sci-chemistry/apbs: Remove redundant python dir after installation

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 148 insertions, 16 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 8d497d360009..256bd9b03968 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.69 2014/10/30 07:30:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.70 2014/10/30 11:52:05 jlec Exp $
+
+*apbs-1.4.1-r2 (30 Oct 2014)
+
+  30 Oct 2014; Justin Lecher <jlec@gentoo.org> +apbs-1.4.1-r2.ebuild:
+  Remove redundant python dir after installation
 
   30 Oct 2014; Justin Lecher <jlec@gentoo.org> apbs-1.4.1-r1.ebuild:
   Fix build problems, #527344
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 8ced89661cb7..069d067b9a73 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -42,24 +42,25 @@ DIST apbs-1.4.1.zip 37999283 SHA256 1156c44fb65bb7c884801f3111ca1cdb1dfba6f53082
 EBUILD apbs-1.2.1b-r4.ebuild 3611 SHA256 0c38e680838e539110402eec44dda6569d12ac70a9f6ae3d4f40c5f4723ce568 SHA512 447a1c810b5b4393fe3e95cea47d2c13d7ff296cdebd0d599b830700bc7ace89f731b6554aba66959687b5b33182193cec10cd5cbbadcb45e932021182a85259 WHIRLPOOL 4bcb114704e4fcba1966680dd882993204a8890777342e2a7130523b52df2d51237c0001b5b652d589e74f5933cfe473342fd09eff5e67da641f9690e5d0594a
 EBUILD apbs-1.3-r3.ebuild 4281 SHA256 9786340ad9fed6e51e16c9dde4c2e3dc35137069a569c3d9687e0e74507a6e8b SHA512 b20a75745a42a0ce3b8af9cecd50fd7cf31d05a4759057c7eb28bc8d72a4784eb34bb6a897a0aad9beb4769009a33667fd7bc965115ded3a61493c377287fe07 WHIRLPOOL 127c0a1a8e9244a538808c887b1d972a62fe744ab0973d91ac2abeb66fda21c4196a1f1e86240bfd901c4c6328160bb3b602ee30695d84b794ae3182e43ef6c8
 EBUILD apbs-1.4.1-r1.ebuild 3086 SHA256 50b5e1bcafe663ee580b982fffa7f67926d0677c36e54aaa7852db03a88ef682 SHA512 3f889ee44eae080dfc426171aa9ce0cb1a2b258427ddddd702b68b71536da303967f25289a332ebd4c661f1e55c39eddc5a8e52a1d438ec3db093b9b66aef4b8 WHIRLPOOL e4794d70a65b80fdff2072d508b63df2f70da061af28e218f45b6df86fb2c7735e92b463e31fe40f71fc5d115919fdb8bdf882ad584e1e4fa260b61dbe4f9a39
-MISC ChangeLog 12121 SHA256 36b9d4f40c4ffdbfea2ca1b3c494357ed17ba49ddf76e00486b534eb1bbf5443 SHA512 afaa3451cba6434d34f9fba2ec84fe5551ffe1f0b8229eb758fbf835253808fc3e2ae2ec027c2e5cbe4508a82f5ad3a82aade24e4e654e8b6e3e80aec213c796 WHIRLPOOL b4a90e4af39a30d7d4a3237f4d03e08afda5d64d68d53c9e5e24cbf90bd734925655653b4a32b60553234086d7cf2cdc44da3e9ac3eed4793cc50a8c42a0e176
+EBUILD apbs-1.4.1-r2.ebuild 3138 SHA256 777e9010f49500d4dfdc066a2a27455db7c9cc8782fdd46a50708bc688de7f3e SHA512 09efc570881bd7f1c84d456be90b297b892853997fc61c2a6a502a95d334c0abb00b79ea1cd079066b284e8dab6332447aa9989932052c7123cd1a44ef76ebc5 WHIRLPOOL 6d82a6b45b4fc031745c0d66f43fefad29b208f983b41bd5ef58d36562305ac225670ea2898be1490d800ce273c843c1571b4665a81efc3d1979850aa38009ba
+MISC ChangeLog 12271 SHA256 19f33b9529093c60d54852ab90f8b7ed6de97c9d535e6abcc1ddc5310a2ec564 SHA512 f05b19678a5828ab4a77328b9bf88249b43f83face8eaf4fdab233aac8114f1e66f115c1bc653ed56e23e952bdf85f753cde0d71ad49f8663761e521ba4c825c WHIRLPOOL b7c287b051a50739289e48d23c675e8f52d05c94d55b1234caffeae99fd9efb3c23bcd27d63eb3e9508f1cfad303a12bc1ca6df180d209bfb8ad895f24440701
 MISC metadata.xml 948 SHA256 ed8d35d9a0f77c758a6699bc5b5baa7e1e59603677dc9d13da6b9d445204f1e9 SHA512 ff99fbdf53cff0078f32fd95fafbd482dc064885dc4e4bc621a654fad3e134d7f6d4087770523ce6220011b33ecfb83dad8d8f749f20f329aba55f9d1c10f59b WHIRLPOOL 4f88e33d5b391fec5b1bdb09f5848be8dc8be0d14644c529d8cc82a04f556821a16bd1fc60838b98a67778405b10600d4409e70cd796432bdf08c77ce4c4ce94
