New version, works with python 2.6, closes bug #269119. Many thanks to Justin Lecher for doing the work, and fauli for a kick in the pants :)

Package-Manager: portage-2.1.6.13/cvs/Linux x86_64

7 files changed, 183 insertions, 17 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 914f2597e868..b637d10b40dd 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.42 2009/05/06 21:06:39 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.43 2009/08/02 14:58:31 je_fro Exp $
+
+*pymol-1.2.1 (02 Aug 2009)
+
+  02 Aug 2009; Jeff Gardner <je_fro@gentoo.org> +pymol-1.2.1.ebuild,
+  +files/1.2.1/pymol-1.2.1-data-path.patch,
+  +files/1.2.1/pymol-1.2.1-shaders.patch:
+  New version, works with python 2.6, closes bug #269119. Many thanks to
+  Justin Lecher for doing the work, and fauli for a kick in the pants :)
 
   06 May 2009; Markus Meier <maekke@gentoo.org> pymol-1.1-r2.ebuild:
   amd64/x86 stable, bug #250903
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index f82d2bab77d3..49d6e16fb331 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,22 +1,16 @@
------BEGIN PGP SIGNED MESSAGE-----
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 AUX 1.1/apbs-070604.patch.bz2 20149 RMD160 886070ebd93b9ac0738c978b3a5fee816916bca9 SHA1 2ef35c7d6662d88a8c2468f9851827a7f3150380 SHA256 b3fc123c4810fe95c1b6ab93ac2dd45bdf6cc48caccd4f26ec2a825fd78cd440
 AUX 1.1/nosplash-gentoo.patch 467 RMD160 a6be474aab95e8c8ffd37f509fe3d40cf4db23f7 SHA1 14862bab327fea0cdc8198070f01827d6f832899 SHA256 c4b5384485242165aa517fe2caf83241201c2354d5c964554f6d82c51ba7fba3
 AUX 1.1/pymol-1.1-r2-data-path.patch 2584 RMD160 c5fdd7884241a493578be5a2b658ac0cd0bff000 SHA1 1e4cd368ad08b87627ef465fad4ca96dcfbef00b SHA256 39e06459105969e0156bfe71f61bdccd3da4c8d7f2ba6e783aa34e63dc62b0a7
 AUX 1.1/pymol-1.1-r2-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
+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 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 2106 RMD160 1912d6b28ecc19ac5837fd985e029e025a526a80 SHA1 26fd3cf04d055dbce8a21534682452970389c0a0 SHA256 c931fda5e8c02cd91317b24806604d5d280b76c9c781f83d2f81816c0b0be8ef
-EBUILD pymol-1.0-r1.ebuild 2093 RMD160 dcc9c7a614f272f01020974e59915064b6d932fc SHA1 31fc6128dd276b73550e8d3c8f31c63531badc99 SHA256 0c29bcbf628201e8c384eb7fdac33a4e7432c966fb0b10e7358097691e333349
+DIST apbs_tools.py.090618.bz2 21329 RMD160 80baed718524dfbaff2f0a3b7263fc75c55bf1d9 SHA1 e2c69bb150679f137ba7ff2cfcd0fe2da000612b SHA256 604803ed58f1827b76cbf5f3b58c35859d31c68d51481da4b37e08a1c0656d6e
+EBUILD pymol-0.99_rc10.ebuild 2125 RMD160 92cb22b6566abc10a6d5f02d6b45be0316f2126d SHA1 4dfd6793fd7b1ee3bd90b12e0ed9c1ded007cb03 SHA256 3a9eb60ad0fff94a55d8614f5ade15225298a05d31efb4de0e1f0aa092d94b24
+EBUILD pymol-1.0-r1.ebuild 2114 RMD160 26354ebc9e4bf91327f0631cf415eb08989bdd89 SHA1 1bb01c6daf8a44a11670dc0c12f63bdb08c136c3 SHA256 30356fe8bc8fc8183c2b04ea7179682476c8bda5673b29f04d2107a41fc37d1d
 EBUILD pymol-1.1-r2.ebuild 3228 RMD160 043fca3d53bad75d9342f2a2fe621cc8b2717a5e SHA1 d4f55783362a9b02e35e1ce5bfe8aeb7f017086f SHA256 af621fe505490733ddbdf5bfd4c97fb69ef6c95bdefd7daa0c779d6421460449
-MISC ChangeLog 9247 RMD160 047fc231090928b79c043a29567fb8b6f46b727f SHA1 8d57ab558f7155412cc876864deb4892007583c5 SHA256 7584cd90e07ebc2a49c511e5caf4e2f637728b011d2f5e2d953f9f8ad45201c6
+EBUILD pymol-1.2.1.ebuild 2969 RMD160 c2d98ec20cf7d6c424ac817e63c3fb58040a884c SHA1 88c983af2bcf7bc3293df92f225c409d494aa24d SHA256 4a69773417d086e230c6120466ba0636bbd0177b84a7c1a6a52d47144760a5e4
+MISC ChangeLog 9577 RMD160 bfe20d3a824633a08e0cda3e7260f239589a0c72 SHA1 766de67f5e5213bcfa214bff68ebd1c70c28ed50 SHA256 7aa381a0478791017e7deafee19e41ed82778d0cdfaef2fd6021ecd1081c168e
 MISC metadata.xml 327 RMD160 d44a69d538eb2125e431b5690abeb3a2fddc425d SHA1 d65dff362b78fc32fa382ff4644e98149da0be5a SHA256 0ec76fa228418dc19e62626f28c73ce3341bce42208ea98704226f5f12cccc0c
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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
new file mode 100644
index 000000000000..86c3fe1f1c27
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch
@@ -0,0 +1,30 @@
+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
new file mode 100644
index 000000000000..06f75682344f
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch
@@ -0,0 +1,10 @@
+--- 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/pymol-0.99_rc10.ebuild b/sci-chemistry/pymol/pymol-0.99_rc10.ebuild
index 93bc63309411..2fbe43a7b397 100644
--- a/sci-chemistry/pymol/pymol-0.99_rc10.ebuild
+++ b/sci-chemistry/pymol/pymol-0.99_rc10.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.99_rc10.ebuild,v 1.8 2009/04/16 13:42:53 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.99_rc10.ebuild,v 1.9 2009/08/02 14:58:31 je_fro Exp $
 
