.
(("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
(string-append (getcwd) "/protobuf-src/src/google")))
@@ -1938,7 +2080,7 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
(string-append (getcwd) "/eigen-src/"))
;; Take Eigen headers from our own package.
(("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
- (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
+ (search-input-directory inputs "/include/eigen3")))
;; Correct the RUNPATH of ops libraries generated for Python.
;; TODO: this doesn't work :(
@@ -1953,11 +2095,21 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
COMPILE_FLAGS ${target_compile_flags} \
INSTALL_RPATH_USE_LINK_PATH TRUE \
INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))))
- (add-after 'build 'build-pip-package
+ (add-after 'unpack 'patch-cmake-file-to-install-c-headers
+ (lambda _
+ (substitute* "tensorflow/contrib/cmake/tf_c.cmake"
+ (("if\\(tensorflow_BUILD_PYTHON_BINDINGS" m)
+ (string-append
+ "install(DIRECTORY ${tensorflow_source_dir}/tensorflow/c/ \
+DESTINATION include/tensorflow/c FILES_MATCHING PATTERN \"*.h\")\n" m)))))
+ (add-after 'build 'build-c-bindings
+ (lambda* (#:key outputs parallel-build? #:allow-other-keys)
+ (invoke "make" "-j" (if parallel-build?
+ (number->string (parallel-job-count))
+ "1")
+ "tf_c")))
+ (add-after 'install 'build-pip-package
(lambda* (#:key outputs parallel-build? #:allow-other-keys)
- (setenv "LDFLAGS"
- (string-append "-Wl,-rpath="
- (assoc-ref outputs "out") "/lib"))
(invoke "make" "-j" (if parallel-build?
(number->string (parallel-job-count))
"1")
@@ -2338,7 +2490,7 @@ learning libraries.")
(define-public xgboost
(package
(name "xgboost")
- (version "1.4.2")
+ (version "1.5.2")
(source
(origin
(method git-fetch)
@@ -2348,7 +2500,7 @@ learning libraries.")
(file-name (git-file-name name version))
(patches (search-patches "xgboost-use-system-dmlc-core.patch"))
(sha256
- (base32 "00liz816ahk9zj3jv3m2fqwlf6xxfbgvpmpl72iklx32vl192w5d"))))
+ (base32 "0qx04y7cz8z7qv6bk9q7d7ba9b7xzj53l83l2x9ykdwhzacc3dn0"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DGOOGLE_TEST=ON")))
@@ -2356,7 +2508,7 @@ learning libraries.")
`(("googletest" ,googletest)
("python" ,python-wrapper)))
(inputs
- `(("dmlc-core" ,dmlc-core)))
+ (list dmlc-core))
(home-page "https://xgboost.ai/")
(synopsis "Gradient boosting (GBDT, GBRT or GBM) library")
(description
@@ -2421,19 +2573,14 @@ in a fast and accurate way.")
" and not test_cv_no_shuffle"
" and not test_cv"
" and not test_training"
- ;; FIXME: May pass in the next version.
- " and not test_pandas"
;; "'['./runexp.sh']' returned non-zero exit status 1"
" and not test_cli_binary_classification"))))))))
(native-inputs
- `(("python-pandas" ,python-pandas)
- ("python-pytest" ,python-pytest)
- ("python-scikit-learn" ,python-scikit-learn)))
+ (list python-pandas python-pytest python-scikit-learn))
(inputs
- `(("xgboost" ,xgboost)))
+ (list xgboost))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)))
+ (list python-numpy python-scipy))
(synopsis "Python interface for the XGBoost library")))
(define-public python-iml
@@ -2449,12 +2596,9 @@ in a fast and accurate way.")
"1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
(build-system python-build-system)
(propagated-inputs
- `(("ipython" ,python-ipython)
- ("numpy" ,python-numpy)
- ("pandas" ,python-pandas)
- ("scipy" ,python-scipy)))
+ (list python-ipython python-numpy python-pandas python-scipy))
(native-inputs
- `(("nose" ,python-nose)))
+ (list python-nose))
(home-page "https://github.com/interpretable-ml/iml")
(synopsis "Interpretable Machine Learning (iML) package")
(description "Interpretable ML (iML) is a set of data type objects,
@@ -2479,13 +2623,10 @@ project, and it will potentially also do the same for the Lime project.")
;; The tests require Keras, but this package is needed to build Keras.
(arguments '(#:tests? #f))
(propagated-inputs
- `(("python-h5py" ,python-h5py)
- ("python-numpy" ,python-numpy)))
+ (list python-h5py python-numpy))
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-pytest-pep8" ,python-pytest-pep8)
- ("python-pytest-xdist" ,python-pytest-xdist)))
+ (list python-pytest python-pytest-cov python-pytest-pep8
+ python-pytest-xdist))
(home-page "https://github.com/keras-team/keras-applications")
(synopsis "Reference implementations of popular deep learning models")
(description
@@ -2506,15 +2647,14 @@ models for use with the Keras deep learning framework.")
