Version BUmp

(Portage version: 2.2.0_alpha90/cvs/Linux x86_64)

4 files changed, 200 insertions, 1 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 10250bc2c153..3aa6322d350e 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.85 2012/02/27 22:53:03 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.86 2012/03/10 09:31:31 jlec Exp $
+
+*pymol-1.5.0.3 (10 Mar 2012)
+
+  10 Mar 2012; Justin Lecher <jlec@gentoo.org> +pymol-1.5.0.3.ebuild,
+  +files/pymol-1.5.0.3-prefix.patch, +files/pymol-1.5.0.3-web.patch:
+  Version BUmp
 
 *pymol-1.5.0.2 (27 Feb 2012)
 
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch b/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch
new file mode 100644
index 000000000000..9b0bad342e19
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch
@@ -0,0 +1,57 @@
+Index: setup.py
+===================================================================
+--- setup.py	(revision 3983)
++++ setup.py	(working copy)
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!@GENTOO_PORTAGE_EPREFIX@/usr/bin/env python
+ #
+ # This script only applies if you are performing a Python Distutils-based
+ # installation of PyMOL.
+@@ -35,7 +35,7 @@
+ 	      "modules/cealign/src/tnt" ]
+     libs=["glut32","opengl32","glu32","png"]
+     pyogl_libs = ["glut32","opengl32","glu32"]
+-    lib_dirs=["/usr/lib/w32api"]
++    lib_dirs=["@GENTOO_PORTAGE_EPREFIX@/usr/lib/w32api"]
+     def_macros=[("_PYMOL_MODULE",None),
+                 ("CYGWIN",None),
+                 ("_PYMOL_LIBPNG",None)]
+@@ -87,7 +87,7 @@
+                   "/sw/include/freetype2/freetype",
+                   "/sw/include/freetype2",
+                   "/sw/include",
+-                  "/usr/X11/include",
++                  "@GENTOO_PORTAGE_EPREFIX@/usr/X11/include",
+ 		  "modules/cealign/src",
+ 		  "modules/cealign/src/tnt",
+ 		  #"contrib/uiuc/plugins/include/",
+@@ -114,8 +114,8 @@
+         ext_comp_args=[]
+         ext_link_args=[
+                        "-L/sw/lib", "-lpng",
+-                       "/usr/X11/lib/libGL.dylib",
+-                       "/usr/X11/lib/libGLU.dylib",
++                       "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGL.dylib",
++                       "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGLU.dylib",
+                        "-lfreeglut",
+                        "-lglew",
+                        "-L/sw/lib/freetype219/lib", "-lfreetype"
+@@ -221,7 +221,7 @@
+                  "layer3",
+                  "layer4",
+                  "layer5",
+-                 "/usr/include/freetype2",
++                 "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2",
+               # VMD plugin support
+               #              "contrib/uiuc/plugins/include",
+               #              "contrib/uiuc/plugins/molfile_plugin/src",
+@@ -242,7 +242,7 @@
+                    "GLU",
+                    "glut",
+                    "GLEW"]
+-    lib_dirs = [ "/usr/X11R6/lib64", ]
++    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/X11R6/lib64", ]
+     def_macros = [ ("_PYMOL_MODULE",None),
+                    ("_PYMOL_INLINE",None),
+                    ("_PYMOL_FREETYPE",None),
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch b/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch
new file mode 100644
index 000000000000..4f48140169cc
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch
@@ -0,0 +1,16 @@
+Index: setup.py
+===================================================================
+--- setup.py	(revision 3983)
++++ setup.py	(working copy)
+@@ -292,10 +292,7 @@
+                  'pymol/opengl/glu',
+                  'pymol/opengl/glut',
+                  'pymol/wizard',
+-                 'pymol2',
+-                 'web',
+-                 'web/examples',
+-                 'web/javascript', ],
++                 'pymol2', ],
+     ext_modules = [
+         Extension("pymol._cmd", [
+                 "modules/cealign/src/ccealignmodule.cpp",
diff --git a/sci-chemistry/pymol/pymol-1.5.0.3.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3.ebuild
new file mode 100644
index 000000000000..b79c7aa3e1ce
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.5.0.3.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.3.ebuild,v 1.1 2012/03/10 09:31:31 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2:2.7"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.* *-jython 2.7-pypy-*"
+PYTHON_USE_WITH="tk"
+PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
+
+inherit distutils eutils fdo-mime prefix versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+	http://dev.gentoo.org/~jlec/distfiles/${PN}.xpm.tar"
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="apbs numpy vmd web"
+
+DEPEND="
+	dev-python/numpy
+	dev-python/pmw
+	media-libs/freetype:2
+	media-libs/glew
+	media-libs/libpng
+	media-video/mpeg-tools
+	sys-libs/zlib
+	media-libs/freeglut
+	apbs? (
+		dev-libs/maloc
+		sci-chemistry/apbs
+		sci-chemistry/pdb2pqr
+		sci-chemistry/pymol-apbs-plugin
+	)
+	web? ( !dev-python/webpy )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-1.5.0.1-setup.py.patch \
+		"${FILESDIR}"/${PN}-1.5.0.1-data-path.patch \
+		"${FILESDIR}"/${PN}-1.5.0.1-flags.patch
+
+	use web || epatch "${FILESDIR}"/${P}-web.patch
+
+	epatch "${FILESDIR}"/${P}-prefix.patch && \
+		eprefixify setup.py
+
+	use vmd && epatch "${FILESDIR}"/${PN}-1.5.0.1-vmd.patch
+
+	if use numpy; then
+		sed \
+			-e '/PYMOL_NUMPY/s:^#::g' \
+			-i setup.py || die
+	fi
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die
+
+	# python 3.* fix
+	# sed '452,465d' -i setup.py
+	distutils_src_prepare
+}
+
+src_configure() {
+	:
+}
+
+src_install() {
+	distutils_src_install
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	cat >> "${T}"/pymol <<- EOF
+	#!/bin/sh
+	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
+	EOF
+
+	dobin "${T}"/pymol
+
+	insinto /usr/share/pymol
+	doins -r test data scripts
+
+	insinto /usr/share/pymol/examples
+	doins -r examples
+
+	dodoc DEVELOPERS README
+
+	doicon "${WORKDIR}"/${PN}.xpm
+	make_desktop_entry pymol PyMol ${PN} "Graphics;Science;Chemistry"
+}
+
+pkg_postinst() {
+	elog "\t USE=shaders was removed,"
+	elog "please use pymol config settings"
+	elog "\t set use_shaders, 1"
+	distutils_pkg_postinst
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}