sci-chemistry/coot: Version Bump, #437304; drop prereleases

(Portage version: 2.2.0_alpha135/cvs/Linux x86_64)

14 files changed, 21 insertions, 356 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 9af9cc16646a..dd59db687c3c 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,22 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.53 2012/07/11 20:38:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.54 2012/10/06 16:19:58 jlec Exp $
+
+*coot-0.7 (06 Oct 2012)
+
+  06 Oct 2012; Justin Lecher <jlec@gentoo.org> -coot-0.7_pre4040.ebuild,
+  -coot-0.7_pre4266.ebuild, +coot-0.7.ebuild,
+  +files/coot-0.7-clipper-config.patch, +files/coot-0.7-goocanvas.patch,
+  +files/coot-0.7-mmdb-config.patch, +files/coot-0.7-ssm.patch,
+  -files/coot-0.7_pre4040-clipper-config.patch,
+  -files/coot-0.7_pre4040-gl.patch, -files/coot-0.7_pre4040-goocanvas.patch,
+  -files/coot-0.7_pre4040-libpng-1.5.patch,
+  -files/coot-0.7_pre4040-mmdb-config.patch, -files/coot-0.7_pre4040-ssm.patch,
+  -files/coot-0.7_pre4040-test.patch,
+  -files/coot-0.7_pre4266-clipper-config.patch,
+  -files/coot-0.7_pre4266-goocanvas.patch,
+  -files/coot-0.7_pre4266-mmdb-config.patch, -files/coot-0.7_pre4266-ssm.patch:
+  Version Bump, #437304; drop prereleases
 
 *coot-0.7_pre4266 (11 Jul 2012)
 
diff --git a/sci-chemistry/coot/coot-0.7_pre4266.ebuild b/sci-chemistry/coot/coot-0.7.ebuild
index 6d331ba735e8..bae7ef02dc0a 100644
--- a/sci-chemistry/coot/coot-0.7_pre4266.ebuild
+++ b/sci-chemistry/coot/coot-0.7.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.7_pre4266.ebuild,v 1.1 2012/07/11 20:38:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.7.ebuild,v 1.1 2012/10/06 16:19:58 jlec Exp $
 
 EAPI=4
 
@@ -19,7 +19,7 @@ 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://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+	http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
 	test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
 
 SLOT="0"
@@ -71,6 +71,8 @@ DEPEND="${RDEPEND}
 	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"
@@ -92,14 +94,6 @@ src_prepare() {
 		-i configure.in || die
 
 	autotools-utils_src_prepare
-
-	cat >> src/svn-revision.cc <<- EOF
-	extern "C" {
-	int svn_revision() {
-		return  ${ESVN_WC_REVISION:-0};
-	}
-	}
-	EOF
 }
 
