Rename all patches, add support for desktop icon, drop nosplash patch and add launch option

(Portage version: 2.2.0_alpha86/cvs/Linux x86_64)

16 files changed, 47 insertions, 185 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index ca714f689b81..753435a0a288 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,21 @@
 # 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 1.82 2012/02/13 22:09:19 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.83 2012/02/14 08:18:11 jlec Exp $
+
+  14 Feb 2012; Justin Lecher <jlec@gentoo.org> -files/1.2.2-data-path.patch,
+  -files/1.2.1/pymol-1.2.1-data-path.patch, -files/1.2.2-prefix.patch,
+  -files/1.2.1/pymol-1.2.1-shaders.patch, -files/1.3.0-vmd.patch,
+  -pymol-1.2.3-r1.ebuild, -files/1.4.1-data-path.patch,
+  pymol-1.3.1_pre3925-r1.ebuild, -files/1.4.1-shaders.patch,
+  pymol-1.4.1.ebuild, -files/1.4-shaders.patch,
+  +files/pymol-1.2.2-data-path.patch, +files/pymol-1.4.1-data-path.patch,
+  -files/1.4-vmd.patch, +files/pymol-1.3.0-vmd.patch,
+  +files/pymol-1.4.1-shaders.patch, -files/1.4.1-web.patch,
+  +files/pymol-1.2.2-prefix.patch, +files/pymol-1.4.1-web.patch,
+  +files/pymol-1.4-shaders.patch, +files/pymol-1.4-vmd.patch,
+  pymol-1.5.0.1.ebuild, -files/pymol-1.5.0.1-nosplash.patch:
+  Rename all patches, add support for desktop icon, drop nosplash patch and add
+  launch option
 
 *pymol-1.5.0.1 (13 Feb 2012)
 
