From 1cc847b5ee999289be29375e316083822fbedc73 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Tue, 28 Jun 2011 17:01:28 +0000 Subject: Version Bump (Portage version: 2.2.0_alpha41/cvs/Linux x86_64) --- sci-chemistry/coot/ChangeLog | 10 +- sci-chemistry/coot/coot-0.6.1.ebuild | 17 +-- sci-chemistry/coot/coot-0.6.2.ebuild | 153 +++++++++++++++++++++ .../coot/files/0.6.2-clipper-config.patch | 17 +++ sci-chemistry/coot/files/0.6.2-gl.patch | 10 ++ sci-chemistry/coot/files/0.6.2-mmdb-config.patch | 18 +++ sci-chemistry/coot/metadata.xml | 2 +- 7 files changed, 217 insertions(+), 10 deletions(-) create mode 100644 sci-chemistry/coot/coot-0.6.2.ebuild create mode 100644 sci-chemistry/coot/files/0.6.2-clipper-config.patch create mode 100644 sci-chemistry/coot/files/0.6.2-gl.patch create mode 100644 sci-chemistry/coot/files/0.6.2-mmdb-config.patch (limited to 'sci-chemistry/coot') 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 + +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 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 @@ -sci-chemistry + sci-chemistry -- cgit v1.2.3-65-gdbad