sci-chemistry/pymol: Backport fix for broken labels

Package-Manager: portage-2.2.8-r1/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 207 insertions, 16 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index f5a97ddc2778..b6626a5e7595 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.109 2014/03/10 07:08:07 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.110 2014/03/13 08:16:23 jlec Exp $
+
+*pymol-1.7.0.4-r1 (13 Mar 2014)
+
+  13 Mar 2014; Justin Lecher <jlec@gentoo.org> +pymol-1.7.0.4-r1.ebuild,
+  +files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch:
+  Backport fix for broken labels
 
 *pymol-1.7.0.4 (10 Mar 2014)
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 3c655f1c5559..f50d973367f6 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -12,6 +12,7 @@ AUX pymol-1.5.0.3-web.patch 545 SHA256 559fbf42497c33a0ec844a11d7cd89178a8e0bae4
 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
+AUX pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch 3073 SHA256 a5bbfc21e3d47e70e597d0b6509251b0720480beb118dff1f85113fc7e59c643 SHA512 96ade2f3d47966fb2322c32d5ab055cc927a065b5ac84bc1de20d798ea6b358a153b6b8c8f85e66f3e3ac04790df416294eb4bbde1b8aad7737c83ecf82158fe WHIRLPOOL bae9e9f38ff0e5bb3fb94d9e4c1d1082d80b40a0ab14e6098733c8a18c5c5289a9dc63725d06299eac917b3f2c6b6b4df68e36ef6fb959f30aa2f2cb283fa79d
 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-1.7.0.0.png.xz 5392 SHA256 4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105 WHIRLPOOL 395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
@@ -28,25 +29,26 @@ EBUILD pymol-1.6.0.0.ebuild 2329 SHA256 72013c55e9e223c76a4643a8b423292b43e2e9e9
 EBUILD pymol-1.6.0_rc1.ebuild 2262 SHA256 468f978ce8800b1db5c55274c912bd67000715454762007286d3c0c1c36dbf24 SHA512 d4d57c77f7bd5805af04260207da63da1e4dbdfb067de2538d4882818d3169e66d2cb1a2bf48977967011d566db591938e0531c1847ade8389f4c698e7ac41c9 WHIRLPOOL 2cc6be852c6c6e502d3a963bdc2eb5393c81fcf28248cc33ce4efb5853cb5606e807cff2b96fc725ee3d8f5a3e2b9b93dead7b0441877780480ef9315f4197f2
 EBUILD pymol-1.7.0.0.ebuild 2477 SHA256 73f2ad6605e9b5dd776904e9d2594e3c2d9322f3095113303169f9859ba94247 SHA512 d6483ad15a56a41d9c517d9f1c2e40cce5050fc0151c48e370b2e11bb0aa57291fbf9b6263fa810e5cf273ca0cc493006e988f16389f28450caadf6e7edd1eb2 WHIRLPOOL 1c16c22aa3db290b67b3a180e42ef2bb8b561e64d742fb8d0122a779c3af2644cba170c41feb3a494343f46d33bcd2ce166002a94d79506cd3c8aa492e389d35
 EBUILD pymol-1.7.0.1.ebuild 2553 SHA256 7fd10ccbf59cb01c992353b8a7363959c9f789f596fff9ebf61f91171fb35714 SHA512 c90dab7fdd09e0e9e38b811126423c1d36ec2f793443fca7d0e40522510bcac7be0359cbed6b190a706cb4de8c6b071f6a1e80c8477f19a8563f8cae569a73a4 WHIRLPOOL 0bf7d047e4774afa0e51f4c61c24458c3396c3ed888d78077dd2d1b8c2eb7c3bfccdf12b4edbb168bf6b17315f04855cc290e4efac24f8175b96f41218656bba
+EBUILD pymol-1.7.0.4-r1.ebuild 2629 SHA256 3c9b53b1f8cf811328e4f6b321a40200f9af8978f3343df42be315d89e7566c6 SHA512 08649f9dc0bec58df5884abe4a534224c32c2648df632bce1b5280fceef580374524a8289d803e267635094cbc637fb24519252b0a05b93b2ec7d177ad259ff8 WHIRLPOOL 911d138d68449d54ffe7c4022d203866c40dfab0d20f3073a10fe84aa7de6c2992286d3ef7a8834c141cf8dd7b3eb138e7d660dd080d2b1fb49ad97d6320edcb
