summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--sci-libs/cctbx/ChangeLog11
-rw-r--r--sci-libs/cctbx/Manifest14
-rw-r--r--sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild191
-rw-r--r--sci-libs/cctbx/metadata.xml12
4 files changed, 213 insertions, 15 deletions
diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
index fcf59b86e86f..52f40f2d49b9 100644
--- a/sci-libs/cctbx/ChangeLog
+++ b/sci-libs/cctbx/ChangeLog
@@ -1,6 +1,13 @@
# ChangeLog for sci-libs/cctbx
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.30 2012/10/19 10:36:38 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.31 2013/03/17 14:44:48 jlec Exp $
+
+*cctbx-2010.03.29.2334-r7 (17 Mar 2013)
+
+ 17 Mar 2013; Justin Lecher <jlec@gentoo.org>
+ +cctbx-2010.03.29.2334-r7.ebuild, metadata.xml:
+ Move to new python eclasses, log all file removals; bump to EAPI=5;add
+ missing die; use usex instead of custom check_use
19 Oct 2012; Justin Lecher <jlec@gentoo.org> cctbx-2010.03.29.2334-r6.ebuild:
Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest
index 5fbbf66d5818..c646037a3889 100644
--- a/sci-libs/cctbx/Manifest
+++ b/sci-libs/cctbx/Manifest
@@ -1,5 +1,5 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
AUX 2010.03.29.2334-boost.patch 18175 SHA256 f6a8a246dfd42e7981687802a0e00d933759d3c749c0344bfbfbfde12814f4d7 SHA512 e722312a878be229a24269471902bd1febe98c5510bfc50e1ba3a841c1a0228cdb7964e69703083850052e49e91899b229bc3543d90485ba50e79e7eceb11e2e WHIRLPOOL f87a78d93a94fb93fd243269fe1e5c0cfcc6beff02d936d2b609cece6ea9fbe08b5201c354f982df6ef5f09b84032a25b8a3cac357abf6279c6b5a5b2468e0e7
AUX 2010.03.29.2334-clipper.patch 2209 SHA256 e7c8bf813bedd3b67de5ce727d5f75e9635568769373f237e7b624ed143351b1 SHA512 cb3fc1f89d9a4008b4add3ef2ecf5b2aa8e875e41e169916859a8e508858bc9548023bb552d4cb3794c46788eaa325c75bb858c7c08799b87f2e31bef57cf69a WHIRLPOOL 84b427cfc9ddba9891197f8185123a8f5831e6a9beaafe58ced2f52ea3d492217cbb5264f3118ec9f27b12746141b788e9464a66b00c56f54b786bd3aada9351
@@ -10,13 +10,13 @@ AUX 2010.03.29.2334-soname.patch 5177 SHA256 dd4ea6dbf34c1b2d9572adec5a33fe6a73b
AUX 2010.03.29.2334-tst_server.py.patch 774 SHA256 df058d16d2dc5beaac9f1a1fbf2e640994c7e881d449eb01ac338dadbfb15ac3 SHA512 490918c3139355ecb0430d908ccafc6d66cb25ec7df285cedbb983d80f3473425c72d0766262c557c0c783626479edd2528eaf83b1decdeba416dde193472d5a WHIRLPOOL cc15b95661d8cba66bc3e06b3589188582c5e637faa860c70a4bbc53450a02afb36ec14c51796fe34441bd74842c06c938e22258a5ea5bf3264237a7afc169bc
DIST cctbx-2010.03.29.2334.tar.gz 15570372 SHA256 e1fae804caaf8593c7a3f32e4544046f4c00293063d9099721578cc8fbd17213 SHA512 7aafd647db49925fc1df16a9ccb4f8caf040b4d73e9601731eb3da3051467c3005fb2cc95b498501c899cd1bd378e6a6135cffe734cb4f93eccacbc13575b2c8 WHIRLPOOL 5954ce6ae8bd3a29deaa5d7f8b354d9468a87a01fc7d6aa9a0545e1d323b1ee209348e88270e2f50d7985b1916a7b5bf687dfdf871013d3ec35925fde253d9a0
EBUILD cctbx-2010.03.29.2334-r6.ebuild 6035 SHA256 dd202b25c89893981b4d4491b3d8b4cda6c1fe370d087c2fe36fac9615d57476 SHA512 0000173efa1d6af8a85dba7e2e9a80a84854742bd13ffd7d06f52ba6259ebe9731405b4894863e4ea15a548ddd3bc6519ddfe005e6710ed78d6038a90f0299a7 WHIRLPOOL c3fdb352659d783d95c80382d205940f3707e26551a30a853978fa1e0625a7053a45163b1664159ca1225fa36efea4e52db2280accb84020448af30b60fb9f73
