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-rw-r--r--gnu/packages/machine-learning.scm821
1 files changed, 576 insertions, 245 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index b4651c80e5..23791dfd03 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -15,12 +15,18 @@
;;; 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 © 2022 Kiran Shila <me@kiranshila.com>
;;; 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>
+;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2024 David Pflug <david@pflug.io>
+;;; Copyright © 2024 Timothee Mathieu <timothee.mathieu@inria.fr>
+;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -70,6 +76,7 @@
#:use-module (gnu packages cran)
#:use-module (gnu packages databases)
#:use-module (gnu packages dejagnu)
+ #:use-module (gnu packages documentation)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
@@ -103,6 +110,7 @@
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages rdf)
#:use-module (gnu packages regex)
#:use-module (gnu packages rpc)
#:use-module (gnu packages serialization)
@@ -516,8 +524,8 @@ Performance is achieved by using the LLVM JIT compiler.")
(deprecated-package "guile-aiscm-next" guile-aiscm))
(define-public llama-cpp
- (let ((commit "f31b5397143009d682db90fd2a6cde83f1ef00eb")
- (revision "0"))
+ (let ((commit "03bf161eb6dea6400ee49c6dc6b69bdcfa9fd3fc")
+ (revision "1"))
(package
(name "llama-cpp")
(version (git-version "0.0.0" revision commit))
@@ -526,10 +534,10 @@ Performance is achieved by using the LLVM JIT compiler.")
(method git-fetch)
(uri (git-reference
(url "https://github.com/ggerganov/llama.cpp")
- (commit (string-append "master-" (string-take commit 7)))))
+ (commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "0ys6n53n032zq1ll9f3vgxk8sw0qq7x3fi7awsyy13adzp3hn08p"))))
+ (base32 "1ag1jash84hasz10h0piw72a8ginm8kzvhihbzzljz96gq2kjm88"))))
(build-system cmake-build-system)
(arguments
(list
@@ -556,8 +564,10 @@ Performance is achieved by using the LLVM JIT compiler.")
(get-string-all input))))))
(chmod (string-append bin script) #o555)))
(mkdir-p bin)
- (make-script "convert-pth-to-ggml")
+ (make-script "convert-hf-to-gguf")
+ (make-script "convert-llama-ggml-to-gguf")
(make-script "convert-lora-to-ggml")
+ (make-script "convert-persimmon-to-gguf")
(make-script "convert"))))
(add-after 'install-python-scripts 'wrap-python-scripts
(assoc-ref python:%standard-phases 'wrap))
@@ -656,6 +666,53 @@ networks) based on simulation of (stochastic) flow in graphs.")
algorithm.")
(license license:gpl3)))
+(define-public openmm
+ (package
+ (name "openmm")
+ (version "8.1.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openmm/openmm")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "064vv6zaci30pj38z5lwfqscxssm67jqxkz30hcya9vm4ng831d5"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ '(list "-DOPENMM_BUILD_SHARED_LIB=TRUE"
+ "-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=TRUE"
+ "-DOPENMM_BUILD_PYTHON_WRAPPERS=TRUE"
+ "-DOPENMM_BUILD_CUDA_LIB=FALSE")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-python-build-system
+ (lambda _
+ (substitute* "wrappers/python/CMakeLists.txt"
+ (("install --root=\\\\\\$ENV\\{DESTDIR\\}/")
+ (string-append "install --prefix=" #$output
+ " --root=/ --single-version-externally-managed")))))
+ (add-after 'install 'install-python
+ (lambda _
+ (invoke "make" "PythonInstall"))))))
+ (inputs
+ (list python-wrapper))
+ (propagated-inputs
+ (list python-numpy))
+ (native-inputs
+ (list doxygen gfortran opencl-headers python-cython swig))
+ (home-page "https://github.com/openmm/openmm/")
+ (synopsis "Toolkit for molecular simulation")
+ (description
+ "OpenMM is a toolkit for molecular simulation. It can be used either as
+a stand-alone application for running simulations, or as a library you call
+from your own code.")
+ ;; See https://github.com/openmm/openmm/issues/4278#issuecomment-1772982471
+ (license license:expat)))
+
(define-public randomjungle
(package
(name "randomjungle")
@@ -812,6 +869,94 @@ 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")
@@ -1524,7 +1669,7 @@ 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)
@@ -1534,20 +1679,28 @@ 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"
+ "-k" (string-append
+ ;; This test tries to access the internet.
