Version bump, thanks to jschmitz and hodak for the kick in the pants :)

Package-Manager: portage-2.2_rc8/cvs/Linux 2.6.26-gentoo-r1 x86_64

9 files changed, 212 insertions, 7 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 962133967f93..ab96922e994c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/pymol
-# Copyright 2002-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.36 2007/08/02 09:08:02 je_fro Exp $
+# Copyright 2002-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.37 2008/08/17 03:06:59 je_fro Exp $
+
+*pymol-1.1-r1 (13 Aug 2008)
+
+  13 Aug 2008; Jeff Gardner <je_fro@gentoo.org>
+  +files/1.1/pymol-1.1-r1-shaders.patch, +files/1.1/nosplash-gentoo.patch,
+  +files/1.1/pymol-1.1-r1-data-path.patch, +files/1.1/apbs-070604.patch.bz2,
+  +pymol-1.1-r1.ebuild:
+  Version bump, thanks to jschmitz and hodak for the kick in the pants :)
 
   02 Aug 2007; Jeff Gardner <je_fro@gentoo.org> pymol-0.99_rc10.ebuild:
   Fix ESVN_REPO_URI wrt bug #187462. Thanks to Michael Mysinger.
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 9ab34ec66c82..c85d79b62ea4 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,7 +1,12 @@
+AUX 1.1/apbs-070604.patch.bz2 20129 RMD160 9de523bed2f5560132bd1638b7b032be4580c1b8 SHA1 b8c7dae81fded36f462328932d2ecaae43e83391 SHA256 4a838c9805767de872e772eb71aedc343d1ae0d50e8d080b13cc72d0f00b65d3
+AUX 1.1/nosplash-gentoo.patch 467 RMD160 a6be474aab95e8c8ffd37f509fe3d40cf4db23f7 SHA1 14862bab327fea0cdc8198070f01827d6f832899 SHA256 c4b5384485242165aa517fe2caf83241201c2354d5c964554f6d82c51ba7fba3
+AUX 1.1/pymol-1.1-r1-data-path.patch 2584 RMD160 c5fdd7884241a493578be5a2b658ac0cd0bff000 SHA1 1e4cd368ad08b87627ef465fad4ca96dcfbef00b SHA256 39e06459105969e0156bfe71f61bdccd3da4c8d7f2ba6e783aa34e63dc62b0a7
+AUX 1.1/pymol-1.1-r1-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
 AUX nosplash-gentoo.patch 332 RMD160 2280fbe9daba8a0d3ca81a3aacfcc55bd06fc7d3 SHA1 275a325f7a9bb076bea72897fd6dd5ed1b014390 SHA256 5e0761591eeea90bcaa06a72c210a80ba46f2542ff985f8dd893af112254a890
 AUX pymol-0.99_rc10-data-path.patch 2969 RMD160 608e0e936fccf0860f6b5269e6739c839fcd32ea SHA1 7a3585d14431b7840eff8f6ee0a5d8324049ff77 SHA256 10c97c3d4d2f620a2884a812a6997f2cf8472f2e0c589c2630a4d0bcf67656de
 AUX pymol-1.0-r1-data-path.patch 3521 RMD160 bbd8722a1f52944f122caa64642db5dc2609a208 SHA1 735871b06d8f874334ef51fe9054ae92a7fbe523 SHA256 ba0c036b1f01338b42f9e31a0252be59292726289e330f4c33cf52ee48ea9172
 EBUILD pymol-0.99_rc10.ebuild 2137 RMD160 149cd67ab02da9fec25b619bba63299a85f6e7e7 SHA1 5c4f2f09a9f09ed5bc294d49845d7f72317e2690 SHA256 8290ac85a81b9ecf0be3ee6ee6709d553466878cd90e099f03e45def93a5de76
-EBUILD pymol-1.0-r1.ebuild 2093 RMD160 c70a982b131a7e6e6bab16764f241e1098f41d1c SHA1 9a661ca1ed87a6d6d5811cf19bb65e4a83a479c3 SHA256 a3727078af51c359426ea4e0619a975961670234340592e16ba3099e422aad62
-MISC ChangeLog 8285 RMD160 00de4ba970526e409c250741c2c3f99591005477 SHA1 03166b5dd6d1ef24755c9de2d1265f60a2ddad10 SHA256 a84169c38b33f5b951e8aa92d3ce2108ab81993b6627f8b4d710ed2bbbb27ed1
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+EBUILD pymol-1.0-r1.ebuild 2093 RMD160 dcc9c7a614f272f01020974e59915064b6d932fc SHA1 31fc6128dd276b73550e8d3c8f31c63531badc99 SHA256 0c29bcbf628201e8c384eb7fdac33a4e7432c966fb0b10e7358097691e333349
+EBUILD pymol-1.1-r1.ebuild 3241 RMD160 27798e58dcf4d331e3ff56470e5427474ab42b03 SHA1 63bdcdee9b8cd6f4728f1a34c2b6324d67ed3575 SHA256 006d77be60f511387a652cd9ffdf0af56435f0372c1ac65bae7726009d08da0e