 src_configure() {
diff --git a/sci-chemistry/coot/coot-0.7_pre4040.ebuild b/sci-chemistry/coot/coot-0.7_pre4040.ebuild
deleted file mode 100644
index 2a7e3fccbfb3..000000000000
--- a/sci-chemistry/coot/coot-0.7_pre4040.ebuild
+++ /dev/null
@@ -1,174 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.7_pre4040.ebuild,v 1.2 2012/03/07 19:33:39 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="2"
-
-AUTOTOOLS_AUTORECONF="true"
-
-inherit autotools-utils 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://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-	test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+openmp static-libs test"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	>=sci-libs/clipper-20090520
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23
-	sci-libs/ssm
-	<sci-libs/monomer-db-1
-	sci-chemistry/reduce
-	<sci-chemistry/refmac-5.6
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	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}
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python_set_active_version 2
-	python_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-clipper-config.patch
-	"${FILESDIR}"/${P}-goocanvas.patch
-	"${FILESDIR}"/${P}-gl.patch
-	"${FILESDIR}"/${P}-mmdb-config.patch
-	"${FILESDIR}"/${P}-test.patch
-	"${FILESDIR}"/${P}-ssm.patch
-	"${FILESDIR}"/${P}-libpng-1.5.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
-
-	autotools-utils_src_prepare
-
-	cat >> src/svn-revision.cc <<- EOF
-	extern "C" {
-	int svn_revision() {
-		return  ${ESVN_WC_REVISION:-0};
-	}
-	}
-	EOF
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-gtk2
-		--with-pygtk
-		$(use_enable openmp)
-		)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	python_convert_shebangs $(python_get_version) "${S}"/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 command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
-}
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-clipper-config.patch b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch
index 311b5e88d84e..311b5e88d84e 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-clipper-config.patch
+++ b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch
index ce0d4a00abba..ce0d4a00abba 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-goocanvas.patch
+++ b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch
index b3b66ab65786..b3b66ab65786 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-mmdb-config.patch
+++ b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-ssm.patch b/sci-chemistry/coot/files/coot-0.7-ssm.patch
index c801da72410a..c801da72410a 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-ssm.patch
+++ b/sci-chemistry/coot/files/coot-0.7-ssm.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-gl.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-gl.patch
deleted file mode 100644
index bbd858c646df..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-gl.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-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/coot-0.7_pre4040-libpng-1.5.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-libpng-1.5.patch
deleted file mode 100644
index bddd251698de..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-libpng-1.5.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- ccp4mg-utils/ppmutil.cc
-+++ ccp4mg-utils/ppmutil.cc
-@@ -2494,15 +2494,21 @@
- 
-   pixels = new unsigned char[width*height*colourspace];
- 
-+  png_colorp palette;
-+  int num_trans;
-+#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
-+  png_bytep trans_alpha;
-+#endif
-+
-   for (int i=0; i<height; i++){
-     if(color_type==PNG_COLOR_TYPE_PALETTE){
-       for (int j=0; j<width; j++){
--        pixels[i*width*colourspace+j*colourspace] = png_ptr->palette[row_pointers[i][j]].red;
--        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){
-+        pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red;
-+        pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green;
-+        pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue;
-+        if(row_pointers[i][j]<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]];
-+         pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]];
- #else
-          pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]];
- #endif
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch
deleted file mode 100644
index 8cb79e65d767..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/testing.cc |    4 +++-
- 1 files changed, 3 insertions(+), 1 deletions(-)
-
-diff --git a/src/testing.cc b/src/testing.cc
-index f767bf6..097b9b9 100644
---- a/src/testing.cc
-+++ b/src/testing.cc
-@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) {
-    const char *c = getenv("COOT_TEST_DATA_DIR");
-    if (c) {
-       dd = c;
-+      dd += "/";
-+      dd += file_name;
-    } else { 
-       const char *d = getenv("HOME");
-       if (d) {
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch
deleted file mode 100644
index 311b5e88d84e..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- 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 $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch
deleted file mode 100644
index ce0d4a00abba..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Index: macros/goo-canvas.m4
-===================================================================
---- macros/goo-canvas.m4	(revision 3307)
-+++ macros/goo-canvas.m4	(working copy)
-@@ -56,9 +56,9 @@
-   fi
- fi
- 
--AC_MSG_CHECKING([for Goocanvas])
-+PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
- 
--LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
-+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
- CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
- #
- # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
-@@ -76,7 +76,7 @@
- if test x$have_goocanvas = xyes; then
- 
-  GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
-- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
-+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
- 
- ifelse([$1], , :, [$1])
- 
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch
deleted file mode 100644
index b3b66ab65786..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Index: macros/mmdb.m4
-===================================================================
---- macros/mmdb.m4	(revision 3579)
-+++ macros/mmdb.m4	(working copy)
-@@ -86,8 +86,12 @@
-  ac_MMDB_LDOPTS="-lmmdb -lm"
- fi
- 
--AC_MSG_CHECKING([for MMDB])
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
-+ac_MMDB_LDOPTS="${MMDB_LIBS}"
-+ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
- 
-+AC_MSG_CHECKING([for CISPEP in MMDB])
-+
- 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
- 	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
- 	#
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch
deleted file mode 100644
index c801da72410a..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch
+++ /dev/null
@@ -1,56 +0,0 @@
- macros/mmdb-ssm.m4 |   42 +-----------------------------------------
- 1 files changed, 1 insertions(+), 41 deletions(-)
-
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 1937a16..6ef547c 100644
---- a/macros/mmdb-ssm.m4
-+++ b/macros/mmdb-ssm.m4
-@@ -22,47 +22,7 @@
- AC_DEFUN([AM_WITH_MMDBSSM],
- [AC_PROVIDE([AM_USE_MMDBSSM])
- 
--
--AC_ARG_WITH(ssmlib-prefix, 
--	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
--	[ with_ssmlib_prefix="$withval" ],
-- with_ssmlib_prefix="")
--
--AC_MSG_CHECKING([for SSMLib])
--
--if test x$with_ssmlib_prefix != x; then
--
--   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
--   MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
--
--ac_mmdb_dirs='
--.
--include
--include/ssm
--include/mmdb
--lib
--src
--lib/src
--lib/src/mmdb'
--
--   for ac_dir in $ac_mmdb_dirs; do
--      if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
--         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
--         break
--      fi
--   done
--
--  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
--  
--else 
--
--   MMDBSSM_CXXFLAGS=""
--   MMDBSSM_LIBS=""
--   with_ssmlib_prefix=no 
--
--fi
--
--AC_MSG_RESULT([$with_ssmlib_prefix])
-+PKG_CHECK_MODULES([MMDBSSM],[ssm])
- 
- AC_SUBST(MMDBSSM_CXXFLAGS)
- AC_SUBST(MMDBSSM_LIBS)