pymol: live version is in the science overlay now

8 files changed, 0 insertions, 235 deletions

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
deleted file mode 100644
index 9d6b93e..0000000
--- a/sci-chemistry/pymol/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX apbs-070604.patch.bz2 20034 RMD160 0244e60a99143fbfd43e849910da798d14259cf5 SHA1 0b4c86a7cd34282efa580866c3f80809a27e3348 SHA256 8d694a2fe726fc1176228beec42bbde9df1bced0148cbef2b2b853995cf0376f
-AUX nosplash-gentoo.patch 467 RMD160 a6be474aab95e8c8ffd37f509fe3d40cf4db23f7 SHA1 14862bab327fea0cdc8198070f01827d6f832899 SHA256 c4b5384485242165aa517fe2caf83241201c2354d5c964554f6d82c51ba7fba3
-AUX pymol-1.1-r1-data-path.patch 2584 RMD160 c5fdd7884241a493578be5a2b658ac0cd0bff000 SHA1 1e4cd368ad08b87627ef465fad4ca96dcfbef00b SHA256 39e06459105969e0156bfe71f61bdccd3da4c8d7f2ba6e783aa34e63dc62b0a7
-AUX pymol-1.1-r1-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
-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
-EBUILD pymol-9999.ebuild 3080 RMD160 d3f1e4b79da10cc654ded67145bbde5b485f5b26 SHA1 94135388aadc09523435bc104dca0c16544425e7 SHA256 8c8b5b36a184624e148008ba7e931202e133194b08e6e22cc3b7e8e6aebc6763
diff --git a/sci-chemistry/pymol/files/apbs-070604.patch.bz2 b/sci-chemistry/pymol/files/apbs-070604.patch.bz2
deleted file mode 100644
index b5095ec..0000000
--- a/sci-chemistry/pymol/files/apbs-070604.patch.bz2
+++ /dev/null
diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
deleted file mode 100644
index 0ef65b1..0000000
--- a/sci-chemistry/pymol/files/nosplash-gentoo.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- modules/pymol/invocation.py.orig	2008-06-26 20:55:25.000000000 +0200
-+++ modules/pymol/invocation.py	2008-06-26 20:56:06.000000000 +0200
-@@ -373,6 +373,4 @@
-         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/pymol-1.1-r1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch
deleted file mode 100644
index 329b682..0000000
--- a/sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch
+++ /dev/null
@@ -1,51 +0,0 @@
-diff -urN pymol-9999.orig/modules/pymol/commanding.py pymol-9999/modules/pymol/commanding.py
---- pymol-9999.orig/modules/pymol/commanding.py	2008-01-11 13:23:32.000000000 +0100
-+++ pymol-9999/modules/pymol/commanding.py	2008-01-11 13:22:57.000000000 +0100
-@@ -198,11 +198,11 @@
-                 _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 -urN pymol-9999.orig/modules/pymol/fitting.py pymol-9999/modules/pymol/fitting.py
-#--- pymol-9999.orig/modules/pymol/fitting.py	2008-01-11 13:23:32.000000000 +0100
-#+++ pymol-9999/modules/pymol/fitting.py	2008-01-11 13:23:00.000000000 +0100
-#@@ -68,7 +68,7 @@
-#         if string.lower(matrix)=='none':
-#             matrix=''
-#         if len(matrix):
-#-            mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
-#+            mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
-#         else:
-#             mfile = ''        
-#         # delete existing alignment object (if asked to reset it)
-#@@ -135,7 +135,7 @@
-#         if string.lower(matrix)=='none':
-#             matrix=''
-#         if len(matrix):
-#-            mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
-#+            mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
-#         else:
-#             mfile = ''
-#         if object==None: object=''
-diff -urN pymol-9999.orig/modules/pymol/importing.py pymol-9999/modules/pymol/importing.py
---- pymol-9999.orig/modules/pymol/importing.py	2008-01-11 13:23:32.000000000 +0100
-+++ pymol-9999/modules/pymol/importing.py	2008-01-11 13:23:02.000000000 +0100
-@@ -171,7 +171,7 @@
