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-rw-r--r--gnu/packages/machine-learning.scm661
1 files changed, 413 insertions, 248 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 460e77cf0b..77f1282a2b 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net>
;;; 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>
@@ -15,12 +15,13 @@
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
-;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; 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>
+;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -812,6 +813,94 @@ SentencePiece allows us to make a purely end-to-end system that does not
depend on language-specific pre- or post-processing.")
(license license:asl2.0)))
+(define-public python-hopcroftkarp
+ ;; This commit fixes a broken import, but has not been released to PyPI.
+ (let ((commit "2846e1dd3265d95d2bddb0cf4190b830cbb4efe6")
+ (revision "1"))
+ (package
+ (name "python-hopcroftkarp")
+ (version (git-version "1.2.5" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/sofiatolaosebikan/hopcroftkarp")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "018ilrp41fcclmb5lsml3aijwbmhbq3m7wy65hr1fryj0avic8fr"))))
+ (build-system pyproject-build-system)
+ (home-page "https://github.com/sofiatolaosebikan/hopcroftkarp")
+ (synopsis "Implementation of the Hopcroft-Karp algorithm")
+ (description
+ "This package implements the Hopcroft-Karp algorithm, producing a maximum
+cardinality matching from a bipartite graph.")
+ (license license:gpl3))))
+
+(define-public python-persim
+ (package
+ (name "python-persim")
+ (version "0.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "persim" version))
+ (sha256
+ (base32 "0q8wfakx8q4h3ryvw8cba0v6z7xn9139qkrzs3mi1ggyzacnx9d7"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-deprecated
+ python-hopcroftkarp
+ python-joblib
+ python-matplotlib
+ python-numpy
+ python-scikit-learn
+ python-scipy))
+ (native-inputs (list python-pytest python-pytest-cov))
+ (home-page "https://persim.scikit-tda.org")
+ (synopsis "Tools for analyzing persistence diagrams in Python")
+ (description
+ "This package includes a variety of tools used to analyze persistence diagrams.
+It currently houses implementations of
+@itemize
+@item Persistence images
+@item Persistence landscapes
+@item Bottleneck distance
+@item Modified Gromov–Hausdorff distance
+@item Sliced Wasserstein kernel
+@item Heat kernel
+@item Diagram plotting
+@end itemize
+")
+ (license license:expat))) ; MIT License
+
+(define-public python-ripser
+ (package
+ (name "python-ripser")
+ (version "0.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ripser" version))
+ (sha256
+ (base32 "1575nwsn6b29z7w1mjk23ri83bxq2b4ld979hpgm174642a3x6vs"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-numpy python-persim python-scikit-learn
+ python-scipy))
+ (native-inputs (list python-cython python-pytest))
+ (home-page "https://ripser.scikit-tda.org")
+ (synopsis "Persistent homology library for Python")
+ (description
+ "This package implements a variety of persistent homology algorithms. It
+provides an interface for
+@itemize
+@item computing persistence cohomology of sparse and dense data sets
+@item visualizing persistence diagrams
+@item computing lowerstar filtrations on images
+@item computing representative cochains
+@end itemize
+")
+ (license license:expat))) ; MIT License
+
(define-public python-sacrebleu
(package
(name "python-sacrebleu")
@@ -1151,6 +1240,11 @@ in terms of new algorithms.")
(build-system python-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ ;; Does this difference really matter?
+ (substitute* "requirements.txt"
+ (("3.20.1") "3.20.2"))))
(add-before 'build 'pass-cmake-arguments
(lambda* (#:key outputs #:allow-other-keys)
;; Pass options to the CMake-based build process.
@@ -1214,6 +1308,35 @@ an extensible computation graph model, as well as definitions of built-in
operators and standard data types.")
(license license:expat)))
+(define-public onnx-for-torch2
+ (package
+ (inherit onnx)
+ (name "onnx")
+ (version "1.13.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/onnx/onnx")
+ (commit (string-append "v" version))))
+ (sha256
+ (base32
+ "16967dbq2j40diqd0s37r19llsab8q8vbxkg1ppgy0p9fpdhfhyp"))
+ (file-name (git-file-name name version))
+ (patches (search-patches "onnx-1.13.1-use-system-googletest.patch"
+ "onnx-shared-libraries.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "third_party")
+ (substitute* "onnx/backend/test/runner/__init__.py"
+ (("urlretrieve\\(.*") "raise unittest.SkipTest('Skipping download')\n"))))))
+ (arguments
+ ;; reuse build system tweaks
+ (substitute-keyword-arguments (package-arguments onnx)
+ ((#:phases phases)
+ #~(modify-phases #$phases
+ (delete 'relax-requirements)))))))
+
(define-public python-onnx
;; This used to be called "python-onnx" because it provided nothing but
;; Python bindings. The package now provides shared libraries and C++
@@ -1239,7 +1362,12 @@ operators and standard data types.")
