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@gentoo.org>

5 files changed, 8 insertions, 122 deletions

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index b660c664cc1d..1d654d7bb605 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 9af014ea2935..6a640625b05a 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -6,7 +6,6 @@
     <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>
   <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 2e0475cce617..000000000000
--- 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 c163b24f41d1..4033493c22f7 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 a16c696f2cf6..7d6aab4313dc 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() {