diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 314 |
1 files changed, 296 insertions, 18 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 53d428bd4f..b19af8a1d5 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -73,6 +73,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages image-processing) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages jupyter) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) @@ -752,7 +753,7 @@ in terms of new algorithms.") (define-public onnx (package (name "onnx") - (version "1.9.0") + (version "1.12.0") (source (origin (method git-fetch) (uri (git-reference @@ -760,7 +761,7 @@ in terms of new algorithms.") (commit (string-append "v" version)))) (sha256 (base32 - "1xnii361f68x0masxgfc4ai7hh3wlxxk56aznwf4m4yr6wqx47ml")) + "1g9f1hviksbn7gi6fnd0dsm7nf0w3yia0mjj33d9mggklrl0db6x")) (file-name (git-file-name name version)) (patches (search-patches "onnx-use-system-googletest.patch" "onnx-shared-libraries.patch" @@ -2821,8 +2822,8 @@ and Darknet.") (define-public xnnpack ;; There's currently no tag on this repo. (let ((version "0.0") - (commit "bbe88243aba847f6a3dd86defec0fea4a0e415a1") - (revision "1")) + (commit "ae108ef49aa5623b896fc93d4298c49d1750d9ba") + (revision "2")) (package (name "xnnpack") (version (git-version version revision commit)) @@ -2833,7 +2834,7 @@ and Darknet.") (file-name (git-file-name name version)) (sha256 (base32 - "19j605x1l2h95mjhcj90zwjh1153pdgmqggl35ya5w0wll628iiz")) + "0q68q2jxiiiblx45q4337k13ppgh5vqjwrwznchcnpb8hawjj3zl")) (patches (search-patches "xnnpack-system-libraries.patch")))) (build-system cmake-build-system) (arguments @@ -2866,10 +2867,11 @@ high-level machine learning frameworks, such as TensorFlow Lite, TensorFlow.js, PyTorch, and MediaPipe.") (license license:bsd-3)))) +;; Please also update python-torchvision when updating this package. (define-public python-pytorch (package (name "python-pytorch") - (version "1.10.2") + (version "1.12.0") (source (origin (method git-fetch) (uri (git-reference @@ -2879,7 +2881,7 @@ TensorFlow.js, PyTorch, and MediaPipe.") (file-name (git-file-name name version)) (sha256 (base32 - "15fi3nr7fx2zc9j2xf0jq627zfmnvs8hijyifg9769arm8kfijs1")) + "0pdqi91qzgyx947zv4pw2fdj9vpqvdhfzw1ydjd4mpqm8g5njgnz")) (patches (search-patches "python-pytorch-system-libraries.patch" "python-pytorch-runpath.patch")) (modules '((guix build utils))) @@ -2899,12 +2901,7 @@ TensorFlow.js, PyTorch, and MediaPipe.") "gloo" "googletest" "ios-cmake" "NNPACK" "onnx" "protobuf" "pthreadpool" "pybind11" "python-enum" "python-peachpy" - "python-six" "tbb" "XNNPACK" "zstd")) - - ;; Adjust references to the onnx-optimizer headers. - (substitute* "caffe2/onnx/backend.cc" - (("onnx/optimizer/") - "onnxoptimizer/")))))) + "python-six" "tbb" "XNNPACK" "zstd")))))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -2915,6 +2912,10 @@ TensorFlow.js, PyTorch, and MediaPipe.") ;; ones. (setenv "USE_SYSTEM_LIBS" "1") + (substitute* "cmake/Dependencies.cmake" + (("if\\(USE_SYSTEM_BIND11\\)") + "if(TRUE)")) + ;; XXX: Disable that for simplicity for now. (setenv "USE_FBGEMM" "0"))) (add-before 'build 'make-things-writable @@ -2942,7 +2943,23 @@ TensorFlow.js, PyTorch, and MediaPipe.") (let ((python-site (site-packages inputs outputs))) (for-each delete-file (find-files python-site - "(^test_cpp_rpc|_test)$")))))) + "(^test_cpp_rpc|_test)$"))))) + (add-after 'install 'remove-caffe2-onnx-scripts + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + ;; Remove 'convert-caffe2-to-onnx' and + ;; 'convert-onnx-to-caffe2': they seem to be + ;; deprecated and they cause a failure of the + ;; 'sanity-check' phase: + ;; + ;; ImportError: cannot import name 'metanet_pb2' from partially initialized module 'caffe2.proto' (most likely due to a circular import) + (for-each delete-file + (find-files bin "^convert-.*caffe2")) + + (substitute* (find-files out "^entry_points\\.txt$") + (("^convert-.