(modules '((guix build utils)))
(snippet '(delete-file-recursively "third_party"))))
(build-system python-build-system)
- (arguments (package-arguments onnx)) ;reuse build system tweaks
+ (arguments
+ ;; reuse build system tweaks
+ (substitute-keyword-arguments (package-arguments onnx)
+ ((#:phases phases)
+ #~(modify-phases #$phases
+ (delete 'relax-requirements)))))
(native-inputs
(list cmake python-pytest python-pytest-runner python-nbval
python-coverage))
@@ -1259,6 +1387,13 @@ aim is to provide all such passes along with ONNX so that they can be re-used
with a single function call.")
(license license:expat)))
+(define-public onnx-optimizer-for-torch2
+ (package
+ (inherit onnx-optimizer)
+ (inputs
+ (modify-inputs (package-inputs onnx-optimizer)
+ (replace "onnx" onnx-for-torch2)))))
+
(define-public rxcpp
(package
(name "rxcpp")
@@ -1478,7 +1613,7 @@ computing environments.")
(define-public python-scikit-learn
(package
(name "python-scikit-learn")
- (version "1.2.2")
+ (version "1.3.2")
(source
(origin
(method git-fetch)
@@ -1488,20 +1623,25 @@ computing environments.")
(file-name (git-file-name name version))
(sha256
(base32
- "0x7gfzvcdadf8jnvpz8m373bi37bc6sndfbjh9lzmn3p39pwm2hl"))))
- (build-system python-build-system)
+ "1hr024vcilbjwlwn32ppadri0ypnzjmkfxhkkw8gih0qjvcvjbs7"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
+ (list
+ #:test-flags
+ '(list "-m" "not network"
+ ;; This test tries to access the internet.
+ "-k" "not test_load_boston_alternative")
+ #:phases
+ '(modify-phases %standard-phases
(add-before 'build 'configure
(lambda _
(setenv "SKLEARN_BUILD_PARALLEL"
(number->string (parallel-job-count)))))
(add-after 'build 'build-ext
(lambda _ (invoke "python" "setup.py" "build_ext" "--inplace"
- "-j" (number->string (parallel-job-count)))))
+ "-j" (number->string (parallel-job-count)))))
(replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
(when tests?
;; Restrict OpenBLAS threads to prevent segfaults while testing!
(setenv "OPENBLAS_NUM_THREADS" "1")
@@ -1512,14 +1652,11 @@ computing environments.")
;; Step out of the source directory to avoid interference;
;; we want to run the installed code with extensions etc.
(with-directory-excursion "/tmp"
- (invoke "pytest" "-vv" "--pyargs" "sklearn"
- "-m" "not network"
- "-n" (number->string (parallel-job-count))
- ;; This test tries to access the internet.
- "-k" "not test_load_boston_alternative"))))))))
+ (apply invoke "pytest" "--pyargs" "sklearn"
+ test-flags))))))))
(inputs (list openblas))
(native-inputs
- (list python-cython
+ (list python-cython-0.29.35
python-pandas
python-pytest
python-pytest-xdist))
@@ -1532,6 +1669,54 @@ computing environments.")
data analysis.")
(license license:bsd-3)))
+(define-public python-scikit-learn-extra
+ (package
+ (name "python-scikit-learn-extra")
+ (version "0.3.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/scikit-learn-contrib/scikit-learn-extra")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0yy6ka94ss88f3r7b6mpjf1l8lnv7aabhsg844pigfj8lfiv0wvl"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #: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")
+
+ ;; Step out of the source directory to avoid interference;
+ ;; we want to run the installed code with extensions etc.
+ (with-directory-excursion "/tmp"
+ (invoke "pytest" "-vv" "--pyargs"
+ "sklearn_extra"
+ ;; ignore tests that require network
+ "-k" "not test_build"))))))))
+ (propagated-inputs (list python-numpy python-scikit-learn python-scipy))
+ (native-inputs (list python-pytest python-pytest-cov python-cython))
+ (home-page "https://github.com/scikit-learn-contrib/scikit-learn-extra")
+ (synopsis "Set of tools for scikit-learn")
+ (description
+ "This package provides a Python module for machine learning that extends
+scikit-learn. It includes algorithms that are useful but do not satisfy the
+scikit-learn inclusion criteria, for instance due to their novelty or lower
+citation number.")
