diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 405 |
1 files changed, 174 insertions, 231 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 3bb09129f5..2f8f2ece3e 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -201,7 +201,7 @@ classification.") (string-append site "libsvm.so.2"))) #t))))) (inputs - `(("python" ,python))) + (list python)) (synopsis "Python bindings of libSVM"))) (define-public ghmm @@ -266,12 +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 @@ -299,7 +299,7 @@ training, HMM clustering, HMM mixtures.") `(#:configure-flags (list "--enable-blast" "CFLAGS=-fcommon"))) (inputs - `(("perl" ,perl))) + (list perl)) (home-page "http://micans.org/mcl/") (synopsis "Clustering algorithm for graphs") (description @@ -355,7 +355,7 @@ networks) based on simulation of (stochastic) flow in graphs.") (("restrict") "restrict_")) #t))))) (native-inputs - `(("ocamlbuild" ,ocamlbuild))) + (list ocamlbuild)) (home-page "https://github.com/fhcrc/mcl") (synopsis "OCaml wrappers around MCL") (description @@ -396,10 +396,7 @@ algorithm.") (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"))) @@ -569,8 +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")) @@ -647,22 +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 @@ -699,17 +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 @@ -748,7 +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 @@ -853,7 +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 @@ -916,9 +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) @@ -977,16 +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 @@ -1034,15 +1017,12 @@ data analysis.") ;; 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 @@ -1066,7 +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 @@ -1086,13 +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 @@ -1129,14 +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 @@ -1158,12 +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 @@ -1189,10 +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 @@ -1218,11 +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 @@ -1256,13 +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") @@ -1303,8 +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=" @@ -1347,17 +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 @@ -1396,20 +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 @@ -1508,21 +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 @@ -1582,11 +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 @@ -2372,7 +2332,7 @@ 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 @@ -2442,14 +2402,11 @@ in a fast and accurate way.") ;; "'['./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 @@ -2495,13 +2452,10 @@ 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 @@ -2522,15 +2476,14 @@ 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 @@ -2586,25 +2539,25 @@ 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 @@ -2639,9 +2592,9 @@ 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 @@ -2671,13 +2624,9 @@ 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") @@ -2726,16 +2675,14 @@ 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 @@ -2769,13 +2716,13 @@ 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 @@ -2869,38 +2816,37 @@ TensorFlow.js, PyTorch, and MediaPipe.") ;; 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-click" ,python-click) - ("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 @@ -2939,13 +2885,10 @@ 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 |