-         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/pymol-1.1-r1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch
deleted file mode 100644
index 7f4a24f..0000000
--- a/sci-chemistry/pymol/files/pymol-1.1-r1-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-9999-data-path.patch b/sci-chemistry/pymol/files/pymol-9999-data-path.patch
deleted file mode 100644
index 86c3fe1..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-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/pymol-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
deleted file mode 100644
index 7f4a24f..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-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/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
deleted file mode 100644
index fcefe73..0000000
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ /dev/null
@@ -1,116 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-NEED_PYTHON=2.4
-PYTHON_MODNAME="chempy pmg_tk pymol"
-
-inherit distutils eutils multilib subversion
-
-ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-
-LICENSE="PSF-2.2"
-IUSE="apbs shaders"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/pmw
-	dev-python/numeric
-	dev-lang/tk
-	media-libs/libpng
-	sys-libs/zlib
-	virtual/glut
-	apbs? ( dev-libs/maloc
-		sci-chemistry/apbs
-		sci-chemistry/pdb2pqr
-	)"
-DEPEND="${RDEPEND}"
-
-pkg_setup() {
-	if ! built_with_use dev-lang/python tk; then
-		eerror "Please reemerge dev-lang/python with 'tk' support or pymol will"
-		eerror "not work. In order to fix this, execute the following:"
-		eerror "echo \"dev-lang/python tk\" >> /etc/portage/package.use"
-		eerror "and reemerge dev-lang/python before emerging pymol."
-		die "requires dev-lang/python with use-flag 'tk'!!"
-	fi
-}
-
-src_unpack() {
-	subversion_src_unpack
-
-	python_version
-
-	epatch "${FILESDIR}"/${PF}-data-path.patch
-
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though.
-	[[ -z "$WANT_SPLASH" ]] && epatch "${FILESDIR}"/nosplash-gentoo.patch
-
-	# Respect CFLAGS
-	sed -i \
-		-e "s:\(ext_comp_args=\).*:\1[]:g" \
-		"${S}"/setup.py
-
-	if use shaders; then
-		epatch "${FILESDIR}"/${PF}-shaders.patch
-	fi
-
-	if use apbs; then
-#		epatch "${FILESDIR}"/apbs-070604.patch.bz2
-		sed "s:LIBANDPYTHON:$(get_libdir)/python${PYVER}:g" \
-			-i modules/pmg_tk/startup/apbs_tools.py || die
-	fi
-}
-
-src_install() {
-	distutils_src_install
-	cd "${S}"
-
-	#The following three lines probably do not do their jobs and should be
-	#changed
-	PYTHONPATH="${D}/usr/$(get_libdir)/python${PYVER}/site-packages" ${python} setup2.py
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-	PYMOL_PATH=/usr/$(get_libdir)/python${PYVER}/site-packages/pymol
-	PYMOL_DATA="/usr/share/pymol/data"
-	PYMOL_SCRIPTS="/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol || die "Failed to install env.d file."
-
-	# Make our own wrapper
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	${python} -O \${PYMOL_PATH}/__init__.py \$*
-	EOF
-
-	if ! use apbs; then
-		rm "${D}"/usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup/apbs_tools.py
-	fi
-
-	exeinto /usr/bin
-	doexe "${T}"/pymol || die "Failed to install wrapper."
-	dodoc DEVELOPERS || die "Failed to install docs."
-
-	mv examples "${D}"/usr/share/doc/${PF}/ || die "Failed moving docs."
-
-	dodir /usr/share/pymol
-	mv test "${D}"/usr/share/pymol/ || die "Failed moving test files."
-	mv data "${D}"/usr/share/pymol/ || die "Failed moving data files."
-	mv scripts "${D}"/usr/share/pymol/ || die "Failed moving scripts."
-}
-
-pkg_postinst() {
-	distutils_pkg_postinst
-
-	if use apbs; then
-		[[ -e /usr/share/apbs-0.5* ]] && \
-		ewarn "You need to reemerge sci-chemistry/apbs!"
-	fi
-}