Version Bump

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

8 files changed, 230 insertions, 17 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/Manifest b/sci-chemistry/coot/Manifest
index 94232e0e2afc..93212e778fab 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 AUX 0.3.1-as-needed.patch 18766 RMD160 00b020d46457f9e335b92c2f48088cdc950fce3a SHA1 bd2835ba0a974c8e01d6fa30f670827e6e72fc70 SHA256 cb395ba53839e16aa9e3248b2cfb16794c137730e02a41ca80927538717c4d83
 AUX 0.3.1-fix-compilation-with-guile-1.8.patch 968 RMD160 8c53c2bd3e78b17de447068646cba56bccf50072 SHA1 a2b74a18fa92021528b704bc95277fb77fc4ed02 SHA256 667246f46ac6324c7c346986221f68ee62922cfa3cdd2d3c9e816943719e5b71
@@ -10,17 +10,23 @@ AUX 0.4_pre2-as-needed.patch 19258 RMD160 a9ad8cbc84f9c2a35edb9ea7ec8926c3c4eb94
 AUX 0.4_pre2-link-against-guile-gtk-properly.patch 800 RMD160 e4a9931de152385d552542e11d9a74a548810964 SHA1 74264270682a9135af92bf40a030c008876252e4 SHA256 c7271c82bb6e9e1ba89096ef0a7416609a81b455a1633637b84952db686d5080
 AUX 0.4_pre2-r549-fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
 AUX 0.6.1-libpng14.patch 950 RMD160 c2d1c298ada419272d79d49972b13e414a234cd3 SHA1 bfd4828ab8e05863ce197c59865901ce3186fb66 SHA256 7b121a0bccd49da0c459003512a2c61368eeab41b33a6726525ace501eb03559
+AUX 0.6.2-clipper-config.patch 431 RMD160 7a00939760bc4c062bbde1a65f53b9556b93c3bc SHA1 0d72c4c898fd29802c74d237b54f715444922956 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f
+AUX 0.6.2-gl.patch 383 RMD160 6460e87e4da57ff845f96f072dec1354ed117bee SHA1 00bc0bbfc7d4fb00ebc8477941469bef2ed6b670 SHA256 9d47a6cf2d0c7644b945f88acdc7af146df4f9a5a8f883a0e72e1bc8ccf8b380
+AUX 0.6.2-mmdb-config.patch 432 RMD160 8418198b08d15af9ee5d80b15ea46bb9efd2b973 SHA1 3e6f5c888b476d8d37da4effa67a8053784a7a3c SHA256 41484424f2f7f61b0555c893a51884d02f7bd471e70c4c0903c8740dcc273f77
 AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
 AUX gtk.m4 8516 RMD160 3860fe211902d5b9290f0a70e7d75ebec6b0ec67 SHA1 98b93b820423a52ebd80e3f1822a8f2bd4b3f15d SHA256 4eb6e0bb2c6863139d1fb4ca2d1d0f0ef07e3a85fdbb5ba98d03373f610f0c37
 DIST coot-0.6.1.tar.gz 12229005 RMD160 76cbf28320ff52f02b40164eea00e7ec8a6b6c2c SHA1 cdd74e394e07dc17b99f56fce7cf180a177d53d7 SHA256 7897eb62e1add5f8deddd16d24ffd9b4c763e784714cd47fa9777beb79f56066
+DIST coot-0.6.2.tar.gz 13597123 RMD160 707eb3df47681a011f42874210b940329a748bc7 SHA1 46b663125cef4c01387330d144e49acb0b0b5709 SHA256 d2f55db4f75c721d120ea33a4ca42c1abf246dff29a75b7f189e604e32709e78
 DIST greg-data-0.6.1.tar.gz 7930213 RMD160 e9a17d1ef2d3f15b3792ea5c7204901e0105b76b SHA1 f4158fa440406b88d0bb72880cdee9a3653c4233 SHA256 658a557b85ee6b90fc446cb3c605556586a2a5a0575ddd11b42265e019eb74a0
-EBUILD coot-0.6.1.ebuild 3854 RMD160 67068c72ae22d2dc2d2db5d7e75ff7b37ef5b601 SHA1 f74e6eb067faa83c7b66122f19a8fc64582c2d94 SHA256 b9ae1eb9646c182652dbd25028040631e5eb765d73267baaaed39abb89094743
-MISC ChangeLog 5324 RMD160 71d7c97325eb7aee6748048ddd3f50a4782875f3 SHA1 c2d7af4a06c6327d5b063792f1fad2f5b8d6477b SHA256 c6afa0c886ed0694f02ec03b77a8d66d47b0152d6581ef7ef986ef7f95c3de7d
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+DIST greg-data-0.6.2.tar.gz 8044588 RMD160 065acee98384540d0c2ffaf2511dfd1aa400b11c SHA1 92cec24dab594d8024f41047af2bf6760e9e7d00 SHA256 c9fedf6e1fa60fda178753bbfb539671c274f64d4daca2b63ab49c59bd4c5856
+EBUILD coot-0.6.1.ebuild 3934 RMD160 6376495fce52056acbaaf0df862fbb502b8a7600 SHA1 0ecc3bfa5760bb663d62c67c98c6146f3f77e707 SHA256 7ac1bd7397140da0386b360ef613067a2932d381d0a85e9ad97218fac20f944d
+EBUILD coot-0.6.2.ebuild 3936 RMD160 d555c38c1d7a9abde9213d6b72055cfa7a20783d SHA1 6f9fc151a4d44cb1c92db27dd1c7b2ab57e6ea80 SHA256 13213900ae562e5f3f409627839dc3c1523d67d7d81a842bbcdab1a48d38bfe1
+MISC ChangeLog 5563 RMD160 60269e4a6be13b0e1739ddb0d5987165da97e046 SHA1 cf08fdeb0f86dadb30413fce86b04fcbe9fb5155 SHA256 8e078912012f172de54bdc9da5ef2f229be00f3207de294ddd4751a853c0ffc2
+MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk1uFH4ACgkQgAnW8HDreRYh3wCcDq0Hcu8Xtr3IibyGITPFqWgQ
-aocAn09oETlkKa47HFeeqlGY/SoHENO8
-=BcCz
+iEYEAREKAAYFAk4KCPIACgkQgAnW8HDreRY40QCgkMFuYZBQwvduioxbzVYuBVyZ
+Il4AnjvQoK9WSqcqJ3KUYh4fqcoP1z3S
+=V0zP
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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>