sci-chemistry/pymol: Backport fix for stereo flickering

Package-Manager: portage-2.2.0_alpha188/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 195 insertions, 5 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 0ce39b4be0f0..c0196b345f6e 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.102 2013/06/18 12:20:13 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.103 2013/07/16 09:12:21 jlec Exp $
+
+*pymol-1.6.0.0-r2 (16 Jul 2013)
+
+  16 Jul 2013; Justin Lecher <jlec@gentoo.org> +pymol-1.6.0.0-r2.ebuild,
+  +files/pymol-1.6.0.0-stereo.patch:
+  Backport fix for stereo flickering
 
 *pymol-1.6.0.0-r1 (18 Jun 2013)
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 0e28e9b667d9..37037029a99e 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -11,6 +11,7 @@ AUX pymol-1.5.0.3-prefix.patch 2278 SHA256 d4bb54dd667011747cf4f201cc4c0ac84ed6e
 AUX pymol-1.5.0.3-web.patch 545 SHA256 559fbf42497c33a0ec844a11d7cd89178a8e0bae437df71a4408b891857ef9b3 SHA512 272a516e8d2780bd5b74e852c9d06c27f8dd645e3c68b17bba1931d0d59af55637bc0565447642539b3b0e73b82e5392c13e51171aa3a2ebf42d717fabf4bce2 WHIRLPOOL 95a5bf25a068da437dd2c04fb22b9b4216646f9b0bd0c3ce333428a5eccc090005a0e6b4fd50279ba22df9a754acb9b61fdec07dfb7a134e3d966e0e8e14cb88
 AUX pymol-1.6.0.0-bg_rgb.patch 9264 SHA256 12fa3a5a83f77ecbff3f5958e40b7c8f0b5f9c9bb7fa2c1e87cff15f2476e83b SHA512 23627c8db8f55bfe8150a7bd4f75033d3f09f308e0f7c39f79e67c6c749fede2402f611df102e30d74cf8c83b27c0143833c7bfbcc54bd04cbae1adefefc0726 WHIRLPOOL dfa0a9918815c9d048a89ed3b8f40409532192f2bdfdb64a1c1495b5aa0641bf4c40889387ba752de5381999809812ab2933a155e5054efa3997a4a7cbad49f9
 AUX pymol-1.6.0.0-labels.patch 17150 SHA256 b1385696a5f781e51adcd61774362f76c4f8443e168e5232b1b577f06a6821b0 SHA512 190353d690656685da0e7912cb74426c161659a177d3cc8b1e9bdeb02513756b9d36b32c0ee351905b5dd31e7a7ea6dfe7ca685533b0ef7651bd51190e2060bc WHIRLPOOL e79fd2debc7b3bb80f0d83fe49c9b90de24d5e3f0e373e2b91452965059874c2d007b3e2731028a2ab4005ddef3c75404ee7f4b6bde6216e930eb5ff2fd1fbf3
+AUX pymol-1.6.0.0-stereo.patch 1839 SHA256 accbb7e142d2f4709605d156c169146836d78d29514af5eeffc5c6121d5e056c SHA512 bd32c26dce36b2a44613470f20ef8916111acc20f6525185b9c4b33c25b03efea4ee00f35ab391f8c12874d3bc9e1be665b5706864e660c85b2432b97a9c80b8 WHIRLPOOL 16a30e3830c17420bc53dc86191dbf6b366be94ef5484798e945600b3fc97f83df742d7cdbcbcfa574cb4a4e7c9ff5501f7301d1f33c3a11682f99aadd52dd82
 DIST pymol-1.5.0.3.tar.xz 7412080 SHA256 b304c2839bc944bd2619403474d36cb846b372ba281c8f05931d3f155a0aec7a SHA512 a3f1dd3089fa4158840f2cb8c3848ef70284d1f859429cfab6ac9b00f649d7274a3ac7697a7fb4996d7643068a916f9ad7b1952c5ff27003cedcc7c89e795485 WHIRLPOOL 82788bf6fce52d76ff00d1d7243e8f3962027b4512addaf0fc2f881aaf5f0da6582cb3b3b56a178ed36572947273a999be3d67ba49845eb887da6cf242c5b5f3