+ "not test_load_boston_alternative"
+ ;; DID NOT RAISE <class 'ValueError'>
+ " and not test_singular_matrix"))
+ #: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")
@@ -1558,14 +1711,11 @@ 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))
@@ -1579,51 +1729,83 @@ data analysis.")
(license license:bsd-3)))
(define-public python-scikit-learn-extra
+ ;; This commit fixes an incompatibility with newer versions of scikit-learn
+ (let ((commit "0f95d8dda4c69f9de4fb002366041adcb1302f3b")
+ (revision "1"))
+ (package
+ (name "python-scikit-learn-extra")
+ (version (git-version "0.3.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/scikit-learn-contrib/scikit-learn-extra")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0a248sff1psfwzmngj465gzyisq20d83nzpwpq2cspxhih51m6j9"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ ;; ignore tests that require network
+ '(list "--pyargs" "sklearn_extra"
+ "-k" "not test_build")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'build 'build-ext
+ (lambda _
+ (invoke "python" "setup.py" "build_ext"
+ "--inplace")))
+ (replace 'check
+ (lambda* (#:key tests? test-flags #: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"
+ (apply invoke "pytest" "-vv" test-flags))))))))
+ (propagated-inputs
+ (list python-numpy
+ python-scikit-learn
+ python-scipy
+ python-packaging))
+ (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-mord
(package
- (name "python-scikit-learn-extra")
- (version "0.3.0")
+ (name "python-mord")
+ (version "0.7")
(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))
+ (method url-fetch)
+ (uri (pypi-uri "mord" version))
(sha256
- (base32 "0yy6ka94ss88f3r7b6mpjf1l8lnv7aabhsg844pigfj8lfiv0wvl"))))
+ (base32 "1cvv9b9w69v0inq0zgcw0vmkiq3zn9q9r6clkynpzjik9rrh405n"))))
(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")
+ ;; v0.7 does not provide any test cases
+ ;; v0.6 relies on deprecated scikit-learn functionality
+ (arguments `(#:tests? #f))
+ (inputs (list python-numpy python-scipy python-scikit-learn))
+ (home-page "https://pypi.org/project/mord/")
+ (synopsis "Ordinal regression models 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.")
+ "This package provides a collection of ordinal regression models for
+machine learning in Python. They are intended to be used with scikit-learn
+and are compatible with its API.")
(license license:bsd-3)))
(define-public python-thinc
@@ -1687,73 +1869,6 @@ 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")
@@ -1797,30 +1912,59 @@ techniques commonly used in datasets showing strong between-class imbalance.
It is compatible with @code{scikit-learn}.")
(license license:expat)))
+(define-public python-hdbscan
+ (package
+ (name "python-hdbscan")
+ (version "0.8.33")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "hdbscan" version))
+ (sha256
+ (base32 "03gr70ys1zrnp15pxzhichvrdj5bj88p6p5k0wj8vx251rgvryjp"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'build-extensions
+ (lambda _
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+ (propagated-inputs (list python-joblib
+ python-numpy
+ python-scikit-learn
+ python-scipy))
+ (native-inputs (list python-cython
+ python-nose
+ python-pytest
+ python-pandas
+ python-networkx))
+ (home-page "https://github.com/scikit-learn-contrib/hdbscan")
+ (synopsis "High performance implementation of HDBSCAN clustering")
+ (description "HDBSCAN - Hierarchical Density-Based Spatial Clustering of
+Applications with Noise. Performs DBSCAN over varying epsilon values and
+integrates the result to find a clustering that gives the best stability over
+epsilon. This allows HDBSCAN to find clusters of varying densities (unlike
+DBSCAN), and be more robust to parameter selection. HDBSCAN is ideal for
+exploratory data analysis; it's a fast and robust algorithm that you can trust
+to return meaningful clusters (if there are any).")
+ (license license:bsd-3)))
+
(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
@@ -1835,7 +1979,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
(define-public python-opentsne
(package
(name "python-opentsne")
- (version "1.0.0")
+ (version "1.0.1")
(source
(origin
(method git-fetch) ; no tests in PyPI release
@@ -1844,7 +1988,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "05qzpq1zjs42bl0z8girfwcj3nfxs1a99c5525vp3589sglk351g"))))
+ (base32 "0xjp0l4rxk1s685skbx50m3m9hwlj78w74qwgswnkmkk6f7c8dsi"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -1913,16 +2057,14 @@ 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
@@ -1931,6 +2073,7 @@ standard feature selection algorithms.")
python-tqdm))
(native-inputs
(list python-pytest
+ python-pytest-lazy-fixture
python-pytorch
python-torchvision))
(home-page "https://cleanlab.ai")
@@ -1994,7 +2137,7 @@ and a few related numerical optimization tools.")
