proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 138 insertions, 0 deletions

diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest
new file mode 100644
index 000000000000..33872db5dc96
--- /dev/null
+++ b/sci-chemistry/phaser/Manifest
@@ -0,0 +1 @@
+DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804
diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
new file mode 100644
index 000000000000..5311cb332785
--- /dev/null
+++ b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
@@ -0,0 +1,13 @@
+diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
+index 3b1bd3a..8939a74 100755
+--- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
++++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
+@@ -802,8 +802,6 @@ class environment:
+     else:
+       action = self.write_bin_sh_dispatcher
+       ext = ""
+-      try: os.chmod(source_file, 0755)
+-      except OSError: pass
+     target_file_ext = target_file + ext
+     remove_or_rename(target_file_ext)
+     try: action(source_file, target_file_ext)
diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml
new file mode 100644
index 000000000000..6b4826474daa
--- /dev/null
+++ b/sci-chemistry/phaser/metadata.xml
@@ -0,0 +1,9 @@
+<?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>
+    <description>ccp4 maintainer</description>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild
new file mode 100644
index 000000000000..86fa57f52603
--- /dev/null
+++ b/sci-chemistry/phaser/phaser-2.1.4.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic python-single-r1 toolchain-funcs
+
+CCP4VER="6.1.13"
+
+DESCRIPTION="A program for phasing macromolecular crystal structures"
+HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser"
+SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz"
+
+LICENSE="|| ( phaser phaser-com ccp4 )"
+SLOT="0"
+#KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
+IUSE="openmp"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+		  app-shells/tcsh"
+
+S="${WORKDIR}"/ccp4-${CCP4VER}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/phaser-2.1.4-chmod.patch \
+		"${FILESDIR}"/phaser-2.1.4-ldflags.patch
+
+	use openmp && append-flags -fopenmp
+
+	for i in ${CXXFLAGS}; do
+		OPTS="${OPTS} \"${i}\","
+	done
+
+	OPTS=${OPTS%,}
+
+	sed -i \
+		-e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
+		"${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
+
+	for i in ${LDFLAGS}; do
+		OPTSLD="${OPTSLD} \"${i}\","
+	done
+
+	sed -i \
+		-e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \
+		-e "s:\[\"-static:\[${OPTSLD} \"-static:g" \
+		"${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
+
+}
+
+src_configure() {
+	local compiler
+	local mtype
+	local mversion
+	local nproc
+
+	# Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc,
+	# unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC,
+	# darwin_c++, darwin_gcc.  The build systems seems to prepend
+	# unix_ all by itself.  Can this be derived from $(tc-getCC)?
+	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+
+	# Breaks cross compilation.
+	mtype=$(src/${PN}/bin/machine_type)
+	mversion=$(src/${PN}/bin/machine_version)
+
+	einfo "Creating build directory"
+	mkdir build
+	cd build
+	ln -sf "${S}/lib/cctbx/cctbx_sources/scons"  scons
+	ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx
+
+	einfo "Configuring phaser components"
+	$(PYTHON) "libtbx/configure.py" \
+		--build=release \
+		--compiler=${compiler} \
+		--repository="${S}"/src/${PN}/source \
+		--repository="${S}"/lib/cctbx/cctbx_sources \
+		--static_libraries \
+		ccp4io="${S}" \
+		mmtbx \
+		phaser || die "configure.py failed"
+}
+
+src_compile() {
+	nproc=`echo "-j1 ${MAKEOPTS}" \
+		| sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"`
+
+	cd build
+	einfo "Setting up build environment"
+	source setpaths.sh
+
+	einfo "Compiling phaser components"
+	libtbx.scons -j ${nproc} || die "libtbx.scons failed"
+}
+
+src_install() {
+	dobin build/exe/phaser || die
+
+	cat >> "${T}"/53${PN} <<- EOF
+	PHASER="${EPREFIX}/usr/bin"
+	PHASER_ENVIRONMENT="1"
+	PHASER_MTYPE="${mtype}"
+	PHASER_MVERSION="${mversion}"
+	PHASER_VERSION="${PV}"
+	EOF
+
+	doenvd "${T}"/53${PN} || die
+}