From e485a2dae896e2724f8506f466e49881dcb94d04 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Wed, 28 Mar 2012 12:34:56 +0000 Subject: Add missing wrong usage of PYMOL_PATH, #409971 (Portage version: 2.2.0_alpha96/cvs/Linux x86_64) --- sci-chemistry/pymol/ChangeLog | 8 +- .../pymol/files/pymol-1.5.0.1-data-path.patch | 18 ++-- sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild | 120 +++++++++++++++++++++ 3 files changed, 138 insertions(+), 8 deletions(-) create mode 100644 sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild (limited to 'sci-chemistry/pymol') diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog index 3aa6322d350e..b32f325782c0 100644 --- a/sci-chemistry/pymol/ChangeLog +++ b/sci-chemistry/pymol/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/pymol # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.86 2012/03/10 09:31:31 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.87 2012/03/28 12:34:56 jlec Exp $ + +*pymol-1.5.0.3-r1 (28 Mar 2012) + + 28 Mar 2012; Justin Lecher + files/pymol-1.5.0.1-data-path.patch, +pymol-1.5.0.3-r1.ebuild: + Add missing wrong usage of PYMOL_PATH, #409971 *pymol-1.5.0.3 (10 Mar 2012) diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch index e865bfd04174..a2b09bb9eee3 100644 --- a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch +++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch @@ -4,8 +4,8 @@ modules/chempy/tinker/__init__.py | 2 +- modules/pymol/commanding.py | 6 +++--- modules/pymol/importing.py | 2 +- - modules/pymol/wizard/mutagenesis.py | 4 ++-- - 7 files changed, 17 insertions(+), 17 deletions(-) + modules/pymol/wizard/mutagenesis.py | 8 ++++---- + 7 files changed, 19 insertions(+), 19 deletions(-) diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c index cc760ae..364277f 100644 @@ -74,7 +74,7 @@ index 23dbe45..795a223 100644 path = os.environ['PYMOL_DATA'] + '/chempy/' elif os.environ.has_key('PYMOL_PATH'): - path = os.environ['PYMOL_PATH'] + '/data/chempy/' -+ path = os.environ['PYMOL_PATH'] + '/chempy/' ++ path = os.environ['PYMOL_PATH'] + '/chempy/' elif os.environ.has_key('FREEMOL_MODULES'): path = os.environ['FREEMOL_MODULES'] + '/chempy/' else: @@ -127,20 +127,24 @@ diff --git a/modules/pymol/wizard/mutagenesis.py b/modules/pymol/wizard/mutagene index 8a5250d..6c1b26c 100644 --- a/modules/pymol/wizard/mutagenesis.py +++ b/modules/pymol/wizard/mutagenesis.py -@@ -53,7 +53,7 @@ class Mutagenesis(Wizard): +@@ -52,8 +52,8 @@ class Mutagenesis(Wizard): + self.dep = default_dep - self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ +- 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 -@@ -218,7 +218,7 @@ class Mutagenesis(Wizard): +@@ -217,8 +217,8 @@ class Mutagenesis(Wizard): + def load_library(self): if self.dep == 'dep': if not hasattr(self,'dep_library'): - self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ +- 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): diff --git a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild new file mode 100644 index 000000000000..c3a348f84c11 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild @@ -0,0 +1,120 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild,v 1.1 2012/03/28 12:34:56 jlec Exp $ + +EAPI=4 + +PYTHON_DEPEND="2:2.7" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.* *-jython 2.7-pypy-*" +PYTHON_USE_WITH="tk" +PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx" + +inherit distutils eutils fdo-mime prefix versionator + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="http://pymol.sourceforge.net/" +SRC_URI=" + http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz + http://dev.gentoo.org/~jlec/distfiles/${PN}.xpm.tar" + +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="apbs numpy vmd web" + +DEPEND=" + dev-python/numpy + dev-python/pmw + media-libs/freetype:2 + media-libs/glew + media-libs/libpng + media-video/mpeg-tools + sys-libs/zlib + media-libs/freeglut + apbs? ( + dev-libs/maloc + sci-chemistry/apbs + sci-chemistry/pdb2pqr + sci-chemistry/pymol-apbs-plugin + ) + web? ( !dev-python/webpy )" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-1.5.0.1-setup.py.patch \ + "${FILESDIR}"/${PN}-1.5.0.1-data-path.patch \ + "${FILESDIR}"/${PN}-1.5.0.1-flags.patch + + use web || epatch "${FILESDIR}"/${P}-web.patch + + epatch "${FILESDIR}"/${P}-prefix.patch && \ + eprefixify setup.py + + use vmd && epatch "${FILESDIR}"/${PN}-1.5.0.1-vmd.patch + + if use numpy; then + sed \ + -e '/PYMOL_NUMPY/s:^#::g' \ + -i setup.py || die + fi + + rm ./modules/pmg_tk/startup/apbs_tools.py || die + + echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die + + # python 3.* fix + # sed '452,465d' -i setup.py + distutils_src_prepare +} + +src_configure() { + : +} + +src_install() { + distutils_src_install + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF + PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + cat >> "${T}"/pymol <<- EOF + #!/bin/sh + $(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$* + EOF + + dobin "${T}"/pymol + + insinto /usr/share/pymol + doins -r test data scripts + + insinto /usr/share/pymol/examples + doins -r examples + + dodoc DEVELOPERS README + + doicon "${WORKDIR}"/${PN}.xpm + make_desktop_entry pymol PyMol ${PN} "Graphics;Science;Chemistry" +} + +pkg_postinst() { + elog "\t USE=shaders was removed," + elog "please use pymol config settings" + elog "\t set use_shaders, 1" + distutils_pkg_postinst + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} -- cgit v1.2.3-65-gdbad