diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 158 |
1 files changed, 102 insertions, 56 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 988fac3b63..badbcd6deb 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -167,7 +167,12 @@ representations and sentence classification.") (sha256 (base32 "1i699a9m5ndnj8cwzjjf2agb77aawhzrzxfbmn5zrkxridxvnypj")))) (build-system pyproject-build-system) - (propagated-inputs (list python-autograd python-scipy)) + (native-inputs + (list python-setuptools + python-wheel)) + (propagated-inputs + (list python-autograd + python-scipy)) (home-page "https://github.com/CamDavidsonPilon/autograd-gamma") (synopsis "Autograd-compatible approximations to the gamma family of functions") @@ -183,7 +188,7 @@ family of functions.") (build-system pyproject-build-system) (propagated-inputs (list python-numpy python-scipy)) (inputs (list fasttext)) - (native-inputs (list pybind11)))) + (native-inputs (list pybind11 python-setuptools python-wheel)))) (define-public python-funsor (package @@ -196,6 +201,8 @@ family of functions.") (sha256 (base32 "0cgysij0dix0fikyz2x4f8jvaskm5s5a04s07chzaz2dw1fpxdq8")))) (build-system pyproject-build-system) + (arguments ; disable flaky test + (list #:test-flags '(list "-k" "not test_integrate_variable[x23-i]"))) (propagated-inputs (list python-makefun python-multipledispatch python-numpy python-opt-einsum python-typing-extensions)) @@ -210,10 +217,12 @@ family of functions.") python-pytest-xdist python-requests python-scipy + python-setuptools python-sphinx python-sphinx-gallery python-sphinx-rtd-theme - python-torchvision)) + python-torchvision + python-wheel)) (home-page "https://github.com/pyro-ppl/funsor") (synopsis "Tensor-like library for functions and distributions") (description @@ -358,7 +367,8 @@ classification.") "-k" "not testJSONConversionBestEffort"))))))) (propagated-inputs (list python-absl-py python-contextlib2 python-pyyaml python-six)) - (native-inputs (list python-mock python-pytest)) + (native-inputs (list python-mock python-pytest python-setuptools + python-wheel)) (home-page "https://github.com/google/ml_collections") (synopsis "Python collections designed for Machine Learning usecases") (description @@ -550,7 +560,7 @@ Performance is achieved by using the LLVM JIT compiler.") (deprecated-package "guile-aiscm-next" guile-aiscm)) (define-public llama-cpp - (let ((tag "b3907")) + (let ((tag "b4137")) (package (name "llama-cpp") (version (string-append "0.0.0-" tag)) @@ -562,14 +572,14 @@ Performance is achieved by using the LLVM JIT compiler.") (commit tag))) (file-name (git-file-name name tag)) (sha256 - (base32 "0vpqng1lq1r09vi7s1mhqgqgkxn69spp19c2s68i6kk3zbcl7i9b")))) + (base32 "0agm0188f9y2pr15v83a2fm0k9b8wag96qb3ryq4l2g6nkysiqlj")))) (build-system cmake-build-system) (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON" - "-DLLAMA_BLAS=ON" - "-DLLAMA_BLAS_VENDOR=OpenBLAS" + "-DGGML_BLAS=ON" + "-DGGML_BLAS_VENDOR=OpenBLAS" (string-append "-DBLAS_INCLUDE_DIRS=" #$(this-package-input "openblas") "/include") @@ -577,12 +587,12 @@ Performance is achieved by using the LLVM JIT compiler.") #$(this-package-input "openblas") "/lib/libopenblas.so") - "-DLLAMA_NATIVE=OFF" ;no '-march=native' - "-DLLAMA_FMA=OFF" ;and no '-mfma', etc. - "-DLLAMA_AVX2=OFF" - "-DLLAMA_AVX512=OFF" - "-DLLAMA_AVX512_VBMI=OFF" - "-DLLAMA_AVX512_VNNI=OFF") + "-DGGML_NATIVE=OFF" ;no '-march=native' + "-DGGML_FMA=OFF" ;and no '-mfma', etc. + "-DGGML_AVX2=OFF" + "-DGGML_AVX512=OFF" + "-DGGML_AVX512_VBMI=OFF" + "-DGGML_AVX512_VNNI=OFF") #:modules '((ice-9 textual-ports) (guix build utils) @@ -836,7 +846,7 @@ sample proximities between pairs of cases.") (properties `((upstream-name . "RcppML"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/zdebruine/RcppML") (synopsis "Rcpp machine learning Library") (description @@ -940,6 +950,7 @@ depend on language-specific pre- or post-processing.") (sha256 (base32 "018ilrp41fcclmb5lsml3aijwbmhbq3m7wy65hr1fryj0avic8fr")))) (build-system