Fixing PYMOL_DATA again per 304259

Package-Manager: portage-2.2_rc62/cvs/Linux i686

4 files changed, 194 insertions, 2 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 29a9fa740110..b5d58281abc3 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.53 2010/02/06 15:26:35 pva Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.54 2010/02/10 11:22:34 jlec Exp $
+
+*pymol-1.2.2-r2 (10 Feb 2010)
+
+  10 Feb 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/1.2.2-data-path.patch, +pymol-1.2.2-r2.ebuild:
+  Fixing PYMOL_DATA again per 304259
 
   06 Feb 2010; Peter Volkov <pva@gentoo.org> pymol-1.2.1.ebuild,
   pymol-1.2.2.ebuild, pymol-1.2.2-r1.ebuild:
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 5012cf57fdc9..269953ab077c 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,6 +1,10 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 1.2.1/nosplash-gentoo.patch 485 RMD160 3b3d85ffe14a253e54c4ff89b210cf35effe7aee SHA1 627affce7ee9763e308cf6dee70b831e09bd829d SHA256 acf8ef1d53719c1b4158b0f49250e8ed7c3aa4c870ef7ce4bdbc8ec97f591e27
 AUX 1.2.1/pymol-1.2.1-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
 AUX 1.2.1/pymol-1.2.1-shaders.patch 442 RMD160 db5ee361cd1e253b9aa012098d08eb7873d95da3 SHA1 881d25514bc744d6f12b5f30bfa1709ed45dba05 SHA256 48042a9baf28c35a55204f646f14eddcf5093e17f518d7de2ffc50cbb7914dda
+AUX 1.2.2-data-path.patch 3361 RMD160 ece520d476cc13a312ba3976902fda9dedf7758d SHA1 3a03308d74372bf8fe62cbe804711bdb58895f8d SHA256 da9dfec59b09b2fd6bad5f0188589a0d04c28296651add308acd35d159f60947
 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
@@ -13,6 +17,14 @@ EBUILD pymol-0.99_rc10.ebuild 2125 RMD160 92cb22b6566abc10a6d5f02d6b45be0316f212
 EBUILD pymol-1.0-r1.ebuild 2114 RMD160 26354ebc9e4bf91327f0631cf415eb08989bdd89 SHA1 1bb01c6daf8a44a11670dc0c12f63bdb08c136c3 SHA256 30356fe8bc8fc8183c2b04ea7179682476c8bda5673b29f04d2107a41fc37d1d
 EBUILD pymol-1.2.1.ebuild 2948 RMD160 e5894b3e057f178dec0ecebf7ae40301ab392239 SHA1 0658797816610b8de962cd7640db3e359f8579c0 SHA256 fe9f60d348ca7b1a4e04cb17235724ee1e614a77eafed3e53c8aeed868a5f296
 EBUILD pymol-1.2.2-r1.ebuild 2402 RMD160 88b63931feec240b644f498c1b82d127fff3f56c SHA1 cc468b3d0486b6a11070d5fd960229e4876e9829 SHA256 0bd3d279c14108686661e2bd25cfec15dfbf332282761409f3a43e6d248a96b6
+EBUILD pymol-1.2.2-r2.ebuild 2391 RMD160 7fd5ccd8f4d504126381695651903d0a280af6fc SHA1 82574dbb7b73c4244d3c05bd6e41f5b7a3316c2e SHA256 563b2f15c8bf0fc640fb4c3e56d9cf1baaac62cee67d5a661c55746980e4f929
 EBUILD pymol-1.2.2.ebuild 2951 RMD160 290195269d3bf42d8a2b0e3c8905dbe64bfcdbbf SHA1 d1cadff92e18f1d74d11da304d0672ecd1774c0b SHA256 22afa35303d15e4e82465204d3fab42fb420ec163e37a2f20287e143cdb1e478
-MISC ChangeLog 11510 RMD160 01b24a52239394aa227d86268321a05db8f20d22 SHA1 c5008b59898aa9042f43693b7e18192c3ad58c73 SHA256 97030cf43eff4f71e65f2f2d850d399392278656d5097c13707af3ea945bc9fc
+MISC ChangeLog 11693 RMD160 166ed35cd8d6dd9fc5e81c11934c2a6a64a4d0a7 SHA1 9b561b9a6edd3f6ca6b256c46e600c44fd376419 SHA256 287a223fa9ebc90c38b5098cf4581676a1a4776720bdb3de8938cafddf6e9cd0
 MISC metadata.xml 494 RMD160 0aec5d84b0aaa7666af93962827613e9b4c7487b SHA1 84282f439939e0fbb2f7ec55c128a92442aa016e SHA256 22ac79b0f91926fe2e275ad46ec31994a0523fd196b3d82e8279d0f3d4250300
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAktylv8ACgkQgAnW8HDreRYKRgCcDWQZdoXK2ooUMbfl/0xKdima
+a6UAn0XUfy0Acpakfl+eSx/MkfNjda2f
+=7Yuy
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pymol/files/1.2.2-data-path.patch b/sci-chemistry/pymol/files/1.2.2-data-path.patch
new file mode 100644
index 000000000000..cf1bf59af0c6
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.2.2-data-path.patch
@@ -0,0 +1,75 @@
+Index: modules/pymol/importing.py
+===================================================================
