diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 167 |
1 files changed, 57 insertions, 110 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index afac56f6f7..509b9c7cdd 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, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2016, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2020, 2021, 2022 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> @@ -16,7 +16,7 @@ ;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net> ;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com> ;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net> -;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1095,8 +1095,13 @@ computing environments.") (arguments `(#: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"))) + (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -1107,13 +1112,15 @@ computing environments.") (setenv "HOME" "/tmp") (invoke "pytest" "sklearn" "-m" "not network" + "-n" (number->string (parallel-job-count)) ;; This test tries to access the internet. "-k" "not test_load_boston_alternative"))))))) - (inputs - (list openblas)) + (inputs (list openblas)) (native-inputs - (list python-pytest python-pandas ;for tests - python-cython)) + (list python-cython + python-pandas + python-pytest + python-pytest-xdist)) (propagated-inputs (list python-numpy python-threadpoolctl python-scipy python-joblib)) (home-page "https://scikit-learn.org/") @@ -1121,55 +1128,8 @@ computing environments.") (description "Scikit-learn provides simple and efficient tools for data mining and data analysis.") - (properties `((python2-variant . ,(delay python2-scikit-learn)))) (license license:bsd-3))) -;; scikit-learn 0.22 and later only supports Python 3, so we stick with -;; an older version here. -(define-public python2-scikit-learn - (let ((base (package-with-python2 (strip-python2-variant python-scikit-learn)))) - (package - (inherit base) - (version "0.20.4") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/scikit-learn/scikit-learn") - (commit version))) - (file-name (git-file-name "python-scikit-learn" version)) - (sha256 - (base32 - "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))) - (arguments - `(#:python ,python-2 - #: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") - - (invoke "pytest" "sklearn" "-m" "not network" - "-k" - (string-append - ;; This test tries to access the internet. - "not test_load_boston_alternative" - ;; This test fails for unknown reasons - " and not test_rank_deficient_design")))))))) - (inputs - (list openblas)) - (native-inputs - (list python2-pytest python2-pandas ;for tests - python2-cython)) - (propagated-inputs - (list python2-numpy python2-scipy python2-joblib))))) - (define-public python-threadpoolctl (package (name "python-threadpoolctl") @@ -1203,13 +1163,13 @@ for scientific computing and data science (e.g. BLAS and OpenMP).") (define-public python-pynndescent (package (name "python-pynndescent") - (version "0.5.5") + (version "0.5.6") (source (origin (method url-fetch) (uri (pypi-uri "pynndescent" version)) (sha256 - (base32 "10pqqqc3jkpw03cyzy04slxmpgyhqnlgbyk0c1cv7kqr5d0zhzbs")))) + (base32 "0p3jsdcprjfzz7qf5674dsqfpvdn6p4wgqikg7b6ki5abf433yv1")))) (build-system python-build-system) (arguments `(#:phases @@ -1217,12 +1177,16 @@ for scientific computing and data science (e.g. BLAS and OpenMP).") (replace 'check (lambda* (#:key inputs outputs tests? #:allow-other-keys) (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest" "--pyargs" "pynndescent"))))))) - (native-inputs - (list python-pytest)) + (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"))))))) + (native-inputs (list python-pytest)) (propagated-inputs - (list python-joblib python-llvmlite python-numba python-scikit-learn + (list python-joblib + python-llvmlite + python-numba + python-scikit-learn python-scipy)) (home-page "https://github.com/lmcinnes/pynndescent") (synopsis "Nearest neighbor descent for approximate nearest neighbors") @@ -1362,9 +1326,6 @@ forward-mode differentiation, and the two can be composed arbitrarily. The main intended application of Autograd is gradient-based optimization.") (license license:expat)))) -(define-public python2-autograd - (package-with-python2 python-autograd)) - (define-public lightgbm (package (name "lightgbm") @@ -1451,38 +1412,6 @@ such as online, hashing, allreduce, reductions, learning2search, active, and interactive learning.") (license license:bsd-3))) -(define-public python2-fastlmm - (package - (name "python2-fastlmm") - (version "0.2.21") - (source - (origin - (method url-fetch) - (uri (pypi-uri "fastlmm" version ".zip")) - (sha256 - (base32 - "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; some test files are missing - #:python ,python-2)) ; only Python 2.7 is supported - (propagated-inputs - (list python2-numpy - python2-scipy - python2-matplotlib - python2-pandas - python2-scikit-learn - python2-pysnptools)) - (native-inputs - (list unzip python2-cython python2-mock python2-nose)) - (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/") - (synopsis "Perform genome-wide association studies on large data sets") - (description - "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed -Models, is a program for performing both single-SNP and SNP-set genome-wide -association studies (GWAS) on extremely large data sets.") - (license license:asl2.0))) - (define-public python-hyperopt (package (name "python-hyperopt") @@ -2785,26 +2714,40 @@ These include a barrier, broadcast, and allreduce.") (define-public python-umap-learn (package (name "python-umap-learn") - (version "0.3.10") + (version "0.5.3") (source (origin - (method url-fetch) - (uri (pypi-uri "umap-learn" version)) + (method git-fetch) ;no tests in pypi release + (uri (git-reference + (url "https://github.com/lmcinnes/umap") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "02ada2yy6km6zgk2836kg1c97yrcpalvan34p8c57446finnpki1")))) + "1315jkb0h1b579y9m59632f0nnpksilm01nxx46in0rq8zna8vsb")))) (build-system python-build-system) - (native-inputs - (list python-joblib python-nose)) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + (invoke "pytest" "-vv" "umap"))))))) + (native-inputs (list python-pytest)) (propagated-inputs - (list python-numba python-numpy python-scikit-learn python-scipy)) + (list python-numba + python-numpy + python-pynndescent + python-scikit-learn + python-scipy + python-tqdm)) (home-page "https://github.com/lmcinnes/umap") - (synopsis - "Uniform Manifold Approximation and Projection") - (description - "Uniform Manifold Approximation and Projection is a dimension reduction -technique that can be used for visualisation similarly to t-SNE, but also for -general non-linear dimension reduction.") + (synopsis "Uniform Manifold Approximation and Projection") + (description "Uniform Manifold Approximation and Projection is a dimension +reduction technique that can be used for visualization similarly to t-SNE, but +also for general non-linear dimension reduction.") (license license:bsd-3))) (define-public nnpack @@ -3046,7 +2989,11 @@ Note: currently this package does not provide GPU support.") (uri (pypi-uri "hmmlearn" version)) (sha256 (base32 - "1my0j3rzp17438idr32ssh0j969a98yjblx5igx5kgiiigr9qa1a")))) + "1my0j3rzp17438idr32ssh0j969a98yjblx5igx5kgiiigr9qa1a")) + (snippet + #~(begin + (use-modules ((guix build utils))) + (delete-file "lib/hmmlearn/_hmmc.c"))))) (build-system python-build-system) (arguments `(#:phases |