diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 77 |
1 files changed, 51 insertions, 26 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 9a3073d3dc..d5cff678d8 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -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. ;;; @@ -1111,8 +1111,13 @@ 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? @@ -1123,13 +1128,15 @@ 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/") @@ -1219,13 +1226,13 @@ 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 @@ -1233,12 +1240,16 @@ 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") @@ -2804,26 +2815,40 @@ 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 |