sci-libs/ccp4-libs: Bump to EAPI=5 and new python eclasses, respect AR and RANLIB, #446350; drop silly PYTHONPATH from init files, #390715

(Portage version: 2.2.0_alpha173/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

3 files changed, 440 insertions, 1 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 79b3660d3f39..13ad4f5536e6 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-libs/ccp4-libs
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.54 2013/02/27 16:46:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.55 2013/05/03 16:19:50 jlec Exp $
+
+*ccp4-libs-6.1.3-r12 (03 May 2013)
+
+  03 May 2013; Justin Lecher <jlec@gentoo.org> +ccp4-libs-6.1.3-r12.ebuild,
+  +files/6.1.3-no-pypath.patch:
+  Bump to EAPI=5 and new python eclasses, respect AR and RANLIB, #446350; drop
+  silly PYTHONPATH from init files, #390715
 
   27 Feb 2013; Justin Lecher <jlec@gentoo.org> files/6.1.3-lapack.patch,
   ccp4-libs-6.1.3-r11.ebuild:
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild
new file mode 100644
index 000000000000..1201077fd3b1
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild
@@ -0,0 +1,345 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild,v 1.1 2013/05/03 16:19:50 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+MY_P="${P/-libs}"
+
+PATCH_TOT="0"
+
+DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
+# patch tarball from upstream
+	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# patches created by us
+	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+
+for i in $(seq $PATCH_TOT); do
+	NAME="PATCH${i}[1]"
+	SRC_URI="${SRC_URI}
+		${SRC}/${PV}/patches/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	!<sci-chemistry/ccp4-6.1.3
+	!<sci-chemistry/ccp4-apps-${PV}-r10
+	app-shells/tcsh
+	dev-lang/tcl
+	>=sci-libs/cbflib-0.9.2.2
+	sci-libs/fftw:2.1
+	sci-libs/mmdb
+	sci-libs/monomer-db
+	sci-libs/ssm
+	virtual/jpeg
+	virtual/lapack
+	virtual/blas"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+MAKEOPTS+=" -j1"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	tc-export PKG_CONFIG RANLIB AR
+
+	sed \
+		-e "/^AR/s:ar:$(tc-getAR):g" \
+		-i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
+
+	einfo "Applying upstream patches ..."
+	for patch in $(seq $PATCH_TOT); do
+		base="PATCH${patch}"
+		dir=$(eval echo \${${base}[0]})
+		p=$(eval echo \${${base}[1]})
+		pushd "${dir}" >& /dev/null
+		ccp_patch "${DISTDIR}/${p}"
+		popd >& /dev/null
+	done
+	einfo "Done."
+	echo
+
+	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+	einfo "Applying Gentoo patches ..."
+	# fix buffer overflows wrt bug 339706
+	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
+
+	# it tries to create libdir, bindir etc on live system in configure
+	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
+
+	# gerror_ gets defined twice on ppc if you're using gfortran/g95
+	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
+
+	# make creation of libccif.so smooth
+	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
+
+	# lets try to build libmmdb seperatly
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
+
+	# unbundle libjpeg and cbflib
+	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
+
+	# Fix missing DESTIDR
+	# not installing during build
+	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
+	sed \
+		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
+		-i configure || die
+
+	# Fix upstreams code
+	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
+
+	# use pkg-config to detect BLAS/LAPACK
+	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
+
+	# proto type changing in version 0.9.2.2
+	ccp_patch "${FILESDIR}"/${PV}-cbf.patch
+
+	# proto type changing in version 0.9.2.2
+	ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	# not needed, we have it extra
+	rm -rf src/rapper/{libxml2,gc7.0} || die
+
+	sed \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		-e 's:-Wl,-rpath,$CLIB::g' \
+		-e 's: -rpath $CLIB::g' \
+		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
+		-e 's:sleep 1:sleep .2:g' \
+		-i configure || die
+
+	gnuconfig_update
+
+	for i in lib/DiffractionImage src/rapper src/pisa; do
+		pushd ${i} > /dev/null
+			sed 's:-g::g' -i configure* || die
+			eautoreconf
+		popd > /dev/null
+	done
+
+	## unbundle libssm
+	sed -e '/libdir/s:ssm::g' -i Makefile.in || die
+	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
+}
+
+src_configure() {
+	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
+
+	# Build system is broken if we set LDFLAGS
+	userldflags="${LDFLAGS}"
+	export SHARED_LIB_FLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "$(tc-getFC)" = "ifort" ]]; then
+		if use ia64; then
+			GENTOO_OSNAME="ia64_linux_intel"
+		else
+			# Should be valid for x86, maybe amd64
+			GENTOO_OSNAME="linux_intel_compilers"
+		fi
+	else
+		# Should be valid for x86 and amd64, at least
+		GENTOO_OSNAME="linux"
+	fi
+
+	# Sets up env
+	ln -s \
+		ccp4.setup-bash \
+		"${S}"/include/ccp4.setup || die
+
+	# We agree to the license by emerging this, set in LICENSE
+	sed -i \
+		-e "s~^\(^agreed=\).*~\1yes~g" \
+		"${S}"/configure || die
+
+	# Fix up variables -- need to reset CCP4_MASTER at install-time
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+		"${S}"/include/ccp4.setup* || die
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=$(tc-getFC)
+	export FOPTIM=${FFLAGS:- -O2}
+
+	export SHARE_LIB="\
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
+		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw="${EPREFIX}/usr" \
+		--with-warnings \
+		--disable-cctbx \
+		--disable-clipper \
+		--disable-ssm \
+		--tmpdir="${TMPDIR}" \
+		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
+		--libdir="${EPREFIX}/usr/$(get_libdir)" \
+		${GENTOO_OSNAME} || die "configure failed"
+}
+
+src_compile() {
+	emake DESTDIR="${D}" onlylib
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	emake \
+		DESTDIR="${D}" \
+		includedir="${EPREFIX}/usr/include" \
+		library_includedir="${EPREFIX}/usr/include" \
