[gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/

[Justin Lecher]

commit:     767b48f97d415ca52c9aa904172fc1e24f5d5533
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 29 13:32:19 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 29 13:32:19 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=767b48f9

Imported changes from tree

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog                       |    5 ++
 sci-chemistry/coot/coot-9999.ebuild                |   46 ++++++++++----------
 sci-chemistry/coot/files/9999-clipper-config.patch |   17 +++++++
 sci-chemistry/coot/files/9999-mmdb-config.patch    |   18 ++++++++
 sci-chemistry/coot/files/9999-test.patch           |   16 +++++++
 sci-chemistry/coot/metadata.xml                    |    8 ++--
 6 files changed, 83 insertions(+), 27 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 2d688c2..c4d7981 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Jun 2011; Justin Lecher <jlec@g.o>
+  +files/9999-clipper-config.patch, +files/9999-mmdb-config.patch,
+  coot-9999.ebuild, +files/9999-test.patch, metadata.xml:
+  Imported changes from tree
+
   15 Jun 2011; Justin Lecher <jlec@g.o> -files/9999-align.patch,
   coot-9999.ebuild:
   Updated to current HEAD

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 5561140..ecb5ff0 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI=3
 
 PYTHON_DEPEND="2"
 
@@ -23,16 +23,17 @@ SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )"
 SLOT="0"
 LICENSE="GPL-3"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
+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-libs/mmdb-1.23
+	<sci-libs/monomer-db-1
 	sci-chemistry/reduce
-	sci-chemistry/refmac
+	<sci-chemistry/refmac-5.6
 	sci-chemistry/probe"
 
 XDEPS="
@@ -67,14 +68,20 @@ DEPEND="${RDEPEND}
 S="${WORKDIR}"
 
 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}-lidia.patch
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-include.patch
 	"${FILESDIR}"/${PV}-gl.patch
+	"${FILESDIR}"/${PV}-mmdb-config.patch
+	"${FILESDIR}"/${PV}-test.patch
 	)
 
 src_unpack() {
@@ -85,12 +92,6 @@ src_unpack() {
 src_prepare() {
 	base_src_prepare
 
-	# Link against single-precision fftw
-	sed -i \
-		-e "s:\}fftw:}sfftw:g" \
-		-e "s:\}rfftw:}srfftw:g" \
-		"${S}"/macros/clipper.m4
-
 	cat >> src/svn-revision.cc <<- EOF
 	extern "C" {
 	int svn_revision() {
@@ -107,17 +108,15 @@ src_configure() {
 	# Yes, this is broken behavior.
 	econf \
 		--includedir='${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-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 \
-		--enable-openmp
+		$(use_enable openmp)
 }
 
 src_compile() {
@@ -133,16 +132,16 @@ src_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 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="${T}"/coot_test
+	export PYTHONHOME="${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="${S}"/data/greg-data
+	export COOT_TEST_DATA_DIR="${S}"/data/greg-data/
 
 	cat > command-line-greg.scm <<- EOF
 	(use-modules (ice-9 greg))
@@ -169,4 +168,5 @@ src_test() {
 	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/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch
new file mode 100644
index 0000000..311b5e8
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-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/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch
new file mode 100644
index 0000000..1d7cbd4
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-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/files/9999-test.patch b/sci-chemistry/coot/files/9999-test.patch
new file mode 100644
index 0000000..8cb79e6
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-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) {

diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml
index d7156cf..702e073 100644
--- a/sci-chemistry/coot/metadata.xml
+++ b/sci-chemistry/coot/metadata.xml
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@g.o</email>
-</maintainer>
+	<herd>sci</herd>
+	<maintainer>
+		<email>sci@g.o</email>
+	</maintainer>
 	<maintainer>
 		<email>jlec@g.o</email>
 		<name>Justin Lecher</name>