pyproject-build-system) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/sofiatolaosebikan/hopcroftkarp") (synopsis "Implementation of the Hopcroft-Karp algorithm") (description @@ -965,7 +976,8 @@ cardinality matching from a bipartite graph.") python-numpy python-scikit-learn python-scipy)) - (native-inputs (list python-pytest python-pytest-cov)) + (native-inputs (list python-pytest python-pytest-cov python-setuptools + python-wheel)) (home-page "https://persim.scikit-tda.org") (synopsis "Tools for analyzing persistence diagrams in Python") (description @@ -996,7 +1008,11 @@ It currently houses implementations of (build-system pyproject-build-system) (propagated-inputs (list python-numpy python-persim python-scikit-learn python-scipy)) - (native-inputs (list python-cython python-pytest)) + (native-inputs + (list python-cython + python-pytest + python-setuptools + python-wheel)) (home-page "https://ripser.scikit-tda.org") (synopsis "Persistent homology library for Python") (description @@ -1047,7 +1063,7 @@ and not test_wmt22_references") python-portalocker python-regex python-tabulate)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/mjpost/sacrebleu") (synopsis "Compute shareable, comparable, and reproducible BLEU, chrF, and TER scores") @@ -1088,7 +1104,7 @@ unsupervised text tokenizer.") (build-system pyproject-build-system) ;; This package depends on spacy, which depends on this package. (arguments (list #:tests? #false)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://spacy.io") (synopsis "Legacy registered functions for spaCy backwards compatibility") (description @@ -1109,7 +1125,7 @@ compatibility.") (build-system pyproject-build-system) ;; This package depends on spacy, which depends on this package. (arguments (list #:tests? #false)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/explosion/spacy-loggers") (synopsis "Logging utilities for SpaCy") (description "This package provides logging utilities for the SpaCy @@ -1415,7 +1431,9 @@ in terms of new algorithms.") python-fb-re2 python-parameterized-next python-pytest - python-pytest-runner) + python-pytest-runner + python-setuptools + python-wheel) (filter (lambda (pkg) (member (or (%current-target-system) @@ -1779,7 +1797,9 @@ computing environments.") (list python-cython-3 python-pandas python-pytest - python-pytest-xdist)) + python-pytest-xdist + python-setuptools + python-wheel)) (propagated-inputs (list python-numpy python-threadpoolctl python-scipy python-joblib)) (home-page "https://scikit-learn.org/") @@ -1840,7 +1860,8 @@ data analysis.") python-scikit-learn python-scipy python-packaging)) - (native-inputs (list python-pytest python-pytest-cov python-cython)) + (native-inputs (list python-pytest python-pytest-cov python-cython + python-setuptools python-wheel)) (home-page "https://github.com/scikit-learn-contrib/scikit-learn-extra") (synopsis "Set of tools for scikit-learn") (description @@ -1905,7 +1926,8 @@ and are compatible with its API.") python-srsly python-typing-extensions python-wasabi)) - (native-inputs (list python-cython python-mock python-pytest)) + (native-inputs (list python-cython python-mock python-pytest + python-setuptools python-wheel)) (home-page "https://github.com/explosion/thinc") (synopsis "Functional take on deep learning") (description @@ -1967,6 +1989,8 @@ for scientific computing and data science (e.g. BLAS and OpenMP).") python-pandas python-pytest python-pytest-cov + python-setuptools + python-wheel tensorflow)) (home-page "https://github.com/scikit-learn-contrib/imbalanced-learn") (synopsis "Toolbox for imbalanced dataset in machine learning") @@ -2002,7 +2026,9 @@ It is compatible with @code{scikit-learn}.") python-nose python-pytest python-pandas - python-networkx)) + python-networkx + python-setuptools + python-wheel)) (home-page "https://github.com/scikit-learn-contrib/hdbscan") (synopsis "High performance implementation of HDBSCAN clustering") (description "HDBSCAN - Hierarchical Density-Based Spatial Clustering of @@ -2025,7 +2051,7 @@ to return meaningful clusters (if there are any).") (sha256 (base32 "0l5dpdsk5vg7rpay81bncp04119hnl5z7zxjv63jrnm9spcwwi3g")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-importlib-metadata python-joblib @@ -2147,7 +2173,9 @@ standard feature selection algorithms.") (list python-pytest python-pytest-lazy-fixture python-pytorch - python-torchvision)) + python-torchvision + python-setuptools + python-wheel)) (home-page "https://cleanlab.ai") (synopsis "Automatically find and fix dataset issues") (description @@ -2179,7 +2207,7 @@ data by providing clean labels during training.") python-scipy python-tqdm)) (native-inputs - (list python-pytest)))) + (list python-pytest python-setuptools python-wheel)))) (define-public python-cma (package @@ -2220,7 +2248,7 @@ and a few related numerical optimization tools.") (base32 "17bk60mhkglz6s7wz6xcyhw1h4mvghc1iid0805dra7jdyafwrfn")) (file-name (git-file-name name version)))) (build-system pyproject-build-system) - (native-inputs (list python-hypothesis)) + (native-inputs (list python-hypothesis python-setuptools python-wheel)) (propagated-inputs (list python-numpy)) (home-page "https://github.com/CyberAgentAILab/cmaes") (synopsis "CMA-ES implementation for Python") @@ -2247,7 +2275,7 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.") (version version) (build-system pyproject-build-system) (native-inputs - (list python-nose python-pytest)) + (list python-nose python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-future python-numpy)) (synopsis "Efficiently computes derivatives of NumPy code") @@ -2386,13 +2414,15 @@ interactive learning.") python-networkx python-numpy python-scipy + python-setuptools ; For pkg_resources. python-six python-tqdm)) (native-inputs (list python-black python-nose python-pymongo - python-pytest)) + python-pytest + python-wheel)) (home-page "https://hyperopt.github.io/hyperopt/") (synopsis "Library for hyperparameter optimization") (description "Hyperopt is a Python library for serial and parallel @@ -2421,7 +2451,8 @@ discrete, and conditional dimensions.") (setenv "HOME" "/tmp")))))) ;; DeepXDE supported backends are TensorFlow (v1 and v2), PyTorch, JAX and ;; PaddlePaddle. We test with PyTorch because we have it up to date. - (native-inputs (list python-pytorch python-setuptools-scm)) + (native-inputs (list python-pytorch python-setuptools + python-setuptools-scm python-wheel)) (propagated-inputs (list python-matplotlib python-numpy python-scikit-learn python-scikit-optimize python-scipy)) @@ -3646,7 +3677,8 @@ in a fast and accurate way.") (symlink libxgboost (string-append xgbdir "/lib" "/libxgboost.so")))))))) (native-inputs - (list python-pandas python-pytest python-scikit-learn)) + (list python-pandas python-pytest python-scikit-learn python-setuptools + python-wheel)) (inputs (list xgboost)) (propagated-inputs @@ -3962,7 +3994,8 @@ These include a barrier, broadcast, and allreduce.") ;; nor is examples/plot_quantum.py " and not test_file_is_generated")))) (propagated-inputs (list python-jsmin python-numpy python-scipy)) - (native-inputs (list python-pytest python-pytest-cov python-sphinx)) + (native-inputs (list python-pytest python-pytest-cov python-sphinx + python-setuptools python-wheel)) (home-page "https://github.com/tensorly/tensorly") (synopsis "Tensor learning in Python") (description @@ -4000,7 +4033,7 @@ methodxs at scale on CPU or GPU.") (add-before 'check 'set-numba-cache-dir (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-numba python-numpy @@ -5020,6 +5053,7 @@ Neural Networks for a wide range of applications related to structured data.") (sha256 (base32 "0mqrhq3s23mn8n4i0q791pshn3dgplp0h9ny0pmmp798q0798dzs")))) + (arguments (list #:tests? #f)) ; no tests in PyPI archive. (build-system pyproject-build-system) (propagated-inputs (list python-click python-fastapi-for-pytorch-lightning @@ -5031,6 +5065,7 @@ Neural Networks for a wide range of applications related to structured data.") python-urllib3 python-uvicorn python-websocket-client)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://lightning.ai") (synopsis "Lightning Cloud command line