"1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-six" ,python-six)))
+ (list python-numpy python-six))
(native-inputs
- `(("python-pandas" ,python-pandas)
- ("python-pillow" ,python-pillow)
- ("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-pytest-xdist" ,python-pytest-xdist)
- ("tensorflow" ,tensorflow)))
+ (list python-pandas
+ python-pillow
+ python-pytest
+ python-pytest-cov
+ python-pytest-xdist
+ tensorflow))
(home-page "https://github.com/keras-team/keras-preprocessing/")
(synopsis "Data preprocessing and augmentation for deep learning models")
(description
@@ -2570,25 +2710,25 @@ with image data, text data, and sequence data.")
;; recent versions.
"and not test_stateful_metrics"))))))))
(propagated-inputs
- `(("python-h5py" ,python-h5py)
- ("python-keras-applications" ,python-keras-applications)
- ("python-keras-preprocessing" ,python-keras-preprocessing)
- ("python-numpy" ,python-numpy)
- ("python-pydot" ,python-pydot)
- ("python-pyyaml" ,python-pyyaml)
- ("python-scipy" ,python-scipy)
- ("python-six" ,python-six)
- ("tensorflow" ,tensorflow)
- ("graphviz" ,graphviz)))
+ (list python-h5py
+ python-keras-applications
+ python-keras-preprocessing
+ python-numpy
+ python-pydot
+ python-pyyaml
+ python-scipy
+ python-six
+ tensorflow
+ graphviz))
(native-inputs
- `(("python-pandas" ,python-pandas)
- ("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-pytest-pep8" ,python-pytest-pep8)
- ("python-pytest-timeout" ,python-pytest-timeout)
- ("python-pytest-xdist" ,python-pytest-xdist)
- ("python-sphinx" ,python-sphinx)
- ("python-requests" ,python-requests)))
+ (list python-pandas
+ python-pytest
+ python-pytest-cov
+ python-pytest-pep8
+ python-pytest-timeout
+ python-pytest-xdist
+ python-sphinx
+ python-requests))
(home-page "https://github.com/keras-team/keras")
(synopsis "High-level deep learning framework")
(description "Keras is a high-level neural networks API, written in Python
@@ -2623,9 +2763,9 @@ that:
"1crmqgybzkgkpbmcx16912gsl5qsj49swa0ikx6mhqgph0chrh11"))))
(build-system cmake-build-system)
(native-inputs
- `(("googletest" ,googletest)))
+ (list googletest))
(inputs
- `(("openssl" ,openssl)))
+ (list openssl))
(arguments
`(#:configure-flags '("-DBUILD_TEST=1")
#:phases
@@ -2655,13 +2795,9 @@ These include a barrier, broadcast, and allreduce.")
"02ada2yy6km6zgk2836kg1c97yrcpalvan34p8c57446finnpki1"))))
(build-system python-build-system)
(native-inputs
- `(("python-joblib" ,python-joblib)
- ("python-nose" ,python-nose)))
+ (list python-joblib python-nose))
(propagated-inputs
- `(("python-numba" ,python-numba)
- ("python-numpy" ,python-numpy)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)))
+ (list python-numba python-numpy python-scikit-learn python-scipy))
(home-page "https://github.com/lmcinnes/umap")
(synopsis
"Uniform Manifold Approximation and Projection")
@@ -2710,16 +2846,14 @@ instead it provides low-level performance primitives leveraged in leading deep
learning frameworks, such as PyTorch, Caffe2, MXNet, tiny-dnn, Caffe, Torch,
and Darknet.")
(inputs
- `(("cpuinfo" ,cpuinfo)
- ("fp16" ,fp16)
- ("fxdiv" ,fxdiv)
- ("psimd" ,psimd)
- ("pthreadpool" ,pthreadpool)
- ("googletest" ,googletest)))
+ (list cpuinfo
+ fp16
+ fxdiv
+ psimd
+ pthreadpool
+ googletest))
(native-inputs
- `(("python" ,python)
- ("python-peachpy" ,python-peachpy)
- ("python-six" ,python-six)))
+ (list python python-peachpy python-six))
(license license:bsd-2))))
(define-public xnnpack
@@ -2753,13 +2887,13 @@ and Darknet.")
;; another target with the same name already exists.
#:tests? #f))
(inputs
- `(("cpuinfo" ,cpuinfo)
- ("pthreadpool" ,pthreadpool)
- ("googletest" ,googletest)
- ("googlebenchmark" ,googlebenchmark)
- ("fxdiv" ,fxdiv)
- ("fp16" ,fp16)
- ("psimd" ,psimd)))
+ (list cpuinfo
+ pthreadpool
+ googletest
+ googlebenchmark
+ fxdiv
+ fp16
+ psimd))
(synopsis "Optimized floating-point neural network inference operators")
(description
"XNNPACK is a highly optimized library of floating-point neural network
@@ -2773,7 +2907,7 @@ TensorFlow.js, PyTorch, and MediaPipe.")