 EBUILD pymol-1.7.0.4.ebuild 2553 SHA256 b31adb810360896cf6784c1a6e7dbf78ee8c4ee5932b39f2ab9385e0b8effc33 SHA512 7eddb5d4dff2fdddb6631ba64a59989258381c6eb63174f0ef0d44c8afa108e9c9cde902daad7c17a44f4eaa6cb44bacd313171c9f213f91af3ba0e3ebc54d26 WHIRLPOOL 70e125d140e350664d1b2fe21439deb65a9c1b8cef2458e77382bffe6468211a86a13b1224f0b2d247a11631fb4d9891a86d38a638ccfa482cf5bd81cc216392
-MISC ChangeLog 5769 SHA256 1636b046bbe6f0b0d6710a06f4b96a77969ab66403bbda62f744d90a6610e048 SHA512 93e3ebee11931074c9535530588ec50c459a428974ceac21f75d54b176fd9ca67b09543a4220d2aac813eb721d52d4f0c3917e3c9e5a328d9f91919d048c4fcf WHIRLPOOL e1063e5ea27f26b0f719f7925f308f4d979f6be5b8c34f2bb506334c1d1d878042f28f8d7fdefd5bea10f1d82421243afb6fc9fe4dc5ab6e624615fbc62b1821
+MISC ChangeLog 5973 SHA256 ef298efbefdfa3a14262883e00db4a9e04cd638f7d51e826e27ccb264b1d97aa SHA512 62be7b42ef4ce36ebe380635784e2572137ae920e0c77fc2e10a0633aa0046a823ff6486cd6a75c98412a8181a1556f53583b860226e3b6c626e181de207e922 WHIRLPOOL 518d0684e50a4f2701a9f3067454bb2907a913ab4a9ccba0bf026d5d192814f244cd007c52aa67b8508eae4897dd85d5407c4a25430b5353659bbf27c8635406
 MISC metadata.xml 491 SHA256 7370aee92bf4088e8dc054dc8812cc30e98be7995570afae89dfacc49eec711b SHA512 319f8924b56ecb64e35892fa10ab94adbca68dc3d9dffc760d54e44fe19feb0e3bf87110aa7e94f25a353792e84610353f2f8684b6032426cd4eaa70fa5a9fdc WHIRLPOOL 93baebbb622f81fd48b7396bb3f98c8ce0d97db41c6a09e28da0cd923261961100cd715ada8f4ff70f79638cca88b0f1ab0b0ff78f9656323efcb871ea0958cf
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diff --git a/sci-chemistry/pymol/files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch b/sci-chemistry/pymol/files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch
new file mode 100644
index 000000000000..359a3bc9c78c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch
@@ -0,0 +1,79 @@
+From 5c744d0dcf3ae717ce774e07e24812a543f4a866 Mon Sep 17 00:00:00 2001
+From: speleo3 <speleo3@21428953-86e3-433d-9a34-2224224d0fc8>
+Date: Mon, 10 Mar 2014 15:50:16 +0000
+Subject: [PATCH] fix broken label scaling on Linux
+
+- label scaling became distorted on window resizing
+- minor readability update in label.vs (no change)
+
+
+git-svn-id: svn://svn.code.sf.net/p/pymol/code/trunk@4069 21428953-86e3-433d-9a34-2224224d0fc8
+---
+ pymol/data/shaders/label.vs | 17 ++++++++---------
+ pymol/layer1/Scene.c        | 10 ----------
+ 2 files changed, 8 insertions(+), 19 deletions(-)
+
+diff --git a/pymol/data/shaders/label.vs b/pymol/data/shaders/label.vs
+index b179530..58d9dad 100644
+--- a/pymol/data/shaders/label.vs
++++ b/pymol/data/shaders/label.vs
+@@ -21,16 +21,15 @@ uniform float fog_enabled; // actually bool
+ 
+ void main()
+ {
+-  vec4 transformedPosition = gl_ModelViewProjectionMatrix * attr_worldpos;
+-  transformedPosition.xyz = transformedPosition.xyz/transformedPosition.w;
+-  transformedPosition.w = 1.;
+-  transformedPosition.xy = transformedPosition.xy + attr_screenworldoffset.xy/(screenSize*screenOriginVertexScale);
+-  transformedPosition.z = transformedPosition.z + attr_screenworldoffset.z/(screenSize.x*screenOriginVertexScale);