(define-public python-cmaes
(package
(name "python-cmaes")
- (version "0.9.1")
+ (version "0.10.0")
(source
(origin
(method git-fetch) ;no tests in PyPI
@@ -2002,7 +2145,7 @@ and a few related numerical optimization tools.")
(url "https://github.com/CyberAgentAILab/cmaes")
(commit (string-append "v" version))))
(sha256
- (base32 "1f3143w8ii6i93bdh65iazrq1lryccd805ndnqww5l8h7qnnzpkm"))
+ (base32 "17bk60mhkglz6s7wz6xcyhw1h4mvghc1iid0805dra7jdyafwrfn"))
(file-name (git-file-name name version))))
(build-system pyproject-build-system)
(native-inputs (list python-hypothesis))
@@ -2188,13 +2331,13 @@ discrete, and conditional dimensions.")
(define-public python-deepxde
(package
(name "python-deepxde")
- (version "1.10.0")
+ (version "1.11.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "DeepXDE" version))
(sha256
(base32
- "0fdxrjrm7l19yx6n8vaklxlhwzx0bw9n08vp8idikzdifybz5gij"))))
+ "0qx6iq8n2j8ab80bs2n85v8g6xi2bnq83vfiaj7a4nsmf62rhkzg"))))
(build-system pyproject-build-system)
(arguments
(list #:tests? #f ; there are no tests
@@ -3392,57 +3535,79 @@ in a fast and accurate way.")
(inherit xgboost)
(name "python-xgboost")
(source (package-source xgboost))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'preparations
- (lambda _
- ;; Move python-package content to parent directory to silence
- ;; some warnings about files not being found if we chdir.
- (rename-file "python-package/xgboost" "xgboost")
- (rename-file "python-package/README.rst" "README.rst")
- (rename-file "python-package/setup.cfg" "setup.cfg")
- (rename-file "python-package/setup.py" "setup.py")
- ;; Skip rebuilding libxgboost.so.
- (substitute* "setup.py"
- (("ext_modules=\\[CMakeExtension\\('libxgboost'\\)\\],") "")
- (("'install_lib': InstallLib,") ""))))
- (add-after 'install 'install-version-and-libxgboost
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (pylib (string-append out "/lib/python"
- ,(version-major+minor
- (package-version python))
- "/site-packages"))
- (xgbdir (string-append pylib "/xgboost"))
- (version-file (string-append xgbdir "/VERSION"))
- (libxgboost (string-append (assoc-ref inputs "xgboost")
- "/lib/libxgboost.so")))
- (with-output-to-file version-file
- (lambda ()
- (display ,(package-version xgboost))))
- (mkdir-p (string-append xgbdir "/lib"))
- (symlink libxgboost (string-append xgbdir "/lib"
- "/libxgboost.so")))))
- (replace 'check
- ;; Python-specific tests are located in tests/python.
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "tests/python"
- ;; FIXME: CLI tests fail with PermissionError.
- "--ignore" "tests/python/test_cli.py" "-k"
- (string-append
- "not test_cli_regression_demo"
- ;; The tests below open a network connection.
- " and not test_model_compatibility"
- " and not test_get_group"
- " and not test_cv_no_shuffle"
- " and not test_cv"
- " and not test_training"
- ;; "'['./runexp.sh']' returned non-zero exit status 1"
- " and not test_cli_binary_classification"))))))))
+ (list
+ #:test-flags
+ '(list "tests/python"
+ ;; FIXME: CLI tests fail with PermissionError.
+ "--ignore" "tests/python/test_cli.py"
+ "-k"
+ (string-append
+ "not test_cli_regression_demo"
+ ;; These tests use the Boston dataset that has been
+ ;; removed from scipy.
