# 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 1.62 2010/05/16 12:52:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.63 2010/06/09 06:49:59 jlec Exp $
+
+ 09 Jun 2010; Justin Lecher <jlec@gentoo.org> -pymol-1.0-r1.ebuild,
+ -files/pymol-1.0-r1-data-path.patch, -pymol-1.2.2.ebuild,
+ -pymol-1.2.2-r2.ebuild, -pymol-1.2.2-r4.ebuild,
+ -files/nosplash-gentoo.patch:
+ removed old version which having problems with PYTHON ABIs stuff
16 May 2010; Justin Lecher <jlec@gentoo.org> pymol-1.2.2-r4.ebuild,
pymol-1.2.3-r1.ebuild:
+++ /dev/null
---- modules/pymol/invocation.py.orig 2003-06-11 13:40:13.000000000 -0400
-+++ modules/pymol/invocation.py 2003-06-11 13:40:29.000000000 -0400
-@@ -179,5 +179,3 @@
-
- else:
- options.deferred.append(a)
-- if options.show_splash and not options.no_gui:
-- options.deferred.insert(0,"_do__ cmd.splash(1)")
+++ /dev/null
-diff -aurN pymol-1.0-orig/modules/pymol/commanding.py pymol-1.0/modules/pymol/commanding.py
---- pymol-1.0-orig/modules/pymol/commanding.py 2007-07-01 17:12:26.000000000 -0500
-+++ pymol-1.0/modules/pymol/commanding.py 2007-07-01 17:16:26.000000000 -0500
-@@ -198,11 +198,11 @@
- _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/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/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/data/pymol/ipymol.png")
- if os.path.exists(png_path):
- _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
- else:
-diff -aurN pymol-1.0-orig/modules/pymol/fitting.py pymol-1.0/modules/pymol/fitting.py
---- pymol-1.0-orig/modules/pymol/fitting.py 2007-07-01 17:12:26.000000000 -0500
-+++ pymol-1.0/modules/pymol/fitting.py 2007-07-01 17:17:51.000000000 -0500
-@@ -68,7 +68,7 @@
- if string.lower(matrix)=='none':
- matrix=''
- if len(matrix):
-- mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
-+ mfile = cmd.exp_path("$PYMOL_DATA/data/pymol/matrices/"+matrix)
- else:
- mfile = ''
- # delete existing alignment object (if asked to reset it)
-diff -aurN pymol-1.0-orig/modules/pymol/importing.py pymol-1.0/modules/pymol/importing.py
---- pymol-1.0-orig/modules/pymol/importing.py 2007-07-01 17:12:26.000000000 -0500
-+++ pymol-1.0/modules/pymol/importing.py 2007-07-01 17:18:52.000000000 -0500
-@@ -170,7 +170,7 @@
- r = DEFAULT_ERROR
-
-
-- tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+ tables = { 'cmyk' : "$PYMOL_DATA/data/pymol/cmyk.png",
- 'pymol' : 'pymol',
- 'rgb' : 'rgb' }
-
-diff -aurN pymol-1.0-orig/modules/pymol/wizard/mutagenesis.py pymol-1.0/modules/pymol/wizard/mutagenesis.py
---- pymol-1.0-orig/modules/pymol/wizard/mutagenesis.py 2007-07-01 17:12:26.000000000 -0500
-+++ pymol-1.0/modules/pymol/wizard/mutagenesis.py 2007-07-01 17:20:44.000000000 -0500
-@@ -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
-@@ -217,8 +217,8 @@
- 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
+++ /dev/null
-# 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 1.4 2009/08/02 14:58:31 je_fro Exp $
-
-inherit distutils eutils multilib subversion
-
-ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b10/pymol"
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-
-LICENSE="pymol"
-
-IUSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-
-DEPEND="dev-lang/python
-dev-python/pmw
-dev-lang/tk
-media-libs/libpng
-sys-libs/zlib
-virtual/glut"
-
-RDEPEND="${DEPEND}"
-
-src_unpack() {
- subversion_src_unpack
-
- epatch "${FILESDIR}"/${PF}-data-path.patch
-
-# Turn off splash screen. Please do make a project contribution
-# if you are able.
