inital commit

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

6 files changed, 218 insertions, 0 deletions

diff --git a/sci-chemistry/aria/ChangeLog b/sci-chemistry/aria/ChangeLog
new file mode 100644
index 000000000000..4f99e2d830ed
--- /dev/null
+++ b/sci-chemistry/aria/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/aria
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/ChangeLog,v 1.1 2010/02/06 21:50:40 jlec Exp $
+
+*aria-2.2_p2 (06 Feb 2010)
+
+  06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/2.2_p2-numpy.patch, +aria-2.2_p2.ebuild, +files/2.2_p2-test.patch,
+  +files/sa_ls_cool2.patch, +metadata.xml:
+  Initial commit
+
diff --git a/sci-chemistry/aria/aria-2.2_p2.ebuild b/sci-chemistry/aria/aria-2.2_p2.ebuild
new file mode 100644
index 000000000000..d3f16a96de4d
--- /dev/null
+++ b/sci-chemistry/aria/aria-2.2_p2.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/aria-2.2_p2.ebuild,v 1.1 2010/02/06 21:50:40 jlec Exp $
+
+EAPI="3"
+
+SUPPORT_PYTHON_ABIS="1"
+PYTHON_USE_WITH="tk"
+
+inherit base python eutils versionator
+
+MY_P="${PN}$(get_version_component_range 1-2 ${PV})"
+
+DESCRIPTION="Software for automated NOE assignment and NMR structure calculation."
+HOMEPAGE="http://aria.pasteur.fr/"
+SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.tar.gz"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples"
+
+RDEPEND="
+	dev-python/numpy
+	dev-python/matplotlib[tk]
+	sci-chemistry/cns[aria,openmp]
+	>=dev-lang/tk-8.3
+	>=dev-python/scientificpython-2.7.3
+	>=sci-chemistry/ccpn-2.0.5
+	>=dev-tcltk/tix-8.1.4"
+DEPEND="${RDEPENED}"
+RESTRICT_PYTHON_ABIS="3.*"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}/${PN}2.2"
+
+src_prepare() {
+	epatch "${FILESDIR}"/sa_ls_cool2.patch
+	epatch "${FILESDIR}"/${PV}-numpy.patch
+	epatch "${FILESDIR}"/${PV}-test.patch
+	python_copy_sources --no-link
+}
+
+pkg_nofetch(){
+	einfo "Go to ${HOMEPAGE}, download ${A}"
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_test(){
+	test() {
+		export CCPNMR_TOP_DIR="${EPREFIX}"/$(python_get_sitedir)
+		export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
+		$(PYTHON) check.py || die
+	}
+	python_execute_function -s test
+}
+
+src_install(){
+	installation() {
+		insinto "$(python_get_sitedir)/${PN}"
+		doins -r src aria2.py || die "failed to install ${PN}"
+		insinto "$(python_get_sitedir)/${PN}"/cns
+		doins -r cns/{protocols,toppar,src/helplib} || die "failed to install cns part"
+	}
+	python_execute_function -s installation
+
+	if use examples; then
+		insinto /usr/share/${P}/
+		doins -r examples
+	fi
+
+	# ENV
+	cat >> "${T}"/20aria <<- EOF
+	ARIA2="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
+	EOF
+
+	doenvd "${T}"/20aria
+
+	# Launch Wrapper
+	cat >> "${T}"/aria <<- EOF
+	#!/bin/sh
+	export CCPNMR_TOP_DIR="${EPREFIX}/$(python_get_sitedir -f)"
+	export PYTHONPATH="${EPREFIX}/$(python_get_sitedir -f)/ccpn/python"
+	exec "$(PYTHON -f)" -O "\${ARIA2}"/aria2.py \$@
+	EOF
+
+	dobin "${T}"/aria || die "failed to install wrapper"
+	dosym aria /usr/bin/aria2
+
+	dodoc README || die
+}
diff --git a/sci-chemistry/aria/files/2.2_p2-numpy.patch b/sci-chemistry/aria/files/2.2_p2-numpy.patch
new file mode 100644
index 000000000000..40d81964d9c2
--- /dev/null
+++ b/sci-chemistry/aria/files/2.2_p2-numpy.patch
@@ -0,0 +1,82 @@
+diff -arNu aria2.2/aria2.py aria2.2.new/aria2.py
+--- aria2.2/aria2.py	2008-02-14 11:02:31.000000000 +0100
++++ aria2.2.new/aria2.py	2009-07-14 12:01:02.000000000 +0200
+@@ -427,7 +427,7 @@
+         
+ def check_numeric_slice():
+ 
+-    msg = "\nThe version of Numeric (%s) is known to be incompatible with ARIA.\nConsider reverting to a more stable version (like 23.8).\n"
++    msg = "\nThe version of Numeric (%s) is known to be incompatible with ARIA.\nSo we are using numpy instead.\n"
+     
+     try:
+         from Numeric import ones, __version__ as NUMERIC_VERSION
+diff -arNu aria2.2/check.py aria2.2.new/check.py
+--- aria2.2/check.py	2009-07-14 11:50:54.000000000 +0200
++++ aria2.2.new/check.py	2009-07-14 12:02:56.000000000 +0200
+@@ -55,18 +55,6 @@
+     failed = 0
+     
+     try:
+-        import Numeric
+-        msg += 'ok (numeric).'
+-        
+-    except:
+-        #msg =  'could not import Numeric module.'
+-        failed = 1
+-
+-    if not failed:
+-        print msg
+-        return 'numeric'#, None
+-
+-    try:
+        import numpy.oldnumeric
+        version = LooseVersion(numpy.oldnumeric.__version__)
+ 
+@@ -79,14 +67,14 @@
+            msg += 'version > %s required for Numpy' % str(NUMPY_MIN_VERSION)
+            
+     except:        
+-        msg += 'could not import Numeric/Numpy module.'
++        msg += 'could not import Numpy module.'
+ 
+     print msg
+     return None
+ 
+ def check_numeric_slice():
+ 
+-    msg = "\nWARNING: This version of Numeric (%s) is known to be incompatible with ARIA.\nConsider reverting to a more stable version (like 23.8).\n"
++    msg = "\nWARNING: This version of Numeric (%s) is known to be incompatible with ARIA.\nSo we use numpy instead.\n"
+     
+     from Numeric import ones, __version__ as NUMERIC_VERSION
+     if not ones(10)[2:]:
+diff -arNu aria2.2/src/py/Merger.py aria2.2.new/src/py/Merger.py
+--- aria2.2/src/py/Merger.py	2007-03-05 16:50:12.000000000 +0100
++++ aria2.2.new/src/py/Merger.py	2009-07-14 12:06:55.000000000 +0200
+@@ -213,12 +213,9 @@
+                 new_long = []
+ 
+                 try:
+-                    from RandomArray import permutation
++                    from numpy.oldnumeric.random_array import permutation
+                 except:
+-                    try:
+-                        from numpy.oldnumeric.random_array import permutation
+-                    except:
+-                        return n, []
++                    return n, []
+ 
+                 ids = permutation(len(long_range))
+            
+diff -arNu aria2.2/src/py/N.py aria2.2.new/src/py/N.py
+--- aria2.2/src/py/N.py	2007-12-04 17:01:46.000000000 +0100
++++ aria2.2.new/src/py/N.py	2009-07-14 12:07:16.000000000 +0200
+@@ -1,7 +1,4 @@
+ try:
+-    from Numeric import *
++    from numpy.oldnumeric import *
+ except:
+-    try:
+-        from numpy.oldnumeric import *
+-    except:
+-        pass
++    pass
diff --git a/sci-chemistry/aria/files/2.2_p2-test.patch b/sci-chemistry/aria/files/2.2_p2-test.patch
new file mode 100644
index 000000000000..991a168ab3a5
--- /dev/null
+++ b/sci-chemistry/aria/files/2.2_p2-test.patch
@@ -0,0 +1,13 @@
+diff --git a/check.py b/check.py
+index 6592951..47772f5 100644
+--- a/check.py
++++ b/check.py
+@@ -170,8 +170,6 @@ if __name__ == '__main__':
+     print 'Checking Python environment...\n'
+ 
+     check_python()
+-    numeric = check_numeric()
+-    check_numeric_slice()
+     scientific = check_scientific()
+     check_tix()
+     check_ccpn()
diff --git a/sci-chemistry/aria/files/sa_ls_cool2.patch b/sci-chemistry/aria/files/sa_ls_cool2.patch
new file mode 100644
index 000000000000..d52666a883f9
--- /dev/null
+++ b/sci-chemistry/aria/files/sa_ls_cool2.patch
@@ -0,0 +1,12 @@
+--- aria2.2/cns/protocols/sa_ls_cool2.cns.orig	2008-05-07 18:39:59.000000000 +0200
++++ aria2.2/cns/protocols/sa_ls_cool2.cns	2008-05-07 18:40:29.000000000 +0200
+@@ -33,8 +33,8 @@
+     masym dist &Data.masy_cool2
+     masym hbon &Data.masy_cool2
+ 
+-    scale ambi &Data.amb_cool2 
+     scale dist &Data.unamb_cool2
++    scale ambi &Data.amb_cool2 
+     scale hbon &Data.hbond_cool2
+ end
+ 
diff --git a/sci-chemistry/aria/metadata.xml b/sci-chemistry/aria/metadata.xml
new file mode 100644
index 000000000000..c6856dc7f2cf
--- /dev/null
+++ b/sci-chemistry/aria/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+</maintainer>
+</pkgmetadata>