Put the 0.99 series back in the testing branch. Fixed references to shared data in the mutagenesis wizard and other modules.

(Portage version: 2.0.54)

6 files changed, 149 insertions, 29 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 0826ca1ed0c5..9422094c67ca 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,17 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 2002-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.12 2006/03/07 16:16:52 spyderous Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.13 2006/03/16 03:41:51 ribosome Exp $
+
+*pymol-0.99_rc6-r1 (16 Mar 2006)
+
+  16 Mar 2006; Olivier Fisette <ribosome@gentoo.org>
+  +files/pymol-0.99_rc6-data-path.patch, pymol-0.99_rc6.ebuild,
+  +pymol-0.99_rc6-r1.ebuild:
+  Put the 0.99 series back in the testing branch. This has not been tested for
+  30 days, and is buggy. (It was commited straight to stable.) Fixed
+  references to shared data in the mutagenesis wizard and other modules
+  (0.99_rc6-r1) (thanks to Pierres-Yves Savard <pys@rsvs.ulaval.ca> for
+  reporting).
 
 *pymol-0.99_rc6 (07 Mar 2006)
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index dd401ac7a7db..368087dc1626 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,39 +1,16 @@
 MD5 8b52c49e991f8a8373ea518bb48e82d8 ChangeLog 4269
-RMD160 7d4d4d8b62ed80448c6b84a1e3d5a6ecebf44ddd ChangeLog 4269
-SHA256 7fc811e36eaa75b6810b48c4b124bf14ceb4ddafc7d506b513654ebd2368bb97 ChangeLog 4269
 MD5 cb324029606a6b5048895957143c7a44 files/digest-pymol-0.97 64
-RMD160 82bd85bb8c6cbae6f0b60382383798597836fab8 files/digest-pymol-0.97 64
-SHA256 963decc23698c04c8b1c6f8cd457331cf482907de2d5418a9caae7f6dff904d4 files/digest-pymol-0.97 64
 MD5 2dbc83e197b07cf99e7b02a03555a3d6 files/digest-pymol-0.98 64
-RMD160 ba61ec28c84e18d817ad92408f30138f886bad6f files/digest-pymol-0.98 64
-SHA256 469c60f72347e1f9b0d544866d26bf615b7e6c424da4a28b8bbfd7fba6d6e839 files/digest-pymol-0.98 64
 MD5 925dc45d0ae6070f5506dffc1d100975 files/digest-pymol-0.99_rc6 247
-RMD160 505a34a7bebbbdd2c60913ea3ec7cd41164eeaff files/digest-pymol-0.99_rc6 247
-SHA256 c6ec27d34304ab8e1d2d24f80537f9b63d14e6e915776434e158eecfa1060aac files/digest-pymol-0.99_rc6 247
+MD5 9c414f568a3de5c4af6aee28e735a7a3 files/digest-pymol-0.99_rc6-r1 67
 MD5 1a6ba582a7928c370c8dfe44c8867e7c files/header_order.patch 905
-RMD160 0a4e2b2f95e2ace2ad21d27740bef5308a4990d5 files/header_order.patch 905
-SHA256 1f181350c2d99e31c59baea2f31b5ce27b16bae61ce6c9438d2f0e1e903b4cce files/header_order.patch 905
 MD5 929741dc2da6577e6e99c5542d68dbd5 files/nosplash-gentoo.patch 332
-RMD160 2280fbe9daba8a0d3ca81a3aacfcc55bd06fc7d3 files/nosplash-gentoo.patch 332
-SHA256 5e0761591eeea90bcaa06a72c210a80ba46f2542ff985f8dd893af112254a890 files/nosplash-gentoo.patch 332
+MD5 035c32a87c619d2c2cf6c0d7466d92e0 files/pymol-0.99_rc6-data-path.patch 2473
 MD5 34d172ef31b5038e071b634d4e645cf1 files/pymol-gentoo.diff 1566
-RMD160 6a566cd0105ba94f9b06be8219c5fbe644281ab9 files/pymol-gentoo.diff 1566
-SHA256 15bdd116551022045c57743f21337c14ca368211a68a2a9763a1a7950f9af9d3 files/pymol-gentoo.diff 1566
 MD5 e42746bf581479c61ff1e7cc5b978edd files/setup.py-gentoo.patch 311