+--- modules/pymol/importing.py	(revision 3889)
++++ modules/pymol/importing.py	(working copy)
+@@ -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',
+                    'greyscale': 'greyscale' }
+Index: modules/pymol/wizard/mutagenesis.py
+===================================================================
+--- modules/pymol/wizard/mutagenesis.py	(revision 3889)
++++ modules/pymol/wizard/mutagenesis.py	(working copy)
+@@ -53,8 +53,8 @@
+ 
+         self.dep = default_dep
+ 
+-        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
++        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
++                                           "/chempy/sidechains/sc_bb_ind.pkl")
+         self.load_library()
+         self.status = 0 # 0 no selection, 1 mutagenizing
+         self.bump_check = 1
+@@ -218,8 +218,8 @@
+     def load_library(self):
+         if self.dep == 'dep':
+             if not hasattr(self,'dep_library'):
+-                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
++                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
++                                           "/chempy/sidechains/sc_bb_dep.pkl")
+             
+     def set_mode(self,mode):
+         cmd=self.cmd
+Index: modules/pymol/commanding.py
+===================================================================
+--- modules/pymol/commanding.py	(revision 3889)
++++ modules/pymol/commanding.py	(working copy)
+@@ -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:
+Index: modules/chempy/tinker/__init__.py
+===================================================================
+--- modules/chempy/tinker/__init__.py	(revision 3889)
++++ modules/chempy/tinker/__init__.py	(working copy)
+@@ -145,9 +145,9 @@
+     bin_path = ''
+     params_path = ''
+ 
+-if os.environ.has_key('PYMOL_PATH'):
+-    pymol_path = os.environ['PYMOL_PATH']
+-    test_path = pymol_path + '/data/chempy/tinker/'
++if os.environ.has_key('PYMOL_DATA'):
++    pymol_path = os.environ['PYMOL_DATA']
++    test_path = pymol_path + '/chempy/tinker/'
+     if os.path.exists(test_path):
+         params_path = test_path
+ 
diff --git a/sci-chemistry/pymol/pymol-1.2.2-r2.ebuild b/sci-chemistry/pymol/pymol-1.2.2-r2.ebuild
new file mode 100644
index 000000000000..d62ccb3dd719
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.2.2-r2.ebuild
@@ -0,0 +1,99 @@
+# 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-1.2.2-r2.ebuild,v 1.1 2010/02/10 11:22:34 jlec Exp $
+
+EAPI="2"
+
+inherit eutils distutils
+
+PYTHON_MODNAME="chempy pmg_tk pymol"
+REV="3859"
+
+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} -> ${P}.tar.gz"
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="apbs numpy shaders vmd"
+
+DEPEND=">=dev-lang/python-2.4[tk]
+		dev-python/numpy
+		dev-python/pmw
+		media-libs/freetype:2
+		media-libs/libpng
+		media-video/mpeg-tools
+		sys-libs/zlib
+		virtual/glut
+		apbs? (
+			dev-libs/maloc
+			sci-chemistry/apbs
+			sci-chemistry/pdb2pqr
+			sci-chemistry/pymol-apbs-plugin
+		)"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+pkg_setup(){
+	python_version
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-data-path.patch \
+		|| die "Failed to apply data-path.patch"
+
+	# 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}"/${P}-shaders.patch
+
+	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
+
+	use numpy && \
+		sed \
+			-e '/PYMOL_NUMPY/s:^#::g' \
+			-i setup.py
+}
+
+src_configure() {
+	:
+}
+
+src_install() {
+	distutils_src_install
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH=$(python_get_sitedir)/${PN}
+		PYMOL_DATA="/usr/share/pymol/data"
+		PYMOL_SCRIPTS="/usr/share/pymol/scripts"
+	EOF
+
+	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."
+
+	rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
+}