*" all) + (string-append "# " all "\n"))))))) ;; XXX: Tests attempt to download data such as ;; <https://raw.githubusercontent.com/pytorch/test-infra/master/stats/slow-tests.json>. @@ -2977,7 +2994,7 @@ TensorFlow.js, PyTorch, and MediaPipe.") python-future python-six python-requests - onnx ;propagated for its Python modules + onnx ;propagated for its Python modules onnx-optimizer cpuinfo)) (home-page "https://pytorch.org/") @@ -2996,7 +3013,105 @@ PyTorch when needed. Note: currently this package does not provide GPU support.") (license license:bsd-3))) -(define-public python-pytorch-for-r-torch python-pytorch) +(define-public python-pytorch-for-r-torch + (package + (inherit python-pytorch) + (name "python-pytorch") + (version "1.11.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pytorch/pytorch") + (commit (string-append "v" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1zbk7y74r0ycsfa7x59jnhwhs1gj5rs3n89p15y0212iszgbljq8")) + (patches (search-patches "python-pytorch-system-libraries.patch" + "python-pytorch-runpath.patch")) + (modules '((guix build utils))) + (snippet + '(begin + ;; XXX: Let's be clear: this package is a bundling fest. We + ;; delete as much as we can, but there's still a lot left. + (for-each (lambda (directory) + (delete-file-recursively + (string-append "third_party/" directory))) + '("benchmark" "cpuinfo" "eigen" + + ;; FIXME: QNNPACK (of which XNNPACK is a fork) + ;; needs these. + ;; "FP16" "FXdiv" "gemmlowp" "psimd" + + "gloo" "googletest" "ios-cmake" "NNPACK" + "onnx" "protobuf" "pthreadpool" + "pybind11" "python-enum" "python-peachpy" + "python-six" "tbb" "XNNPACK" "zstd")))))))) + +;; Keep this in sync with python-pytorch +(define-public python-torchvision + (package + (name "python-torchvision") + (version "0.13.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pytorch/vision") + (commit (string-append "v" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "19f6s3ffwkdvjjbvib18c8n7vhysg58smxzq3rvii1c0z4g3b0cw")))) + (build-system python-build-system) + (arguments + `(#:tests? #false ;the test suite is expensive and there is no easy way + ;to subset it. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) + (inputs + (list libpng + libjpeg-turbo)) + (propagated-inputs + (list python-numpy + python-typing-extensions + python-requests + python-pillow + python-pillow-simd + python-pytorch)) + (native-inputs + (list which python-pytest)) + (home-page "https://pytorch.org/vision/stable/index.html") + (synopsis " Datasets, transforms and models specific to computer vision") + (description + "The torchvision package consists of popular datasets, model architectures, +and common image transformations for computer vision.") + (license license:bsd-3))) + +(define-public python-torchfile + (package + (name "python-torchfile") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "torchfile" version)) + (sha256 + (base32 + "0vhklj6krl9r0kdynb4kcpwp8y1ihl2zw96byallay3k9c9zwgd5")))) + (build-system python-build-system) + (arguments '(#:tests? #false)) ;there are no tests + (propagated-inputs + (list python-numpy)) + (home-page "https://github.com/bshillingford/python-torchfile") + (synopsis "Torch7 binary serialized file parser") + (description "This package enables you to deserialize Lua torch-serialized objects from +Python.") + (license license:bsd-3))) (define-public python-hmmlearn (package @@ -3039,7 +3154,7 @@ of Hidden Markov Models.") (define-public liblantern (package (name "liblantern") - (version "0.7.2") + (version "0.8.0") (source (origin (method git-fetch) @@ -3048,7 +3163,7 @@ of Hidden Markov Models.