diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 747 |
1 files changed, 460 insertions, 287 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index db8c8dedc8..1cd2fd1308 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -141,20 +141,28 @@ 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 +201,7 @@ classification.") (string-append site "libsvm.so.2"))) #t))))) (inputs - `(("python" ,python))) + (list python)) (synopsis "Python bindings of libSVM"))) (define-public ghmm @@ -258,12 +266,12 @@ classification.") `(("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 @@ -288,9 +296,10 @@ 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 @@ -326,7 +335,7 @@ 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. @@ -339,14 +348,14 @@ 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 @@ -376,16 +385,18 @@ 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"))) @@ -555,8 +566,7 @@ 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")) @@ -633,22 +643,18 @@ 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 @@ -685,17 +691,12 @@ 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 @@ -734,7 +735,7 @@ 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 @@ -839,7 +840,7 @@ 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 @@ -902,9 +903,9 @@ 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) @@ -926,7 +927,7 @@ computing environments.") (define-public python-scikit-learn (package (name "python-scikit-learn") - (version "0.24.2") + (version "1.0.1") (source (origin (method git-fetch) @@ -936,7 +937,7 @@ computing environments.") (file-name (git-file-name name version)) (sha256 (base32 - "0hm92biqwwc87bqnr56lwa5bz77lr7k9q21rdwksnfzq3vsdp2nm")))) + "07k92y78sk4074vh5hp8y63pwl592wgl8azrfp0q84chxk8igfx9")))) (build-system python-build-system) (arguments `(#:phases @@ -944,14 +945,17 @@ 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 $HOME. + (setenv "HOME" "/tmp") - (invoke "pytest" "sklearn" "-m" "not network"))) + (invoke "pytest" "sklearn" "-m" "not network" + ;; This test tries to access the internet. + "-k" "not test_load_boston_alternative")))) (add-before 'reset-gzip-timestamps 'make-files-writable (lambda* (#:key outputs #:allow-other-keys) ;; Make sure .gz files are writable so that the @@ -960,16 +964,12 @@ computing environments.") (for-each make-file-writable (find-files out "\\.gz$")))))))) (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 @@ -994,16 +994,35 @@ 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 @@ -1027,7 +1046,7 @@ 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 @@ -1047,13 +1066,10 @@ for scientific computing and data science (e.g. BLAS and OpenMP).") (base32 "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (propagated-inputs - `(("python-joblib" ,python-joblib) - ("python-llvmlite" ,python-llvmlite) - ("python-numba" ,python-numba) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy))) + (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 @@ -1090,14 +1106,12 @@ for k-neighbor-graph construction and approximate nearest neighbor search.") (setenv "NUMBA_CACHE_DIR" "/tmp") #t))))) (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 @@ -1119,12 +1133,9 @@ visualizing high-dimensional data sets.") (build-system python-build-system) ;; Pandas is only needed to run the tests. (native-inputs - `(("python-pandas" ,python-pandas))) + (list python-pandas)) (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 @@ -1150,10 +1161,10 @@ 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 @@ -1179,11 +1190,9 @@ 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 @@ -1217,13 +1226,11 @@ 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") @@ -1264,8 +1271,7 @@ 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=" @@ -1308,17 +1314,14 @@ 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 @@ -1357,20 +1360,20 @@ 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 @@ -1469,21 +1472,21 @@ 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 @@ -1543,11 +1546,7 @@ 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 @@ -1730,7 +1729,7 @@ Python.") ((guix build python-build-system) #:select (python-version))) #:imported-modules (,@%cmake-build-system-modules - (guix build python-build-system)) + (guix build python-build-system)) #:phases (modify-phases %standard-phases (add-after 'unpack 'set-source-file-times-to-1980 @@ -1740,9 +1739,9 @@ 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") @@ -1760,8 +1759,16 @@ 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 + (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) @@ -1853,8 +1860,7 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive " (("tf_core_cpu grpc") "tf_core_cpu")) ;; This directory is a dependency of many targets. - (mkdir-p "protobuf") - #t)) + (mkdir-p "protobuf"))) (add-after 'configure 'unpack-third-party-sources (lambda* (#:key inputs #:allow-other-keys) ;; This is needed to configure