Add fixes for boost-1.48 and its PyABI specific libs, #401393

Package-Manager: portage-2.2.0_alpha85/cvs/Linux x86_64

3 files changed, 222 insertions, 3 deletions

diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
index 8f241264f1f0..eb6bad5ee285 100644
--- a/sci-libs/cctbx/ChangeLog
+++ b/sci-libs/cctbx/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/cctbx
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.21 2011/12/04 19:03:25 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.22 2012/02/10 20:20:48 jlec Exp $
+
+*cctbx-2010.03.29.2334-r6 (10 Feb 2012)
+
+  10 Feb 2012; Justin Lecher <jlec@gentoo.org>
+  +cctbx-2010.03.29.2334-r6.ebuild:
+  Add fixes for boost-1.48 and its PyABI specific libs, #401393
 
 *cctbx-2010.03.29.2334-r5 (04 Dec 2011)
 
diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest
index d7fa74d755b5..c8705fba4de0 100644
--- a/sci-libs/cctbx/Manifest
+++ b/sci-libs/cctbx/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX 2010.03.29.2334-boost.patch 18175 RMD160 cf972e6d792d98d152eb18453f0349c87efbbb97 SHA1 f9dac88aea0e898259537a343650cbcd53b6f01f SHA256 f6a8a246dfd42e7981687802a0e00d933759d3c749c0344bfbfbfde12814f4d7
 AUX 2010.03.29.2334-clipper.patch 2209 RMD160 1bfc13f0834e837a55f0e41554649acd1e45b80c SHA1 a81ee2cc94805b6ef1e609c2ea402a1c9f429d62 SHA256 e7c8bf813bedd3b67de5ce727d5f75e9635568769373f237e7b624ed143351b1
 AUX 2010.03.29.2334-flags.patch 3336 RMD160 fdbb0b71499e00c666629e1ff04b5bdcbe376b13 SHA1 ef97099dbd93727bd356015f22e82480a48e1a0c SHA256 769edb3e5dcb608b54ab4d33c5933b523f73ff62c6cb627c4eb4b1a2086e40b1
@@ -8,5 +11,13 @@ DIST cctbx-2010.03.29.2334.tar.gz 15570372 RMD160 e543578dbe6568f5f8f80b3ce7a20b
 EBUILD cctbx-2010.03.29.2334-r3.ebuild 6033 RMD160 595dcb177bdc263203bb34911cd526a0d464c0fe SHA1 4291cecbdd0308ec84cd139caf4d1c25a2f9c959 SHA256 870992421ec6aa56c303d18efb999fa7fb8909952bddc91e695c1b9f1b8b0860
 EBUILD cctbx-2010.03.29.2334-r4.ebuild 6073 RMD160 67c2c2d0bd3d709d094e443ad53769cad1e7c38d SHA1 29c0c3edaee63dbd896b0e670835263055584895 SHA256 e6b8b4f69ac23fd7ade90a03d481eb47d002187f157ab0e420e77ca5a668f38b
 EBUILD cctbx-2010.03.29.2334-r5.ebuild 5767 RMD160 b101169cf17740d657442f0a0653a393189c9d92 SHA1 3d50ecd149c7dc66589f2e802d676997f6cfed8a SHA256 750a609b11c6f66aa9cd93c38a8161ebec00c4f4ede9ded85d709f3e6e36cfaa
-MISC ChangeLog 4082 RMD160 b1c5d40f088221ed98ae7b6e08a2d206b0c12487 SHA1 80f40fb723ec712f08770e2f81a012ab21830f8d SHA256 497a14e028392b8eaf35b36fec2fdea903c64a297c72a57f9f5c004653ed3c39
+EBUILD cctbx-2010.03.29.2334-r6.ebuild 5922 RMD160 e397381e98b0277339299849bf4844bcb7530dce SHA1 fac114f740aa3d46dfafb8d263df55de65915a99 SHA256 8f836373246b89b51884835087bf0b50989aadd76ad8b05270d4a61ccde0548f
+MISC ChangeLog 4271 RMD160 f8ffee7a3b36ed278707f031706f23399887bad5 SHA1 8ddd9e285aea225bb4f7ff6f698a6f138d0fbe68 SHA256 bdb958c11747897abb2f3d525142ca52bde1a8dd30dc15577cf784badd59b7d3
 MISC metadata.xml 765 RMD160 1ee2d6fab10061444dcb6f76effe52f1256ea0ac SHA1 929f35f80d2da1d8eacba6dcf715b5421a7f1393 SHA256 0bc826997f2850e1cdd72cc009127023696e9878caa1a615accd3205b234fc89
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.18 (GNU/Linux)
