Version Bump

Package-Manager: portage-2.2.0_alpha89/cvs/Linux x86_64

5 files changed, 174 insertions, 4 deletions

diff --git a/sci-chemistry/pointless/ChangeLog b/sci-chemistry/pointless/ChangeLog
index d8ecf5bb48c1..63ee687b3cb7 100644
--- a/sci-chemistry/pointless/ChangeLog
+++ b/sci-chemistry/pointless/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/pointless
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pointless/ChangeLog,v 1.30 2011/12/27 12:06:24 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pointless/ChangeLog,v 1.31 2012/02/28 20:52:39 jlec Exp $
+
+*pointless-1.6.14 (28 Feb 2012)
+
+  28 Feb 2012; Justin Lecher <jlec@gentoo.org> +pointless-1.6.14.ebuild:
+  Version Bump
 
 *pointless-1.6.11 (27 Dec 2011)
 
diff --git a/sci-chemistry/pointless/pointless-1.6.14.ebuild b/sci-chemistry/pointless/pointless-1.6.14.ebuild
new file mode 100644
index 000000000000..7761bf5f28a9
--- /dev/null
+++ b/sci-chemistry/pointless/pointless-1.6.14.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pointless/pointless-1.6.14.ebuild,v 1.1 2012/02/28 20:52:39 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils fortran-2 multilib python toolchain-funcs
+
+DESCRIPTION="Scores crystallographic Laue and space groups"
+HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
+SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="
+	sci-chemistry/ccp4-apps
+	>=sci-libs/ccp4-libs-6.1.3-r10
+	sci-libs/clipper
+	sci-libs/fftw:2.1
+	sci-libs/mmdb
+	>=sci-libs/cctbx-2010.03.29.2334-r3
+	virtual/fortran"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	python_set_active_version 2
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/1.5.1-gcc4.4.patch
+}
+
+src_compile() {
+	emake  \
+		-f Makefile.make \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		CFLAGS="${CFLAGS}" \
+		CXXFLAGS="${CXXFLAGS}" \
+		LFLAGS="${LDFLAGS}" \
+		CLIB="${EPREFIX}/usr/$(get_libdir)" \
+		CCTBX_VERSION=2010 \
+		ICCP4=-I"${EPREFIX}/usr/include/ccp4" \
+		ITBX="-I${EPREFIX}/usr/include" \
+		ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \
+		LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
+		SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" \
+		|| die
+}
+
+src_install() {
+	dobin pointless othercell || die
+}
diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog
index 34098ba595bf..0c625968b996 100644
--- a/sci-chemistry/xia2/ChangeLog
+++ b/sci-chemistry/xia2/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/xia2
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.11 2011/10/16 12:30:09 ssuominen Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.12 2012/02/28 20:57:14 jlec Exp $
+
+*xia2-0.3.4.0 (28 Feb 2012)
+
+  28 Feb 2012; Justin Lecher <jlec@gentoo.org> +files/0.3.4.0-fix-syntax.patch,
+  +xia2-0.3.4.0.ebuild:
+  Version Bump
 
   16 Oct 2011; Samuli Suominen <ssuominen@gentoo.org> xia2-0.3.3.1.ebuild:
   amd64 restable
diff --git a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
new file mode 100644
index 000000000000..9ba4c94495ea
--- /dev/null
+++ b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
@@ -0,0 +1,28 @@
+diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
+index 1a3b0e2..e0b8a1e 100755
+--- a/xia2-0.3.4.0/Applications/xia2find.py
++++ b/xia2-0.3.4.0/Applications/xia2find.py
+@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
+ from Experts.FindImages import image2template_directory
+ 
+ known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
+-                          'osc', 'cbf', 'mar2000']]
++                          'osc', 'cbf', 'mar2000']
+ known_sweeps = { }
+ 
+ def is_image_name(file):
+diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
+index 88f9218..5fb6f2a 100644
+--- a/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py
++++ b/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py
+@@ -49,8 +49,8 @@ def Cad(DriverType = None):
+             self.add_command_line(hklin)
+ 
+             self.set_task('Rewriting reflections %s => %s' % 
+-                      `   (os.path.split(hklin)[-1],
+-                       `   os.path.split(self.getHklout())[-1]))
++                         (os.path.split(hklin)[-1],
++                          os.path.split(self.getHklout())[-1]))
+ 
+             self.start()
+ 
diff --git a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild
new file mode 100644
index 000000000000..e1301a9ebb75
--- /dev/null
+++ b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.4.0.ebuild,v 1.1 2012/02/28 20:57:14 jlec Exp $
+
+EAPI=3
+
+PYTHON_DEPEND="2"
+
+inherit eutils python
+
+DESCRIPTION="An automated data reduction system for crystallography"
+HOMEPAGE="http://www.ccp4.ac.uk/xia/"
+SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	>=sci-chemistry/ccp4-apps-6.1.2
+	sci-chemistry/mosflm
+	sci-chemistry/pointless
+	>=sci-libs/ccp4-libs-6.1.2
+	sci-libs/cctbx"
+DEPEND="${RDEPEND}"
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+src_prepare() {
+	find . -name '*.bat' -delete || die
+
+	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
+	python_convert_shebangs -r $(python_get_version) .
+}
+
+src_install() {
+	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
+
+	insinto /usr/share/ccp4/XIAROOT/
+	doins -r * || die
+
+	# Set programs executable
+# fperms cannot handle wildcards
+	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
+	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
+
+	cat >> "${T}"/23XIA <<- EOF
+	XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT"
+	XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}"
+	XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}"
+	PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications"
+	EOF
+
+	doenvd "${T}"/23XIA
+}
+
+pkg_postinst() {
+	python_mod_optimize /usr/share/ccp4/XIAROOT
+	echo ""
+	elog "In order to use the package, you need to"
+	elog "\t source ${EPREFIX}/etc/profile"
+	echo ""
+}
+
+pkg_postrm() {
+	python_mod_cleanup /usr/share/ccp4/XIAROOT
+}