-RMD160 483f63778aa928bf2ce4de99edbc45af98abab8c files/setup.py-gentoo.patch 311
-SHA256 850bae1aef6007f159abf8d2f3ba3342ea5a7aaff8f4798c6829fc879d08d5ed files/setup.py-gentoo.patch 311
 MD5 af2da92225ab57969d18d16ed60324ce files/setup2.py-gentoo.patch 493
-RMD160 2d6bbabc01f6e4eb8ddafb9b0215ece50a639923 files/setup2.py-gentoo.patch 493
-SHA256 dc721d4d3fd557c684ddb1ec43e07e05c38f13750393cd1665148e18c5e6a959 files/setup2.py-gentoo.patch 493
 MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156
-RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156
-SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 metadata.xml 156
 MD5 2e14ab661047ad8d8c2fe6b21b72c5cc pymol-0.97.ebuild 1131
-RMD160 b0488b3652781f924bb09cd8bf50ab64d3ef984c pymol-0.97.ebuild 1131
-SHA256 3c78bd24c24de4861e5b37925fa872164fa20c032dcea3d30d93bc3900208047 pymol-0.97.ebuild 1131
 MD5 178d73732fb90d64350e98c172b9b594 pymol-0.98.ebuild 1131
-RMD160 74c9af0b01ad3f38d1b7ebc80ec176774069d228 pymol-0.98.ebuild 1131
-SHA256 d1a682ccf38e792d76529b104594e583e7b076a8b1095ed92866f7f23e5fa7dc pymol-0.98.ebuild 1131
+MD5 3f0682912b1fa26b97ea540041dc9456 pymol-0.99_rc6-r1.ebuild 1807
 MD5 edbf14350463e3f1e1d9219720e5e3e0 pymol-0.99_rc6.ebuild 1719
-RMD160 83e729365272481f5748c7deeb1592d6b89debc3 pymol-0.99_rc6.ebuild 1719
-SHA256 bd324dd4a32d8fee6cc15b9a01990858890dfc2b4af7e70ae76cd869a9abd64a pymol-0.99_rc6.ebuild 1719
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.99_rc6-r1 b/sci-chemistry/pymol/files/digest-pymol-0.99_rc6-r1
new file mode 100644
index 000000000000..fd7a889871f4
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.99_rc6-r1
@@ -0,0 +1 @@
+MD5 cb29385ab523f648d4db47a222b1d03e pymol-0_99rc6-src.tgz 4198816
diff --git a/sci-chemistry/pymol/files/pymol-0.99_rc6-data-path.patch b/sci-chemistry/pymol/files/pymol-0.99_rc6-data-path.patch
new file mode 100644
index 000000000000..2ecad7f21b5f
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-0.99_rc6-data-path.patch
@@ -0,0 +1,57 @@
+--- commanding.py.old	2006-03-15 21:10:36.000000000 -0500
++++ commanding.py	2006-03-15 21:12:27.000000000 -0500
+@@ -121,7 +121,7 @@
+         r = DEFAULT_ERROR
+         mode = int(mode)
+         if mode == 1: # just show PNG
+-            png_path = cmd.exp_path("$PYMOL_PATH/data/pymol/splash.png")
++            png_path = cmd.exp_path("$PYMOL_DATA/pymol/splash.png")
+             if os.path.exists(png_path):
+                 cmd.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
+                 r = DEFAULT_SUCCESS
+--- fitting.py.old	2006-03-15 21:14:01.000000000 -0500
++++ fitting.py	2006-03-15 21:13:24.000000000 -0500
+@@ -61,7 +61,7 @@
+         r = DEFAULT_ERROR
+         source = selector.process(source)
+         target = selector.process(target)
+-        mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
++        mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
+         if object==None: object=''
+         try:
+             lock()
+--- importing.py.old	2006-03-15 21:15:34.000000000 -0500
++++ importing.py	2006-03-15 21:15:04.000000000 -0500
+@@ -176,7 +176,7 @@
+         r = DEFAULT_ERROR
+         