+MISC ChangeLog 8613 RMD160 d9d3b7e28268e337fa1481ba6a241e36d5edf8d9 SHA1 eea96ffe740f262dea5d2f086e64e9fd4b44fe5a SHA256 e6e994004a6e56ff77b31d735fe2a8e11fae78e5b754d34cda481b58bae06ac3
+MISC metadata.xml 327 RMD160 d44a69d538eb2125e431b5690abeb3a2fddc425d SHA1 d65dff362b78fc32fa382ff4644e98149da0be5a SHA256 0ec76fa228418dc19e62626f28c73ce3341bce42208ea98704226f5f12cccc0c
diff --git a/sci-chemistry/pymol/files/1.1/apbs-070604.patch.bz2 b/sci-chemistry/pymol/files/1.1/apbs-070604.patch.bz2
new file mode 100644
index 000000000000..1fdda203058a
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.1/apbs-070604.patch.bz2
diff --git a/sci-chemistry/pymol/files/1.1/nosplash-gentoo.patch b/sci-chemistry/pymol/files/1.1/nosplash-gentoo.patch
new file mode 100644
index 000000000000..0ef65b1d80fd
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.1/nosplash-gentoo.patch
@@ -0,0 +1,9 @@
+--- 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/1.1/pymol-1.1-r1-data-path.patch b/sci-chemistry/pymol/files/1.1/pymol-1.1-r1-data-path.patch
new file mode 100644
index 000000000000..329b68292877
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.1/pymol-1.1-r1-data-path.patch
@@ -0,0 +1,51 @@
+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/1.1/pymol-1.1-r1-shaders.patch b/sci-chemistry/pymol/files/1.1/pymol-1.1-r1-shaders.patch
new file mode 100644
index 000000000000..7f4a24f48243
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.1/pymol-1.1-r1-shaders.patch
@@ -0,0 +1,11 @@
+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/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 9ac9ffdb3a41..3af1ef48ed3f 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -2,4 +2,8 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 <herd>sci-chemistry</herd>
+<use>
+		<flag name="apbs">Build the apbs plugin tool.</flag>
+		<flag name="shaders">Build with Shaders support - good for high-end 3D video cards.</flag>
+</use>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-1.0-r1.ebuild b/sci-chemistry/pymol/pymol-1.0-r1.ebuild
index a9e5df512230..948171be7872 100644
--- a/sci-chemistry/pymol/pymol-1.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.0-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2007 Gentoo Foundation
+# Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.0-r1.ebuild,v 1.2 2007/07/11 19:26:37 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.0-r1.ebuild,v 1.3 2008/08/17 03:06:59 je_fro Exp $
 
 inherit distutils eutils multilib subversion
 
diff --git a/sci-chemistry/pymol/pymol-1.1-r1.ebuild b/sci-chemistry/pymol/pymol-1.1-r1.ebuild
new file mode 100644
index 000000000000..f8a36b640b81
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.1-r1.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.1-r1.ebuild,v 1.1 2008/08/17 03:06:59 je_fro Exp $
+
+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"
+ESVN_UPDATE_CMD="svn -r 3395 update"
+
+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}"/${PV}/${PF}-data-path.patch
+
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though.
+	[[ -z "$WANT_SPLASH" ]] && epatch "${FILESDIR}"/${PV}/nosplash-gentoo.patch
+
+	# Respect CFLAGS
+	sed -i \
+		-e "s:\(ext_comp_args=\).*:\1[]:g" \
+		"${S}"/setup.py
+
+	if use shaders; then
+		epatch "${FILESDIR}"/${PV}/${PF}-shaders.patch
+	fi
+
+	if use apbs; then
+		epatch "${FILESDIR}"/${PV}/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
+}