diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 276 |
1 files changed, 235 insertions, 41 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index cc20ef68dd..f50398b555 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2016, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2020-2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> @@ -20,6 +20,7 @@ ;;; Copyright © 2022, 2023 Nicolas Graves <ngraves@ngraves.fr> ;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe> ;;; Copyright © 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de> +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -239,7 +240,7 @@ classification.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq")))) + "07kdsngvr4n1qxpqzv1nlay7g41d6jzjppa8vzmrg220s8ing87z")))) (build-system gnu-build-system) (arguments `(#:imported-modules (,@%gnu-build-system-modules @@ -1470,26 +1471,17 @@ with your favorite libraries.") (define-public python-threadpoolctl (package (name "python-threadpoolctl") - (version "2.1.0") + (version "3.1.0") (source (origin (method url-fetch) (uri (pypi-uri "threadpoolctl" version)) (sha256 (base32 - "0szsxcm2fbxrn83iynn42bnvrdh7mfsmkhfn8pdn7swblfb7rifx")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "pytest")) - #t))))) + "100k76nmajf408lbn5ipis1gilklcs6sbqyqy3hhlh54zanbldd3")))) + (build-system pyproject-build-system) (native-inputs - (list python-pytest)) + (list python-flit-core 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 @@ -1497,6 +1489,73 @@ number of threads used in the threadpool-backed of common native libraries used for scientific computing and data science (e.g. BLAS and OpenMP).") (license license:bsd-3))) +(define-public python-tslearn + (package + (name "python-tslearn") + (version "0.6.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tslearn-team/tslearn") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fhs8c28hdqsyj8kdhzrmrxrh4w92x6nf3gm026xapp9divvljd6")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + (string-append + ;; This one fails because of a difference in accuracy. + "not test_all_estimators[LearningShapelets-LearningShapelets]" + ;; XXX: It's embarrassing to disable these two, but the truth is + ;; that there's only so much we can do to force this package to + ;; work with Tensorflow 1.9. It's still worth having this + ;; package, because it can be used without the Tensorflow + ;; backend. + ;; TypeError: cannot pickle '_thread.RLock' object + " and not test_shapelets" + ;; TypeError: Expected binary or unicode string, got 2 + " and not test_serialize_shapelets")) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "tslearn/tests/sklearn_patches.py" + (("_pairwise_estimator_convert_X") + "_enforce_estimator_tags_X") + (("pairwise_estimator_convert_X\\(([^,]+), ([^,\\)]+)" _ a b) + (string-append "pairwise_estimator_convert_X(" b ", " a))) + (substitute* "tslearn/tests/test_shapelets.py" + (("tf.optimizers.Adam") + "tf.keras.optimizers.Adam")) + (substitute* "tslearn/shapelets/shapelets.py" + (("tf.keras.utils.set_random_seed") + "tf.set_random_seed") + (("def __call__\\(self, shape, dtype=None\\):") + "def __call__(self, shape, dtype=None, partition_info=None):") + (("tf.math.is_finite") + "tf.is_finite"))))))) + (propagated-inputs (list python-cesium + python-h5py + python-joblib + python-numba + python-numpy + python-pandas + python-scipy + python-scikit-learn + tensorflow + python-wheel)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/tslearn-team/tslearn") + (synopsis "Machine learning toolkit for time series data") + (description "This is a Python library for time series data mining. +It provides tools for time series classification, clustering +and forecasting.") + (license license:bsd-2))) + (define-public python-imbalanced-learn (package (name "python-imbalanced-learn") @@ -2394,7 +2453,7 @@ Python.") ;; "ZIP does not support timestamps before 1980". Luckily, ;; SOURCE_DATE_EPOCH is respected, which we set to some time in ;; 1980. - (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t)) + (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800"))) (add-after 'unpack 'python3.10-compatibility (lambda _ ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913 @@ -2435,6 +2494,8 @@ Python.") (substitute* "tensorflow/python/keras/callbacks.py" (("from collections import Iterable") "from collections.abc import Iterable")) + (substitute* "tensorflow/python/ops/variable_scope.py" + (("collections_lib.Sequence") "collections_lib.abc.Sequence")) ;; XXX: it is not clear if this is a good idea, but the build ;; system tries to overwrite the __or__ and __ror__ methods of @@ -2450,7 +2511,20 @@ Python.") (("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,")))) + "void CompareUFunc(char** args, npy_intp const* dimensions, npy_intp const* steps,")) + + ;; ...and for numpy >= 1.23 + (substitute* "tensorflow/python/framework/tensor_util.py" + (("np.asscalar\\(x\\[0\\]\\)") "x[0].item()") + (("np.asscalar\\(x\\)") "x.item()") + (("np.asscalar\\(v\\)") "np.ndarray.item(v)") + (("return np.asscalar") "return np.ndarray.item")) + (substitute* "tensorflow/python/kernel_tests/cwise_ops_test.py" + (("np.asscalar\\(np.random.rand\\(1\\) \\* 100.\\)") + "(np.random.rand(1) * 100.).item()")) + (substitute* '("tensorflow/python/framework/fast_tensor_util.pyx" + "tensorflow/python/estimator/canned/linear_testing_utils.py") + (("np.asscalar") "np.ndarray.item")))) (add-after 'python3.10-compatibility 'chdir (lambda _ (chdir "tensorflow/contrib/cmake"))) (add-after 'chdir 'disable-downloads @@ -2794,15 +2868,15 @@ DESTINATION include/tensorflow/c FILES_MATCHING PATTERN \"*.h\")\n" m))))) ("swig" ,swig) ("unzip" ,unzip))) (propagated-inputs - `(("python-absl-py" ,python-absl-py) - ("python-astor" ,python-astor) - ("python-gast" ,python-gast) - ("python-grpcio" ,python-grpcio) - ("python-numpy" ,python-numpy) - ("python-protobuf" ,python-protobuf-3.6) - ("python-six" ,python-six) - ("python-termcolo" ,python-termcolor) - ("python-wheel" ,python-wheel))) + (list python-absl-py + python-astor + python-gast + python-grpcio + python-numpy + python-protobuf-3.6 + python-six + python-termcolor + python-wheel)) (inputs `(("c-ares" ,c-ares) ("eigen" ,eigen-for-tensorflow) @@ -3206,46 +3280,115 @@ with image data, text data, and sequence data.") (define-public python-keras (package (name "python-keras") - (version "2.2.4") + (version "2.3.1") (source (origin (method url-fetch) (uri (pypi-uri "Keras" version)) - (patches (search-patches "python-keras-integration-test.patch")) (sha256 (base32 - "1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh")))) + "1k68xd8n2y9ldijggjc8nn4d6d1axw0p98gfb0fmm8h641vl679j")) + (modules '((guix build utils))) + (snippet + '(substitute* '("keras/callbacks/callbacks.py" + "keras/engine/training_utils.py" + "keras/engine/training.py" + "keras/engine/training_generator.py" + "keras/utils/generic_utils.py") + (("from collections import Iterable") + "from collections.abc import Iterable") + (("collections.Container") + "collections.abc.Container") + (("collections.Mapping") + "collections.abc.Mapping") + (("collections.Sequence") + "collections.abc.Sequence"))))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'remove-tests-for-unavailable-features + (add-after 'unpack 'tf-compatibility + (lambda _ + (substitute* "keras/backend/tensorflow_backend.py" + (("^get_graph = .*") + "get_graph = tf.get_default_graph") + (("tf.compat.v1.nn.fused_batch_norm") + "tf.nn.fused_batch_norm") + ;; categorical_crossentropy does not support axis + (("from_logits=from_logits, axis=axis") + "from_logits=from_logits") + ;; dropout accepts a level number, not a named rate argument. + (("dropout\\(x, rate=level,") + "dropout(x, level,") + (("return x.shape.rank") + "return len(x.shape)")))) + (add-after 'unpack 'hdf5-compatibility + (lambda _ + ;; The truth value of an array with more than one element is ambiguous. + (substitute* "tests/keras/utils/io_utils_test.py" + ((" *assert .* == \\[b'(asd|efg).