diff --git a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch
deleted file mode 100644
index 86c3fe1f1c27..000000000000
--- a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/commanding.py
---- pymol/modules/pymol/commanding.py	2009-03-31 12:43:14.585834066 +0200
-+++ pymol.new/modules/pymol/commanding.py	2009-03-31 12:44:26.436354330 +0200
-@@ -219,11 +219,11 @@
-                 _self.unlock(0,_self)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
-diff -arNu -uarN pymol/modules/pymol/importing.py pymol.new/modules/pymol/importing.py
---- pymol/modules/pymol/importing.py	2009-03-31 12:43:14.546250540 +0200
-+++ pymol.new/modules/pymol/importing.py	2009-03-31 12:44:48.876657949 +0200
-@@ -191,7 +191,7 @@
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb' }
-         
diff --git a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch
deleted file mode 100644
index 06f75682344f..000000000000
--- a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- pymol-1.2_rc1/setup.py.old  2009-07-17 00:05:10.339203020 -0500
-+++ pymol-1.2_rc1/setup.py      2009-07-17 00:09:03.375274561 -0500
-@@ -138,6 +138,7 @@
-                 ("_PYMOL_INLINE",None),
-                 ("_PYMOL_FREETYPE",None),
-                 ("_PYMOL_LIBPNG",None),
-+                ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support   
diff --git a/sci-chemistry/pymol/files/1.2.2-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
index cf1bf59af0c6..cf1bf59af0c6 100644
--- a/sci-chemistry/pymol/files/1.2.2-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
diff --git a/sci-chemistry/pymol/files/1.2.2-prefix.patch b/sci-chemistry/pymol/files/pymol-1.2.2-prefix.patch
index 211881435123..211881435123 100644
--- a/sci-chemistry/pymol/files/1.2.2-prefix.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.2-prefix.patch
diff --git a/sci-chemistry/pymol/files/1.3.0-vmd.patch b/sci-chemistry/pymol/files/pymol-1.3.0-vmd.patch
index 0f34a02ea01b..0f34a02ea01b 100644
--- a/sci-chemistry/pymol/files/1.3.0-vmd.patch
+++ b/sci-chemistry/pymol/files/pymol-1.3.0-vmd.patch
diff --git a/sci-chemistry/pymol/files/1.4-shaders.patch b/sci-chemistry/pymol/files/pymol-1.4-shaders.patch
index 853ebff9da81..853ebff9da81 100644
--- a/sci-chemistry/pymol/files/1.4-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4-shaders.patch
diff --git a/sci-chemistry/pymol/files/1.4-vmd.patch b/sci-chemistry/pymol/files/pymol-1.4-vmd.patch
index 2fd909ffd540..2fd909ffd540 100644
--- a/sci-chemistry/pymol/files/1.4-vmd.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4-vmd.patch
diff --git a/sci-chemistry/pymol/files/1.4.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.4.1-data-path.patch
index 903714cd223a..903714cd223a 100644
--- a/sci-chemistry/pymol/files/1.4.1-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4.1-data-path.patch
diff --git a/sci-chemistry/pymol/files/1.4.1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.4.1-shaders.patch
index 2caac2dc4bce..2caac2dc4bce 100644
--- a/sci-chemistry/pymol/files/1.4.1-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4.1-shaders.patch
diff --git a/sci-chemistry/pymol/files/1.4.1-web.patch b/sci-chemistry/pymol/files/pymol-1.4.1-web.patch
index 2d6957df594d..2d6957df594d 100644
--- a/sci-chemistry/pymol/files/1.4.1-web.patch
+++ b/sci-chemistry/pymol/files/pymol-1.4.1-web.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch
deleted file mode 100644
index b296285e89ca..000000000000
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- modules/pymol/invocation.py |    2 --
- 1 files changed, 0 insertions(+), 2 deletions(-)
-
-diff --git a/modules/pymol/invocation.py b/modules/pymol/invocation.py
-index de47849..c5f4487 100644
---- a/modules/pymol/invocation.py
-+++ b/modules/pymol/invocation.py
-@@ -397,7 +397,5 @@ if __name__=='pymol.invocation':
-         if loaded_something and (options.after_load_script!=""):
-             options.deferred.append(options.after_load_script)
-         options.deferred.extend(final_actions)
--        if options.show_splash and not options.no_gui and not restricted:
--            options.deferred.insert(0,"_do__ cmd.splash(1)")
-         if options.full_screen:
-             options.deferred.append("_do__ full_screen on")
diff --git a/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild b/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild
deleted file mode 100644
index 30dd9790aeda..000000000000
--- a/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild,v 1.9 2010/09/19 19:32:44 jlec Exp $
-
-EAPI="3"
-
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_DEPEND="2:2.6"
-PYTHON_USE_WITH="tk"
-REV="3891"
-
-inherit eutils distutils prefix
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol.tar.gz?view=tar&pathrev=${REV} -> ${P}.tar.gz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy shaders vmd"
-
-DEPEND="
-		dev-python/numpy
-		dev-python/pmw
-		media-libs/freetype:2
-		media-libs/libpng
-		media-video/mpeg-tools
-		sys-libs/zlib
-		media-libs/freeglut
-		apbs? (
-			dev-libs/maloc
-			sci-chemistry/apbs
-			sci-chemistry/pdb2pqr
-			sci-chemistry/pymol-apbs-plugin
-		)"
-RDEPEND="${DEPEND}"
-RESTRICT_PYTHON_ABIS="3.* 2.4 2.5"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	epatch "${FILESDIR}"/1.2.2-data-path.patch
-
-	epatch "${FILESDIR}"/1.2.2-prefix.patch && \
-	eprefixify setup.py
-
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though. #299020
-	epatch "${FILESDIR}"/1.2.1/nosplash-gentoo.patch
-
-	# Respect CFLAGS
-	sed -i \
-		-e "s:\(ext_comp_args=\).*:\1[]:g" \
-		"${S}"/setup.py || die "Failed running sed on setup.py"
-
-	use shaders && epatch "${FILESDIR}"/${PN}-1.2.2-shaders.patch
-
-	use vmd && epatch "${FILESDIR}"/${PN}-1.2.2-vmd.patch
-
-	use numpy && \
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-	# python 3.* fix
-	# sed '452,465d' -i setup.py
-	distutils_src_prepare
-}
-
-src_configure() {
-	:
-}
-
-src_install() {
-	distutils_src_install
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${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 || die "Failed to install env.d file."
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
-	EOF
-
-	dobin "${T}"/pymol || die "Failed to install wrapper."
-
-	insinto /usr/share/pymol
-	doins -r test data scripts || die "no shared data"
-
-	insinto /usr/share/pymol/examples
-	doins -r examples || die "Failed to install docs."
-
-	dodoc DEVELOPERS README || die "Failed to install docs."
-
-#	rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
-}
diff --git a/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild b/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
index 49210fa0f430..047cb181440a 100644
--- a/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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-1.3.1_pre3925-r1.ebuild,v 1.3 2011/05/24 18:44:14 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.3.1_pre3925-r1.ebuild,v 1.4 2012/02/14 08:18:11 jlec Exp $
 
 EAPI="3"
 
@@ -13,7 +13,7 @@ REV="3925"
 
 inherit eutils distutils prefix
 
-DESCRIPTION="A Python-extensible molecular graphics system."
+DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://pymol.sourceforge.net/"
 #SRC_URI="http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol.tar.gz?view=tar&pathrev=${REV} -> ${P}.tar.gz"
 SRC_URI="mirror://gentoo/${PF}.tar.gz"
@@ -42,9 +42,9 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}"/${PN}
 
 src_prepare() {
-	epatch "${FILESDIR}"/1.2.2-data-path.patch
+	epatch "${FILESDIR}"/${PN}-1.2.2-data-path.patch
 
