diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/burrow-owl/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild | 52 | ||||
| -rw-r--r-- | sci-chemistry/pymol/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-chemistry/pymol/pymol-1.5.0.1.ebuild | 4 | ||||
| -rw-r--r-- | sci-chemistry/pymol/pymol-1.5.0.2.ebuild | 120 |
5 files changed, 187 insertions, 4 deletions
diff --git a/sci-chemistry/burrow-owl/ChangeLog b/sci-chemistry/burrow-owl/ChangeLog index 39655e33fbac..ef6ef0946133 100644 --- a/sci-chemistry/burrow-owl/ChangeLog +++ b/sci-chemistry/burrow-owl/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/burrow-owl # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/burrow-owl/ChangeLog,v 1.5 2012/02/14 19:58:49 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/burrow-owl/ChangeLog,v 1.6 2012/02/27 22:50:44 jlec Exp $ + +*burrow-owl-1.5.1 (27 Feb 2012) + + 27 Feb 2012; Justin Lecher <jlec@gentoo.org> +burrow-owl-1.5.1.ebuild: + Version Bump *burrow-owl-1.5 (14 Feb 2012) diff --git a/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild new file mode 100644 index 000000000000..9021afe8e3f8 --- /dev/null +++ b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild,v 1.1 2012/02/27 22:50:44 jlec Exp $ + +EAPI=4 + +inherit autotools-utils + +DESCRIPTION="Visualize multidimensional nuclear magnetic resonance (NMR) spectra" +HOMEPAGE="http://burrow-owl.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${P}.tar.gz + examples? ( mirror://sourceforge/${PN}/burrow-demos.tar )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples static-libs" + +RDEPEND=" + dev-libs/g-wrap + dev-libs/glib:2 + dev-scheme/guile[networking,regex] + dev-scheme/guile-cairo + dev-scheme/guile-gnome-platform + sci-libs/starparse + x11-libs/gtk+:2" +DEPEND="${RDEPEND} + dev-util/indent + dev-util/pkgconfig + doc? ( app-doc/doxygen ) +" + +src_configure() { + local myeconfargs=( + $(use_with doc doxygen doxygen) + ) + autotools-utils_src_configure +} + +src_test () { + autotools-utils_src_compile -C test-suite check +} + +src_install() { + use doc && HTML_DOCS=("${AUTOTOOLS_BUILD_DIR}/doc/api/html/") + autotools-utils_src_install + + use examples && \ + insinto /usr/share/${PN} && \ + doins -r "${WORKDIR}"/burrow-demos/* +} diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog index c46ca1931d60..10250bc2c153 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 1.84 2012/02/26 06:10:49 patrick Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.85 2012/02/27 22:53:03 jlec Exp $ + +*pymol-1.5.0.2 (27 Feb 2012) + + 27 Feb 2012; Justin Lecher <jlec@gentoo.org> pymol-1.5.0.1.ebuild, + +pymol-1.5.0.2.ebuild: + Version Bump 26 Feb 2012; Patrick Lauer <patrick@gentoo.org> pymol-1.3.1_pre3925-r1.ebuild, pymol-1.4.1.ebuild, pymol-1.5.0.1.ebuild: diff --git a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild index 050bfca4b455..c0511e130639 100644 --- a/sci-chemistry/pymol/pymol-1.5.0.1.ebuild +++ b/sci-chemistry/pymol/pymol-1.5.0.1.ebuild @@ -1,6 +1,6 @@ # 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-1.5.0.1.ebuild,v 1.3 2012/02/26 06:10:49 patrick Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.1.ebuild,v 1.4 2012/02/27 22:53:03 jlec Exp $ EAPI=4 @@ -104,7 +104,7 @@ src_install() { dodoc DEVELOPERS README doicon "${WORKDIR}"/${PN}.xpm - make_desktop_entry pymol PyMol ${PN}.xpm "Graphics;Science;Chemistry" + make_desktop_entry pymol PyMol ${PN} "Graphics;Science;Chemistry" } pkg_postinst() { diff --git a/sci-chemistry/pymol/pymol-1.5.0.2.ebuild b/sci-chemistry/pymol/pymol-1.5.0.2.ebuild new file mode 100644 index 000000000000..40ff66f76107 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.5.0.2.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-1.5.0.2.ebuild,v 1.1 2012/02/27 22:53:03 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 "${FILESDIR}"/${PN}-1.5.0.1-web.patch + + epatch "${FILESDIR}"/${PN}-1.5.0.1-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 +} |