*") "")) + (substitute* "tests/test_model_saving.py" + (("h5py.File\\('does not matter',") + "h5py.File('does not matter', 'w',")) + (substitute* "keras/utils/io_utils.py" + (("h5py.File\\('in-memory-h5py', driver='core', backing_store=False\\)") + "h5py.File('in-memory-h5py', 'w', driver='core', backing_store=False)") + (("h5file.fid.get_file_image") + "h5file.id.get_file_image")) + (substitute* "keras/engine/saving.py" + (("\\.decode\\('utf-?8'\\)") "")))) + (add-after 'unpack 'delete-unavailable-backends (lambda _ (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"))) + (delete-file "keras/backend/cntk_backend.py"))) (replace 'check (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)) + ;; This one uses the theano backend that we don't have. + "--ignore=tests/test_api.py" + "--ignore=tests/keras/backend/backend_test.py" + ;; Our Tensorflow version does not have the coder ops library. + "--ignore=tests/keras/callbacks/callbacks_test.py" + ;; ...nor do we have tensorboard + "--ignore=tests/keras/callbacks/tensorboard_test.py" "-k" (string-append + ;; See https://github.com/keras-team/keras/pull/7033 + "not test_TimeDistributed_learning_phase " + ;; XXX fails because no closure is provided + "and not test_func_dump_and_load_backwards_compat " + ;; XXX real bug? These are all tests that fail due to + ;; shape mismatch, e.g. "got logits shape [12,3] and + ;; labels shape [9]" + "and not test_model_with_crossentropy_losses_channels_first " + "and not test_masking_correctness_output_size_not_equal_to_first_state_size " + "and not test_convolutional_recurrent " + "and not test_axis " + + ;; XXX fails because of 3/15 values have unexpected differences. + "and not test_masking_correctness_output_not_equal_to_first_state " + ;; XXX fails because of a difference of about 0.1 + "and not test_sample_weighted " + ;; XXX fails because of a difference of about 0.3 + "and not test_scalar_weighted " + ;; XXX fails because of a difference of about 0.2 + "and not test_unweighted " + + ;; XXX I cannot reproduce this in an interactive + ;; Python session, because l2_norm works just fine. + "and not test_weighted " ;TestCosineSimilarity + "and not test_config " ;TestCosineSimilarity + ;; The following test fails only in the build ;; container; skip it. - "not test_selu " + "and not test_selu " ;; The following test was found flaky and removed in ;; recent versions. "and not test_stateful_metrics")))))))) @@ -3261,12 +3404,15 @@ with image data, text data, and sequence data.") tensorflow graphviz)) (native-inputs - (list python-pandas + (list python-flaky + python-markdown + python-pandas python-pytest python-pytest-cov python-pytest-pep8 python-pytest-timeout python-pytest-xdist + python-pyux python-sphinx python-requests)) (home-page "https://github.com/keras-team/keras") @@ -3722,6 +3868,51 @@ AI services.") Actions for the Lightning suite of libraries.") (license license:asl2.0))) +(define-public python-captum + (package + (name "python-captum") + (version "0.6.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pytorch/captum") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1h4n91ivhjxm6wj0vgqpfss2dmq4sjcp0appd08cd5naisabjyb5")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + ;; These two tests (out of more than 1000 tests) fail because of + ;; accuracy problems. + "not test_softmax_classification_batch_multi_target\ + and not test_softmax_classification_batch_zero_baseline"))) + (propagated-inputs (list python-matplotlib python-numpy python-pytorch)) + (native-inputs (list jupyter + python-annoy + python-black + python-flake8 + python-flask + python-flask-compress + python-ipython + python-ipywidgets + python-mypy + python-parameterized + python-pytest + python-pytest-cov + python-scikit-learn)) + (home-page "https://captum.ai") + (synopsis "Model interpretability for PyTorch") + (description "Captum is a model interpretability and understanding library +for PyTorch. Captum contains general purpose implementations of integrated +gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. +It has quick integration for models built with domain-specific libraries such +as torchvision, torchtext, and others.") + (license license:bsd-3))) + (define-public python-readchar (package (name "python-readchar") @@ -4573,6 +4764,9 @@ Brian 2 simulator.") (sha256 (base32 "1jgmb5kl0bf4a2zfn94zlb117672r9lvvkkmwl86ihlyr1mpr3d0")))) (build-system cmake-build-system) + (arguments (if (target-riscv64?) + (list #:configure-flags #~'("-DDNNL_CPU_RUNTIME=SEQ")) + '())) (home-page "https://github.com/oneapi-src/oneDNN") (synopsis "Deep Neural Network Library") (description |