gnu: Add ghmm.

* gnu/packages/machine-learning.scm (ghmm): New variable.
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Ricardo Wurmus 2016-05-23 12:52:00 +02:00 committed by Ricardo Wurmus
parent a5dd8db4ff
commit 23aab4ab2c
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@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
@ -22,12 +22,15 @@ (define-module (gnu packages machine-learning)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix svn-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages gcc)
#:use-module (gnu packages maths)
#:use-module (gnu packages pkg-config)
@ -108,6 +111,95 @@ (define-public python-libsvm
`(("python" ,python)))
(synopsis "Python bindings of libSVM")))
(define-public ghmm
;; The latest release candidate is several years and a couple of fixes have
;; been published since. This is why we download the sources from the SVN
;; repository.
(let ((svn-revision 2341))
(package
(name "ghmm")
(version (string-append "0.9-rc3-0." (number->string svn-revision)))
(source (origin
(method svn-fetch)
(uri (svn-reference
(url "http://svn.code.sf.net/p/ghmm/code/trunk")
(revision svn-revision)))
(file-name (string-append name "-" version))
(sha256
(base32
"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-dir
(lambda _ (chdir "ghmm") #t))
(add-after 'enter-dir 'fix-PYTHONPATH
(lambda* (#:key outputs #:allow-other-keys)
;; The Python tests fail as the library is assumed to be stored
;; in ./build/lib.linux-i686-*. To fix this we detect the CPU
;; and use it in the path.
(substitute* "configure.in"
(("AM_INIT_AUTOMAKE" line)
(string-append line "\nAC_CANONICAL_HOST\n")))
(substitute* "ghmmwrapper/Makefile.am"
(("i686") "@host_cpu@"))
#t))
(add-after 'enter-dir 'fix-runpath
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "ghmmwrapper/setup.py"
(("^(.*)extra_compile_args = \\[" line indent)
(string-append indent
"extra_link_args = [\"-Wl,-rpath="
(assoc-ref outputs "out") "/lib\"],\n"
line
"\"-Wl,-rpath="
(assoc-ref outputs "out")
"/lib\", ")))
#t))
(add-after 'enter-dir 'disable-broken-tests
(lambda _
(substitute* "tests/Makefile.am"
;; GHMM_SILENT_TESTS is assumed to be a command.
(("TESTS_ENVIRONMENT.*") "")
;; Do not build broken tests.
(("chmm .*") "")
(("read_fa .*") "")
(("mcmc .*") "")
(("label_higher_order_test.*$")
"label_higher_order_test\n"))
;; These Python unittests are broken as there is no gato.
;; See https://sourceforge.net/p/ghmm/support-requests/3/
(substitute* "ghmmwrapper/ghmmunittests.py"
(("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
line indent)
(string-append indent
"@unittest.skip(\"Disabled by Guix\")\n"
line)))
#t))
(add-before 'configure 'autogen
(lambda _
(zero? (system* "bash" "./autogen.sh")))))))
(inputs
`(("python" ,python-2) ; only Python 2 is supported
("libxml2" ,libxml2)))
(native-inputs
`(("pkg-config" ,pkg-config)
("dejagnu" ,dejagnu)
("swig" ,swig)
("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
(home-page "http://ghmm.org")
(synopsis "Hidden Markov Model library")
(description
"The General Hidden Markov Model library (GHMM) is a C library with
additional Python bindings implementing a wide range of types of @dfn{Hidden
Markov Models} (HMM) and algorithms: discrete, continous emissions, basic
training, HMM clustering, HMM mixtures.")
(license license:lgpl2.0+))))
(define-public randomjungle
(package
(name "randomjungle")