+-  transformedPosition.x = transformedPosition.x + aspectRatioAdjustment * attr_screenoffset.x * 2./screenSize.x;
+-  transformedPosition.y = transformedPosition.y + attr_screenoffset.y * 2./screenSize.y;
+-  gl_Position = transformedPosition;
++  vec4 pos = gl_ModelViewProjectionMatrix * attr_worldpos;
++  pos /= pos.w;
++  pos.xyz += attr_screenworldoffset / (screenSize.xyx * screenOriginVertexScale);
++  pos.xy += attr_screenoffset.xy * 2. / screenSize * vec2(aspectRatioAdjustment, 1.);
++
++  gl_Position = pos;
+   textureLookup = attr_texcoords;
+-  normalizedViewCoordinate = (gl_Position.xyz/gl_Position.w) / 2.0 + 0.5;
++  normalizedViewCoordinate = pos.xyz / 2.0 + 0.5;
++
+   if (fog_enabled > 0.5) {
+     vec3 eye_pos = vec3(gl_ModelViewMatrix * attr_worldpos);
+     fog = max(0.0, (gl_Fog.end - abs(eye_pos.z)) * gl_Fog.scale);
+diff --git a/pymol/layer1/Scene.c b/pymol/layer1/Scene.c
+index 639f737..59ee89e 100644
+--- a/pymol/layer1/Scene.c
++++ b/pymol/layer1/Scene.c
+@@ -1972,13 +1972,8 @@ void SceneGetImageSize(PyMOLGlobals * G, int *width, int *height)
+ void SceneGetImageSizeFast(PyMOLGlobals * G, int *width, int *height)
+ {
+   register CScene *I = G->Scene;
+-  if(I->Image) {
+-    *width = I->Image->width;
+-    *height = I->Image->height;
+-  } else {
+     *width = I->Width;
+     *height = I->Height;
+-  }
+ }
+ void SceneGetImageSizeFastAdjustForGrid(PyMOLGlobals * G, int *width, int *height){
+   register CScene *I = G->Scene;
+@@ -1986,13 +1981,8 @@ void SceneGetImageSizeFastAdjustForGrid(PyMOLGlobals * G, int *width, int *heigh
+     *width = I->grid.cur_viewport_size[0];
+     *height = I->grid.cur_viewport_size[1];
+   } else {
+-    if(I->Image) {
+-      *width = I->Image->width;
+-      *height = I->Image->height;
+-    } else {
+       *width = I->Width;
+       *height = I->Height;
+-    }
+   }
+ }
+ 
+-- 
+1.9.0
+
diff --git a/sci-chemistry/pymol/pymol-1.7.0.4-r1.ebuild b/sci-chemistry/pymol/pymol-1.7.0.4-r1.ebuild
new file mode 100644
index 000000000000..29c0fe58de9d
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.7.0.4-r1.ebuild
@@ -0,0 +1,104 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.0.4-r1.ebuild,v 1.1 2014/03/13 08:16:23 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://www.pymol.org/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
+	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+"
+#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="apbs web"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pmw[${PYTHON_USEDEP}]
+	dev-python/pyopengl[${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[${PYTHON_USEDEP}]
+	)
+	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${P}/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-broken-label-scaling-on-Linux.patch
+)
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
+		-e "/import/s:argparse:argparseX: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
+
+	distutils-r1_python_prepare_all
+}
+
+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 "${T}"/20pymol
+
+	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.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
+}