diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 245 |
1 files changed, 206 insertions, 39 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 1cd2fd1308..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) @@ -281,6 +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") @@ -927,7 +1080,7 @@ computing environments.") (define-public python-scikit-learn (package (name "python-scikit-learn") - (version "1.0.1") + (version "1.0.2") (source (origin (method git-fetch) @@ -937,7 +1090,7 @@ computing environments.") (file-name (git-file-name name version)) (sha256 (base32 - "07k92y78sk4074vh5hp8y63pwl592wgl8azrfp0q84chxk8igfx9")))) + "1rli53544vlsnmx4v4xcb8fdqcy5n3zksl4plwp76gsmrppb2lig")))) (build-system python-build-system) (arguments `(#:phases @@ -955,14 +1108,7 @@ computing environments.") (invoke "pytest" "sklearn" "-m" "not network" ;; This test tries to access the internet. - "-k" "not test_load_boston_alternative")))) - (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$")))))))) + "-k" "not test_load_boston_alternative"))))))) (inputs (list openblas)) (native-inputs @@ -1057,16 +1203,24 @@ 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 - (list python-nose)) + (list python-pytest)) (propagated-inputs (list python-joblib python-llvmlite python-numba python-scikit-learn python-scipy)) @@ -1080,17 +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 @@ -1098,13 +1251,15 @@ 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 (list python-cython)) (inputs @@ -1123,17 +1278,15 @@ 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 - (list python-pandas)) + (arguments '(#:tests? #f)) ;no tests on PyPI and no tags in repo (propagated-inputs (list python-numpy python-scipy python-scikit-learn python-joblib)) (home-page "https://epistasislab.github.io/scikit-rebate/") @@ -1679,7 +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 @@ -1862,7 +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 @@ -1900,7 +2055,11 @@ 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") @@ -1936,11 +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") @@ -2321,7 +2490,7 @@ learning libraries.") (define-public xgboost (package (name "xgboost") - (version "1.4.2") + (version "1.5.2") (source (origin (method git-fetch) @@ -2331,7 +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"))) @@ -2404,8 +2573,6 @@ 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 |