Version Bump

(Portage version: 2.2.0_alpha41/cvs/Linux x86_64)

7 files changed, 217 insertions, 10 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index cfaa1c5dad28..1208728cdcab 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.36 2011/03/02 09:57:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.37 2011/06/28 17:01:28 jlec Exp $
+
+*coot-0.6.2 (28 Jun 2011)
+
+  28 Jun 2011; Justin Lecher <jlec@gentoo.org>
+  +files/0.6.2-clipper-config.patch, +files/0.6.2-gl.patch,
+  +files/0.6.2-mmdb-config.patch, coot-0.6.1.ebuild, +coot-0.6.2.ebuild,
+  metadata.xml:
+  Version Bump
 
   02 Mar 2011; Justin Lecher <jlec@gentoo.org> coot-0.6.1.ebuild:
   Correct Slots for gtk 3 introduction to tree
diff --git a/sci-chemistry/coot/coot-0.6.1.ebuild b/sci-chemistry/coot/coot-0.6.1.ebuild
index 004f9f761af9..9274fc43c921 100644
--- a/sci-chemistry/coot/coot-0.6.1.ebuild
+++ b/sci-chemistry/coot/coot-0.6.1.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.6.1.ebuild,v 1.12 2011/03/02 09:57:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.6.1.ebuild,v 1.13 2011/06/28 17:01:28 jlec Exp $
 
-EAPI="3"
+EAPI=3
 
 PYTHON_DEPEND="2"
 
@@ -89,13 +89,13 @@ src_configure() {
 	# Yes, this is broken behavior.
 	econf \
 		--includedir='${prefix}/include/coot' \
-		--with-gtkcanvas-prefix="${EPREFIX}"/usr \
-		--with-clipper-prefix="${EPREFIX}"/usr \
-		--with-mmdb-prefix="${EPREFIX}"/usr \
-		--with-ssmlib-prefix="${EPREFIX}"/usr \
-		--with-gtkgl-prefix="${EPREFIX}"/usr \
+		--with-gtkcanvas-prefix="${EPREFIX}/usr" \
+		--with-clipper-prefix="${EPREFIX}/usr" \
+		--with-mmdb-prefix="${EPREFIX}/usr" \
+		--with-ssmlib-prefix="${EPREFIX}/usr" \
+		--with-gtkgl-prefix="${EPREFIX}/usr" \
 		--with-guile \
-		--with-python="${EPREFIX}"/usr \
+		--with-python="${EPREFIX}/usr" \
 		--with-guile-gtk \
 		--with-gtk2 \
 		--with-pygtk
@@ -149,5 +149,6 @@ src_test() {
 	einfo "CLIBD_MON ${CLIBD_MON}"
 	einfo "SYMINFO ${SYMINFO}"
 