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diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
new file mode 100644
index 000000000000..c7e432777f37
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
@@ -0,0 +1,126 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild,v 1.1 2014/10/30 11:52:05 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
+
+GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
+
+DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
+HOMEPAGE="http://www.poissonboltzmann.org/apbs/"
+#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
+SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug doc examples fast +fetk mpi openmp python tools"
+
+REQUIRED_USE="
+	mpi? ( !python )
+	python? ( tools fetk ${PYTHON_REQUIRED_USE} )"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	dev-libs/maloc[mpi=]
+	virtual/blas
+	sys-libs/readline
+	fetk? (
+		sci-libs/fetk
+		sci-libs/amd
+		sci-libs/umfpack
+		sci-libs/superlu
+	)
+	mpi? ( virtual/mpi )
+	python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${DEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen )
+"
+
+S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-multilib.patch
+	"${FILESDIR}"/${P}-manip.patch
+	"${FILESDIR}"/${P}-python.patch
+)
+
+src_prepare() {
+	cmake-utils_src_prepare
+	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+
+	sed \
+		-e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \
+		-e "/TOOLS_PATH/d" \
+		-i CMakeLists.txt || die
+	use doc && MAKEOPTS+=" -j1"
+	if use python; then
+		unset PATCHES || die
+		cd tools/python && distutils-r1_src_prepare
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_SKIP_RPATH=ON
+		-DTOOLS_PATH="${ED}"/usr
+		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
+		-DLIBRARY_INSTALL_PATH=$(get_libdir)
+		-DFETK_PATH="${EPREFIX}"/usr/
+		-DBUILD_SHARED_LIBS=ON
+		-DENABLE_QUIT=OFF
+		$(cmake-utils_use_build doc DOC)
+		$(cmake-utils_use_build tools TOOLS)
+		-DENABLE_BEM=OFF
+# ENABLE_BEM: Boundary element method using TABIPB
+		$(cmake-utils_use_enable debug DEBUG)
+		$(cmake-utils_use_enable debug VERBOSE_DEBUG)
+		$(cmake-utils_use_enable fast FAST)
+		$(cmake-utils_use_enable fetk FETK)
+		$(cmake-utils_use_enable mpi MPI)
+		$(cmake-utils_use_enable python PYTHON)
+# ENABLE_TINKER: Enable TINKER support
+# ENABLE_iAPBS: Enable iAPBS
+		-DENABLE_iAPBS=ON
+# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
+	)
+	cmake-utils_src_configure
+	if use python; then
+		cd tools/python && distutils-r1_src_configure
+	fi
+}
+
+src_compile(){
+	cmake-utils_src_compile
+	if use python; then
+		append-ldflags -L"${S}"/lib
+		cd tools/python && distutils-r1_src_compile
+	fi
+}
+
+src_test() {
+	cd tests || die
+	"${PYTHON}" apbs_tester.py -l log || die
+	grep -q 'FAILED' log && die "Tests failed"
+}
+
+src_install() {
+	dodir /usr/bin
+	cmake-utils_src_install
+	local i
+	for i in "${ED}"/usr/bin/*; do
+		if [[ ! "${i}" =~ .*apbs$ ]]; then
+			mv "${i}" "${i}-apbs" || die
+		fi
+	done
+	if use python; then
+		cd tools/python && distutils-r1_src_install
+		rm -rf "${ED}"/usr/share/apbs/tools/python || die
+	fi
+}