diff options
Diffstat (limited to 'sci-chemistry/xia2')
| -rw-r--r-- | sci-chemistry/xia2/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch | 61 | ||||
| -rw-r--r-- | sci-chemistry/xia2/xia2-0.3.1.6.ebuild | 66 |
3 files changed, 134 insertions, 1 deletions
diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog index efa260c601ff..8c2b6f02db5d 100644 --- a/sci-chemistry/xia2/ChangeLog +++ b/sci-chemistry/xia2/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/xia2 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.1 2010/02/06 23:36:47 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.2 2010/04/22 19:25:30 jlec Exp $ + +*xia2-0.3.1.6 (22 Apr 2010) + + 22 Apr 2010; Justin Lecher <jlec@gentoo.org> + +files/0.3.1.6-fix-syntax.patch, +xia2-0.3.1.6.ebuild: + Version Bump #316579, fixes for PYTHON ABIs things *xia2-0.3.1.0 (06 Feb 2010) diff --git a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch new file mode 100644 index 000000000000..7770a53c4451 --- /dev/null +++ b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch @@ -0,0 +1,61 @@ +diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py +index 1a3b0e2..e0b8a1e 100755 +--- a/xia2-0.3.1.6/Applications/xia2find.py ++++ b/xia2-0.3.1.6/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/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py +index 28b1dc3..dba3ef7 100644 +--- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py ++++ b/xia2-0.3.1.6/Experts/DRStrategyExpert.py +@@ -48,24 +48,24 @@ strategy_dict = { + 'default':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'default':{ + 'score':2, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} ++ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, + 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':1, + 'pipeline':{ +- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} ++ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, + 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', + 'pointless-1.1.0.4']}, + 'mosaic':{ + 'score':2, + 'pipeline':{ +- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} ++ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, + 'depends-on':['xds', 'xscale']} + } +diff --git a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py +index 88f9218..5fb6f2a 100644 +--- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py ++++ b/xia2core-0.3.1.6/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/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild new file mode 100644 index 000000000000..d52ea9274094 --- /dev/null +++ b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.6.ebuild,v 1.1 2010/04/22 19:25:30 jlec Exp $ + +EAPI="3" + +PYTHON_DEPEND="2" + +inherit eutils python + +DESCRIPTION="An automated data reduction system for crystallography" +HOMEPAGE="http://www.xia2.org/xia/" +SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +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 4 . +} + +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 +} + +pkg_postrm() { + python_mod_cleanup /usr/share/ccp4/XIAROOT +} |