+ (license license:bsd-3)))
+
(define-public python-thinc
(package
(name "python-thinc")
@@ -1593,115 +1778,45 @@ 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 "0.6.2")
- (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
- "0l9l21jy78mhajdfwyx8rskw08597vg55ff22bjkv6xrjjr9g4ac"))))
- (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")
- (version "0.9.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "imbalanced-learn" version))
- (sha256
- (base32
- "0qnrmysnqpc8ii1w5n8mci20gcjhmjr7khvk7f2apdbqc2pgf52f"))))
+ (version "0.11.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "imbalanced-learn" version))
+ (sha256
+ (base32 "1p4gdgc8nsq0vjmw4y4d2bp9g0m1c23d0zgrzs90pnz6b24ax0km"))))
(build-system pyproject-build-system)
(arguments
(list
- #:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'unbreak-tests
- (lambda _
- ;; The doctests require tensorflow
- (substitute* "setup.cfg"
- (("--doctest-modules") ""))
- ;; Some tests require a home directory
- (setenv "HOME" (getcwd))
- ;; We don't have keras
- (delete-file "imblearn/keras/tests/test_generator.py")
- ;; We don't have tensorflow
- (delete-file "imblearn/tensorflow/tests/test_generator.py"))))))
- (propagated-inputs
- (list python-joblib
- python-numpy
- python-scikit-learn
- python-scipy
- python-threadpoolctl))
- (native-inputs
- (list python-black
- python-flake8
- python-mypy
- python-pandas
- python-pytest
- python-pytest-cov))
+ #:test-flags '(list "-k"
+ ;; Although we cannot satify the Tensorflow and Keras requirements
+ ;; (python-keras >= 2.4.3 and tensorflow >= 2.4.3), all tests
+ ;; besides these pass.
+ "not balanced_batch_generator and not BalancedBatchGenerator")
+ #:phases '(modify-phases %standard-phases
+ (add-after 'unpack 'unbreak-tests
+ (lambda _
+ ;; Some tests require a home directory
+ (setenv "HOME"
+ (getcwd)))))))
+ (propagated-inputs (list python-joblib python-numpy python-scikit-learn
+ python-scipy python-threadpoolctl))
+ (native-inputs (list python-black
+ python-flake8
+ python-keras
+ python-mypy
+ python-numpydoc
+ python-pandas
+ python-pytest
+ python-pytest-cov
+ tensorflow))
(home-page "https://github.com/scikit-learn-contrib/imbalanced-learn")
(synopsis "Toolbox for imbalanced dataset in machine learning")
- (description "This is a Python package offering a number of re-sampling
+ (description
+ "This is a Python package offering a number of re-sampling
techniques commonly used in datasets showing strong between-class imbalance.
It is compatible with @code{scikit-learn}.")
(license license:expat)))
@@ -1709,27 +1824,18 @@ It is compatible with @code{scikit-learn}.")
(define-public python-pynndescent
(package
(name "python-pynndescent")
- (version "0.5.10")
+ (version "0.5.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pynndescent" version))
(sha256
- (base32 "1bc8aa6jfw28y6sb0nvfdrfgh66a42bqb4znvpimzx9yq21wcpax"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "pytest" "--pyargs" "pynndescent"
- ;; wminkowski no longer exists in scipy 1.8.0 (see:
- ;; https://github.com/lmcinnes/pynndescent/issues/177)
- "-k" "not test_weighted_minkowski")))))))
+ (base32 "0l5dpdsk5vg7rpay81bncp04119hnl5z7zxjv63jrnm9spcwwi3g"))))
+ (build-system pyproject-build-system)
(native-inputs (list python-pytest))
(propagated-inputs
- (list python-joblib
+ (list python-importlib-metadata
+ python-joblib
python-llvmlite
python-numba
python-scikit-learn
@@ -1744,7 +1850,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
(define-public python-opentsne
(package
(name "python-opentsne")
- (version "0.7.1")
+ (version "1.0.0")
(source
(origin
(method git-fetch) ; no tests in PyPI release
@@ -1753,7 +1859,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "12wp98mh67v6v683yi7wbv8zhpafrfz21z349bww4wgi2q7bl3il"))))
+ (base32 "05qzpq1zjs42bl0z8girfwcj3nfxs1a99c5525vp3589sglk351g"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -1822,16 +1928,14 @@ standard feature selection algorithms.")
