Version BUmp

Package-Manager: portage-2.2.0_alpha90/cvs/Linux x86_64

5 files changed, 208 insertions, 5 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/Manifest b/sci-chemistry/pymol/Manifest
index 27b0fdfb37f6..b55c37e028e8 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -19,21 +19,25 @@ AUX pymol-1.5.0.1-prefix.patch 1746 RMD160 2bab80e0881a7180887a0259121c46fd09b73
 AUX pymol-1.5.0.1-setup.py.patch 893 RMD160 3060484fe43632743eec4503d8b73cff28d9b3a4 SHA1 01353b2578867a413b31a6b063f5ca561a218ddb SHA256 3a03cb19878a772caff5c6931ff7bb1fdcd022147ec0e8a23593d4ae61cf1593
 AUX pymol-1.5.0.1-vmd.patch 1723 RMD160 7e0d0677d3dd498bfdf47e2055720d365a97ec37 SHA1 03157e315ad840bf129b02dede3cc45ebd12fcd4 SHA256 9a31ff39838484ce0df7658b896b8da137740871901bdc66db5dc4c46c293e50
 AUX pymol-1.5.0.1-web.patch 634 RMD160 8c7c2bec3dae9c154f11ae5436a63fa99f2bce39 SHA1 6b68a4220a6ce4058ceb5b10e88a0ed397d1966e SHA256 7c30f0c030c3f2e30cbd1f37c58910592a71ee2d5c5a351130e0bde13104c49e
+AUX pymol-1.5.0.3-prefix.patch 2278 RMD160 864cbd2e330d07e960681f690f4c2105d7d7c328 SHA1 b95a6a192053cbbaa3e2cd7ef6d021582b0d5136 SHA256 d4bb54dd667011747cf4f201cc4c0ac84ed6eb59cb066c374d6f89097a3914cc
+AUX pymol-1.5.0.3-web.patch 545 RMD160 5d1049532c89b2e1c72f7a3a227bf9d9dfae3718 SHA1 d2c271549ba5ea4b64eb6b3c19fdc1cf87e17c8c SHA256 559fbf42497c33a0ec844a11d7cd89178a8e0bae437df71a4408b891857ef9b3
 DIST pymol-1.3.1_pre3925-r1.tar.gz 8185909 RMD160 fcd6bdcedda369af7d51c41fc708c69a878b1aa1 SHA1 990b1acd0d5c84f7b93dc1c9a550f95b74c67e4b SHA256 74d3a3dd1972e2f47458e80c3d157871c361ad81119c76d1edd40b5e491cb50e
 DIST pymol-1.4.1.tar.xz 6831544 RMD160 6478b14215d0c502bff3bdec0cae3c903a9004e0 SHA1 d4da217ebf2c059f4712f564b55daa81a839b259 SHA256 af020e3103360defa3749ed31c16938a00032d4c2bf40f8455c746919aeaffd6
 DIST pymol-1.5.0.2.tar.xz 7389704 RMD160 5164221a8f14f8855a4113d6e16ab6ef2a2fc8b1 SHA1 85c5851b95760cb91fa6352e5eabbdeba299e722 SHA256 22761608a0f7f815b7399830050ec759b2ada8edfe1700e2f299047d0e9254fc
+DIST pymol-1.5.0.3.tar.xz 7412080 RMD160 019905f04f6108daff7a0c5c29dbc4371b0e8e17 SHA1 0b1fe58094c423ad7abc1cd05da5668ba00a4ef2 SHA256 b304c2839bc944bd2619403474d36cb846b372ba281c8f05931d3f155a0aec7a
 DIST pymol-v1.5.0.1.tar.bz2 9695855 RMD160 1e5fd51299f2bbe0249a9a07117c068af49ec095 SHA1 b59ff50437d34f21ca8ffd007a600de4df684073 SHA256 16c0cfbacbbd967b23654dd3708ef6ba877ab2a6c0985ff806a17186427de49c
 DIST pymol.xpm.tar 10240 RMD160 86b01bbe6aa8bf0251a982718d343c61c781c6e3 SHA1 af1ae2c9e2479efcd600c7ba01313b5dd7ef5b87 SHA256 813c450b5acc399387ddc33cc2d747c02afb515e1c3f216be7f7284a09e64819
 EBUILD pymol-1.3.1_pre3925-r1.ebuild 2703 RMD160 73f891e9c3d8f56b154c38c8b18261df50a196af SHA1 0390bf80786231bc5f9ca679f91a2a936dab8876 SHA256 662ffbfb4b7c725095d59dd1490d97a2d2a650b29b394f25f43da763c64597e2
 EBUILD pymol-1.4.1.ebuild 2807 RMD160 f3d2f58327812613dc80aeb1b1287cc637fc6aa3 SHA1 9b0ca9e0abbcb6b7459ae28ea22b10a943a10528 SHA256 c4713c5d289c6a00093a2c89afb918c5411de8dee91082fe22fc708b38463067
 EBUILD pymol-1.5.0.1.ebuild 2800 RMD160 253f9636af0a4611c36ea5bc0871d914af6f270a SHA1 f915cd2add9592fd2a597b0fb552f5b70f596ba6 SHA256 df5d9ba7bf2c044ae4fff1d50948f1be519b96feee97b2f6b4416fc4a54a55f3
 EBUILD pymol-1.5.0.2.ebuild 2814 RMD160 7d177d6ece8a5ffb095e03ba0c4b5e4136abf6a0 SHA1 793b74bb2d08b242b785b1047321e7eb6c44432c SHA256 e30f4c555c3e4278d97b4e7638ffb7dbfecb9f16e939e7168023e82fd7921b77
-MISC ChangeLog 1896 RMD160 d2a4060f4d511b6ba5057fbb020e4f5308283dc6 SHA1 3a43c627bfd0d561fa1946df3e9f58fa01c24c10 SHA256 d955aeec45aca065654a8511bac471727fa391a36ce2257be780a1a99eee9685
+EBUILD pymol-1.5.0.3.ebuild 2796 RMD160 b6dfb9807830d8e9c0030e7bb350802e54a808b4 SHA1 19992731ba6d8c52fb3bf77c1b3ff13e717c22b6 SHA256 41d6dd2821a207bd7a3bd4f79b5c70489690dff01b07db810437969d23a0598f
+MISC ChangeLog 2081 RMD160 d70a82eebeb784bf5017c38de1845183d8adab3d SHA1 18a518d469d553310486efde2ec7ac73ec58fee9 SHA256 53a48b1d113cff204c52892eb871c1e1cfa9c7b773ba7b3f13f34b10b0b6a0a5
 MISC metadata.xml 569 RMD160 edfb6f78a19d49eb7f18fb0d8336a0c5f97c3f34 SHA1 c75951bdda3dcb4564d23b873e30773bc9ed7fc7 SHA256 6f2b2746c7b2182262554076f11159b11d671695c40509bf7014c7546d719ff2
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-0gUAoMl5TakI85LsyNawoEOKRikRoQWm
-=bBa3
+iEYEAREKAAYFAk9bH3gACgkQgAnW8HDreRbvqQCgiZoYP7X/7tUxF/HgxQ86RqpK
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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
+}