pymol cleanup to move to the tree as requested by fauli in bug 269119

13 files changed, 24 insertions, 176 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 86657f0fb..ba0467f7c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,23 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*pymol-1.2.1 (31 Jul 2009)
+*pymol-1.2.0 (31 Jul 2009)
+
+  31 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -pymol-1.2_rc0.ebuild, -pymol-1.2_rc1.ebuild, 
+  -files/1.2_beta8-nosplash-gentoo.patch, -pymol-1.2_beta8.ebuild, 
+  -pymol-1.2_rc0.ebuild, -pymol-1.2_rc1.ebuild,
+  -files/pymol-1.2_beta8-data-path.patch,
+  +files/pymol-1.2.0-data-path.patch, -files/pymol-1.2_beta8-shaders.patch,
+  -files/pymol-1.2_rc1-data-path.patch, +pymol-1.2.0.ebuild,
+  +files/pymol-1.2.0-shaders.patch, -files/pymol-1.2_rc0-data-path.patch,
+  -files/pymol-1.2_rc1-shaders.patch, +pymol-1.2.1.ebuild,
+  +files/pymol-1.2.1-data-path.patch, -files/pymol-1.2_rc0-shaders.patch,
+  +files/pymol-1.2.1-shaders.patch, -files/apbs-070604-r3550.patch.bz2:
+  mv to correct versions
+  cleanup old uneeded versions
+
   17 Jul 2009; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
   Fix up patch to apply to rc1
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 90a67f69a..8d95cd459 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,18 +1,13 @@
-AUX 1.2_beta8-nosplash-gentoo.patch 466 RMD160 2e6afc0b62abc7e8a007c12b887238ece57d323e SHA1 977f2acef4e1a7c30da9dd0510b926ccf56f08c5 SHA256 59fd77f8c7e60e13bb1347c865432574d238a9ce0c705517e291df5880a11768
-AUX apbs-070604-r3550.patch.bz2 20283 RMD160 e7fc42934dea043000ba81e4f27b99b6062e4b12 SHA1 1708de792a53ac4819dfe4ec11cc9ee54b3d5fb9 SHA256 ad8ce064ee2ce3310f862b60b8f762ef713f9952fef0ebd329204a2d25b42db5
 AUX nosplash-gentoo.patch 485 RMD160 3b3d85ffe14a253e54c4ff89b210cf35effe7aee SHA1 627affce7ee9763e308cf6dee70b831e09bd829d SHA256 acf8ef1d53719c1b4158b0f49250e8ed7c3aa4c870ef7ce4bdbc8ec97f591e27
-AUX pymol-1.2_beta8-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
-AUX pymol-1.2_beta8-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
-AUX pymol-1.2_rc0-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
-AUX pymol-1.2_rc0-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
-AUX pymol-1.2_rc1-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
-AUX pymol-1.2_rc1-shaders.patch 442 RMD160 db5ee361cd1e253b9aa012098d08eb7873d95da3 SHA1 881d25514bc744d6f12b5f30bfa1709ed45dba05 SHA256 48042a9baf28c35a55204f646f14eddcf5093e17f518d7de2ffc50cbb7914dda
+AUX pymol-1.2.0-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
+AUX pymol-1.2.0-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
+AUX pymol-1.2.1-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
+AUX pymol-1.2.1-shaders.patch 442 RMD160 db5ee361cd1e253b9aa012098d08eb7873d95da3 SHA1 881d25514bc744d6f12b5f30bfa1709ed45dba05 SHA256 48042a9baf28c35a55204f646f14eddcf5093e17f518d7de2ffc50cbb7914dda
 AUX pymol-9999-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
 AUX pymol-9999-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
 DIST apbs_tools.py.090618.bz2 21329 RMD160 80baed718524dfbaff2f0a3b7263fc75c55bf1d9 SHA1 e2c69bb150679f137ba7ff2cfcd0fe2da000612b SHA256 604803ed58f1827b76cbf5f3b58c35859d31c68d51481da4b37e08a1c0656d6e
-EBUILD pymol-1.2_beta8.ebuild 2707 RMD160 8329ceb3b22bbebe66e62d6bb5f78e39edd9ce22 SHA1 062f9887da79aa83325463ae350e290a275dfef4 SHA256 efa34926bd8545b707728c05184b1a5cf8c2bbd2bcd796439577e5e996fe7c4a
-EBUILD pymol-1.2_rc0.ebuild 2726 RMD160 e4fbf3696379427d95b88e1631748c0a7ef2deff SHA1 d79acbbc0a5a8602330c3735cdc7311ff3a94f77 SHA256 4a97a8c7da7056d19a9a1ab8ec58b5311b6868d5267c793fc9e6b782d6f9f5e0