 DIST pymol-1.6.0_rc1.tar.xz 6592108 SHA256 7353c9bdfa272b516bd43efaea7df16a6e1632b013ac6091eb5ec34b1f8676bc SHA512 971f03b41db1ed6b1095e91cea49ca5ffb819bf9b97e34dab215112462da02d7bb1b608c462d07556998dfd49631663f3d2cbf27368980f3d69bf134002224a8 WHIRLPOOL 2368fb3a20cbb2d490b1f4b370f770aa7b89921c5827414715ec7616ad66e991bb7f378ed7c379db78b9391dea0bcae9d56362bd705978d667858af8ef46ebb4
 DIST pymol-icons.tar.xz 38100 SHA256 03500f28256f67abfbb7d08b798b11aaa208f0ae1473ef2a7205b3c012ddb06a SHA512 5af51014d4fcbc85ef1fecd7667224709c9305b9b72bfdfd89ece2b4420fa8a81bf8c85fcc5903e2a670f44403f12764808f6a16ef42f111bbd0e7ed8e412d54 WHIRLPOOL 6104d378928c56b39f8cbe29184629b73f87da09e81e41ddc08b9b291876f1a30ccaf9ec257f47798c6d03253816f80c14567073c419fa48dd1520fa3fa58ecd
@@ -18,14 +19,25 @@ DIST pymol-v1.6.0.0.tar.bz2 8695114 SHA256 a37eb1a1bd882da14ac9c03617f62f6a49eea
 EBUILD pymol-1.5.0.3-r1.ebuild 3131 SHA256 3381ef60e5dc156116f2ca0e8cd9631c58d38e188f7de4b00e91a39b099f50e3 SHA512 4a34c1416d871da56dc8d753ad46b97a0167dd63a14919d59e601143ad60236b8267b0d779fecc970e1e5b4c8ce1716cca8d125977b92af1d8adf7e2a045f1e0 WHIRLPOOL a05f2b444bb281b78d4199c23c462663d3184735cd66c946f2d32e673593f442876027b142e0cdf6206247574b539526e7aff7f6863f4ce97f878cd783828fe8
 EBUILD pymol-1.5.0.3-r2.ebuild 3048 SHA256 10f44dc1054724a3abf111b5232bbcbf18920066778afdeb965da10bbc7e92e5 SHA512 31441e2cd38615bf977273e5ad7114a99a6680bc9e096625724eef4c71a53186e2d84e41977fc95650728cd0dd0201f3081af42d31019029a24b9154f85d2490 WHIRLPOOL 46cef085836c28f9b41693af62c9a2f5371f6cd54b8bd00013fb799a1cd7c04016a2934728dc0128693b8ddd7be78a22947283c490aa9f2c3ca5fc0fa604e6c6
 EBUILD pymol-1.6.0.0-r1.ebuild 2419 SHA256 7bd6cebcd5d308e5facd47705b857689da698359fef1c866346880f1470470ee SHA512 0a599151b7bcf6f8de25f2f15bdf5a4d80e1c25e94ba5cf5311c608d7a2d2dda4eb3f52af5525a4a8c6c3d4e7b600db28f490f3119fc26b901725b307d058601 WHIRLPOOL 2ca9788e2031f62dc803648e86f7cb2d681e1dcde7efbaac00d7dcb04a73dca1109b3682ab237e4ba68a37f908e16d5d51c4e10e316fa60ae367535404e86db5
+EBUILD pymol-1.6.0.0-r2.ebuild 2452 SHA256 01f212ffafbd5030f0dcbf6a47af22002a876a8cd4c5fcef5cfa67bca42eff80 SHA512 a621d6a9017a31bd0816df591890bfbc3de7e315ba21ad22a9145fae2d5802f8fa23608e703a0dc2bffd1227d2f8b75ad046956a83ac4f70af7eb6d1392e708a WHIRLPOOL 3c6f2e4667acbcecfcc25c51ca6d14d14774166c4b1dbb77874127ae536c4bbbec722babb904795faae191655c7c856ecf843c3fb509e3826fc5088e67b28422
 EBUILD pymol-1.6.0.0.ebuild 2337 SHA256 a6df3b85b342539aa4743164511f5c39361db0141cb3acffda7242bd1837d398 SHA512 104221e52fa572aadf58ecaaa817510fee4c7defe47ad826b9b8bbef416cad3be632624343ad38f6265c73ea51255dacbe1df4f19b912c680ea9f1a072b84853 WHIRLPOOL 54524d364491f913e66b4c0a3b5cc0eabf38afde975eedc38e0d8d5376a6bcf274ad0ef8a55c3f634ad59d9982221a8b78e59291fa0aea5e694d12821b2add62
