Version Bump

(Portage version: 2.2_rc67/cvs/Linux x86_64)

3 files changed, 170 insertions, 1 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 2501a7b31b6b..48e64b6093fd 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.23 2010/04/25 11:37:01 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.24 2010/05/17 10:30:52 jlec Exp $
+
+*coot-0.6.1 (17 May 2010)
+
+  17 May 2010; Justin Lecher <jlec@gentoo.org> +files/0.6.1-libpng14.patch,
+  +coot-0.6.1.ebuild:
+  Version Bump
 
   22 Apr 2010; Justin Lecher <jlec@gentoo.org> coot-0.6.ebuild:
   Fixes for Python ABIs
diff --git a/sci-chemistry/coot/coot-0.6.1.ebuild b/sci-chemistry/coot/coot-0.6.1.ebuild
new file mode 100644
index 000000000000..d1c572cdc20c
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.6.1.ebuild
@@ -0,0 +1,146 @@
+# Copyright 1999-2010 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 1.1 2010/05/17 10:30:52 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit autotools base eutils python 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/${MY_P}.tar.gz
+	test? ( mirror://gentoo/greg-data-${PV}.tar.gz  )"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86"
+IUSE="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
+	media-libs/libpng
+	virtual/glut
+	>=x11-libs/gtk+-2.2
+	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}
+	${SCHEMEDEPS}
+	dev-python/pygtk
+	>=dev-libs/gmp-4.2.2-r2
+	>=net-misc/curl-7.19.6"
+DEPEND="${RDEPEND}
+	dev-lang/swig
+	test? ( dev-scheme/greg )"
+
+S="${WORKDIR}/${MY_P}"
+#S="${WORKDIR}/${MY_S2_P}"
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+src_prepare() {
+	base_src_prepare
+
+	# Link against single-precision fftw
+	sed -i \
+		-e "s:lfftw:lsfftw:g" \
+		-e "s:lrfftw:lsrfftw:g" \
+		"${S}"/macros/clipper.m4
+
+	epatch "${FILESDIR}"/${PV}-libpng14.patch
+
+	eautoreconf
+}
+
+src_configure() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix="${EPREFIX}"/usr \
+		--with-clipper-prefix="${EPREFIX}"/usr \
+		--with-mmdb-prefix="${EPREFIX}"/usr \
+		--with-ssmlib-prefix="${EPREFIX}"/usr \
+		--with-gtkgl-prefix="${EPREFIX}"/usr \
+		--with-guile \
+		--with-python="${EPREFIX}"/usr \
+		--with-guile-gtk \
+		--with-gtk2 \
+		--with-pygtk
+}
+
+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() {
+	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="${T}"/coot_test
+
+	export COOT_TEST_DATA_DIR="${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 ${CCP4_SCR}"
+
+	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
+}
diff --git a/sci-chemistry/coot/files/0.6.1-libpng14.patch b/sci-chemistry/coot/files/0.6.1-libpng14.patch
new file mode 100644
index 000000000000..cb09759ed1a2
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.1-libpng14.patch
@@ -0,0 +1,17 @@
+http://code.google.com/p/coot/source/diff?spec=svn2956&old=2307&r=2907&format=unidiff&path=%2Ftrunk%2Fccp4mg-utils%2Fppmutil.cc
+diff --git a/ccp4mg-utils/ppmutil.cc b/ccp4mg-utils/ppmutil.cc
+index 4f0fb5e..20b1d0d 100644
+--- a/ccp4mg-utils/ppmutil.cc
++++ b/ccp4mg-utils/ppmutil.cc
+@@ -2501,7 +2501,11 @@ void image_info::readpng(const char *filename){
+         pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green;
+         pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue;
+         if(row_pointers[i][j]<png_ptr->num_trans){
++#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
++         pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]];
++#else
+          pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]];
++#endif
+         }else
+          pixels[i*width*colourspace+j*colourspace+3] = 255;
+       }