+
+iEYEAREKAAYFAk81fCsACgkQgAnW8HDreRb88gCgwfq6ROeZNbOJqv4ol8SbETOV
+fV0AniAnUV+fYxPkDarYEVuIfwlvpkWs
+=oxdV
+-----END PGP SIGNATURE-----
diff --git a/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild
new file mode 100644
index 000000000000..6ba4b3f82bea
--- /dev/null
+++ b/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild
@@ -0,0 +1,202 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild,v 1.1 2012/02/10 20:20:48 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils fortran-2 prefix python toolchain-funcs
+
+MY_PV="${PV//./_}"
+
+DESCRIPTION="Computational Crystallography Toolbox"
+HOMEPAGE="http://cctbx.sourceforge.net/"
+SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"
+
+LICENSE="cctbx-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="+minimal openmp threads"
+
+RDEPEND="
+	virtual/fortran
+	>dev-libs/boost-1.48[python]
+	sci-libs/clipper
+	sci-libs/fftw
+	!minimal? (
+		sci-chemistry/cns
+		sci-chemistry/shelx )"
+DEPEND="${RDEPEND}
+	>=dev-util/scons-1.2"
+
+S="${WORKDIR}"
+MY_S="${WORKDIR}"/cctbx_sources
+MY_B="${WORKDIR}"/cctbx_build
+
+pkg_setup() {
+	use openmp && FORTRAN_NEED_OPENMP="1"
+	fortran-2_pkg_setup
+	if use openmp && ! tc-has-openmp; then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc"
+		ewarn "If you want to build ${PN} with OpenMP, abort now,"
+		ewarn "and switch CC to an OpenMP capable compiler"
+	fi
+	python_set_active_version 2
+}
+
+src_prepare() {
+	local opts
+	local optsld
+
+	epatch \
+		"${FILESDIR}"/${PV}-tst_server.py.patch \
+		"${FILESDIR}"/${PV}-boost.patch \
+		"${FILESDIR}"/${PV}-clipper.patch \
+		"${FILESDIR}"/${PV}-flags.patch \
+		"${FILESDIR}"/${PV}-soname.patch \
+		"${FILESDIR}"/${PV}-gcc-4.6.patch
+
+	eprefixify "${MY_S}"/scitbx/libtbx_refresh.py
+
+	rm -rf "${MY_S}/scons" "${MY_S}/boost" "${MY_S}/PyCifRW" || die
+	find "${MY_S}/clipper" -name "*.h" -delete || die
+
+	sed \
+		-e "/LIBS/s:boost_python:boost_python-${PYTHON_ABI}:g" \
+		-i "${MY_S}"/boost_adaptbx/SConscript "${MY_S}"/scitbx/boost_python/SConscript || die
+
+	echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py
+}
+
+src_configure() {
+	local compiler
+	local myconf
+
+	myconf="${MY_S}/libtbx/configure.py"
+
+	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+	myconf="${myconf} --compiler=${compiler}"
+
+	# Additional USE flag usage
+	check_use openmp
+	myconf="${myconf} --enable-openmp-if-possible=${USE_openmp}"
+
+	use threads && USEthreads="--enable-boost-threads" && \
+		ewarn "If using boost threads openmp support is disabled"
+
+	myconf="${myconf} ${USE_threads} --scan-boost --use_environment_flags"
+
+	mkdir "${MY_B}" && myconf="${myconf} --current_working_directory=${MY_B}"
+	cd "${MY_B}"
+
+	myconf="${myconf} --build=release fftw3tbx rstbx smtbx mmtbx clipper_adaptbx fable"
+	einfo "configuring with ${python} ${myconf}"
+
+	$(PYTHON) ${myconf} || die "configure failed"
+}
+
+src_compile() {
+	local makeopts_exp
+
+	cd "${MY_B}"
+
+	makeopts_exp=${MAKEOPTS/j/j }
+	makeopts_exp=${makeopts_exp%-l[0-9]*}
+
+	source setpaths_all.sh
+
+	einfo "compiling with libtbx.scons ${makeopts_exp}"
