sci-libs/ghmm: Drop obsolete tools, #163; correctly support python modules; add optional support for gsl and lapack

Package-Manager: portage-2.2.7

6 files changed, 138 insertions, 14 deletions

diff --git a/sci-libs/ghmm/ChangeLog b/sci-libs/ghmm/ChangeLog
index a55592121..886fd6a4c 100644
--- a/sci-libs/ghmm/ChangeLog
+++ b/sci-libs/ghmm/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-libs/ghmm
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  20 Dec 2013; Justin Lecher <jlec@gentoo.org> ghmm-9999.ebuild,
+  +files/ghmm-9999-link.patch, +files/ghmm-9999-obsolete.patch,
+  +files/ghmm-9999-out-of-source.patch, +files/ghmm-9999-respect.patch:
+  Drop obsolete tools, #163; correctly support python modules; add optional
+  support for gsl and lapack
+
   25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Fixed herd entry in metadata.xml
 
diff --git a/sci-libs/ghmm/files/ghmm-9999-link.patch b/sci-libs/ghmm/files/ghmm-9999-link.patch
new file mode 100644
index 000000000..9b4e919ec
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-link.patch
@@ -0,0 +1,24 @@
+Index: tools/Makefile.am
+===================================================================
+--- tools/Makefile.am	(revision 2332)
++++ tools/Makefile.am	(working copy)
+@@ -23,5 +23,5 @@
+ smix_hmm_SOURCES = smix_hmm.c
+ smo2xml_SOURCES = smo2xml.c
+ 
+-LDADD = $(top_builddir)/ghmm/.libs/libghmm.a
++LDADD = $(top_builddir)/ghmm/libghmm.la
+ bin_SCRIPTS = ghmm-config
+Index: tests/Makefile.am
+===================================================================
+--- tests/Makefile.am	(revision 2332)
++++ tests/Makefile.am	(working copy)
+@@ -34,7 +34,7 @@
+ 		  read_fa \
+                   mcmc
+ 
+-LDADD = $(top_builddir)/ghmm/.libs/libghmm.a
++LDADD = $(top_builddir)/ghmm/libghmm.la
+ 
+ TESTS_ENVIRONMENT = GHMM_SILENT_TESTS
+ TESTS =           root_finder_test \
diff --git a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch
new file mode 100644
index 000000000..2e6be54d0
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch
@@ -0,0 +1,13 @@
+Index: configure.in
+===================================================================
+--- configure.in	(revision 2332)
++++ configure.in	(working copy)
+@@ -293,7 +293,7 @@
+ CFLAGS="$CFLAGS $LIBXML2_CFLAGS"
+ 
+ dnl final configuration
+-SUBDIRS="ghmm tools tests"
++SUBDIRS="ghmm"
+ 
+ dnl python wrapper can be switched on or off
+ AC_ARG_WITH(python,
diff --git a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch
new file mode 100644
index 000000000..6197d9ba1
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch
@@ -0,0 +1,40 @@
+Index: tools/Makefile.am
+===================================================================
+--- tools/Makefile.am	(revision 2332)
++++ tools/Makefile.am	(working copy)
+@@ -12,7 +12,7 @@
+ MAINTAINERCLEANFILES = Makefile.in
+ 
+ BUILT_SOURCES = 
+-INCLUDES = -I$(top_srcdir)
++INCLUDES = -I$(top_srcdir) -I$(top_builddir)/ghmm
+ 
+ bin_PROGRAMS = probdist cluster scluster smix_hmm $(OBSOLETE_TOOLS)
+ EXTRA_PROGRAMS = smo2xml
+Index: tests/Makefile.am
+===================================================================
+--- tests/Makefile.am	(revision 2332)
++++ tests/Makefile.am	(working copy)
+@@ -15,7 +15,7 @@
+ MAINTAINERCLEANFILES = Makefile.in
+ # stuff from dejagnu
+ 
+-INCLUDES=-I$(top_srcdir)
++INCLUDES=-I$(top_srcdir) -I$(top_builddir)/ghmm
+ 
+ #these tests will not be installed
+ # in progress: test_sdfoba nullmodel ciscreen test_sdmodel 
+Index: ghmmwrapper/Makefile.am
+===================================================================
+--- ghmmwrapper/Makefile.am	(revision 2332)
++++ ghmmwrapper/Makefile.am	(working copy)
+@@ -47,7 +47,9 @@
+                  testdata/model_label.xml \
+                  testdata/tiny.txt.sqd
+ 
++INCLUDES=-I$(top_builddir)
+ 
++
+ EXTRA_DIST = ${SWIG_INTERFACE_FILES} ${EXTENSION_C_FILES} ${PYTHON_FILES} ${PYTHON_GATO_FILES} ${TESTDATA_FILES}
+ 
+ all: setup.py ghmm.py ${SWIG_INTERFACE_FILES}
diff --git a/sci-libs/ghmm/files/ghmm-9999-respect.patch b/sci-libs/ghmm/files/ghmm-9999-respect.patch
new file mode 100644
index 000000000..09c8721c9
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-respect.patch
@@ -0,0 +1,12 @@
+Index: ghmmwrapper/setup.py
+===================================================================
+--- ghmmwrapper/setup.py	(revision 2332)
++++ ghmmwrapper/setup.py	(working copy)
+@@ -48,7 +48,6 @@
+                                include_dirs = ['..'],
+                                library_dirs = ['../ghmm/.libs'],
+                                libraries = ['ghmm', 'm', 'pthread', 'xml2', 'z'],
+-                               extra_compile_args = ["-O2", "-pipe", "-Wall"], # -g might help debugging
+                                depends = ['wrapper_alphabet.i', 'wrapper_cmodel.i', 'wrapper_cseq.i',
+                                           'wrapper_dmodel.i', 'wrapper_dpmodel.i', 'wrapper_dpseq.i',
+                                           'wrapper_dseq.i', 'wrapper_xmlfile.i']
diff --git a/sci-libs/ghmm/ghmm-9999.ebuild b/sci-libs/ghmm/ghmm-9999.ebuild
index 514d454af..5981be5f5 100644
--- a/sci-libs/ghmm/ghmm-9999.ebuild
+++ b/sci-libs/ghmm/ghmm-9999.ebuild
@@ -1,38 +1,67 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mauvealigner/mauvealigner-9999.ebuild,v 1.1 2009/04/17 18:03:19 weaver Exp $
 