+ " and not test_sklearn_demo"
+ " and not test_sklearn_parallel_demo"
+ " and not test_predict_shape"
+ " and not test_num_parallel_tree"
+ " and not test_boston_housing_regression"
+ " and not test_boston_housing_rf_regression"
+ " and not test_parameter_tuning"
+ " and not test_regression_with_custom_objective"
+ " and not test_RFECV"
+ ;; Pandas incompatibility? Says:
+ ;; '_CalibratedClassifier' object has no attribute
+ ;; 'base_estimator'
+ " and not test_pandas_input"
+ ;; Accuracy problems?
+ " and not test_exact"
+ " and not test_approx"
+ " and not test_hist"
+ ;; The tests below open a network connection.
+ " and not test_model_compatibility"
+ " and not test_get_group"
+ " and not test_cv_no_shuffle"
+ " and not test_cv"
+ " and not test_training"
+ ;; "'['./runexp.sh']' returned non-zero exit status 1"
+ " and not test_cli_binary_classification"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'preparations
+ (lambda _
+ ;; Move python-package content to parent directory to silence
+ ;; some warnings about files not being found if we chdir.
+ (rename-file "python-package/xgboost" "xgboost")
+ (rename-file "python-package/README.rst" "README.rst")
+ (rename-file "python-package/setup.cfg" "setup.cfg")
+ (rename-file "python-package/setup.py" "setup.py")
+ ;; Skip rebuilding libxgboost.so.
+ (substitute* "setup.py"
+ (("ext_modules=\\[CMakeExtension\\('libxgboost'\\)\\],") "")
+ (("'install_lib': InstallLib,") ""))
+ ;; Remove bad dataset. This has been removed in scipy.
+ (substitute* "tests/python/testing.py"
+ (("TestDataset\\('boston', get_boston, 'reg:squarederror', 'rmse'\\),")
+ "")
+ (("datasets.load_boston")
+ "datasets.load_digits"))))
+ (add-after 'install 'install-version-and-libxgboost
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((pylib (string-append #$output "/lib/python"
+ #$(version-major+minor
+ (package-version python))
+ "/site-packages"))
+ (xgbdir (string-append pylib "/xgboost"))
+ (version-file (string-append xgbdir "/VERSION"))
+ (libxgboost (string-append (assoc-ref inputs "xgboost")
+ "/lib/libxgboost.so")))
+ (with-output-to-file version-file
+ (lambda ()
+ (display #$(package-version xgboost))))
+ (mkdir-p (string-append xgbdir "/lib"))
+ (symlink libxgboost (string-append xgbdir "/lib"
+ "/libxgboost.so"))))))))
(native-inputs
(list python-pandas python-pytest python-scikit-learn))
(inputs
@@ -3772,46 +3937,26 @@ 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
@@ -4101,6 +4246,61 @@ PyTorch when needed.
Note: currently this package does not provide GPU support.")
(license license:bsd-3)))
+(define-public python-pytorch2
+ (package
+ (inherit python-pytorch)
+ (name "python-pytorch")
+ (version "2.2.1")
+ (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
+ "0hdr0d6n072qd0nq2dkxhc9pva6vggj9hpzc0glpc60vfgk0cgzb"))
+ (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-peachpy"
+ "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-fsspec
+ python-jinja2
+ python-networkx
+ python-opt-einsum
+ python-sympy)
+ (replace "onnx" onnx-for-torch2)
+ (replace "onnx-optimizer" onnx-optimizer-for-torch2)))))
+
(define-public python-pytorch-for-r-torch
(package
(inherit python-pytorch)
@@ -4155,6 +4355,86 @@ Note: currently this package does not provide GPU support.")
(replace "onnx" onnx-for-torch2)
(replace "onnx-optimizer" onnx-optimizer-for-torch2)))))
+(define-public python-pytorch-geometric
+ (package
+ (name "python-pytorch-geometric")
+ (version "2.4.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyg-team/pytorch_geometric/")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0hrs579asjsph16hyb4ablkbgfwd5j9y5s6ny7ahn3qrbkl2ji1g"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ ;; Hangs with AttributeError: 'NoneType' object has no attribute 'rpc_async'
+ '(list "--ignore=test/distributed/test_rpc.py"
+ ;; A message passing jinja template is missing
+ "--ignore=test/nn/conv/test_message_passing.py"
+ "--ignore=test/nn/test_sequential.py"
+ "--ignore=test/nn/models/test_basic_gnn.py"
+ ;; These all fail with a size mismatch error such as
+ ;; RuntimeError: shape '[-1, 2, 1, 1]' is invalid for input of size 3
+ "--ignore=test/explain/algorithm/test_captum_explainer.py"
+ "-k" (string-append
+ ;; Permissions error
+ "not test_packaging"
+ ;; This can fail due to accuracy problems
+ " and not test_gdc"
+ ;; These refuse to be run on CPU and really want a GPU
+ " and not test_add_random_walk_pe"
+ " and not test_asap"
+ " and not test_two_hop"))
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'delete-top-level-directories
+ (lambda _
+ ;; The presence of these directories confuses the pyproject build
+ ;; system.