+		install
+
+	sed \
+		-e "330,1000d" \
+		-i "${S}"/include/ccp4.setup-sh || die
+
+	sed \
+		-e "378,1000d" \
+		-i "${S}"/include/ccp4.setup-csh || die
+
+	sed \
+		-e "s:-${PV/-r*/}::g" \
+		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
+		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
+		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
+		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
+		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
+		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
+		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
+		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
+		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
+		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
+		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
+		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
+		-e "s:^\(.*export CLIBS=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*setenv CLIBS \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*export CLIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*setenv CLIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
+		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
+		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
+		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
+		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
+		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
+		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
+		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
+		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
+		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
+		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
+		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
+		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
+		-e "/CCP4_HELPDIR/d" \
+		-e "/IMOSFLM_VERSION/d" \
+		-i "${S}"/include/ccp4.setup* || die
+
+	# Don't check for updates on every sourcing of /etc/profile
+	sed -i \
+		-e "s:\(eval python.*\):#\1:g" \
+		"${S}"/include/ccp4.setup* || die
+
+	# Libs
+	for file in "${S}"/lib/*; do
+		if [[ -d ${file} ]]; then
+			continue
+		elif [[ -x ${file} ]]; then
+			dolib.so ${file}
+		else
+			insinto /usr/$(get_libdir)
+			doins ${file}
+		fi
+	done
+
+	prune_libtool_files
+
+	sed \
+		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
+		-i "${S}"/include/ccp4.setup-sh || die
+
+	# Setup scripts
+	insinto /etc/profile.d
+	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
+	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
+	rm -f "${S}"/include/ccp4.setup*
+
+	# Data
+	insinto /usr/share/ccp4/data/
+	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
+
+	# Environment files, setup scripts, etc.
+	rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
+	insinto /usr/share/ccp4/
+	doins -r "${S}"/include
+
+	dodoc "${S}"/lib/data/*.doc
+	newdoc "${S}"/lib/data/README DATA-README
+}
+
+pkg_postinst() {
+	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
+	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch b/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch
new file mode 100644
index 000000000000..6a0cb5be7c3d
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch
@@ -0,0 +1,87 @@
+ include/ccp4.setup-bash |  8 --------
+ include/ccp4.setup-csh  | 11 -----------
+ include/ccp4.setup-sh   |  8 --------
+ include/ccp4.setup-zsh  | 10 ----------
+ 4 files changed, 37 deletions(-)
+
+diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash
+index 3a67791..80aef23 100755
+--- a/include/ccp4.setup-bash
++++ b/include/ccp4.setup-bash
+@@ -185,14 +185,6 @@ else
+   fi
+ fi
+ 
+-#Python path for the subprocess fixed module
+-
+-if [ $ccp4_first_in_path -eq 1 ]; then
+-    setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+-else
+-    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
+-fi
+-
+ ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
+ setenv PLOT_COMMAND   'lp -s -dmicrolaser'  
+ setenv PRINT_COMMAND  'lp -s -denscript'    
+diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh
+index 10d3ab8..72cc479 100755
+--- a/include/ccp4.setup-csh
++++ b/include/ccp4.setup-csh
+@@ -177,17 +177,6 @@ else
+   endif
+ endif
+ 
+-#Python path for the subprocess fixed module
+-if (${?PYTHONPATH}) then
+-  if ($ccp4_first_in_path) then
+-      setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+-  else
+-      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
+-  endif
+-else
+-    setenv PYTHONPATH ${CCP4}/share/python
+-endif
+-
+ ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
+ setenv PLOT_COMMAND   'lp -s -dmicrolaser'  
+ setenv PRINT_COMMAND  'lp -s -denscript'    
+diff --git a/include/ccp4.setup-sh b/include/ccp4.setup-sh
+index 2298bba..44643ab 100755
+--- a/include/ccp4.setup-sh
++++ b/include/ccp4.setup-sh
+@@ -225,14 +225,6 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
+ 
+ ################### EXPERIENCED USERS STOP HERE #####################
+ 
+-#Python path for the subprocess fixed module
+-
+-if test $ccp4_first_in_path -eq 1; then
+-    export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
+-else
+-    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
+-fi
+-
+ ################### THE REST SHOULDN'T NEED EDITING #####################
+ 
+ ### dbCCP4i database handler setup ###
+diff --git a/include/ccp4.setup-zsh b/include/ccp4.setup-zsh
+index 660b35b..e453db9 100755
+--- a/include/ccp4.setup-zsh
++++ b/include/ccp4.setup-zsh
+@@ -154,16 +154,6 @@ export CCP4_BIN=$CBIN
+ CLASSPATH=$CBIN:$CLASSPATH               # edit this if necessary
+ export CLASSPATH
+ 
+-#Python path for the subprocess fixed module
+-
+-if ($ccp4_first_in_path) then
+-    PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
+-    export PYTHONPATH
+-else
+-    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
+-    export PYTHONPATH
+-fi
+-
+ ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
+ export PLOT_COMMAND='lpr'  
+ export PRINT_COMMAND='lpr'