 EBUILD pymol-1.6.0_rc1.ebuild 2270 SHA256 4a7a7bea1ce4c0c96c0dc6a2a624a33ab779b783776a6293b38a11d6c028a751 SHA512 826ee97eec01fe34ca34cfdee1c4a85e994e861297fbf7dd93b63e347aa83800c84f21aee8c7052d4930bc6a299fcab97d34ca7849e7ff80e5394c609beda2fd WHIRLPOOL 70ec2a72a1ace006b1d0b98958d22d916b60447a7383c0a7891db028c33ace1a12c649626428cc3aea1ef58632e646c04c1731332c7c638393253d3308427bc9
-MISC ChangeLog 4817 SHA256 7e8de1cc4dc9dd518be7a0219a22311e79425a4d3f14c9f619be84062be522dc SHA512 8f41509c9c00b5e8d26196f02d5dca0aec24985657876fda1e78875cebdd6df9223e0e51a0e435aea44dfcec7eeca139b5e6c6f9ace1adc352a0ff8db445d5df WHIRLPOOL 8d2758be534c7756ce25c54d1068d022a302bb6c66507da1bd89b277bbc800e8d5ff54af243574c967d1addc03a39fae0ab73966fc4a7f6bed829c07c6ab6b31
+MISC ChangeLog 4998 SHA256 3123b14b6e0a62350c8162ded013cd1c51a157cbda26a265d6be84e68c232c12 SHA512 101a26807e67bf580da6423e04542b1d8a9e8979e73420b4980ddb629db4156fda26466bc109aaf65034913d9bf64c0369643e5416f3aa272de8dc9a3199a2e1 WHIRLPOOL bb23836aad43a9d321b2f1fbf87f7f88fb452046c8618be6c8e3b06983370259764092e86d63bd3b16e514355ffced211d4e07452ceff52d321f62314c0e0157
 MISC metadata.xml 491 SHA256 7370aee92bf4088e8dc054dc8812cc30e98be7995570afae89dfacc49eec711b SHA512 319f8924b56ecb64e35892fa10ab94adbca68dc3d9dffc760d54e44fe19feb0e3bf87110aa7e94f25a353792e84610353f2f8684b6032426cd4eaa70fa5a9fdc WHIRLPOOL 93baebbb622f81fd48b7396bb3f98c8ce0d97db41c6a09e28da0cd923261961100cd715ada8f4ff70f79638cca88b0f1ab0b0ff78f9656323efcb871ea0958cf
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diff --git a/sci-chemistry/pymol/files/pymol-1.6.0.0-stereo.patch b/sci-chemistry/pymol/files/pymol-1.6.0.0-stereo.patch
new file mode 100644
index 000000000000..6d0f2e16833d
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.6.0.0-stereo.patch
@@ -0,0 +1,72 @@
+From 4920977eeeebdc944a824e2c589272324ea5e74e Mon Sep 17 00:00:00 2001
+From: speleo3 <speleo3@21428953-86e3-433d-9a34-2224224d0fc8>
+Date: Mon, 15 Jul 2013 14:01:10 +0000
+Subject: [PATCH] fixed flickering ortho problems on some machines
+
+git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4034 21428953-86e3-433d-9a34-2224224d0fc8
+---
+ pymol/ChangeLog      |  4 ++++
+ pymol/layer1/Ortho.c | 26 ++++++++++++++++++++------
+ 2 files changed, 24 insertions(+), 6 deletions(-)
+
+diff --git a/pymol/layer1/Ortho.c b/pymol/layer1/Ortho.c
+index 4d79114..9dd5d45 100644
+--- a/pymol/layer1/Ortho.c
++++ b/pymol/layer1/Ortho.c
+@@ -1517,7 +1517,7 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
+   int overlay, text;
+   int rightSceneMargin;
+   int internal_feedback;
+-  int times = 1;
++  int times = 1, origtimes = 0;
+   int double_pump = false;