-	epatch "${FILESDIR}"/1.2.2-prefix.patch && \
+	epatch "${FILESDIR}"/${PN}-1.2.2-prefix.patch && \
 	eprefixify setup.py
 
 	# Turn off splash screen.  Please do make a project contribution
@@ -58,7 +58,7 @@ src_prepare() {
 
 	use shaders && epatch "${FILESDIR}"/${PN}-1.2.2-shaders.patch
 
-	use vmd && epatch "${FILESDIR}"/1.3.0-vmd.patch
+	use vmd && epatch "${FILESDIR}"/${PN}-1.3.0-vmd.patch
 
 	use numpy && \
 		sed \
diff --git a/sci-chemistry/pymol/pymol-1.4.1.ebuild b/sci-chemistry/pymol/pymol-1.4.1.ebuild
index e52f29d26142..aad9eee68429 100644
--- a/sci-chemistry/pymol/pymol-1.4.1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.4.1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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-1.4.1.ebuild,v 1.2 2011/06/02 08:39:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.4.1.ebuild,v 1.3 2012/02/14 08:18:11 jlec Exp $
 
 EAPI="3"
 
@@ -12,7 +12,7 @@ PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
 
 inherit eutils distutils prefix versionator
 
-DESCRIPTION="A Python-extensible molecular graphics system."
+DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://pymol.sourceforge.net/"
 SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
 
@@ -41,12 +41,12 @@ RDEPEND="${DEPEND}"
 
 src_prepare() {
 	epatch \
-		"${FILESDIR}"/${PV}-data-path.patch \
-		"${FILESDIR}"/${PV}-shaders.patch
+		"${FILESDIR}"/${P}-data-path.patch \
+		"${FILESDIR}"/${P}-shaders.patch
 
-	use web || epatch "${FILESDIR}"/${PV}-web.patch
+	use web || epatch "${FILESDIR}"/${P}-web.patch
 
-	epatch "${FILESDIR}"/1.2.2-prefix.patch && \
+	epatch "${FILESDIR}"/${PN}-1.2.2-prefix.patch && \
 		eprefixify setup.py
 
 	# Turn off splash screen.  Please do make a project contribution
@@ -58,7 +58,7 @@ src_prepare() {
 		-e "s:\(ext_comp_args=\).*:\1[]:g" \
 		"${S}"/setup.py || die "Failed running sed on setup.py"
 
-	use vmd && epatch "${FILESDIR}"/$(get_version_component_range 1-2)-vmd.patch
+	use vmd && epatch "${FILESDIR}"/${PN}-$(get_version_component_range 1-2)-vmd.patch
 
 	use numpy && \
 		sed \
diff --git a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
index 829d4fad273d..381a14bfce07 100644
--- a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild
@@ -1,6 +1,6 @@
 # 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-1.5.0.1.ebuild,v 1.1 2012/02/13 22:09:19 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.1.ebuild,v 1.2 2012/02/14 08:18:11 jlec Exp $
 
 EAPI=4
 
@@ -10,11 +10,13 @@ RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.*"
 PYTHON_USE_WITH="tk"
 PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
 
-inherit eutils distutils prefix versionator
+inherit distutils eutils fdo-mime prefix versionator
 
-DESCRIPTION="A Python-extensible molecular graphics system."
+DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${PN}-v${PV}.tar.bz2"
+SRC_URI="
+	mirror://sourceforge/project/${PN}/${PN}/${PV}/${PN}-v${PV}.tar.bz2
+	http://dev.gentoo.org/~jlec/distfiles/${PN}.xpm.tar"
 
 LICENSE="PSF-2.2"
 SLOT="0"
@@ -52,10 +54,6 @@ src_prepare() {
 	epatch "${FILESDIR}"/${P}-prefix.patch && \
 		eprefixify setup.py
 
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though. #299020
-	epatch "${FILESDIR}"/${P}-nosplash.patch
-
 	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
 
 	if use numpy; then
@@ -92,7 +90,7 @@ src_install() {
 
 	cat >> "${T}"/pymol <<- EOF
 	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
+	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
 	EOF
 
 	dobin "${T}"/pymol
@@ -104,6 +102,9 @@ src_install() {
 	doins -r examples
 
 	dodoc DEVELOPERS README
+
+	doicon "${WORKDIR}"/${PN}.xpm
+	make_desktop_entry pymol PyMol ${PN}.xpm "Graphics;Science;Chemistry"
 }
 
 pkg_postinst() {
@@ -111,4 +112,11 @@ pkg_postinst() {
 	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
 }