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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/pymol | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-chemistry/pymol')
-rw-r--r-- | sci-chemistry/pymol/Manifest | 4 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch | 11 | ||||
-rw-r--r-- | sci-chemistry/pymol/metadata.xml | 12 | ||||
-rw-r--r-- | sci-chemistry/pymol/pymol-1.7.0.1.ebuild | 101 | ||||
-rw-r--r-- | sci-chemistry/pymol/pymol-1.7.4.0.ebuild | 106 | ||||
-rw-r--r-- | sci-chemistry/pymol/pymol-1.7.6.0.ebuild | 113 |
6 files changed, 347 insertions, 0 deletions
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest new file mode 100644 index 000000000000..3e0a1ca939e5 --- /dev/null +++ b/sci-chemistry/pymol/Manifest @@ -0,0 +1,4 @@ +DIST pymol-1.7.0.0.png.xz 5392 SHA256 4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105 WHIRLPOOL 395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b +DIST pymol-1.7.0.1.tar.xz 6550492 SHA256 e8c6f6a465aec78171daf5cd981ebd1614dfa5e014e13c85a044cfbb591841c8 SHA512 a09277cd827f832c4f4e307f6117613d2ee8250643d129a5c34a30ceab2bfe8cea195c71a138fff09b6c69e9427153b917d7d3a7262d154ada5f323ec9635087 WHIRLPOOL 1803b55ade1b04de5963fd4a3bbe1354cda8759e15254c644952e25d7dcc904bc7b9fd91da75fdb8c6a96fd118a5a21bec9c8bba368744b44436747faca5cd9c +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 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/metadata.xml b/sci-chemistry/pymol/metadata.xml new file mode 100644 index 000000000000..ace2d8e58ce8 --- /dev/null +++ b/sci-chemistry/pymol/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@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> +</pkgmetadata> diff --git a/sci-chemistry/pymol/pymol-1.7.0.1.ebuild b/sci-chemistry/pymol/pymol-1.7.0.1.ebuild new file mode 100644 index 000000000000..fbd2fd858c86 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.7.0.1.ebuild @@ -0,0 +1,101 @@ +# 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=" + 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${PV}.tar.bz2 + +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="apbs web" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/pmw[${PYTHON_USEDEP}] + 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} + +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-1.7.4.0.ebuild b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild new file mode 100644 index 000000000000..20f49ba45a55 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild @@ -0,0 +1,106 @@ +# 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=" + 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/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/pmw[${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 new file mode 100644 index 000000000000..d3ec32637cee --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild @@ -0,0 +1,113 @@ +# 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 flag-o-matic 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/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/pmw[${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} + +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 + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + + append-cxxflags -std=c++0x + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1d' \ + -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ + -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ + -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + + python_foreach_impl python_doscript "${T}"/${PN} + + # 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}/usr/share/pymol" + 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 +} |