@@ 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 @@
#: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 @@ classification.")
`(("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")