(build-system pyproject-build-system)
(arguments
(list
- #:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'disable-bad-tests
- (lambda _
- ;; XXX This requires pytest lazy_fixture
- (delete-file "tests/test_multilabel_classification.py")
- ;; Requires tensorflow
- (delete-file "tests/test_frameworks.py")
+ #:test-flags
+ ;; This test fails because the newer version of scikit learn returns one
+ ;; more classification result than expected. This should be harmless.
+ '(list "-k" "not test_aux_inputs"
+ ;; Requires Tensorflow
+ "--ignore=tests/test_frameworks.py"
;; Tries to download datasets from the internet at runtime.
- (delete-file "tests/test_dataset.py"))))))
+ "--ignore=tests/test_dataset.py")))
(propagated-inputs
(list python-numpy
python-pandas
@@ -1840,6 +1944,7 @@ standard feature selection algorithms.")
python-tqdm))
(native-inputs
(list python-pytest
+ python-pytest-lazy-fixture
python-pytorch
python-torchvision))
(home-page "https://cleanlab.ai")
@@ -1923,9 +2028,9 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
(license license:expat)))
(define-public python-autograd
- (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
+ (let* ((commit "c6d81ce7eede6db801d4e9a92b27ec5d409d0eab")
(revision "0")
- (version (git-version "0.0.0" revision commit)))
+ (version (git-version "1.5" revision commit)))
(package
(name "python-autograd")
(home-page "https://github.com/HIPS/autograd")
@@ -1936,19 +2041,14 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
(commit commit)))
(sha256
(base32
- "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
+ "04kljgydng42xlg044h6nbzxpban1ivd6jzb8ydkngfq88ppipfk"))
(file-name (git-file-name name version))))
(version version)
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(native-inputs
(list python-nose python-pytest))
(propagated-inputs
(list python-future python-numpy))
- (arguments
- `(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "py.test" "-v"))))))
(synopsis "Efficiently computes derivatives of NumPy code")
(description "Autograd can automatically differentiate native Python and
NumPy code. It can handle a large subset of Python's features, including loops,
@@ -2102,13 +2202,13 @@ discrete, and conditional dimensions.")
(define-public python-deepxde
(package
(name "python-deepxde")
- (version "1.9.3")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "DeepXDE" version))
(sha256
(base32
- "1zw2gqssc0s3maf4gdjckxmzx1d3036hbp1iir26kd08hxj93vzs"))))
+ "1lgn4sa9bnmhsccddb9vjz7nsvdnccxqkvv7xssxmfb413dpg1mz"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #f ; there are no tests
@@ -3069,7 +3169,7 @@ advanced research.")
(define-public tensorflow-lite
(package
(name "tensorflow-lite")
- (version "2.13.0")
+ (version "2.13.1")
(source
(origin
(method git-fetch)
@@ -3079,7 +3179,7 @@ advanced research.")
(file-name (git-file-name name version))
(sha256
(base32
- "07g6vlrs0aayrg2mfdl15gxg5dy103wx2xlqkran15dib40nkbj6"))
+ "09mfskmpvpbq919wibnw3bnhi1y3hkx3qrzm72gdr0gsivn1yb3w"))
(patches (search-patches "tensorflow-lite-unbundle.patch"))))
(build-system cmake-build-system)
(arguments
@@ -3686,46 +3786,26 @@ methodxs at scale on CPU or GPU.")
