;;; 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.
;;;
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
#:use-module (gnu packages xml)
"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 _
(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
;; 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
`(("python" ,python)
("numpy" ,python-numpy)
("r-minimal" ,r-minimal)
- ("octave" ,octave)
+ ("octave" ,octave-cli)
("swig" ,swig)
("eigen" ,eigen)
("hdf5" ,hdf5)
(define-public python-scikit-learn
(package
(name "python-scikit-learn")
- (version "0.19.1")
+ (version "0.20.1")
(source
(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/scikit-learn/scikit-learn/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/scikit-learn/scikit-learn.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))
- (patches (search-patches
- "python-scikit-learn-fix-test-non-determinism.patch"))))
+ "0fkhwg3xn1s7ln9q1szq6kwc4jhwvjh8w4kmv9wcrqy7cq3lbv0d"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- (delete 'check)
- (add-after 'install 'check
- ;; Running tests from the source directory requires
- ;; an "inplace" build with paths relative to CWD.
- ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing
- ;; Use the installed version instead.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- ;; some tests require access to "$HOME"
+ (add-after 'build 'build-ext
+ (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
+ (replace 'check
+ (lambda _
+ ;; 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 just to be sure.
- (chdir "..")
- (invoke "nosetests" "-v" "sklearn"))))))
+
+ (invoke "pytest" "sklearn" "-m" "not network")))
+ ;; FIXME: This fails with permission denied
+ (delete 'reset-gzip-timestamps))))
(inputs
`(("openblas" ,openblas)))
(native-inputs
- `(("python-nose" ,python-nose)
+ `(("python-pytest" ,python-pytest)
+ ("python-pandas" ,python-pandas) ;for tests
("python-cython" ,python-cython)))
(propagated-inputs
`(("python-numpy" ,python-numpy)
(home-page "http://scikit-learn.org/")
(synopsis "Machine Learning in Python")
(description
- "Scikit-learn provides simple and efficient tools for data
-mining and data analysis.")
+ "Scikit-learn provides simple and efficient tools for data mining and
+data analysis.")
(license license:bsd-3)))
(define-public python2-scikit-learn
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
+ `(#:python ,python-2)) ; only Python 2.7 is supported
+ (propagated-inputs
+ `(("python2-numpy" ,python2-numpy)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-matplotlib" ,python2-matplotlib)
+ ("python2-pandas" ,python2-pandas)
+ ("python2-scikit-learn" ,python2-scikit-learn)
+ ("python2-pysnptools" ,python2-pysnptools)))
+ (native-inputs
+ `(("unzip" ,unzip)
+ ("python2-cython" ,python2-cython)
+ ("python2-mock" ,python2-mock)
+ ("python2-nose" ,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)))
HCoop / jackhill / guix / guix.git / blobdiff