+	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
 	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
 }
diff --git a/sci-chemistry/coot/coot-0.6.2.ebuild b/sci-chemistry/coot/coot-0.6.2.ebuild
new file mode 100644
index 000000000000..f89ddc8338e9
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.6.2.ebuild
@@ -0,0 +1,153 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.6.2.ebuild,v 1.1 2011/06/28 17:01:28 jlec Exp $
+
+EAPI=3
+
+PYTHON_DEPEND="2"
+
+inherit autotools base eutils python toolchain-funcs versionator
+
+MY_S2_PV=$(replace_version_separator 2 - ${PV})
+MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
+MY_S_P=${MY_S2_P}-${PR/r/revision-}
+MY_PV=${PV}
+MY_P=${PN}-${MY_PV}
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
+SRC_URI="
+	http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
+	test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+openmp test"
+
+SCIDEPS="
+	>=sci-libs/ccp4-libs-6.1
+	>=sci-libs/clipper-20090520
+	>=sci-libs/coot-data-2
+	>=sci-libs/gsl-1.3
+	sci-libs/mmdb
+	sci-chemistry/reduce
+	sci-chemistry/refmac
+	sci-chemistry/probe"
+
+XDEPS="
+	gnome-base/libgnomecanvas
+	gnome-base/librsvg:2
+	media-libs/libpng
+	media-libs/freeglut
+	x11-libs/gtk+:2
+	x11-libs/gtkglext"
+
+SCHEMEDEPS="
+	dev-scheme/net-http
+	dev-scheme/guile-gui
+	>=dev-scheme/guile-lib-0.1.6
+	dev-scheme/guile-www
+	>=x11-libs/guile-gtk-2.1"
+
+RDEPEND="
+	${SCIDEPS}
+	${XDEPS}
+	${SCHEMEDEPS}
+	dev-python/pygtk:2
+	>=dev-libs/gmp-4.2.2-r2
+	>=net-misc/curl-7.19.6
+	net-dns/libidn"
+DEPEND="${RDEPEND}
+	dev-lang/swig
+	sys-devel/bc
+	test? ( dev-scheme/greg )"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	if use openmp; then
+		tc-has-openmp || die "Please use an OPENMP capable compiler"
+	fi
+	python_set_active_version 2
+}
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-clipper-config.patch
+	"${FILESDIR}"/${PV}-gl.patch
+	"${FILESDIR}"/${PV}-mmdb-config.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+
+	eautoreconf
+}
+
+src_configure() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix="${EPREFIX}/usr" \
+		--with-ssmlib-prefix="${EPREFIX}/usr" \
+		--with-gtkgl-prefix="${EPREFIX}/usr" \
+		--with-guile \
+		--with-python="${EPREFIX}/usr" \
+		--with-guile-gtk \
+		--with-gtk2 \
+		--with-pygtk \
+		$(use_enable openmp)
+}
+
+src_compile() {
+	emake || die "emake failed"
+	python_convert_shebangs $(python_get_version) src/coot_gtk2.py
+	cp "${S}"/src/coot_gtk2.py python/coot.py || die
+}
+
+src_test() {
+	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
+	mkdir "${T}"/coot_test
+
+	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
+	export COOT_SCHEME_DIR="${S}/scheme/"
+	export COOT_RESOURCES_FILE="${S}/cootrc"
+	export COOT_PIXMAPS_DIR="${S}/pixmaps"
+	export COOT_DATA_DIR="${S}"
+	export COOT_PYTHON_DIR="${S}/python"
+	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
+	export PYTHONHOME="${EPREFIX}"/usr
+	export CCP4_SCR="${T}"/coot_test
+	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
+	export SYMINFO="${S}/syminfo.lib"
+
+	export COOT_TEST_DATA_DIR="${WORKDIR}/data/greg-data"
+
+	cat > command-line-greg.scm <<- EOF
+	(use-modules (ice-9 greg))
+		(set! greg-tools (list "greg-tests"))
+			(set! greg-debug #t)
+			(set! greg-verbose 5)
+			(let ((r (greg-test-run)))
+				(if r
+				(coot-real-exit 0)
+				(coot-real-exit 1)))
+	EOF
+
+	einfo "Running test with following paths ..."
+	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
+	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
+	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
+	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
+	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
+	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
+	einfo "PYTHONPATH $PYTHONPATH"
+	einfo "PYTHONHOME $PYTHONHOME"
+	einfo "CCP4_SCR ${CCP4_SCR}"
+	einfo "CLIBD_MON ${CLIBD_MON}"
+	einfo "SYMINFO ${SYMINFO}"
+
+	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
+	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
+}
diff --git a/sci-chemistry/coot/files/0.6.2-clipper-config.patch b/sci-chemistry/coot/files/0.6.2-clipper-config.patch
new file mode 100644
index 000000000000..311b5e88d84e
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-clipper-config.patch
@@ -0,0 +1,17 @@
+ macros/clipper.m4 |    3 +++
+ 1 files changed, 3 insertions(+), 0 deletions(-)
+
+diff --git a/macros/clipper.m4 b/macros/clipper.m4
+index 0bf087a..d0e8b6b 100644
+--- a/macros/clipper.m4
++++ b/macros/clipper.m4
+@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
+         ;;
+ esac
+ 
++CLIPPER_CXXFLAGS=`clipper-config --cflags`
++CLIPPER_LDOPTS=`clipper-config --libs`
++
+ AC_MSG_CHECKING([for Clipper])
+ 
+ 	LIBS="$save_LIBS $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/0.6.2-gl.patch b/sci-chemistry/coot/files/0.6.2-gl.patch
new file mode 100644
index 000000000000..bbd858c646df
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-gl.patch
@@ -0,0 +1,10 @@
+Index: coot-surface/Makefile.am
+===================================================================
+--- coot-surface/Makefile.am	(revision 3478)
++++ coot-surface/Makefile.am	(working copy)
+@@ -29,4 +29,4 @@
+ 
+ libcoot_surface_la_LIBADD = \
+ 	$(top_builddir)/surface/libccp4mg-surface.la \
+-	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) 
++	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) -lGL
diff --git a/sci-chemistry/coot/files/0.6.2-mmdb-config.patch b/sci-chemistry/coot/files/0.6.2-mmdb-config.patch
new file mode 100644
index 000000000000..1d7cbd452f7b
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-mmdb-config.patch
@@ -0,0 +1,18 @@
+ macros/mmdb.m4 |    4 ++++
+ 1 files changed, 4 insertions(+), 0 deletions(-)
+
+diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
+index b477597..d05cf66 100644
+--- a/macros/mmdb.m4
++++ b/macros/mmdb.m4
+@@ -86,6 +86,10 @@ else
+  ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+ 
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
++ac_MMDB_LDOPTS="${MMDB_LIBS}"
++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
++
+ AC_MSG_CHECKING([for MMDB])
+ 
+ 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml
index 9ac9ffdb3a41..e42d0af60f42 100644
--- a/sci-chemistry/coot/metadata.xml
+++ b/sci-chemistry/coot/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
+	<herd>sci-chemistry</herd>
 </pkgmetadata>