gentoo resync : 02.06.2019

3 files changed, 4 insertions, 121 deletions

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 1bbeb6cfbd8e..53adcde9c072 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,8 +1,6 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
-DIST pymol-2.2.0.tar.gz 10514753 BLAKE2B 54bf7c639ec1af0c318438f6dcbe5878aded5cc360dee3a5f1dee4b6eea588f4242865ae8adf1e044628ad5f71aa8f6d58d0cc71baf7c1f20eed3045ed3a1cb1 SHA512 56776586276208d42cc4bd4c3cb7d6b9a08e7239186b8f398c75cb57f85e05ebf51aaa8cdec5672e56beeda26f1cd9d14c6de7fba1a741f9c8ec22c1292b9c63
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
 DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3 SHA512 73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
 EBUILD pymol-1.8.4.0-r1.ebuild 3009 BLAKE2B a076dd994e90f886e65cbb5b3f976e75eacd0a6f153c1b9417c476b53d2169495b08b6d3361ab5fcb55102a2e93a86b7f0ac6d0f25bca947f6b13f52dadde6bd SHA512 c696905b2e28c28249bf458e37dfe05237b307e3af1727fe17ebfd6a818322e6f9dc947d720df7ee29d694fe6501791f3a2f6fdc554a8e7dd43adf9727c8ece8
-EBUILD pymol-2.2.0.ebuild 3123 BLAKE2B d5d39aca27089614f5f095eaef2d89bc783f1b3144a944b5e03fa80c2eb3a15402a6041dbe7e59af8c04e9b5e4668d93073cc6173495079f803537485390830c SHA512 4c6a01df6417ea2e28f1a90a2e690b078b853e7bfc4d42f418a095ae605b7fcd316b57e201e1b0debcd15fb8102f9c6e20e7a0a7067af3e1f4372eef76faa635
-EBUILD pymol-2.3.0.ebuild 3142 BLAKE2B d03631d7794b9557c6dcac84895bb0a10766a97a5b81a93ce2a54f8b6d89c0f27f2249109e51c8a8f315948786ba6f49f716f23810d438c36de9fd1237c11de4 SHA512 c90b2798a36403c316f36a483fbc2887d84e55afea4667704543c388a5803ed678830276c4621b7499fb759ea67a29545c399acdea4d88a1c22feb9b31ca2aeb
+EBUILD pymol-2.3.0-r1.ebuild 3134 BLAKE2B 5dac0f4ca3041d02d27d9484bd3a6fe9ac037ffd367e36308ace5c6e5b3389c42cdcde5939c3a5af03f782ebb2fee994547e3251747e02f1c2df610dda17f9f1 SHA512 2fdffad45d70aa2117f295027701ebb2c6d6b523c939caf2c4d128f40e557d118377a5e93612ce1db247341509740274c8520af9f11d121cf66bb502565229d5
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.2.0.ebuild b/sci-chemistry/pymol/pymol-2.2.0.ebuild
deleted file mode 100644
index 1e53d9ab3397..000000000000
--- a/sci-chemistry/pymol/pymol-2.2.0.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils xdg-utils flag-o-matic
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
-	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	"
-# git archive -v --prefix=${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[${PYTHON_USEDEP}]
-	media-libs/freeglut
-	media-libs/freetype:2
-	media-libs/glew:0=
-	media-libs/glm
-	media-libs/libpng:0=
-	media-video/mpeg-tools
-	sys-libs/zlib
-	virtual/python-pmw[${PYTHON_USEDEP}]
-	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-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
-	sed \
-		-e "s:\['msgpackc'\]:\['msgpack'\]: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() {
-	xdg_desktop_database_update
-	xdg_mimeinfo_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	xdg_desktop_database_update
-	xdg_mimeinfo_database_update
-}
diff --git a/sci-chemistry/pymol/pymol-2.3.0.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
index 0f1975780234..89aef82c8e96 100644
--- a/sci-chemistry/pymol/pymol-2.3.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
@@ -4,9 +4,8 @@
 EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
 
-inherit distutils-r1 eutils xdg-utils flag-o-matic
+inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://www.pymol.org/"
@@ -14,7 +13,6 @@ SRC_URI="
 	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
 	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
 	"
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
 RESTRICT="mirror"
 LICENSE="PSF-2.2"
 SLOT="0"
@@ -26,7 +24,8 @@ DEPEND="
 	dev-libs/mmtf-cpp
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freeglut
+	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
 	media-libs/freetype:2
 	media-libs/glew:0=
 	media-libs/glm