Added fix for python import

Package-Manager: portage-2.2.0_alpha66/cvs/Linux x86_64

4 files changed, 137 insertions, 5 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/Manifest b/sci-chemistry/aria/Manifest
index b11b8b3090b8..cd995f46c718 100644
--- a/sci-chemistry/aria/Manifest
+++ b/sci-chemistry/aria/Manifest
@@ -1,18 +1,20 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA512
 
+AUX aria-2.3.2-python.patch 963 RMD160 a59437b4e83c211ac1298fc0f08c444d7c4806dc SHA1 ba8142cd4f676225ddb802814f2acd7e243121a8 SHA256 87f5f27484eddb6ce47fab2a2df6da15fa37cdef24c39e3da7b93555a22e512d
 AUX aria-2.3.2-through-space.patch 5040 RMD160 b4f80987195d45bf956b2dbd8084b4a3a6e0b5e3 SHA1 717d1ff0034d675509d27365806ae81f82157e2d SHA256 99c547ad5fb85401c39187b9a708fc7332c36be6e467bd834cb551a723fd84fb
 DIST aria2.3.1.tar.gz 1833973 RMD160 f2ee0bfc7e3164b5c34c81abb74256c5d76f53d7 SHA1 b257094bdaf6ba5b64645b8251d9243654e6d0fc SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc
 DIST aria2.3.2.tar.gz 1836270 RMD160 cd96f19c7a229694d561824dcca9ee22845c6a4f SHA1 74fc1cb6640b2a3f97851ac88042023f1a9c07ce SHA256 30727ea8bdc2e3b44e5970545008fcfa07fa59aa28b76824956a2aa71daa9615
 EBUILD aria-2.3.1.ebuild 2022 RMD160 e176a7b25c8d06287c91bb2c4d97f0d160dcc6d5 SHA1 28677a59f666d2ec9173ae86cfac37bc4a76f719 SHA256 0a83e234e39fbff3ffa65f21df768b7e0fea23ac13ad17008ab72e6103e3c96d
 EBUILD aria-2.3.2-r1.ebuild 2091 RMD160 441211d98653e9e08ef2794208ee23f94492b821 SHA1 2b2c0fd51bf23c84a00000ba8a43fabda25cf1e0 SHA256 e571030ad00d304613f3bdce32a578ee850735cdaccc591bec1e686afaf21292
+EBUILD aria-2.3.2-r2.ebuild 2131 RMD160 02922d3d831aa7dbe7804624e644fddf2ac826a4 SHA1 7df4de9b931467177905912ad870449da4f717db SHA256 6de02f396ba98c2eeec1cfbe3f10744db95f6287a965c100b401eeb70e8683be
 EBUILD aria-2.3.2.ebuild 2022 RMD160 f17276f2346ef63e9fbd25145f9fb26d85113018 SHA1 180e90a7f4e92d7a47d0a428bccd0155bcf002cf SHA256 738fa89aff5df458c4c61a64dd6e8ad839fdd43df50c141a34d6750f4055ebd9
-MISC ChangeLog 1596 RMD160 5868290e0b0c0033861c8f681b40d8010ebc3e63 SHA1 d9c0d4c51a78045ea5f596e7f8ecdbb9fd316aaa SHA256 0ebc72558b921ec6e4fc2d0652934cedb0d5705405f38808e9c5df944e56f54d
+MISC ChangeLog 1761 RMD160 d399961264b4acad93ff23d762947619f4f0daa8 SHA1 e033627d03f58e49b1cd7040326d71970b7c5a79 SHA256 df9abc63528bb73e51a5d826ae6cfb82ebfcabc11a75632144716f7d80f4ed39
 MISC metadata.xml 219 RMD160 e9da2d4271f89b9dbac478d145a519318f0f3314 SHA1 6d4a101013d6a40cd61cb2d8c6b517c443013bc7 SHA256 0be94b46df4c9a73494034f33b1371769951f52890e5c857ebe1dc9bc729d0a8
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-=kJFp
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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]