(define-public python-pytorch
(package
(name "python-pytorch")
- (version "1.9.0")
+ (version "1.10.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2783,7 +2917,7 @@ TensorFlow.js, PyTorch, and MediaPipe.")
(file-name (git-file-name name version))
(sha256
(base32
- "0cznsh68hwk5761gv7iijb4g6jgjpvs3bbixwpzzmkbkbn2q96c1"))
+ "1ihsjw48qqbikmhxxn17bcdvk2zsjabvkq61q6pvj7dzvrdpkb60"))
(patches (search-patches "python-pytorch-system-libraries.patch"
"python-pytorch-runpath.patch"))
(modules '((guix build utils)))
@@ -2834,13 +2968,10 @@ TensorFlow.js, PyTorch, and MediaPipe.")
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
;; Run the test suite following the instructions in
;; 'CONTRIBUTING.md'. XXX: Unfortunately this doesn't
- ;; work, unless you set PYTHONPATH presumably.
+ ;; work, unless you set GUIX_PYTHONPATH presumably.
(when tests?
- (let ((python-site (site-packages inputs outputs)))
- (setenv "PYTHONPATH"
- (string-append python-site ":"
- (getenv "PYTHONPATH")))
- (invoke "python" "test/run_test.py")))))
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "test/run_test.py"))))
(add-after 'install 'remove-test-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Remove test executables, but keep other executables
@@ -2853,39 +2984,40 @@ TensorFlow.js, PyTorch, and MediaPipe.")
;; XXX: Tests attempt to download data such as
;; <https://raw.githubusercontent.com/pytorch/test-infra/master/stats/slow-tests.json>.
+ ;; We're also missing some Python modules, such as expecttest.
#:tests? #f))
(native-inputs
- `(("cmake" ,cmake)
- ("ninja" ,ninja)))
+ (list cmake ninja))
(inputs
- `(("eigen" ,eigen)
- ;; ("fmt" ,fmt)
- ("fp16" ,fp16)
- ("gemmlowp" ,gemmlowp)
- ("googletest" ,googletest)
- ("googlebenchmark" ,googlebenchmark)
- ("gloo" ,gloo)
- ("nnpack" ,nnpack)
- ("openblas" ,openblas)
- ("openmpi" ,openmpi)
- ("pthreadpool" ,pthreadpool)
- ("protobuf" ,protobuf)
- ("pybind11" ,pybind11)
- ("sleef" ,sleef)
- ("xnnpack" ,xnnpack)
- ("zstd" ,zstd)))
+ (list eigen
+ ;; ("fmt" ,fmt)
+ fp16
+ gemmlowp
+ googletest
+ googlebenchmark
+ gloo
+ nnpack
+ openblas
+ openmpi
+ pthreadpool
+ protobuf
+ pybind11
+ sleef
+ xnnpack
+ zstd))
(propagated-inputs
- `(("python-astunparse" ,python-astunparse)
- ("python-numpy" ,python-numpy)
- ("python-pyyaml" ,python-pyyaml)
- ("python-cffi" ,python-cffi)
- ("python-typing-extensions" ,python-typing-extensions)
- ("python-future" ,python-future)
- ("python-six" ,python-six)
- ("python-requests" ,python-requests)
- ("onnx" ,onnx) ;propagated for its Python modules
- ("onnx-optimizer" ,onnx-optimizer)
- ("cpuinfo" ,cpuinfo)))
+ (list python-astunparse
+ python-click
+ python-numpy
+ python-pyyaml
+ python-cffi
+ python-typing-extensions
+ python-future
+ python-six
+ python-requests
+ onnx ;propagated for its Python modules
+ onnx-optimizer
+ cpuinfo))
(home-page "https://pytorch.org/")
(synopsis "Python library for tensor computation and deep neural networks")
(description
@@ -2924,13 +3056,10 @@ Note: currently this package does not provide GPU support.")
(with-directory-excursion (string-append (assoc-ref outputs "out") "/lib")
(invoke "python" "-m" "pytest"))))))))
(propagated-inputs
- `(("python-cython" ,python-cython)
- ("python-numpy" ,python-numpy)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)
- ("python-setuptools-scm" ,python-setuptools-scm)))
+ (list python-cython python-numpy python-scikit-learn python-scipy
+ python-setuptools-scm))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-pytest))
(home-page "https://github.com/hmmlearn/hmmlearn")
(synopsis "Hidden Markov Models with scikit-learn like API")
(description
generated by cgit v1.2.3 (git 2.50.1) at 2025-08-08 02:33:31 +0000