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1nam375ych4nr7gk2dpbnzlanr2jc7akqjhmfs0ar9l34zmzz9m9")))) + (base32 "1xkqyj1clj1r70yrp5qpbpyf0xmh9c128005idshi7vk883wfp77")))) (build-system cmake-build-system) (arguments (list @@ -3096,3 +3211,166 @@ of Hidden Markov Models.") (description "Lantern provides a C API to the libtorch machine learning library.") (license license:expat))) + +(define-public python-lap + (package + (name "python-lap") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "lap" version)) + (sha256 + (base32 + "0fqfxpq4jg9h4wxjw540gjmvfg1ccc1nssk7i9njg7qfdybxknn4")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (invoke "python" "setup.py" "build" + "--cpu-baseline=sse2"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; The tests must be run from elsewhere. + (mkdir-p "/tmp/test") + (copy-recursively "lap/tests" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest" "-vv")))))))) + (propagated-inputs + (list python-numpy + python-scipy)) + (native-inputs + (list python-cython python-pytest)) + (home-page "https://github.com/gatagat/lap") + (synopsis "Linear Assignment Problem solver (LAPJV/LAPMOD).") + (description "Lap is a linear assignment problem solver using Jonker-Volgenant +algorithm for dense (LAPJV) or sparse (LAPMOD) matrices.") + (license license:bsd-2))) + +(define-public python-visdom + (package + (name "python-visdom") + (version "0.1.8.9") + (source (origin + (method url-fetch) + (uri (pypi-uri "visdom" version)) + (sha256 + (base32 + "09kiczx2i5asqsv214fz7sx8wlyldgbqvxwrd0alhjn24cvx4fn7")))) + (build-system python-build-system) + (propagated-inputs + (list python-jsonpatch + python-numpy + python-pillow + python-pyzmq + python-requests + python-scipy + python-six + python-torchfile + python-tornado + python-websocket-client)) + (home-page "https://github.com/fossasia/visdom") + (synopsis "Visualizations of live, rich data for Torch and Numpy") + (description + "This package provides a tool for visualizing live, rich data for Torch +and Numpy.") + (license license:asl2.0))) + +(define-public python-pyro-api + (package + (name "python-pyro-api") + (version "0.1.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyro-api" version)) + (sha256 + (base32 + "086r2h6x9i5d9ayl1x65lx6p84rlydzsn8xingxc588ab3ch1fd1")))) + (build-system python-build-system) + (arguments '(#:tests? #false)) ;requires pyro + (native-inputs + (list python-flake8 + python-ipython + python-pytest + python-sphinx + python-sphinx-rtd-theme)) + (home-page "https://github.com/pyro-ppl/pyro-api") + (synopsis "Generic API for dispatch to Pyro backends.") + (description "This package provides a generic API for dispatch to Pyro backends.") + (license license:asl2.0))) + +(define-public python-pyro-ppl + (package + (name "python-pyro-ppl") + (version "1.8.1") + ;; The sources on pypi don't include tests. + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pyro-ppl/pyro") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ns20mr8qgjshzbplrfzaz1xhb9ldbgvrj2rzlsxvns2bi1ddyl5")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + ;; This tests features that are only implemented when non-free + ;; software is available (Intel MKL or CUDA). + (for-each delete-file + (list "tests/distributions/test_spanning_tree.py" + "tests/infer/mcmc/test_mcmc_api.py")) + + ;; Four test_gamma_elbo tests fail with bad values for unknown + ;; reasons. + (delete-file "tests/distributions/test_rejector.py") + ;; This test fails sometimes. + (delete-file "tests/optim/test_optim.py") + (invoke "pytest" "-vv" "--stage=unit")))))) + (propagated-inputs + (list python-numpy + python-opt-einsum + python-pyro-api + python-pytorch + python-tqdm)) + (native-inputs + (list ninja + jupyter + python-black + python-flake8 + python-graphviz + python-isort + python-lap + python-matplotlib + python-mypy + python-nbformat + python-nbsphinx + python-nbstripout + python-nbval + python-pandas + python-pillow + python-pypandoc + python-pytest + python-pytest-cov + python-pytest-xdist + python-scikit-learn + python-scipy + python-seaborn + python-sphinx + python-sphinx-rtd-theme + python-torchvision + python-visdom + python-wget + python-yapf)) + (home-page "https://pyro.ai") + (synopsis "Python library for probabilistic modeling and inference") + (description + "This package provides a Python library for probabilistic modeling and +inference.") + (license license:asl2.0))) |