-EBUILD pymol-1.2_rc1.ebuild 2726 RMD160 cc3392e76e4ba82a886e1bf2925e4cabdc7a4a63 SHA1 afada6e399c2d405fc9741d9dcb7abe1ec04bf0d SHA256 741949fedda03f738b248fe34f504b65cd59de734a660d5b2c6b1bdf8902607d
+EBUILD pymol-1.2.0.ebuild 2726 RMD160 e4fbf3696379427d95b88e1631748c0a7ef2deff SHA1 d79acbbc0a5a8602330c3735cdc7311ff3a94f77 SHA256 4a97a8c7da7056d19a9a1ab8ec58b5311b6868d5267c793fc9e6b782d6f9f5e0
+EBUILD pymol-1.2.1.ebuild 2726 RMD160 cc3392e76e4ba82a886e1bf2925e4cabdc7a4a63 SHA1 afada6e399c2d405fc9741d9dcb7abe1ec04bf0d SHA256 741949fedda03f738b248fe34f504b65cd59de734a660d5b2c6b1bdf8902607d
 EBUILD pymol-9999.ebuild 2981 RMD160 1d609dd649eadf68293340adb19c3b05b206e5f5 SHA1 b161cc3344f98660cb18e7a97621cf311c297d5f SHA256 3b315033850b04249d94a211b0c5105fcd76f1b938688a44f2e9a274d808f3f9
-MISC ChangeLog 4664 RMD160 28887c1bb0f6c7f0943072c752209081b3352117 SHA1 f7bb690593a580b11d2c7dfff6284cf1838a4623 SHA256 d05dde7827ea9786b30f414b2b7c4d6a422cb737794b55d92182a43ab6e5c330
+MISC ChangeLog 5456 RMD160 15cfbbbb68320ea9d3c173e2ae2867c387cbd15b SHA1 48139fc4a56532234beb57d4f8eac1be2afc40c0 SHA256 d2cb7186c17f1d035358bc8a182d8c78ef885eaf74c28d07688659a6451ac88b
 MISC metadata.xml 412 RMD160 9c33c90cdb3bc60af7dbee004b7f1cffd1b43aa6 SHA1 efd4a32d739fe54f0f464edc0843c81e9fb23437 SHA256 ee0056aa8c9e40b6da007fa8c895e15c17cb25004212b91d48dad03f6123483c
diff --git a/sci-chemistry/pymol/files/1.2_beta8-nosplash-gentoo.patch b/sci-chemistry/pymol/files/1.2_beta8-nosplash-gentoo.patch
deleted file mode 100644
index 18f228524..000000000
--- a/sci-chemistry/pymol/files/1.2_beta8-nosplash-gentoo.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- modules/pymol/invocation.py	2009-06-30 14:27:39.000000000 +0200
-+++ modules/pymol/invocation.py.new	2009-06-30 14:30:01.000000000 +0200
-@@ -372,6 +372,4 @@
-         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:
--            options.deferred.insert(0,"_do__ cmd.splash(1)")
-         
diff --git a/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2 b/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2
deleted file mode 100644
index 396a4d26d..000000000
--- a/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2
+++ /dev/null
diff --git a/sci-chemistry/pymol/files/pymol-1.2_beta8-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.0-data-path.patch
index 86c3fe1f1..86c3fe1f1 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_beta8-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.0-data-path.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_beta8-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2.0-shaders.patch
index 7f4a24f48..7f4a24f48 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_beta8-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.0-shaders.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc0-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.1-data-path.patch
index 86c3fe1f1..86c3fe1f1 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_rc0-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.1-data-path.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2.1-shaders.patch
index 06f756823..06f756823 100644
--- a/sci-chemistry/pymol/files/pymol-1.2_rc1-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-1.2.1-shaders.patch
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc0-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2_rc0-shaders.patch
deleted file mode 100644
index 7f4a24f48..000000000
--- a/sci-chemistry/pymol/files/pymol-1.2_rc0-shaders.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff -uarN pymol-9999.orig/setup.py pymol-9999/setup.py
