Adding pre release version from svn

(Portage version: 2.2.0_alpha90/cvs/Linux x86_64)

10 files changed, 357 insertions, 10 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 76d80d4a687d..957c8f24cffd 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,16 @@
 # 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 1.50 2011/10/23 20:07:55 ssuominen Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.51 2012/03/06 15:31:19 jlec Exp $
+
+*coot-0.7_pre4040 (06 Mar 2012)
+
+  06 Mar 2012; Justin Lecher <jlec@gentoo.org> coot-0.6.2-r1.ebuild,
+  +coot-0.7_pre4040.ebuild, +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:
+  Adding pre release version from svn
 
   23 Oct 2011; Samuli Suominen <ssuominen@gentoo.org>
   -files/0.6.1-libpng14.patch, -coot-0.6.1.ebuild:
diff --git a/sci-chemistry/coot/coot-0.6.2-r1.ebuild b/sci-chemistry/coot/coot-0.6.2-r1.ebuild
index 077441b0e84a..be31a70d7af9 100644
--- a/sci-chemistry/coot/coot-0.6.2-r1.ebuild
+++ b/sci-chemistry/coot/coot-0.6.2-r1.ebuild
@@ -1,11 +1,13 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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-0.6.2-r1.ebuild,v 1.2 2011/10/07 09:37:25 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.6.2-r1.ebuild,v 1.3 2012/03/06 15:31:19 jlec Exp $
 
 EAPI=3
 
 PYTHON_DEPEND="2"
 
+AUTOTOOLS_AUTORECONF="true"
+
 inherit autotools-utils flag-o-matic python toolchain-funcs versionator
 
 MY_S2_PV=$(replace_version_separator 2 - ${PV})
@@ -86,12 +88,6 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-libpng15.patch
 	)
 
-src_prepare() {
-	autotools-utils_src_prepare
-
-	eautoreconf
-}
-
 src_configure() {
 	# All the --with's are used to activate various parts.
 	# Yes, this is broken behavior.
diff --git a/sci-chemistry/coot/coot-0.7_pre4040.ebuild b/sci-chemistry/coot/coot-0.7_pre4040.ebuild
new file mode 100644
index 000000000000..519ac27bad9f
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.7_pre4040.ebuild
@@ -0,0 +1,170 @@
+# 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 1.1 2012/03/06 15:31:19 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() {
+	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_pre4040-clipper-config.patch
new file mode 100644
index 000000000000..311b5e88d84e
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4040-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/coot-0.7_pre4040-gl.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-gl.patch
new file mode 100644
index 000000000000..bbd858c646df
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4040-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) $(MMDB_LIBS) -lGL
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-goocanvas.patch
new file mode 100644
index 000000000000..ce0d4a00abba
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4040-goocanvas.patch
@@ -0,0 +1,25 @@
+Index: macros/goo-canvas.m4
+===================================================================
+--- macros/goo-canvas.m4	(revision 3307)
++++ macros/goo-canvas.m4	(working copy)
+@@ -56,9 +56,9 @@
+   fi
+ fi
+ 
+-AC_MSG_CHECKING([for Goocanvas])
++PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
+ 
+-LIBS="$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_pre4040-libpng-1.5.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-libpng-1.5.patch
new file mode 100644
index 000000000000..bddd251698de
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4040-libpng-1.5.patch
@@ -0,0 +1,29 @@
+--- 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-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-mmdb-config.patch
new file mode 100644
index 000000000000..b3b66ab65786
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4040-mmdb-config.patch
@@ -0,0 +1,18 @@
+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 $ac_MMDB_CXXFLAGS"
+ 	#
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-ssm.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-ssm.patch
new file mode 100644
index 000000000000..c801da72410a
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4040-ssm.patch
@@ -0,0 +1,56 @@
+ macros/mmdb-ssm.m4 |   42 +-----------------------------------------
+ 1 files changed, 1 insertions(+), 41 deletions(-)
+
+diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
+index 1937a16..6ef547c 100644
+--- a/macros/mmdb-ssm.m4
++++ b/macros/mmdb-ssm.m4
+@@ -22,47 +22,7 @@
+ AC_DEFUN([AM_WITH_MMDBSSM],
+ [AC_PROVIDE([AM_USE_MMDBSSM])
+ 
+-
+-AC_ARG_WITH(ssmlib-prefix, 
+-	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
+-	[ with_ssmlib_prefix="$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)
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch
new file mode 100644
index 000000000000..8cb79e65d767
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch
@@ -0,0 +1,16 @@
+ 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) {