+	libtbx.scons ${makeopts_exp} .|| die "make failed"
+}
+
+src_test(){
+	source "${MY_B}"/setpaths_all.sh
+	libtbx.python $(libtbx.show_dist_paths boost_adaptbx)/tests/tst_rational.py && \
+	libtbx.python ${SCITBX_DIST}/run_tests.py ${MAKEOPTS_EXP} && \
+	libtbx.python ${CCTBX_DIST}/run_tests.py  ${MAKEOPTS_EXP} \
+	|| die "test failed"
+}
+
+src_install(){
+	local lib baselib
+#	find cctbx_build/ -type f \( -name "*.py" -o -name "*sh" \) -exec \
+#	sed -e "s:${MY_S}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
+#	    -e "s:${MY_B}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build:g"  \
+#	    -i '{}' \; || die "Fail to correct path"
+
+	sed \
+		-e "s:${MY_B}:${EPREFIX}/usr:g" \
+		-e "s:${MY_S}:${EPREFIX}/$(python_get_sitedir):g" \
+		-i "${MY_B}/libtbx_env" || die
+
+	insinto /usr/share/cctbx
+	doins "${MY_B}/libtbx_env" || die
+
+	ebegin "removing unnessary files"
+		rm -r "${S}"/cctbx_sources/{clipper,ccp4io,ucs-fonts,TAG} || die "failed to remove uneeded scons"
+		find -O3 "${S}" -type f \
+			\( -name "*conftest*" -o -name "*.o" -o -name "*.c" -o -name "*.f" -o -name "*.cpp" -o \
+			-name "*.pyc" -o -name "SCons*" -o -name "Makefile" -o -name "config.log" \) -delete || die
+		find "${S}" -type d -empty -delete || die
+		find "${MY_B}" -maxdepth 1 -type f -delete || die
+	eend
+
+	dobin "${MY_B}"/bin/* || die
+	rm -rf "${MY_B}/bin"
+	dolib.so "${MY_B}"/lib/lib* || die
+	mv "${ED}"/usr/$(get_libdir)/libscitbx_min{,i}pack.so || die
+	rm -f "${MY_B}"/lib/lib*
+
+	for lib in "${ED}"/usr/$(get_libdir)/*.so; do
+		baselib=$(basename ${lib})
+		mv ${lib}{,.0.0}
+		dosym ${baselib}.0.0 /usr/$(get_libdir)/${baselib}
+	done
+
+	insinto /usr/include
+	doins -r "${MY_B}"/include/* || die
+	rm -rf "${MY_B}/include"
+
+	insinto /usr/libexec/${PN}
+	doins -r "${MY_B}"/* || die
+	find "${ED}"/usr/libexec/${PN} -type f -exec chmod 755 '{}' \;
+
+	cd "${MY_S}"
+	insinto $(python_get_sitedir)
+	doins -r * || die
+	exeinto $(python_get_sitedir)
+	doexe "${MY_B}"/lib/* || die
+	rm -rf "${MY_B}/lib"
+
+	sed \
+		-e "/PYTHONPATH/s:${MY_S}:$(python_get_sitedir):g" \
+		-e "/PYTHONPATH/s:${MY_B}:$(python_get_sitedir):g" \
+		-e "/LD_LIBRARY_PATH/s:${MY_B}/lib:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "/PATH/s:${MY_B}/bin:${EPREFIX}/usr/bin:g" \
+		-e "/PATH/s:${MY_B}/exe:${EPREFIX}/usr/bin:g" \
+		-e "/exec/s:${MY_S}:$(python_get_sitedir):g" \
+		-e "/LIBTBX_BUILD/s:${MY_B}:${EPREFIX}/usr/share/cctbx:g" \
+		-e "s:${MY_B}/exe_dev/:${EPREFIX}/usr/libexec/${PN}/exe_dev/:g" \
+		-i "${ED}"/usr/bin/* || die
+
+}
+
+pkg_postinst () {
+	python_mod_optimize boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx chiltbx clipper_adaptbx crys3d fable fftw3tbx gltbx iotbx libtbx mmtbx omptbx rstbx scitbx smtbx spotfinder tntbx
+}
+
+pkg_postrm () {
+	python_mod_cleanup boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx chiltbx clipper_adaptbx crys3d fable fftw3tbx gltbx iotbx libtbx mmtbx omptbx rstbx scitbx smtbx spotfinder tntbx
+}
+
+check_use() {
+	for var in $@; do
+		if use ${var}; then
+			printf -v "USE_$var" True
+		else
+			printf -v "USE_$var" False
+		fi
+	shift
+	done
+}