+   float *bg_color;
+   int skip_prompt = 0;
+@@ -1627,6 +1627,7 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
+ 
+     SceneGLClearColor(0.0, 0.0, 0.0, 1.0);
+ 
++    origtimes = times;
+     while(times--) {
+ 
+       switch (times) {
+@@ -1678,7 +1679,7 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
+ 	  } else {
+ 	    OrthoRenderCGO(G);
+ 	    OrthoPopMatrix(G);
+-	    return;
++	    continue;
+ 	  }
+ 	}
+       }
+@@ -1925,10 +1926,23 @@ void OrthoDoDraw(PyMOLGlobals * G, int render_mode)
+ 	CGOStop(I->orthoCGO);
+ 	I->orthoCGO->use_shader = true;
+       }
+-
+-      OrthoPushMatrix(G);
+-      OrthoRenderCGO(G);
+-      OrthoPopMatrix(G);
++      
++      while(origtimes--){
++	switch (origtimes){
++	case 1:
++	  OrthoDrawBuffer(G, GL_BACK_LEFT);
++	  break;
++	case 0:
++	  if(double_pump) {
++	    OrthoDrawBuffer(G, GL_BACK_RIGHT);
++	  } else
++	    OrthoDrawBuffer(G, GL_BACK);
++	  break;
++	}
++	OrthoPushMatrix(G);
++	OrthoRenderCGO(G);
++	OrthoPopMatrix(G);
++      }
+     }
+   }
+ 
+-- 
+1.8.3.2
+
diff --git a/sci-chemistry/pymol/pymol-1.6.0.0-r2.ebuild b/sci-chemistry/pymol/pymol-1.6.0.0-r2.ebuild
new file mode 100644
index 000000000000..45912bc342be
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.6.0.0-r2.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.6.0.0-r2.ebuild,v 1.1 2013/07/16 09:12:21 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 fdo-mime versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="
+	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
+	http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz"
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="apbs web"
+
+DEPEND="
+	dev-python/pmw[${PYTHON_USEDEP}]
+	media-libs/freetype:2
+	media-libs/glew
+	media-libs/libpng
+	media-video/mpeg-tools
+	sys-libs/zlib
+	media-libs/freeglut
+	apbs? (
+		dev-libs/maloc
+		sci-chemistry/apbs
+		sci-chemistry/pdb2pqr
+		sci-chemistry/pymol-apbs-plugin
+	)
+	web? ( !dev-python/webpy )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-labels.patch
+	"${FILESDIR}"/${P}-bg_rgb.patch
+	"${FILESDIR}"/${P}-stereo.patch
+	)
+
+python_prepare_all() {
+	distutils-r1_python_prepare_all
+	sed \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
+		-i setup.py || die
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
+}
+
+python_install() {
+	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	python_export python2_7 EPYTHON
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="$(python_get_sitedir)/${PN}"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	doicon "${WORKDIR}"/${PN}.{xpm,png}
+	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
+
+	if ! use web; then
+		rm -rf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}