commit: 01222e4f46e52148f0c9e200129a6420d6b3f8fb Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Thu Nov 12 16:20:32 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Thu Nov 12 16:20:32 2015 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=01222e4f
sci-chemistry/pymol: Always use included apbs plugin Correctly block files collisions Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=565600 Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-chemistry/pymol/Manifest | 1 - sci-chemistry/pymol/metadata.xml | 1 - sci-chemistry/pymol/pymol-1.7.4.0.ebuild | 106 ------------------------------- sci-chemistry/pymol/pymol-1.7.6.0.ebuild | 11 ++-- sci-chemistry/pymol/pymol-1.7.7.2.ebuild | 11 ++-- 5 files changed, 8 insertions(+), 122 deletions(-) diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index b660c66..1d654d7 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,4 +1,3 @@ DIST pymol-1.7.0.0.png.xz 5392 SHA256 4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105 WHIRLPOOL 395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b -DIST pymol-1.7.4.0.tar.xz 6528964 SHA256 5a732aeb8a02797a185f54c3bd8bb477a1a11976eb9f982f6cf79ce887ce3a4a SHA512 fa53e90413cb1e02797a30b21b4254901504edc029104567fd2d4c5ef630eb8c2eb9f5065b2b9e65f657aaa30ca8ac85c3314c6c7fbb89148d89a9a0964de3cf WHIRLPOOL 1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf333371cd38c78917e1f4b0a3a684b4807972546180d69 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d WHIRLPOOL 3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2 DIST pymol-1.7.7.2.tar.xz 6527780 SHA256 fc15fc8fbf23b422c5d19babd20e19b7d7ab8ee9532012c7b3a27b87af44fdae SHA512 faf3715cd6b9e7115f6501fc4480a6f71fe53d3b02b2eeefdd07a57d7c15b3621c05fd3894bb92ac4042edaa224d99c2be7488a762254d069c581974a0146179 WHIRLPOOL b52683ce1dc265fe302c974ccc1bfa9e55365e8502f944cf6527c0071f207fcb54e8b3ad38fd684b66c66f85fa6a03f2f1178b90fd406b9f7561d956c704fb9a diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml index 9af014e..6a64062 100644 --- a/sci-chemistry/pymol/metadata.xml +++ b/sci-chemistry/pymol/metadata.xml @@ -6,7 +6,6 @@ <email>j...@gentoo.org</email> </maintainer> <use> - <flag name="apbs">Install the apbs plugin</flag> <flag name="web">Install Pymodule needed for web app support</flag> </use> <upstream> diff --git a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild deleted file mode 100644 index 2e0475c..0000000 --- a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild +++ /dev/null @@ -1,106 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -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=" - https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz - https://dev.gentoo.org/~jlec/distfiles/${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/pyopengl[${PYTHON_USEDEP}] - media-libs/freeglut - media-libs/freetype:2 - media-libs/glew:0= - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib - virtual/python-pmw[${PYTHON_USEDEP}] - apbs? ( - sci-chemistry/apbs[${PYTHON_USEDEP}] - sci-chemistry/pdb2pqr[${PYTHON_USEDEP}] - sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] - ) - web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/${P}/${PN} - -PATCHES=( - "${FILESDIR}"/${PN}-1.7.3.1-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/${PN}/LICENSE || die -} - -pkg_postinst() { - fdo-mime_desktop_database_update - fdo-mime_mime_database_update -} - -pkg_postrm() { - fdo-mime_desktop_database_update - fdo-mime_mime_database_update -} diff --git a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild index c163b24..4033493 100644 --- a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild +++ b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild @@ -7,7 +7,7 @@ EAPI=5 PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" -inherit distutils-r1 fdo-mime flag-o-matic versionator +inherit distutils-r1 eutils fdo-mime flag-o-matic versionator DESCRIPTION="A Python-extensible molecular graphics system" HOMEPAGE="http://www.pymol.org/"; @@ -21,7 +21,7 @@ SRC_URI=" LICENSE="PSF-2.2" SLOT="0" KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="apbs web" +IUSE="web" DEPEND=" dev-python/numpy[${PYTHON_USEDEP}] @@ -33,11 +33,7 @@ DEPEND=" media-video/mpeg-tools sys-libs/zlib virtual/python-pmw[${PYTHON_USEDEP}] - apbs? ( - sci-chemistry/apbs[${PYTHON_USEDEP}] - sci-chemistry/pdb2pqr[${PYTHON_USEDEP}] - !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] - ) + !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" RDEPEND="${DEPEND}" @@ -105,6 +101,7 @@ python_install_all() { pkg_postinst() { fdo-mime_desktop_database_update fdo-mime_mime_database_update + optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr } pkg_postrm() { diff --git a/sci-chemistry/pymol/pymol-1.7.7.2.ebuild b/sci-chemistry/pymol/pymol-1.7.7.2.ebuild index a16c696..7d6aab4 100644 --- a/sci-chemistry/pymol/pymol-1.7.7.2.ebuild +++ b/sci-chemistry/pymol/pymol-1.7.7.2.ebuild @@ -7,7 +7,7 @@ EAPI=5 PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" -inherit distutils-r1 fdo-mime flag-o-matic versionator +inherit distutils-r1 eutils fdo-mime flag-o-matic versionator DESCRIPTION="A Python-extensible molecular graphics system" HOMEPAGE="http://www.pymol.org/"; @@ -21,7 +21,7 @@ SRC_URI=" LICENSE="PSF-2.2" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="apbs web" +IUSE="web" DEPEND=" dev-python/numpy[${PYTHON_USEDEP}] @@ -33,11 +33,7 @@ DEPEND=" media-video/mpeg-tools sys-libs/zlib virtual/python-pmw[${PYTHON_USEDEP}] - apbs? ( - sci-chemistry/apbs[${PYTHON_USEDEP}] - sci-chemistry/pdb2pqr[${PYTHON_USEDEP}] - !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] - ) + !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" RDEPEND="${DEPEND}" @@ -105,6 +101,7 @@ python_install_all() { pkg_postinst() { fdo-mime_desktop_database_update fdo-mime_mime_database_update + optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr } pkg_postrm() {