- [[ -n "$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" ${python} setup2.py
-
-# These environment variables should not go in the wrapper script, or else
-# it will be impossible to use the PyMOL libraries from Python.
- cat >> "${T}"/20pymol << EOF
- PYMOL_PATH=/usr/$(get_libdir)/python${PYVER}/site-packages/pymol
- PYMOL_DATA="/usr/share/pymol/data"
- PYMOL_SCRIPTS="/usr/share/pymol/scripts"
-EOF
-
- doenvd "${T}"/20pymol || die "Failed to install env.d file."
-
-# Make our own wrapper
- cat >> "${T}"/pymol << EOF
-#!/bin/sh
- ${python} \${PYMOL_PATH}/__init__.py \$*
-EOF
-
- exeinto /usr/bin
- doexe "${T}"/pymol || die "Failed to install wrapper."
- dodoc DEVELOPERS || die "Failed to install docs."
-
- mv examples "${D}"/usr/share/doc/${PF}/ || die "Failed moving docs."
-
- dodir /usr/share/pymol
- mv test "${D}"/usr/share/pymol/ || die "Failed moving test files."
- mv data "${D}"/usr/share/pymol/ || die "Failed moving data files."
- mv scripts "${D}"/usr/share/pymol/ || die "Failed moving scripts."
-}
+++ /dev/null
-# 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
-}
+++ /dev/null
-# 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-r4.ebuild,v 1.3 2010/05/16 12:52:12 jlec Exp $
-
-EAPI="3"
-
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_USE_WITH="tk"
-REV="3859"
-
-inherit eutils distutils prefix
-
-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} -> ${P}.tar.gz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy shaders vmd"
-
-DEPEND="
- dev-python/numpy
- dev-python/pmw
- media-libs/freetype:2
- media-libs/libpng
- media-video/mpeg-tools
- sys-libs/zlib
- virtual/glut
- apbs? (
- dev-libs/maloc
- sci-chemistry/apbs
- sci-chemistry/pdb2pqr
- sci-chemistry/pymol-apbs-plugin
- )"
-RDEPEND="${DEPEND}"
-RESTRICT_PYTHON_ABIS="3.* 2.4 2.5"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
- epatch "${FILESDIR}"/${PV}-data-path.patch
-
- epatch "${FILESDIR}"/${PV}-prefix.patch && \
- eprefixify setup.py
-
- # 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}"/${P}-vmd.patch
-
- use numpy && \
- sed \
- -e '/PYMOL_NUMPY/s:^#::g' \
- -i setup.py
-
- rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
- # python 3.* fix
- # sed '452,465d' -i setup.py
- distutils_src_prepare
-}
-
-src_configure() {
- :
-}
-
-src_install() {
- distutils_src_install
-
- # These environment variables should not go in the wrapper script, or else
- # it will be impossible to use the PyMOL libraries from Python.
- cat >> "${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 || die "Failed to install env.d file."
-
- cat >> "${T}"/pymol <<- EOF
- #!/bin/sh
- $(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
- EOF
-
- dobin "${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
-}
+++ /dev/null
-# 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.ebuild,v 1.5 2010/02/06 15:26:35 pva Exp $
-
-EAPI="2"
-
-inherit eutils distutils
-
-PYTHON_MODNAME="chempy pmg_tk pymol"
-APBS_PATCH="090618"
-REV="3859"
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="apbs? ( mirror://gentoo/apbs_tools.py.${APBS_PATCH}.bz2 )
- http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol.tar.gz?view=tar&pathrev=${REV} -> ${P}.tar.gz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="apbs shaders"
-
-DEPEND="dev-python/pmw
- dev-python/numpy
- media-libs/freetype:2
- >=dev-lang/python-2.4[tk]
- media-libs/libpng
- sys-libs/zlib
- virtual/glut
- media-video/mpeg-tools
- apbs? ( dev-libs/maloc
- sci-chemistry/apbs
- sci-chemistry/pdb2pqr
- )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-pkg_setup(){
- python_version
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/1.2.1/${PN}-1.2.1-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}"/${P}-shaders.patch
-
- if use apbs; then
- cp -f "${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
-}
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