[gentoo-commits] proj/sci:ccp4 commit in: sci-chemistry/xia2/, sci-chemistry/xia2/files/

[Justin Lecher]

commit:     c6ebc0dc5e591060000b7157a390e416f0d4315a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu May 30 15:26:21 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  1 08:35:20 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c6ebc0dc

sci-chemistry/xia2: Version BUmp

Package-Manager: portage-2.2.0_alpha177

---
 sci-chemistry/xia2/ChangeLog                       | 69 +++++++++++++++++++
 .../xia2/files/xia2-0.3.6.0-fix-syntax.patch       | 28 ++++++++
 sci-chemistry/xia2/metadata.xml                    |  8 +++
 sci-chemistry/xia2/xia2-0.3.6.0.ebuild             | 78 ++++++++++++++++++++++
 4 files changed, 183 insertions(+)

diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog
new file mode 100644
index 0000000..5fb3985
--- /dev/null
+++ b/sci-chemistry/xia2/ChangeLog
@@ -0,0 +1,69 @@
+# ChangeLog for sci-chemistry/xia2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.13 2012/04/14 09:54:22 nativemad Exp $
+
+*xia2-0.3.6.0 (30 May 2013)
+
+  30 May 2013; Justin Lecher <jlec@g.o> +xia2-0.3.6.0.ebuild,
+  +files/xia2-0.3.6.0-fix-syntax.patch, +metadata.xml:
+  Version BUmp
+
+  14 Apr 2012; Andreas Schuerch <nativemad@g.o> xia2-0.3.3.1.ebuild:
+  x86 stable, see bug 375917, thanks all.
+
+*xia2-0.3.4.0 (28 Feb 2012)
+
+  28 Feb 2012; Justin Lecher <jlec@g.o> +files/0.3.4.0-fix-syntax.patch,
+  +xia2-0.3.4.0.ebuild:
+  Version Bump
+
+  16 Oct 2011; Samuli Suominen <ssuominen@g.o> xia2-0.3.3.1.ebuild:
+  amd64 restable
+
+  08 Oct 2011; Samuli Suominen <ssuominen@g.o> xia2-0.3.3.1.ebuild:
+  Revert back to ~arch for security and libpng porting.
+
+  06 Oct 2011; Tony Vroon <chainsaw@g.o> xia2-0.3.3.1.ebuild:
+  Marked stable on AMD64 based on arch testing by Agostino "ago" Sarubbo in bug
+  #351753.
+
+*xia2-0.3.3.3 (04 Oct 2011)
+
+  04 Oct 2011; Justin Lecher <jlec@g.o> +files/0.3.3.3-fix-syntax.patch,
+  +xia2-0.3.3.3.ebuild:
+  Version Bump
+
+  23 Jul 2011; Justin Lecher <jlec@g.o> xia2-0.3.3.1.ebuild:
+  Added pstins msg
+
+*xia2-0.3.3.1 (25 Jun 2011)
+
+  25 Jun 2011; Justin Lecher <jlec@g.o> +files/0.3.3.1-fix-syntax.patch,
+  xia2-0.3.1.0.ebuild, xia2-0.3.1.6.ebuild, xia2-0.3.1.7.ebuild,
+  +xia2-0.3.3.1.ebuild, metadata.xml:
+  Version BUmp
+
+  16 Jan 2011; Kacper Kowalik <xarthisius@g.o> xia2-0.3.1.7.ebuild:
+  marked ~ppc wrt #303931
+
+*xia2-0.3.1.7 (27 Jul 2010)
+
+  27 Jul 2010; Justin Lecher <jlec@g.o>
+  +files/0.3.1.7-fix-syntax.patch, +xia2-0.3.1.7.ebuild:
+  Version bump
+
+  22 Apr 2010; Justin Lecher <jlec@g.o> xia2-0.3.1.6.ebuild:
+  Keyworded for ~*-linux
+
+*xia2-0.3.1.6 (22 Apr 2010)
+
+  22 Apr 2010; Justin Lecher <jlec@g.o>
+  +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)
+
+  06 Feb 2010; Justin Lecher (jlec) <jlec@g.o>
+  +files/0.3.1.0-fix-syntax.patch, +xia2-0.3.1.0.ebuild, +metadata.xml:
+  Splitted xia2 from ccp4
+

diff --git a/sci-chemistry/xia2/files/xia2-0.3.6.0-fix-syntax.patch b/sci-chemistry/xia2/files/xia2-0.3.6.0-fix-syntax.patch
new file mode 100644
index 0000000..83741af
--- /dev/null
+++ b/sci-chemistry/xia2/files/xia2-0.3.6.0-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/Applications/xia2find.py
++++ b/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/core/Python/Examples/CCP4/Cad.py b/core/Python/Examples/CCP4/Cad.py
+index 88f9218..5fb6f2a 100644
+--- a/core/Python/Examples/CCP4/Cad.py
++++ b/core/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/metadata.xml b/sci-chemistry/xia2/metadata.xml
new file mode 100644
index 0000000..4bf6dbc
--- /dev/null
+++ b/sci-chemistry/xia2/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>sci@g.o</email>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-chemistry/xia2/xia2-0.3.6.0.ebuild b/sci-chemistry/xia2/xia2-0.3.6.0.ebuild
new file mode 100644
index 0000000..6a5f2dc
--- /dev/null
+++ b/sci-chemistry/xia2/xia2-0.3.6.0.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2013 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=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils python-r1
+
+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="${RDEPEND}"
+
+src_prepare() {
+	find . -name '*.bat' -delete || die
+
+	epatch "${FILESDIR}"/${P}-fix-syntax.patch
+}
+
+src_install() {
+	local bin
+	dohtml html/*
+	rm -rf html || die
+
+	dodoc readme.txt
+	rm -f *txt setup.* || die
+
+	installation() {
+		python_moduleinto ${PN}
+		python_domodule *
+	}
+
+	python_foreach_impl installation
+
+	insinto /usr/share/ccp4/${PN}
+	doins -r *
+
+	cat >> "${T}"/23XIA <<- EOF
+	XIA2_ROOT="${EPREFIX}/usr/share/ccp4/${PN}"
+	XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/${PN}/core"
+	EOF
+
+	doenvd "${T}"/23XIA
+
+	cd Applications || die
+	rm __init__.py || die
+
+	sed \
+		-e '1i#!/usr/bin/python' \
+		-i xia2hdr.py || die
+
+	for bin in *.py; do
+		python_foreach_impl python_newscript ${bin} ${bin#.py}
+	done
+
+	dobin xia2html x1335 pydiffdump2xds pychef cbfdump aimless2gnuplot
+}
+
+pkg_postinst() {
+	echo ""
+	elog "In order to use the package, you need to"
+	elog "\t source ${EPREFIX}/etc/profile"
+	echo ""
+}