Added fix for python import

(Portage version: 2.2.0_alpha66/cvs/Linux x86_64)

3 files changed, 131 insertions, 1 deletions

diff --git a/sci-chemistry/aria/ChangeLog b/sci-chemistry/aria/ChangeLog
index 51206a1a1b8c..040317c19665 100644
--- a/sci-chemistry/aria/ChangeLog
+++ b/sci-chemistry/aria/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/aria
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/ChangeLog,v 1.10 2011/10/07 19:23:04 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/ChangeLog,v 1.11 2011/10/11 14:24:22 jlec Exp $
+
+*aria-2.3.2-r2 (11 Oct 2011)
+
+  11 Oct 2011; Justin Lecher <jlec@gentoo.org> +aria-2.3.2-r2.ebuild,
+  +files/aria-2.3.2-python.patch:
+  Added fix for python import
 
 *aria-2.3.2-r1 (07 Oct 2011)
 
diff --git a/sci-chemistry/aria/aria-2.3.2-r2.ebuild b/sci-chemistry/aria/aria-2.3.2-r2.ebuild
new file mode 100644
index 000000000000..a24da015ef34
--- /dev/null
+++ b/sci-chemistry/aria/aria-2.3.2-r2.ebuild
@@ -0,0 +1,94 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/aria-2.3.2-r2.ebuild,v 1.1 2011/10/11 14:24:22 jlec Exp $
+
+EAPI=3
+
+PYTHON_DEPEND="2"
+PYTHON_USE_WITH="tk"
+
+inherit base eutils python versionator
+
+MY_P="${PN}$(get_version_component_range 1-2 ${PV})"
+
+DESCRIPTION="Automated NOE assignment and NMR structure calculation"
+HOMEPAGE="http://aria.pasteur.fr/"
+SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2.tar.gz"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-chemistry/clashlist
+	sci-chemistry/procheck
+	sci-libs/clashscore-db
+	dev-python/numpy
+	dev-python/matplotlib[tk]
+	>=sci-chemistry/cns-1.2.1-r7[aria,openmp]
+	>=dev-lang/tk-8.3
+	>=sci-chemistry/ccpn-2.0.5
+	>=dev-tcltk/tix-8.1.4"
+DEPEND="${RDEPEND}"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_nofetch(){
+	einfo "Go to ${HOMEPAGE}, download ${A}"
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-python.patch \
+		"${FILESDIR}"/${P}-through-space.patch
+}
+
+src_test(){
+	export CCPNMR_TOP_DIR="${EPREFIX}"/$(python_get_sitedir)
+	export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
+	$(PYTHON) check.py || die
+}
+
+src_install(){
+	insinto "$(python_get_sitedir)/${PN}"
+	doins -r src aria2.py || die "failed to install ${PN}"
+	insinto "$(python_get_sitedir)/${PN}"/cns
+	doins -r cns/{protocols,toppar,src/helplib} || die "failed to install cns part"
+
+	if use examples; then
+		insinto /usr/share/${P}/
+		doins -r examples || die
+	fi
+
+	# ENV
+	cat >> "${T}"/20aria <<- EOF
+	ARIA2="${EPREFIX}/$(python_get_sitedir)/${PN}"
+	EOF
+
+	doenvd "${T}"/20aria
+
+	# Launch Wrapper
+	cat >> "${T}"/aria <<- EOF
+	#!/bin/sh
+	export CCPNMR_TOP_DIR="${EPREFIX}/$(python_get_sitedir)"
+	export PYTHONPATH="${EPREFIX}/$(python_get_sitedir)/ccpn/python"
+	exec "$(PYTHON)" -O "\${ARIA2}"/aria2.py \$@
+	EOF
+
+	dobin "${T}"/aria || die "failed to install wrapper"
+	dosym aria /usr/bin/aria2
+
+	dodoc README || die
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/aria/files/aria-2.3.2-python.patch b/sci-chemistry/aria/files/aria-2.3.2-python.patch
new file mode 100644
index 000000000000..1f9ae1fcc5f6
--- /dev/null
+++ b/sci-chemistry/aria/files/aria-2.3.2-python.patch
@@ -0,0 +1,30 @@
+ src/py/aria/legacy/QualityChecks/Descriptive.py |    5 +++--
+ 1 files changed, 3 insertions(+), 2 deletions(-)
+
+diff --git a/src/py/aria/legacy/QualityChecks/Descriptive.py b/src/py/aria/legacy/QualityChecks/Descriptive.py
+index ae5913c..550d20c 100644
+--- a/src/py/aria/legacy/QualityChecks/Descriptive.py
++++ b/src/py/aria/legacy/QualityChecks/Descriptive.py
+@@ -1,3 +1,6 @@
++from math import *
++from numpy import *
++
+ class Descriptive:
+     """
+     some basic statistics
+@@ -55,7 +58,6 @@ class Descriptive:
+ 
+     def getStdDev(self):
+ 	if( len(self.myData) == 0): return None
+-	from math import *
+ 	if( (self.count - 1) > 0 ):
+ 	    return sqrt( self.pseudoVariance/ (self.count - 1))
+ 	else:
+@@ -89,7 +91,6 @@ class Descriptive:
+     def getMedian(self):
+ 	if( len(self.myData) == 0): return None
+ 	if( self.median == None ):
+-	    from numpy import *
+ 	    sort(self.myData)
+ 	    if( self.count%2 == 1):
+ 		self.median = self.myData[(self.count-1)/2]