 inherit distutils eutils multilib subversion
 
@@ -20,6 +20,8 @@ media-libs/libpng
 sys-libs/zlib
 virtual/glut"
 
+RDEPEND="${DEPEND}"
+
 src_unpack() {
 	subversion_src_unpack
 
diff --git a/sci-chemistry/pymol/pymol-1.0-r1.ebuild b/sci-chemistry/pymol/pymol-1.0-r1.ebuild
index 948171be7872..271f37596af7 100644
--- a/sci-chemistry/pymol/pymol-1.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.0-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 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 1.3 2008/08/17 03:06:59 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.0-r1.ebuild,v 1.4 2009/08/02 14:58:31 je_fro Exp $
 
 inherit distutils eutils multilib subversion
 
@@ -22,6 +22,8 @@ media-libs/libpng
 sys-libs/zlib
 virtual/glut"
 
+RDEPEND="${DEPEND}"
+
 src_unpack() {
 	subversion_src_unpack
 
diff --git a/sci-chemistry/pymol/pymol-1.2.1.ebuild b/sci-chemistry/pymol/pymol-1.2.1.ebuild
new file mode 100644
index 000000000000..e7e1fb391e1e
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.2.1.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.2.1.ebuild,v 1.1 2009/08/02 14:58:31 je_fro Exp $
+
+EAPI="2"
+
+inherit distutils subversion
+
+PYTHON_MODNAME="chempy pmg_tk pymol"
+APBS_PATCH="090618"
+REV="3825"
+
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="apbs? ( mirror://gentoo/apbs_tools.py.${APBS_PATCH}.bz2 )"
+ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol@${REV}"
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="apbs shaders"
+
+DEPEND="dev-python/pmw
+		dev-python/numpy
+		>=dev-lang/python-2.4[tk]
+		media-libs/libpng
+		sys-libs/zlib
+		virtual/glut
+		media-video/mpeg-tools
+		apbs? ( dev-libs/maloc
+			sci-chemistry/apbs
+			sci-chemistry/pdb2pqr
+		)"
+RDEPEND="${DEPEND}"
+
+pkg_setup(){
+	python_version
+}
+
+src_unpack() {
+	use apbs && unpack ${A}
+	subversion_src_unpack
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}/${P}-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.
+	[[ -n ${WANT_SPLASH} ]] || epatch "${FILESDIR}"/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}"/${PV}/${P}-shaders.patch
+
+	if use apbs; then
+		cp -f "${WORKDIR}"/apbs_tools.py.${APBS_PATCH} modules/pmg_tk/startup/apbs_tools.py \
+			|| die "Failed to copy apbs_tools.py"
+
+		sed "s:LIBANDPYTHON:$(python_get_libdir):g" \
+			-i modules/pmg_tk/startup/apbs_tools.py \
+				|| die "Failed running sed on apbs_tools.py"
+	fi
+}
+
+src_configure() {
+	:
+}
+
+src_install() {
+	distutils_src_install
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH=$(python_get_sitedir)/${PN}
+		PYMOL_DATA="/usr/share/pymol/data"
+		PYMOL_SCRIPTS="/usr/share/pymol/scripts"
+	EOF
+
+	if use apbs; then
+		echo "APBS_PSIZE=$(python_get_sitedir)/pdb2pqr/src/psize.py" >> "${T}"/20pymol
+	fi
+
+	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
+}
+