+ (for-each delete-file-recursively
+ '("conda" "docker" "graphgym")))))))
+ (propagated-inputs
+ (list onnx
+ python-captum
+ python-graphviz
+ python-h5py
+ python-jinja2
+ python-matplotlib
+ python-networkx
+ python-numba
+ python-numpy
+ python-opt-einsum
+ python-pandas
+ python-protobuf
+ python-psutil
+ python-pyparsing
+ python-pytorch-lightning
+ python-rdflib
+ python-requests
+ python-scikit-image
+ python-scikit-learn
+ python-scipy
+ python-statsmodels
+ python-sympy
+ python-tabulate
+ python-torchmetrics
+ python-tqdm))
+ (native-inputs
+ (list python-flit-core
+ python-pytest
+ python-pytest-cov))
+ (home-page "https://pyg.org")
+ (synopsis "Graph Neural Network library for PyTorch")
+ (description
+ "PyG is a library built upon PyTorch to easily write and train Graph
+Neural Networks for a wide range of applications related to structured data.")
+ (license license:expat)))
+
(define-public python-lightning-cloud
(package
(name "python-lightning-cloud")
@@ -4205,7 +4485,7 @@ 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
@@ -4214,7 +4494,7 @@ 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
@@ -4224,7 +4504,8 @@ 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
@@ -4738,24 +5019,23 @@ and Numpy.")
(file-name (git-file-name name version))
(sha256
(base32 "0n1vsih99pvswcaygdxkc6kq6r48ny130z6ca8pp3281396r2ykw"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
+ (list
+ #:test-flags
+ '(list "-vv" "--stage=unit"
;; 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"))
-
+ "--ignore=tests/distributions/test_spanning_tree.py"
+ "--ignore=tests/infer/mcmc/test_mcmc_api.py"
+ ;; This test fails sometimes.
+ "--ignore=tests/optim/test_optim.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"))))))
+ "--ignore=tests/distributions/test_rejector.py"
+ ;; This looks like a test system failure. All of these fail
+ ;; because x is an array of functions, not an array of numbers.
+ "-k" "not test_sample")))
(propagated-inputs
(list python-numpy
python-opt-einsum
@@ -5168,3 +5448,54 @@ Brian 2 simulator.")
"OneAPI Deep Neural Network Library (oneDNN) is a cross-platform
performance library of basic building blocks for deep learning applications.")
(license license:asl2.0)))
+
+(define-public python-gguf
+ (package
+ (name "python-gguf")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gguf" version))
+ (sha256
+ (base32 "0rbyc2h3kpqnrvbyjvv8a69l577jv55a31l12jnw21m1lamjxqmj"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #false))
+ (inputs (list poetry python-pytest))
+ (propagated-inputs (list python-numpy))
+ (home-page "https://ggml.ai")
+ (synopsis "Read and write ML models in GGUF for GGML")
+ (description "A Python library for reading and writing GGUF & GGML format ML models.")
+ (license license:expat)))
+
+(define-public python-gymnasium
+ (package
+ (name "python-gymnasium")
+ (version "0.29.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gymnasium" version))
+ (sha256
+ (base32 "1cab4wsnlsxn2z90qmymv8ppmsq8yq2amiqwid3r0xfbxx92flqs"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-cloudpickle python-farama-notifications
+ python-importlib-metadata python-numpy
+ python-typing-extensions))
+ (native-inputs (list python-pytest python-scipy))
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'create-tests-module
+ (lambda _
+ (with-output-to-file "tests/__init__.py"
+ (lambda _ (display ""))))))))
+ (home-page "https://gymnasium.farama.org/")
+ (synopsis
+ "Standard API for reinforcement learning and a set of reference environments")
+ (description
+ "This package provides a standard API for reinforcement learning and a
+diverse set of reference environments (formerly Gym).")
+ (license license:expat)))
generated by cgit v1.2.3 (git 2.50.1) at 2025-08-14 14:48:49 +0000