-EAPI="2"
+EAPI=5
 
-ESVN_REPO_URI="https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm"
+AUTOTOOLS_AUTORECONF=true
+
+PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit subversion
+inherit autotools-utils distutils-r1 subversion
 
 DESCRIPTION="General Hidden Markov Model library - efficient data structures and algorithms for HMMs"
 HOMEPAGE="http://ghmm.sourceforge.net/"
 SRC_URI=""
+ESVN_REPO_URI="https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm"
 
 LICENSE="LGPL-2.1"
 SLOT="0"
-IUSE=""
 KEYWORDS=""
+IUSE="gsl lapack +python static-libs"
 
-CDEPEND=""
-DEPEND="${CDEPEND}"
-RDEPEND="${CDEPEND}"
+RDEPEND="
+	dev-libs/libxml2
+	gsl? ( sci-libs/gsl )
+	lapack? (
+		sci-libs/clapack
+		virtual/lapack
+		)"
+DEPEND="${RDEPEND}"
 
 S="${WORKDIR}/${PN}"
 
+ESVN_BOOTSTRAP="autotools-utils_src_prepare"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-out-of-source.patch
+	"${FILESDIR}"/${P}-link.patch
+	"${FILESDIR}"/${P}-respect.patch
+	"${FILESDIR}"/${P}-obsolete.patch
+)
+
 src_prepare() {
-	./autogen.sh
+	use python && AUTOTOOLS_IN_SOURCE_BUILD=1
+	autotools-utils_src_prepare
+	use python && cd "${S}"/ghmmwrapper && distutils-r1_python_prepare
 }
 
 src_configure() {
-	econf
-	# fixme: hack
-	sed -i 's|^prefix = \(.*\)|prefix = ${D}/usr|' {ghmmwrapper,HMMEd}/Makefile || die
+	local myeconfargs=(
+		--without-python
+		--disable-obsolete
+		$(use_enable gsl)
+		$(use_enable lapack atlas)
+	)
+	autotools-utils_src_configure
+}
+
+src_compile() {
+	autotools-utils_src_compile
+	use python && cd "${S}"/ghmmwrapper && distutils-r1_src_compile
 }
 
 src_install() {
-	einstall || die
+	autotools-utils_src_install
+	use python && cd "${S}"/ghmmwrapper && distutils-r1_src_install
 }