-MISC ChangeLog 5543 SHA256 3ac1d5a6487c91307c4bd8986ed4f6b1fc87cff1b0987f3404e8ea67907c9c51 SHA512 cbad3dc64ca456d98953338a9f5c5ef7d34c95a644126173c2340845ee183b2fd63c48933ddf18b672f36638ac9256738a1a4c03eb1e3bff54d37811b94b842a WHIRLPOOL c1c1650573c1381483d9862e205ddc985672dac2b8499dd4a817567aad25200f5ea492a5a97cf235e942149c81734c87b31ee6ea0681040da6795e910324bc28
-MISC metadata.xml 765 SHA256 0bc826997f2850e1cdd72cc009127023696e9878caa1a615accd3205b234fc89 SHA512 3a1f6f8da7869ab6093e002135a6cfb266edbdc72d5ced047b526c27fd8e9a7330df9f5e1a7b10c0ca63f99da58cab26420dbe6899c52004f1508e48fc1b99e3 WHIRLPOOL c9aec1f4c7d8dc8f3e337ede705de7e5dd597c05e271227341b73e05105aa44a8e3cc6822216d35e7fb4f7bdce67709ee52c81cab18ba19b1271979a391202a6
+EBUILD cctbx-2010.03.29.2334-r7.ebuild 5796 SHA256 f424ffc9c31d264e59afe5fc4fe1011cc219da13b9a5bffe9ddae8ef863b8a0b SHA512 99c147f6777d72d86f41480d4a9a6028cb408758e159004a15771632bb74e3c7f051043dba0846a7d42494480de89394d5a563116dbe39f1c34d09f68aab69e0 WHIRLPOOL 03f79fad16101c027fce89107c133fc5472ffe22ab7d203d1286db42813acbe4a9eb90216e54183d1e67c9ce79526f1edd6e1e7034e59a7071aba1f680a5ae33
+MISC ChangeLog 5807 SHA256 c63540eff4b069e90a89bbda9d564e1bdafd629ab69c4b8c9651f22e713a3f8e SHA512 a05b49af96f283d468316316871e6abfd2ea7c9936c2dcf90b489d09887b694fd35e4251a62aa578eb00205f356b5f82fed3b7a9f672f3ed4eceeef88e2718d1 WHIRLPOOL 81db74ae27ad6e5dc91326aecf5b3ea3f1ee3cebec0e36c3cfae77a6430506ca5e5dfe925975ffc43446aeef455fb172ebc71e205d997d02a19f965660c835c3
+MISC metadata.xml 773 SHA256 6d424e7d549ba25e0ed4efaa2114679116006dca9592bac473a78baef48af1f0 SHA512 81ddc8d7808b9ca772955e865e49bcff68fc686672679758433d0d3bf8d27047f9dfeb29b36e72bd0b5c86c4a1e50ecd01bce96c71d0790084a0ef5894094899 WHIRLPOOL dee8ca57313ed6cecef6f4108f06feb614fe4f450f2feeacf88a9da534a0a6ebb7b791abb19fed1f9cff771579fec96883a63caf6d4b2c3b3c2e8cf6ff799746
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.19 (GNU/Linux)
-Comment: GPGTools - http://gpgtools.org
-iEYEAREIAAYFAlCBLTcACgkQgAnW8HDreRaCaACguLxjDuYVW7crdZj3YutRUvTi
-7xMAoK0enMbzgR1U391QsNwoKnlMH9y3
-=PQP2
+iEYEAREKAAYFAlFF1uUACgkQgAnW8HDreRbviQCgve8ONmbG8e2xr/h9WwMpI7T6
+IWEAmwZkxpEXSQuMjXvciU+lejwP0sT0
+=bVRm
-----END PGP SIGNATURE-----
diff --git a/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild
new file mode 100644
index 000000000000..d8e23ec40267
--- /dev/null
+++ b/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild
@@ -0,0 +1,191 @@
+# Copyright 1999-2013 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-r7.ebuild,v 1.1 2013/03/17 14:44:48 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+PYTHON_DEPEND="2"
+
+inherit eutils fortran-2 prefix python-single-r1 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 -> ${P}.tar.gz"
+
+LICENSE="cctbx-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="+minimal openmp threads"
+
+REQUIRED_USE="?? ( openmp threads )"
+
+RDEPEND="
+ >=dev-libs/boost-1.48[python]
+ sci-libs/clipper
+ sci-libs/fftw
+ !minimal? (
+ sci-chemistry/cns
+ sci-chemistry/shelx )"
+DEPEND="${RDEPEND}
+ !prefix? ( >=dev-util/scons-1.2[${PYTHON_USEDEP}] )"
+
+S="${WORKDIR}"
+MY_S="${WORKDIR}"/cctbx_sources
+MY_B="${WORKDIR}"/cctbx_build
+
+pkg_setup() {
+ use openmp && FORTRAN_NEED_OPENMP="1"