(define-public python-umap-learn
(package
(name "python-umap-learn")
- (version "0.5.3")
+ (version "0.5.5")
(source
(origin
(method git-fetch) ;no tests in pypi release
(uri (git-reference
(url "https://github.com/lmcinnes/umap")
- (commit version)))
+ (commit (string-append "release-" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "1315jkb0h1b579y9m59632f0nnpksilm01nxx46in0rq8zna8vsb"))))
- (build-system python-build-system)
+ "0ijyiaqycynwj1383cxp519c765gjbg1f6fjwbvqj1gims710w3d"))))
+ (build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
- (add-after 'unpack 'numpy-compatibility
- (lambda _
- (substitute* "umap/tests/test_umap_metrics.py"
- ;; See commit a714b59bd9e2ca2e63312bc3491b2b037a42f2f2
- (("sparse_binary_data.todense\\(\\),")
- "np.asarray(sparse_binary_data.todense()),")
- ;; See commit c7d05683325589ad432a55e109cacb9d631cfaa9
- (("sparse_spatial_data.todense\\(\\),")
- "np.asarray(sparse_spatial_data.todense()),"))
- ;; See commit 949abd082524fce8c45dfb147bcd8e8ef49eade3
- (substitute* "umap/tests/test_umap_ops.py"
- (("np.random,") "None,"))))
;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir
(lambda _
- (setenv "NUMBA_CACHE_DIR" "/tmp")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (setenv "HOME" "/tmp")
- (invoke "pytest" "-vv" "umap"
- ;; This test can fail because trust may only be
- ;; 0.9679405204460967 >= 0.97
- "-k" "not test_densmap_trustworthiness_on_iris_supervised")))))))
+ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(native-inputs (list python-pytest))
(propagated-inputs
(list python-numba
@@ -3838,6 +3918,34 @@ high-level machine learning frameworks, such as TensorFlow Lite,
TensorFlow.js, PyTorch, and MediaPipe.")
(license license:bsd-3))))
+(define-public xnnpack-for-torch2
+ ;; There's currently no tag on this repo.
+ (let ((version "0.0")
+ (commit "51a987591a6fc9f0fc0707077f53d763ac132cbf")
+ (revision "3"))
+ (package
+ (inherit xnnpack)
+ (name "xnnpack")
+ (version (git-version version revision commit))
+ (home-page "https://github.com/google/XNNPACK") ;fork of QNNPACK
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1rzby82xq8d0rl1d148yz88jh9cpsw5c8b2yw7yg39mi7qmr55rm"))
+ (patches (search-patches "xnnpack-for-torch2-system-libraries.patch"))))
+ (arguments
+ (list
+ #:tests? #false
+ #:configure-flags '(list "-DXNNPACK_USE_SYSTEM_LIBS=YES"
+ "-DBUILD_SHARED_LIBS=ON"
+ "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
+ "-DXNNPACK_LIBRARY_TYPE=shared"
+ "-DXNNPACK_BUILD_TESTS=FALSE" ;FIXME: see below
+ "-DXNNPACK_BUILD_BENCHMARKS=FALSE"))))))
+
;; Please also update python-torchvision when updating this package.
(define-public python-pytorch
(package
@@ -3987,7 +4095,59 @@ 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 "2.0.1")
+ (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
+ "14m7v54zyd2qg2xk9mqdpbf4ps7091mdzinzh4vq9p5k4bpznj65"))
+ (patches (search-patches "python-pytorch2-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"))
+ (substitute* "caffe2/CMakeLists.txt"
+ (("target_link_libraries\\(\\$\\{test_name\\}_\\$\\{CPU_CAPABILITY\\} c10 sleef gtest_main\\)")
+ "target_link_libraries(${test_name}_${CPU_CAPABILITY} c10 sleef gtest gtest_main)"))
+ (substitute* "functorch/CMakeLists.txt"
+ (("\\$\\{_rpath_portable_origin\\}/../torch/lib")
+ "$ORIGIN/../torch/lib"))))))
+ (inputs
+ (modify-inputs (package-inputs python-pytorch)
+ (replace "xnnpack" xnnpack-for-torch2)))
+ (propagated-inputs
+ (modify-inputs (package-propagated-inputs python-pytorch)
+ (append python-filelock
+ python-jinja2
+ python-networkx
+ python-opt-einsum
+ python-sympy)
+ (replace "onnx" onnx-for-torch2)
+ (replace "onnx-optimizer" onnx-optimizer-for-torch2)))))
(define-public python-lightning-cloud
(package
@@ -4039,7 +4199,7 @@ Actions for the Lightning suite of libraries.")
(define-public python-captum
(package
(name "python-captum")
- (version "0.6.0")
+ (version "0.7.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -4048,7 +4208,7 @@ Actions for the Lightning suite of libraries.")
(file-name (git-file-name name version))
(sha256
(base32
- "1h4n91ivhjxm6wj0vgqpfss2dmq4sjcp0appd08cd5naisabjyb5"))))
+ "0bgfwnlsi50hbmknn7qljiy93fi6ggwz3k7yk9kj7s37mhzaylym"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -4058,7 +4218,8 @@ Actions for the Lightning suite of libraries.")
;; 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))
+ (propagated-inputs
+ (list python-matplotlib python-numpy python-pytorch python-tqdm))
(native-inputs (list jupyter
python-annoy
python-black
@@ -4400,70 +4561,74 @@ of Hidden Markov Models.")
