sci-chemistry/pymol: Version Bump

(Portage version: 2.2.14_rc1/cvs/Linux x86_64, RepoMan options: --force, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 124 insertions, 1 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index ca274c591808..eadece7d5c3c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.118 2014/09/15 08:20:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.119 2014/10/17 06:54:03 jlec Exp $
+
+*pymol-1.7.3.1 (17 Oct 2014)
+
+  17 Oct 2014; Justin Lecher <jlec@gentoo.org> +pymol-1.7.3.1.ebuild,
+  +files/pymol-1.7.3.1-maeffplugin.cpp.patch:
+  Version Bump
 
 *pymol-1.7.3.0 (15 Sep 2014)
 
diff --git a/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch b/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch
new file mode 100644
index 000000000000..cd4650bbf4e0
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch
@@ -0,0 +1,11 @@
+--- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin_orig.cpp	2014-02-07 19:50:50.132261610 -0800
++++ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp	2014-02-07 19:52:12.527797099 -0800
+@@ -1983,7 +1983,7 @@
+       }
+     }
+     catch (std::exception &e) {
+-      fprintf(stderr, e.what());
++      fprintf(stderr, "%s", e.what());
+       return MOLFILE_ERROR;
+     }
+     return MOLFILE_SUCCESS;
diff --git a/sci-chemistry/pymol/pymol-1.7.3.1.ebuild b/sci-chemistry/pymol/pymol-1.7.3.1.ebuild
new file mode 100644
index 000000000000..37b77d5f35be
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.7.3.1.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.3.1.ebuild,v 1.1 2014/10/17 06:54:03 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 fdo-mime versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
+	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+"
+#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="apbs web"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pmw[${PYTHON_USEDEP}]
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	media-libs/freetype:2
+	media-libs/glew
+	media-libs/libpng
+	media-video/mpeg-tools
+	sys-libs/zlib
+	media-libs/freeglut
+	apbs? (
+		sci-chemistry/apbs
+		sci-chemistry/pdb2pqr
+		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+	)
+	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${P}/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-maeffplugin.cpp.patch
+	)
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+		-e "/import/s:argparse:argparseX:g" \
+		-i setup.py || die
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_install() {
+	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	python_export python2_7 EPYTHON
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="$(python_get_sitedir)/${PN}"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
+	make_desktop_entry ${PN} PyMol ${PN} \
+		"Graphics;Education;Science;Chemistry;" \
+		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
+
+	if ! use web; then
+		rm -rf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}