From: Olivier Fisette Date: Thu, 16 Mar 2006 03:41:54 +0000 (+0000) Subject: Put the 0.99 series back in the testing branch. Fixed references to shared data in... X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=a8605fd31654f1e986b7bdb14885e24a6b8e979f;p=gentoo.git Put the 0.99 series back in the testing branch. Fixed references to shared data in the mutagenesis wizard and other modules. Package-Manager: portage-2.0.54 --- 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 + +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 for + reporting). *pymol-0.99_rc6 (07 Mar 2006) diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index dd401ac7a7db..51b809fd0d4b 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 9c6fb81bdd4f2b19aa43ca96c1bdccbd ChangeLog 4755 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 edbf14350463e3f1e1d9219720e5e3e0 pymol-0.99_rc6.ebuild 1719 -RMD160 83e729365272481f5748c7deeb1592d6b89debc3 pymol-0.99_rc6.ebuild 1719 -SHA256 bd324dd4a32d8fee6cc15b9a01990858890dfc2b4af7e70ae76cd869a9abd64a pymol-0.99_rc6.ebuild 1719 +MD5 03c375c56799851b4df5b75cdb5f2720 pymol-0.99_rc6-r1.ebuild 1811 +MD5 e339da592644e001ae3b497400f08716 pymol-0.99_rc6.ebuild 1720 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