;; Keep this in sync with the r-torch package.
(define-public liblantern
- (package
- (name "liblantern")
- (version "0.10.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/mlverse/torch")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "12480fac9xq7rgw0q5f2cnvmakhakjsnq1gvh2ncjfwxz34n8fl7"))))
- (build-system cmake-build-system)
- (arguments
- (list
- #:tests? #false ;no test target
- #:phases
- (let ((python-version (version-major+minor (package-version python))))
- #~(modify-phases %standard-phases
- (add-after 'unpack 'chdir
- (lambda _ (chdir "src/lantern")))
- (add-after 'chdir 'do-not-download-binaries
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "CMakeLists.txt"
- (("find_package\\(Torch.*") "set(TORCH_CXX_FLAGS \"-ltorch\")\n")
- (("retrieve_lib\\(.*") ""))
- (let ((site-packages (string-append "/lib/python"
- #$python-version
- "/site-packages")))
- (setenv "LIBRARY_PATH"
- (string-append
- (search-input-directory
- inputs (string-append site-packages "/torch/lib"))
- ":" (or (getenv "LIBRARY_PATH") "")))
- (setenv "CPLUS_INCLUDE_PATH"
- (string-append
- (search-input-directory
- inputs (string-append
- site-packages "/torch/include/torch/csrc/api/include/"))
- ":"
- (search-input-directory
- inputs (string-append site-packages "/torch/include/"))
- ":"
- (or (getenv "CPLUS_INCLUDE_PATH") "")))
- (setenv "C_INCLUDE_PATH"
- (string-append
- (search-input-directory
- inputs (string-append site-packages "/torch/include/"))
- ":"
- (or (getenv "C_INCLUDE_PATH") ""))))))
- (replace 'install
- (lambda _
- (install-file
- "../build/liblantern.so"
- (string-append #$output "/lib"))
- (copy-recursively
- "../lantern/include"
- (string-append #$output "/include"))))))))
- (inputs (list python-pytorch-for-r-torch))
- (home-page "https://github.com/mlverse/torch/")
- (synopsis "C API to libtorch")
- (description
- "Lantern provides a C API to the libtorch machine learning library.")
- (license license:expat)))
+ ;; There has been no release or tagged commit for r-torch 0.12.0. The
+ ;; selected commit corresponds to the 0.12.0 release.
+ (let ((commit "4d83bd087be581f7db321c27f55897ff021d2537")
+ (revision "1"))
+ (package
+ (name "liblantern")
+ (version (git-version "0.11.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mlverse/torch")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1xxc6vr7sr2mg0va0hc2fs4f6v5b78mx43dp2shzzbcgw90mgpvk"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ #:tests? #false ;no test target
+ #:phases
+ (let ((python-version (version-major+minor (package-version python))))
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "src/lantern")))
+ (add-after 'chdir 'do-not-download-binaries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "CMakeLists.txt"
+ (("find_package\\(Torch.*") "set(TORCH_CXX_FLAGS \"-ltorch\")\n")
+ (("retrieve_lib\\(.*") ""))
+ (let ((site-packages (string-append "/lib/python"
+ #$python-version
+ "/site-packages")))
+ (setenv "LIBRARY_PATH"
+ (string-append
+ (search-input-directory
+ inputs (string-append site-packages "/torch/lib"))
+ ":" (or (getenv "LIBRARY_PATH") "")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append
+ (search-input-directory
+ inputs (string-append
+ site-packages "/torch/include/torch/csrc/api/include/"))
+ ":"
+ (search-input-directory
+ inputs (string-append site-packages "/torch/include/"))
+ ":"
+ (or (getenv "CPLUS_INCLUDE_PATH") "")))
+ (setenv "C_INCLUDE_PATH"
+ (string-append
+ (search-input-directory
+ inputs (string-append site-packages "/torch/include/"))
+ ":"
+ (or (getenv "C_INCLUDE_PATH") ""))))))
+ (replace 'install
+ (lambda _
+ (install-file
+ "../build/liblantern.so"
+ (string-append #$output "/lib"))
+ (copy-recursively
+ "../lantern/include"
+ (string-append #$output "/include"))))))))
+ (inputs (list python-pytorch-for-r-torch))
+ (home-page "https://github.com/mlverse/torch/")
+ (synopsis "C API to libtorch")
+ (description
+ "Lantern provides a C API to the libtorch machine learning library.")
+ (license license:expat))))
(define-public python-lap
(package
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-24 20:21:15 +0000