reinit the tree, so we can have metadata

4 files changed, 239 insertions, 0 deletions

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
new file mode 100644
index 000000000000..bfc21a112425
--- /dev/null
+++ b/sci-chemistry/pymol/Manifest
@@ -0,0 +1,8 @@
+DIST pymol-1.8.4.0.png.xz 19528 SHA256 e2c956b39965130a3dc51c2c1b1090bee6bf591885069b2ddb77c0991e9e4928 SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c WHIRLPOOL 1336c20e068b71cdf35118c84b5df8485c86bc51eed7f542a483fb78ce374ca76e4aed3518aced0a6f8ea49e0b180004e567cc059ac52a27a3d616adb282cea2
+DIST pymol-v1.8.4.0.tar.bz2 8717344 SHA256 b6147befe74844dd23550461b831b2fa6d170d4456f0059cf93fb1e8cb43d279 SHA512 73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe WHIRLPOOL 3943a619ca00cc2bfb51ff4dffa0166856b4425c7518d91b1ff2a048caa53dcb7411c64b246014b860b7f036de582e9efdc09783b3918283f0a96ee5130c7287
+DIST pymol-v1.8.6.0.tar.bz2 8717164 SHA256 7eaaf90ac1e1be0969291cdb1154b3631b5b6403cce1d697133d90cd37a3c565 SHA512 bd08e6890382af1503d6af16b27b43af09b372a1229cc9d8e2de311873918b5e7b06e8a2365ce73a5f52cb31ac795f5d91b2ae6ef62890d9c2bf0ea25f856658 WHIRLPOOL 950d655a48b3801de2657b6d8935404ca0069525719b9c88a117ad819c37366a55e42dbe51a253b960b79413e5df9d781b9ada8839ca06e1e01dde965044efe4
+EBUILD pymol-1.8.4.0-r1.ebuild 3009 SHA256 a5f968aa75695834f878c9c18ed98c30461ea2d0f8ec70e0cb1b52b4eb9b19dc SHA512 c696905b2e28c28249bf458e37dfe05237b307e3af1727fe17ebfd6a818322e6f9dc947d720df7ee29d694fe6501791f3a2f6fdc554a8e7dd43adf9727c8ece8 WHIRLPOOL 65730bcce7ade5900a90fb5a24207cba2d2433ab1312ab91a9af9c48ca98bad216d2732d59ce5e4e95e5b0f5cf064a7b221ae2973f712ac47c1890c4574f43f9
+EBUILD pymol-1.8.6.0.ebuild 3052 SHA256 8b239353bac4386400100d0fcf889c16eef5f8323b03e62b938fe085ea1a08cb SHA512 f065ffbdade1cc02734a35f6f785670417e113299ec6b92d1b9c7ffdaaeba0ca5353dcc0ae09e206eb1a83474487db89234ab22c65c0a75e768e7b4cb5982f86 WHIRLPOOL f7aef767f1d264f14a93010385f8e0e4890f5dfe1619af0a2caf81e2b51d17fc93c35745bd44490c9e24b3476024bb1c073b6837fdc8fa5847b3b3f14957991e
+MISC ChangeLog 5319 SHA256 e58797f1ec06da23cc79f421c1cf011d4ba4deff3198daa02c23b4aed4731ba0 SHA512 75974a75951abe5a2d9a0b615a4d2176f39dce7f06bbec2859efa08a9814f5fae299124529a8fd18eb6c983f62b1d9f91ba9cfc90596ecfcc413563d99a5001b WHIRLPOOL 8ee424fcf377c91456fabd4e54dca753d517019768a39a378f0d4f2f9b0320e937d56094982fc68dd7a8c7cf7f1bc6f8b79ae225ed5f94e0ea6e8f1dcda11560
+MISC ChangeLog-2015 9337 SHA256 c462188628a8604c4023b896438c60be3fadb47cae8259d22847ef5bb1cd8a8b SHA512 29c5ce09d595262a27750f13adf918ec0a0bfea21eb787c3f9048a4cc9cc8f053b53d9faf178be34ae9fe23d07933a0a3d5dcdf857ce9ae2cc70cec18b24dbcb WHIRLPOOL 4d8adb760612b09ac2cc823b156cfd0dfe6a6533d99b81eb56d7c0d83f79df52c993bf7f5cc93fa14007e0c306ffb955ebdcb7b9560c88c2a388193e6b6b9f25
+MISC metadata.xml 439 SHA256 ee9fdf7e53b518562aa334a006889f3a7ffd56cb635f54b18171f08700678cee SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4 WHIRLPOOL 88c38bd335bafc9105e94d743229edc6244d426ea040aa6fba7f33f01eea69268aa0963d79b2479a96457332dec8b4b60983915c6668d6c29fb32f81191fbac6
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
new file mode 100644
index 000000000000..156735fe0d36
--- /dev/null
+++ b/sci-chemistry/pymol/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <use>
+    <flag name="web">Install Pymodule needed for web app support</flag>
+  </use>
+  <upstream>
+    <remote-id type="sourceforge">pymol</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
new file mode 100644
index 000000000000..c2bedf7ca9db
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -0,0 +1,108 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${P}.png.xz
+	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
+	"
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+	dev-python/numpy[${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}]
+	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${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}"/${P}.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/${PN}/LICENSE || die
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
diff --git a/sci-chemistry/pymol/pymol-1.8.6.0.ebuild b/sci-chemistry/pymol/pymol-1.8.6.0.ebuild
new file mode 100644
index 000000000000..8fd0a78a12a1
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.8.6.0.ebuild
@@ -0,0 +1,109 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
+	"
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+	dev-libs/msgpack[cxx]
+	dev-python/numpy[${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}]
+	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${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}-1.8.4.0.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
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}