---- pymol-9999.orig/setup.py	2008-06-18 11:47:58.000000000 +0200
-+++ pymol-9999/setup.py	2008-06-18 11:48:52.000000000 +0200
-@@ -143,6 +143,7 @@
-     def_macros=[("_PYMOL_MODULE",None),
-                     ("_PYMOL_INLINE",None),
-                     ("_PYMOL_FREETYPE",None),
-+                    ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                        ("_PYMOL_NUMPY",None),
- # VMD plugin support                    
diff --git a/sci-chemistry/pymol/files/pymol-1.2_rc1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2_rc1-data-path.patch
deleted file mode 100644
index 86c3fe1f1..000000000
--- a/sci-chemistry/pymol/files/pymol-1.2_rc1-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/pymol-1.2_rc0.ebuild b/sci-chemistry/pymol/pymol-1.2.0.ebuild
index 5b872e771..5b872e771 100644
--- a/sci-chemistry/pymol/pymol-1.2_rc0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.2.0.ebuild
diff --git a/sci-chemistry/pymol/pymol-1.2_rc1.ebuild b/sci-chemistry/pymol/pymol-1.2.1.ebuild
index 60eb583ee..60eb583ee 100644
--- a/sci-chemistry/pymol/pymol-1.2_rc1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.2.1.ebuild
diff --git a/sci-chemistry/pymol/pymol-1.2_beta8.ebuild b/sci-chemistry/pymol/pymol-1.2_beta8.ebuild
deleted file mode 100644
index 1ff55eb49..000000000
--- a/sci-chemistry/pymol/pymol-1.2_beta8.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-PYTHON_MODNAME="chempy pmg_tk pymol"
-APBS_PATCH="090618"
-REV="3761"
-
-inherit distutils subversion
-
-ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol@${REV}"
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="apbs? ( http://dev.gentooexperimental.org/~jlec/distfiles/apbs_tools.py.${APBS_PATCH}.bz2 )"
-
-LICENSE="PSF-2.2"
-IUSE="apbs shaders"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/pmw
-		dev-python/numpy
-		>=dev-lang/python-2.4[tk]
-		media-libs/libpng
-		sys-libs/zlib
-		virtual/glut
-		apbs? ( dev-libs/maloc
-				sci-chemistry/apbs
-				sci-chemistry/pdb2pqr
-		)"
-DEPEND="${RDEPEND}"
-
-pkg_setup(){
-	python_version
-}
-
-src_unpack() {
-	use apbs && unpack ${A}
-	subversion_src_unpack
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-data-path.patch || die
-
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though.
-	[[ -n ${WANT_SPLASH} ]] || epatch "${FILESDIR}"/${PV}-nosplash-gentoo.patch
-
-	# Respect CFLAGS
-	sed -i \
-		-e "s:\(ext_comp_args=\).*:\1[]:g" \
-		"${S}"/setup.py
-
-	use shaders && epatch "${FILESDIR}"/${P}-shaders.patch
-
-	if use apbs; then
-		cp -f "${WORKDIR}"/apbs_tools.py.${APBS_PATCH} modules/pmg_tk/startup/apbs_tools.py || die
-		sed "s:LIBANDPYTHON:$(python_get_libdir):g" \
-			-i modules/pmg_tk/startup/apbs_tools.py || die
-	fi
-}
-
-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 >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH=$(python_get_sitedir)/${PN}
-		PYMOL_DATA="/usr/share/pymol/data"
-		PYMOL_SCRIPTS="/usr/share/pymol/scripts"
-	EOF
-
-	use apbs && \
-	echo "APBS_PSIZE=$(python_get_sitedir)/pdb2pqr/src/psize.py" >> "${T}"/20pymol
-
-	doenvd "${T}"/20pymol || die "Failed to install env.d file."
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	${python} -O \${PYMOL_PATH}/__init__.py \$*
-	EOF
-
-	dobin "${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."
-
-	if ! use apbs; then
-		rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
-	fi
-}
-
-pkg_postinst(){
-	distutils_pkg_postinst
-
-	# The apbs ebuild was just corrected and not bumped #213616
-	if use apbs; then
-		[ -e /usr/share/apbs-0.5* ] && \
-		ewarn "You need to reemerge sci-chemistry/apbs!"
-	fi
-}