client") (description "This package provides a command line interface for Lightning @@ -5048,9 +5083,14 @@ AI services.") (base32 "016zikn39apig3y6xyipw34w0w02c73z483radddbf68ivpjgz3r")))) (build-system pyproject-build-system) - (propagated-inputs (list python-importlib-metadata python-packaging - python-typing-extensions)) - (native-inputs (list python-coverage)) + (native-inputs + (list python-coverage + python-setuptools + python-wheel)) + (propagated-inputs + (list python-importlib-metadata + python-packaging + python-typing-extensions)) (home-page "https://github.com/Lightning-AI/utilities") (synopsis "PyTorch Lightning sample project") (description "This package provides common Python utilities and GitHub @@ -5093,7 +5133,8 @@ Actions for the Lightning suite of libraries.") python-parameterized python-pytest python-pytest-cov - python-scikit-learn)) + python-scikit-learn + python-setuptools)) (home-page "https://captum.ai") (synopsis "Model interpretability for PyTorch") (description "Captum is a model interpretability and understanding library @@ -5123,6 +5164,7 @@ as torchvision, torchtext, and others.") (lambda _ (delete-file "readchar/_win_read.py")))))) (propagated-inputs (list python-setuptools)) + (native-inputs (list python-wheel)) (home-page "https://github.com/magmax/python-readchar") (synopsis "Library to easily read single chars and key strokes") (description "This package provides a Python library to easily read single @@ -5391,7 +5433,7 @@ implementations and an easy-to-use API to create custom metrics. It offers: python-pillow-simd python-pytorch)) (native-inputs - (list which python-pytest)) + (list which python-pytest python-setuptools python-wheel)) (home-page "https://pytorch.org/vision/stable/index.html") (synopsis "Datasets, transforms and models specific to computer vision") (description @@ -5422,32 +5464,34 @@ Python.") (define-public python-hmmlearn (package (name "python-hmmlearn") - (version "0.2.8") + (version "0.3.3") (source (origin (method url-fetch) (uri (pypi-uri "hmmlearn" version)) (sha256 (base32 - "1yd5l9ra37mks41mn5bigav7xpb161a9yqlcnz4ir076vkik2sb9")))) - (build-system python-build-system) + "1v24rkqjjf67w2rys25qxa3vk30bf23m7zn1ilihqzi5qp25sg0x")))) + (properties + '((updater-extra-native-inputs . ("pybind11" "python-setuptools-scm")))) + (build-system pyproject-build-system) (arguments (list #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (with-directory-excursion (string-append #$output "/lib") - (invoke "python" "-m" "pytest")))))))) + '(modify-phases %standard-phases + (add-after 'unpack 'set-core-count + (lambda _ + ;; "Could not find the number of physical cores", so we tell it + ;; how many cores to use. + (setenv "LOKY_MAX_CPU_COUNT" "1"))) + (add-before 'check 'build-extensions + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs - (list pybind11 - python-numpy - python-scikit-learn - python-scipy - python-setuptools-scm)) + (list python-numpy python-scikit-learn python-scipy)) (native-inputs - (list python-pytest)) + (list pybind11 python-pytest python-setuptools-scm + util-linux)) ;for lscpu (home-page "https://github.com/hmmlearn/hmmlearn") (synopsis "Hidden Markov Models with scikit-learn like API") (description @@ -5661,6 +5705,7 @@ inference.") (native-inputs (list python-flake8 python-flake8-print python-pytest + python-setuptools python-setuptools-scm python-twine)) (home-page "https://github.com/cornellius-gp/linear_operator/") @@ -5693,6 +5738,7 @@ linear algebra routines needed for structured matrices (or operators).") python-flake8-print python-nbval python-pytest + python-setuptools python-twine)) (home-page "https://gpytorch.ai") (synopsis "Implementation of Gaussian Processes in PyTorch") @@ -5992,7 +6038,7 @@ fi" ;; Required by codegen. python-setuptools python-sympy)) - (native-inputs (list python-pytest python-pytest-xdist)) + (native-inputs (list python-pytest python-pytest-xdist python-wheel)) (home-page "https://briansimulator.org/") (synopsis "Clock-driven simulator for spiking neural networks") (description |