+         
+-        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
++        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
+                       'pymol' : 'pymol',
+                       'rgb' : 'rgb' }
+ 
+--- wizard/mutagenesis.py.old	2006-03-15 21:44:06.000000000 -0500
++++ wizard/mutagenesis.py	2006-03-15 21:57:48.000000000 -0500
+@@ -35,8 +35,8 @@
+ 
+         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
+@@ -107,8 +107,8 @@
+     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):
+         if mode in self.modes:
diff --git a/sci-chemistry/pymol/pymol-0.99_rc6-r1.ebuild b/sci-chemistry/pymol/pymol-0.99_rc6-r1.ebuild
new file mode 100644
index 000000000000..df13ddc2e237
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-0.99_rc6-r1.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.99_rc6-r1.ebuild,v 1.1 2006/03/16 03:41:54 ribosome Exp $
+
+inherit distutils eutils multilib
+
+MY_PV=${PV/_}
+MY_S_P="${PN}-${MY_PV}"
+MY_PV=${MY_PV/./_}
+MY_P="${PN}-${MY_PV}"
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="mirror://sourceforge/pymol/${MY_P}-src.tgz"
+
+LICENSE="PSF-2.2"
+IUSE=""
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+
+DEPEND="dev-lang/python
+	dev-python/pmw
+	dev-python/numeric
+	dev-lang/tk
+	media-libs/libpng
+	sys-libs/zlib
+	virtual/glut"
+S="${WORKDIR}/${MY_S_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"/modules/${PN}
+	epatch "${FILESDIR}"/${P}-data-path.patch
+	cd "${S}"
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though.
+	[[ -n "$WANT_NOSPLASH" ]] && epatch "${FILESDIR}"/nosplash-gentoo.patch
+
+	# Respect CFLAGS
+	sed -i \
+		-e "s:\(ext_comp_args=\).*:\1[]:g" \
+		"${S}"/setup.py
+}
+
+src_install() {
+	python_version
+
+	distutils_src_install
+	cd "${S}"
+
+	#The following three lines probably do not do their jobs and should be
+	#changed
+	PYTHONPATH="${D}/usr/$(get_libdir)/site-packages" ${python} setup2.py
+
+	# Make our own wrapper
+cat >> "${T}"/pymol << EOF
+#!/bin/sh
+PYMOL_PATH=/usr/lib/python${PYVER}/site-packages/pymol
+PYMOL_DATA="/usr/share/pymol/data"
+PYMOL_SCRIPTS="/usr/share/pymol/scripts"
+export PYMOL_PATH PYMOL_DATA PYMOL_SCRIPTS
+${python} \${PYMOL_PATH}/__init__.py \$*
+EOF
+
+	exeinto /usr/bin
+	doexe "${T}"/pymol
+	dodoc DEVELOPERS CHANGES
+
+	mv examples "${D}"/usr/share/doc/${PF}/
+
+	dodir /usr/share/pymol
+	mv test "${D}"/usr/share/pymol/
+	mv data "${D}"/usr/share/pymol/
+	mv scripts "${D}"/usr/share/pymol/
+}
diff --git a/sci-chemistry/pymol/pymol-0.99_rc6.ebuild b/sci-chemistry/pymol/pymol-0.99_rc6.ebuild
index 8dc6b66afa02..954372945693 100644
--- a/sci-chemistry/pymol/pymol-0.99_rc6.ebuild
+++ b/sci-chemistry/pymol/pymol-0.99_rc6.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.99_rc6.ebuild,v 1.1 2006/03/07 16:16:52 spyderous Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.99_rc6.ebuild,v 1.2 2006/03/16 03:41:54 ribosome Exp $
 
 inherit distutils eutils multilib
 
@@ -15,7 +15,7 @@ SRC_URI="mirror://sourceforge/pymol/${MY_P}-src.tgz"
 LICENSE="PSF-2.2"
 IUSE=""
 SLOT="0"
-KEYWORDS="~amd64 ppc x86"
+KEYWORDS="~amd64 ~ppc ~x86"
 
 DEPEND="dev-lang/python
 	dev-python/pmw