diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 53 |
1 files changed, 20 insertions, 33 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 990a6c771a..084e62cca4 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -8,6 +8,8 @@ ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org> ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com> +;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> +;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -300,7 +302,9 @@ networks) based on simulation of (stochastic) flow in graphs.") "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110")))) (build-system ocaml-build-system) (arguments - `(#:phases + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:phases (modify-phases %standard-phases (add-before 'configure 'patch-paths (lambda _ @@ -328,15 +332,17 @@ algorithm.") (origin (method url-fetch) (uri (string-append - "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/" - "randomjungle-" version ".tar_.gz")) + "https://www.imbs.uni-luebeck.de/fileadmin/files/Software" + "/randomjungle/randomjungle-" version ".tar_.gz")) + (patches (search-patches "randomjungle-disable-static-build.patch")) (sha256 (base32 "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w")))) (build-system gnu-build-system) (arguments `(#:configure-flags - (list (string-append "--with-boost=" + (list "--disable-static" + (string-append "--with-boost=" (assoc-ref %build-inputs "boost"))) #:phases (modify-phases %standard-phases @@ -356,7 +362,7 @@ algorithm.") ;; Non-portable assembly instructions are used so building fails on ;; platforms other than x86_64 or i686. (supported-systems '("x86_64-linux" "i686-linux")) - (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/") + (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224") (synopsis "Implementation of the Random Forests machine learning method") (description "Random Jungle is an implementation of Random Forests. It is supposed to @@ -489,7 +495,7 @@ sample proximities between pairs of cases.") `(("python" ,python) ("numpy" ,python-numpy) ("r-minimal" ,r-minimal) - ("octave" ,octave) + ("octave" ,octave-cli) ("swig" ,swig) ("eigen" ,eigen) ("hdf5" ,hdf5) @@ -703,7 +709,7 @@ computing environments.") (define-public python-scikit-learn (package (name "python-scikit-learn") - (version "0.19.2") + (version "0.20.1") (source (origin (method git-fetch) @@ -713,9 +719,7 @@ computing environments.") (file-name (git-file-name name version)) (sha256 (base32 - "1dk9hdj01c0bny4ps78b7869fjw9gr6qklxf6wyql8h6nh4k19xm")) - (patches (search-patches - "python-scikit-learn-fix-test-non-determinism.patch")))) + "0fkhwg3xn1s7ln9q1szq6kwc4jhwvjh8w4kmv9wcrqy7cq3lbv0d")))) (build-system python-build-system) (arguments `(#:phases @@ -726,11 +730,11 @@ computing environments.") (lambda _ ;; Restrict OpenBLAS threads to prevent segfaults while testing! (setenv "OPENBLAS_NUM_THREADS" "1") - ;; Disable tests that require network access - (delete-file "sklearn/datasets/tests/test_mldata.py") - (delete-file "sklearn/datasets/tests/test_rcv1.py") - (invoke "pytest" "sklearn") - #t)) + + ;; Some tests require write access to $HOME. + (setenv "HOME" "/tmp") + + (invoke "pytest" "sklearn" "-m" "not network"))) ;; FIXME: This fails with permission denied (delete 'reset-gzip-timestamps)))) (inputs @@ -750,24 +754,7 @@ data analysis.") (license license:bsd-3))) (define-public python2-scikit-learn - (let ((parent (package-with-python2 python-scikit-learn))) - (package (inherit parent) - (arguments - (substitute-keyword-arguments (package-arguments parent) - ((#:phases phases) - `(modify-phases ,phases - (replace 'check - (lambda _ - ;; Restrict OpenBLAS threads to prevent segfaults while testing! - (setenv "OPENBLAS_NUM_THREADS" "1") - ;; Some tests expect to be able to write to HOME. - (setenv "HOME" "/tmp") - ;; Disable tests that require network access - (delete-file "sklearn/datasets/tests/test_kddcup99.py") - (delete-file "sklearn/datasets/tests/test_mldata.py") - (delete-file "sklearn/datasets/tests/test_rcv1.py") - (invoke "pytest" "sklearn") - #t))))))))) + (package-with-python2 python-scikit-learn)) (define-public python-autograd (let* ((commit "442205dfefe407beffb33550846434baa90c4de7") |