gentoo resync : 10.02.2020

2 files changed, 28 insertions, 46 deletions

diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 911dbff7ccca..d057f25d651e 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -3,5 +3,5 @@ AUX pdb2pqr 263 BLAKE2B 3cbd33cf9fb9fd6469c71d8d167ed0fb85ad7b87b6caf27dabb2490b
 AUX pdb2pqr-1.9.0-flags.patch 1392 BLAKE2B b6b6ac64f98944d85fc93c076d7258c8f980a0391d2cf086edc46bca3f4ef15a5cb720ef8ae2dc38007962a462fb88e92eb4f439c4f3267a5d1d83de5a848dd6 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b
 AUX pdb2pqr-1.9.0-install-py.patch 578 BLAKE2B 91ad4b40ce3d13b574ad6d9ea84e55b08803fa018490a7327dae5621a371adfeda509188c049144301cbc023f4407f6c0daf7b57e7d3c10d95d78ab570a6f540 SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2
 DIST pdb2pqr-src-1.9.0.tar.gz 9051969 BLAKE2B bacb2c65d319fb918a7a15b772c250398ffa991a93ee731ec15c8ae907304daf57282bf83c24f84d11945349a7f93f6f934575c117d4ce24d6530f14e60f3730 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f
-EBUILD pdb2pqr-1.9.0-r2.ebuild 2961 BLAKE2B b8aa0bba7cb9d94f8a8fcc3246ae63d6c8a92f8148fbf28b73b683425b00bedb58069250b06e6e08e21ca483343723738c70c8c7e19309559d05c032c5bb4d62 SHA512 5e613fe7a2e927634fde7f685a8ab9429f171d469280a21c8004dd718a22e4ed5bcfb30e0d5ea6426744e0a75f4ffd366ae93d7c458d6bd72e0269e7dcb006a4
+EBUILD pdb2pqr-1.9.0-r3.ebuild 2679 BLAKE2B 882e244c9764c317df96195e4c9049a8a23872c458487ed4e897263cc99b5e1fa8bb7a3a70bf34fda447d71767ee4eb59fa49c4beecbd04fd2577438bb8aaf8e SHA512 f5037488f9ecdc9be44fb1dcc15ec55db932fc4268b61db7d95375e0e22d9f54f0315a5c0eb4398919f8620c167adbdd5e632bcdb241724ebc77efb7e7442802
 MISC metadata.xml 511 BLAKE2B 70a1bf9ff6db44bdbae39b1f58ac5b80769738b2ce8fbb19b3bcb9fbf7cec2a9eab215a7a922025b9110673cb834255240adf10613fd78a8fea47fa7be4fbba9 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
index ad95f8f410fa..179e6448d605 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r2.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild
@@ -5,7 +5,7 @@ EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs
+inherit scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
 
 DESCRIPTION="Automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
 HOMEPAGE="https://www.poissonboltzmann.org/"
@@ -19,13 +19,15 @@ KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="${PYTHON_DEPS}
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
-	opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
-	pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+		sci-chemistry/openbabel-python[${PYTHON_MULTI_USEDEP}]
+		opal? ( dev-python/zsi[${PYTHON_MULTI_USEDEP}] )
+	')
+	pdb2pka? ( sci-chemistry/apbs[${PYTHON_SINGLE_USEDEP},-mpi] )"
 DEPEND="${RDEPEND}
 	dev-lang/swig:0"
 
@@ -43,6 +45,7 @@ pkg_setup() {
 		einfo "Allow usage of ${MAXATOMS} during calculations"
 	fi
 	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
 }
 
 src_prepare() {
@@ -54,15 +57,10 @@ src_prepare() {
 	epatch "${PATCHES[@]}"
 	tc-export CXX
 	rm -rf scons || die
-
-	python_copy_sources
 }
 
 src_configure() {
-	python_configure() {
-		cd "${BUILD_DIR}" || die
-
-		cat > build_config.py <<- EOF
+	cat > build_config.py <<- EOF
 		PREFIX="${D}/$(python_get_sitedir)/${PN}"
 		#URL="http://<COMPUTER NAME>/pdb2pqr/"
 		APBS="${EPREFIX}/usr/bin/apbs"
@@ -71,51 +69,35 @@ src_configure() {
 		MAX_ATOMS=${MAXATOMS}
 		BUILD_PDB2PKA=$(usex pdb2pka True False)
 		REBUILD_SWIG=True
-		EOF
-	}
-
-	python_foreach_impl python_configure
+	EOF
 }
 
 src_compile() {
-	python_compile() {
-		cd "${BUILD_DIR}" || die
-		escons
-	}
-	python_foreach_impl python_compile
+	escons
 }
 
 src_test() {
-	python_test() {
-		local myesconsargs=( -j1 )
-		cd "${BUILD_DIR}" || die
-		escons test
-		escons advtest
-		escons complete-test
-	}
-	python_foreach_impl python_test
+	local myesconsargs=( -j1 )
+	escons test
+	escons advtest
+	escons complete-test
 }
 
 src_install() {
 	dodir /usr/share/doc/${PF}/html
-	python_install() {
-		local lib
-
-		cd "${BUILD_DIR}" || die
+	local lib
 
-		escons install
+	escons install
 
-		find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
+	find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die
 
-		python_doscript "${FILESDIR}"/{${PN},pdb2pka}
+	python_doscript "${FILESDIR}"/{${PN},pdb2pka}
 
-		for lib in apbslib.py{,c,o}; do
-			dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
-		done
-		dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
-		python_optimize
-	}
-	python_foreach_impl python_install
+	for lib in apbslib.py{,c,o}; do
+		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
+	done
+	dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
+	python_optimize
 
 	if use doc; then
 		pushd doc > /dev/null