sci-chemistry/pdb2pqr: Allow multi py ABI installations, clean installation

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 180 insertions, 1 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 0cea88aff125..73a419d9d14a 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.42 2014/10/27 17:17:03 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.43 2014/10/28 09:00:32 jlec Exp $
+
+*pdb2pqr-1.9.0-r1 (28 Oct 2014)
+
+  28 Oct 2014; Justin Lecher <jlec@gentoo.org> +pdb2pqr-1.9.0-r1.ebuild,
+  +files/pdb2pka, +files/pdb2pqr-1.9.0-install-py.patch, +files/pdb2pqr:
+  Allow multi py ABI installations, clean installation
 
   27 Oct 2014; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.9.0.ebuild:
   Add missing PYTHON_USEDEP
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pka b/sci-chemistry/pdb2pqr/files/pdb2pka
new file mode 100644
index 000000000000..2406b0c4773f
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pka
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+
+import subprocess
+import site
+import sys
+import os
+
+sitepackages = site.getsitepackages()[0]
+
+_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pka", "pka.py")]
+_cmd.extend(sys.argv[1:])
+
+subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr b/sci-chemistry/pdb2pqr/files/pdb2pqr
new file mode 100644
index 000000000000..8c0635aea94e
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+
+import subprocess
+import site
+import sys
+import os
+
+sitepackages = site.getsitepackages()[0]
+
+_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pqr.py")]
+_cmd.extend(sys.argv[1:])
+
+subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr)
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
new file mode 100644
index 000000000000..2695b013c66a
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch
@@ -0,0 +1,15 @@
+ SConscript-install.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/SConscript-install.py b/SConscript-install.py
+index e2f9f09..1fdf1a8 100644
+--- a/SConscript-install.py
++++ b/SConscript-install.py
+@@ -41,6 +41,7 @@ def installFile(file_name, build_target='install'):
+ 		if GetOption("clean"):

+ 			env.Default(result)

+ 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), result))

++		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))

+ 	else:

+ 		Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))

+ 

diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
new file mode 100644
index 000000000000..8c6e54ee0316
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild
@@ -0,0 +1,132 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild,v 1.1 2014/10/28 09:00:32 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs
+
+DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+HOMEPAGE="http://www.poissonboltzmann.org/"
+SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+IUSE="doc examples opal +pdb2pka"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-chemistry/openbabel[python]
+	sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
+	opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
+	pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
+DEPEND="${RDEPEND}
+	dev-lang/swig:0"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-flags.patch
+	"${FILESDIR}"/${P}-install-py.patch
+)
+
+pkg_setup() {
+	if [[ -z ${MAXATOMS} ]]; then
+		einfo "If you like to have support for more then 10000 atoms,"
+		einfo "export MAXATOMS=\"your value\""
+		export MAXATOMS=10000
+	else
+		einfo "Allow usage of ${MAXATOMS} during calculations"
+	fi
+	fortran-2_pkg_setup
+}
+
+src_prepare() {
+	find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
+
+	export CXXFLAGS="${CXXFLAGS}"
+	export LDFLAGS="${LDFLAGS}"
+
+	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
+		PREFIX="${ED}/$(python_get_sitedir)/${PN}"
+		#URL="http://<COMPUTER NAME>/pdb2pqr/"
+		APBS="${EPREFIX}/usr/bin/apbs"
+		#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
+		#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"
+		MAX_ATOMS=${MAXATOMS}
+		BUILD_PDB2PKA=$(usex pdb2pka True False)
+		REBUILD_SWIG=True
+		EOF
+	}
+
+	python_foreach_impl python_configure
+}
+
+src_compile() {
+	python_compile() {
+		cd "${BUILD_DIR}" || die
+		escons
+	}
+	python_foreach_impl python_compile
+}
+
+src_test() {
+	python_test() {
+		local myesconsargs=( -j1 )
+		cd "${BUILD_DIR}" || die
+		escons test
+		escons advtest
+		escons complete-test
+	}
+	python_foreach_impl python_test
+}
+
+src_install() {
+	dodir /usr/share/doc/${PF}/html
+	python_install() {
+		local lib
+
+		cd "${BUILD_DIR}" || die
+
+		escons install
+
+		find "${ED}"$(python_get_sitedir)/${PN}/{jmol,examples,doc,contrib} -delete || die
+
+		python_doscript "${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
+
+	if use doc; then
+		pushd doc > /dev/null
+		docinto html
+		dodoc -r *.html images pydoc
+		popd > /dev/null
+	fi
+
+	use examples && \
+		insinto /usr/share/${PN}/ && \
+		doins -r examples
+
+
+	dodoc *md NEWS
+}