bundled packages properly. @@ -1901,8 +1907,7 @@ set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive " (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" ;; Take protobuf source files from our source package. @@ -1932,17 +1937,20 @@ COMPILE_FLAGS ${target_compile_flags} \ INSTALL_RPATH_USE_LINK_PATH TRUE \ INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n"))))) (add-after 'build 'build-pip-package - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key outputs parallel-build? #:allow-other-keys) (setenv "LDFLAGS" (string-append "-Wl,-rpath=" (assoc-ref outputs "out") "/lib")) - (invoke "make" "tf_python_build_pip_package"))) + (invoke "make" "-j" (if parallel-build? + (number->string (parallel-job-count)) + "1") + "tf_python_build_pip_package"))) (add-after 'build-pip-package 'install-python (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) (wheel (car (find-files "../build/tf_python/dist/" "\\.whl$"))) (python-version (python-version - (assoc-ref inputs "python")))) + (assoc-ref inputs "python")))) (invoke "python" "-m" "pip" "install" wheel (string-append "--prefix=" out)) @@ -2211,7 +2219,7 @@ advanced research.") (install-file file target-dir))) (find-files "." "\\.h$"))))))))) (inputs - `(("abseil-cpp" ,abseil-cpp) + `(("abseil-cpp" ,abseil-cpp-20200923.3) ("eigen" ,eigen-for-tensorflow-lite) ("flatbuffers" ,flatbuffers) ("python" ,python))) @@ -2282,6 +2290,132 @@ learning models. This package provides the \"lite\" variant for mobile devices.") (license license:asl2.0))) +(define-public dmlc-core + (package + (name "dmlc-core") + (version "0.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dmlc/dmlc-core") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1x4ad1jhn84fywlk031fmv1kxyiscclmrqn9hhj8gz0mh7z9vcrh")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGOOGLE_TEST=ON"))) + (native-inputs + `(("googletest" ,googletest) + ("python" ,python-wrapper))) + (home-page "https://github.com/dmlc/dmlc-core") + (synopsis "Common bricks library for machine learning") + (description + "DMLC-Core is the backbone library to support all DMLC projects, +offers the bricks to build efficient and scalable distributed machine +learning libraries.") + (license license:asl2.0))) + +(define-public xgboost + (package + (name "xgboost") + (version "1.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dmlc/xgboost") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (patches (search-patches "xgboost-use-system-dmlc-core.patch")) + (sha256 + (base32 "00liz816ahk9zj3jv3m2fqwlf6xxfbgvpmpl72iklx32vl192w5d")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags (list "-DGOOGLE_TEST=ON"))) + (native-inputs + `(("googletest" ,googletest) + ("python" ,python-wrapper))) + (inputs + (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 python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'preparations + (lambda _ + ;; Move python-package content to parent directory to silence + ;; some warnings about files not being found if we chdir. + (rename-file "python-package/xgboost" "xgboost") + (rename-file "python-package/README.rst" "README.rst") + (rename-file "python-package/setup.cfg" "setup.cfg") + (rename-file "python-package/setup.py" "setup.py") + ;; Skip rebuilding libxgboost.so. + (substitute* "setup.py" + (("ext_modules=\\[CMakeExtension\\('libxgboost'\\)\\],") "") + (("'install_lib': InstallLib,") "")))) + (add-after 'install 'install-version-and-libxgboost + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (pylib (string-append out "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages")) + (xgbdir (string-append pylib "/xgboost")) + (version-file (string-append xgbdir "/VERSION")) + (libxgboost (string-append (assoc-ref inputs "xgboost") + "/lib/libxgboost.so"))) + (with-output-to-file version-file + (lambda () + (display ,(package-version xgboost)))) + (mkdir-p (string-append xgbdir "/lib")) + (symlink libxgboost (string-append xgbdir "/lib" + "/libxgboost.so"))))) + (replace 'check + ;; Python-specific tests are located in tests/python. + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "tests/python" + ;; FIXME: CLI tests fail with PermissionError. + "--ignore" "tests/python/test_cli.py" "-k" + (string-append + "not test_cli_regression_demo" + ;; The tests below open a network connection. + " and not test_model_compatibility" + " and not test_get_group" + " and not test_cv_no_shuffle" + " and not test_cv" + " and not test_training" + ;; FIXME: May pass in the next version. + " and not test_pandas" + ;; "'['./runexp.sh']' returned non-zero exit status 1" + " and not test_cli_binary_classification")))))))) + (native-inputs + (list python-pandas python-pytest python-scikit-learn)) + (inputs + (list xgboost)) + (propagated-inputs + (list python-numpy python-scipy)) + (synopsis "Python interface for the XGBoost library"))) + (define-public python-iml (package (name "python-iml") @@ -2295,12 +2429,9 @@ devices.") "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, @@ -2325,13 +2456,10 @@ 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 @@ -2352,15 +2480,14 @@ 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 @@ -2390,51 +2517,57 @@ with image data, text data, and sequence data.") (delete-file "keras/backend/theano_backend.py") (delete-file "keras/backend/cntk_backend.py") (delete-file "tests/keras/backend/backend_test.py") - ;; FIXME: This doesn't work because Tensorflow is missing the ;; coder ops library. - (delete-file "tests/keras/test_callbacks.py") - #t)) + (delete-file "tests/keras/test_callbacks.py"))) (replace 'check - (lambda _ - ;; These tests attempt to download data files from the internet. - (delete-file "tests/integration_tests/test_datasets.py") - (delete-file "tests/integration_tests/imagenet_utils_test.py") - ;; Backport https://github.com/keras-team/keras/pull/12479. - (substitute* "tests/keras/engine/test_topology.py" - (("np.ones\\(\\(3, 2\\)\\)") - "1.")) - (invoke "python" "-m" "pytest" - ;; The following test fail only in the build container; - ;; skip it. - "-k" "not test_selu")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; These tests attempt to download data files from the internet. + (delete-file "tests/integration_tests/test_datasets.py") + (delete-file "tests/integration_tests/imagenet_utils_test.py") + ;; Backport https://github.com/keras-team/keras/pull/12479. + (substitute* "tests/keras/engine/test_topology.py" + (("np.ones\\(\\(3, 2\\)\\)") + "1.")) + (invoke "python" "-m" "pytest" "tests" + "-p" "no:pep8" + ;; FIXME: python-build-system lacks PARALLEL-TESTS? + "-n" (number->string (parallel-job-count)) + "-k" + (string-append + ;; The following test fails only in the build + ;; container; skip it. + "not test_selu " + ;; The following test was found flaky and removed in + ;; 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 and capable of running on top of TensorFlow. It was developed with a focus on enabling fast experimentation. Use Keras if you need a deep learning library that: - @itemize @item Allows for easy and fast prototyping (through user friendliness, modularity, and extensibility). @@ -2463,9 +2596,9 @@ 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 @@ -2495,13 +2628,9 @@ 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") @@ -2511,6 +2640,55 @@ technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.") (license license:bsd-3))) +(define-public nnpack + (let ((version "0.0") + (commit "c07e3a0400713d546e0dea2d5466dd22ea389c73") + (revision "1")) + (package + (name "nnpack") + (version (git-version version revision commit)) + (home-page "https://github.com/Maratyszcza/NNPACK") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0s0kk3a35w3yzf0q447p72350sbsh4qhg6vm3y2djbj4xpg7jc8v")) + (patches (search-patches "nnpack-system-libraries.patch")))) + (build-system cmake-build-system) + ;; XXX: The test suite runs but it's very expensive, and on x86_64 CPUs + ;; that lack the right ISA extensions, tests fail with: + ;; + ;; Expected equality of these values: + ;; nnp_status_success + ;; Which is: 0 + ;; status + ;; Which is: 51 + ;; + ;; where 51 is 'nnp_status_unsupported_hardware'. + (arguments '(#:tests? #f)) + (synopsis "Acceleration package for neural network computations") + (description + "NNPACK is an acceleration package for neural network computations. +NNPACK aims to provide high-performance implementations of convnet layers for +multi-core CPUs. + +NNPACK is not intended to be directly used by machine learning researchers; +instead it provides low-level performance primitives leveraged in leading deep +learning frameworks, such as PyTorch, Caffe2, MXNet, tiny-dnn, Caffe, Torch, +and Darknet.") + (inputs + (list cpuinfo + fp16 + fxdiv + psimd + pthreadpool + googletest)) + (native-inputs + (list python python-peachpy python-six)) + (license license:bsd-2)))) + (define-public xnnpack ;; There's currently no tag on this repo. (let ((version "0.0") @@ -2542,13 +2720,13 @@ general non-linear dimension reduction.") ;; 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 @@ -2562,7 +2740,7 @@ 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 @@ -2572,7 +2750,7 @@ 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))) @@ -2589,7 +2767,7 @@ TensorFlow.js, PyTorch, and MediaPipe.") ;; needs these. ;; "FP16" "FXdiv" "gemmlowp" "psimd" - "gloo" "googletest" "ios-cmake" + "gloo" "googletest" "ios-cmake" "NNPACK" "onnx" "protobuf" "pthreadpool" "pybind11" "python-enum" "python-peachpy" "python-six" "tbb" "XNNPACK" "zstd")) @@ -2623,13 +2801,10 @@ 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 @@ -2642,39 +2817,40 @@ 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) - ("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-peachpy" ,python-peachpy) - ("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 @@ -2713,13 +2889,10 @@ 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 |