+ 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 ${PN} with OpenMP, abort now,"
+ ewarn "and switch CC to an OpenMP capable compiler"
+ FORTRAN_NEED_OPENMP=1
+ fi
+ fortran-2_pkg_setup
+ python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ local opts
+ local optsld
+
+ epatch \
+ "${FILESDIR}"/${PV}-tst_server.py.patch \
+ "${FILESDIR}"/${PV}-boost.patch \
+ "${FILESDIR}"/${PV}-clipper.patch \
+ "${FILESDIR}"/${PV}-flags.patch \
+ "${FILESDIR}"/${PV}-soname.patch \
+ "${FILESDIR}"/${PV}-gcc-4.6.patch \
+ "${FILESDIR}"/${PV}-gcc-4.7.patch
+
+ eprefixify "${MY_S}"/scitbx/libtbx_refresh.py
+
+ rm -rvf "${MY_S}/boost" "${MY_S}/PyCifRW" >> "${T}"/clean.log || die
+ if ! use prefix; then
+ rm -rvf "${MY_S}/scons" >> "${T}"/clean.log || die
+ echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py || die
+ fi
+
+ find "${MY_S}/clipper" -name "*.h" -print -delete >> "${T}"/clean.log || die
+
+ sed \
+ -e "/LIBS/s:boost_python:boost_python-$(echo ${EPYTHON} | sed 's/python//'):g" \
+ -i "${MY_S}"/boost_adaptbx/SConscript "${MY_S}"/scitbx/boost_python/SConscript || die
+}
+
+src_configure() {
+ local compiler
+ local myconf
+
+ myconf="${MY_S}/libtbx/configure.py"
+
+ compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+ myconf="${myconf} --compiler=${compiler}"
+
+ # Additional USE flag usage
+ myconf="${myconf} --enable-openmp-if-possible=$(usex openmp true false)"
+
+ use threads && USEthreads="--enable-boost-threads"
+
+ 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}"
+
+ ${EPYTHON} ${myconf} || die "configure failed"
+}
+
+src_compile() {
+ local makeopts_exp
+
+ cd "${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 \
+ -print >> "${T}"/clean.log || die
+ find "${S}" -type d -empty -delete -print >> "${T}"/clean.log || die
+ find "${MY_B}" -maxdepth 1 -type f -delete -print >> "${T}"/clean.log || die
+ eend
+
+ dobin "${MY_B}"/bin/*
+ rm -vrf "${MY_B}/bin" >> "${T}"/clean.log || die
+ dolib.so "${MY_B}"/lib/lib*
+ mv "${ED}"/usr/$(get_libdir)/libscitbx_min{,i}pack.so || die
+ rm -vf "${MY_B}"/lib/lib* >> "${T}"/clean.log || die
+
+ for lib in "${ED}"/usr/$(get_libdir)/*.so; do
+ baselib=$(basename ${lib})
+ mv ${lib}{,.0.0} || die
+ dosym ${baselib}.0.0 /usr/$(get_libdir)/${baselib}
+ done
+
+ insinto /usr/include
+ doins -r "${MY_B}"/include/* || die
+ rm -rvf "${MY_B}/include" >> "${T}"/clean.log || die
+
+ 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 *
+ exeinto $(python_get_sitedir)
+ doexe "${MY_B}"/lib/*
+ rm -rvf "${MY_B}/lib" >> "${T}"/clean.log || die
+
+ 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
+
+ python_optimize
+}
diff --git a/sci-libs/cctbx/metadata.xml b/sci-libs/cctbx/metadata.xml
index 4648e788d94d..a259ded7c025 100644
--- a/sci-libs/cctbx/metadata.xml
+++ b/sci-libs/cctbx/metadata.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- <name>Justin Lecher (jlec)</name>
- </maintainer>
- <longdescription>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ <name>Justin Lecher (jlec)</name>
+ </maintainer>
+ <longdescription>
The Computational Crystallography Toolbox (cctbx) is being developed
as the open source component of the PHENIX system. The goal of
the PHENIX project is to advance automation of macromolecular structure