Version bump and fix bug #450378

(Portage version: 2.2.01.22124-prefix/cvs/Linux x86_64, signed Manifest commit with key 0x13CB1360)

8 files changed, 147 insertions, 146 deletions

diff --git a/sci-libs/gerris/ChangeLog b/sci-libs/gerris/ChangeLog
index 8cb71447eb05..004923d2a39f 100644
--- a/sci-libs/gerris/ChangeLog
+++ b/sci-libs/gerris/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-libs/gerris
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/gerris/ChangeLog,v 1.18 2013/02/21 22:03:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/gerris/ChangeLog,v 1.19 2013/07/22 22:42:13 bicatali Exp $
+
+*gerris-20130531 (22 Jul 2013)
+
+  22 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/gerris-20130531-hypre-no-mpi.patch,
+  +files/gerris-20130531-lis-matrix-csr.patch,
+  +files/gerris-20130531-use-blas-lapack-system.patch, +gerris-20130531.ebuild,
+  -files/gerris-20100519-autotools.patch,
+  -files/gerris-20111123-autotools.patch, metadata.xml:
+  Version bump and fix bug #450378
 
   21 Feb 2013; Justin Lecher <jlec@gentoo.org> -gerris-20100519.ebuild,
   -gerris-20111123.ebuild, gerris-20120731.ebuild, metadata.xml:
diff --git a/sci-libs/gerris/files/gerris-20100519-autotools.patch b/sci-libs/gerris/files/gerris-20100519-autotools.patch
deleted file mode 100644
index 2bab3f3a2d07..000000000000
--- a/sci-libs/gerris/files/gerris-20100519-autotools.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 8b07f68..678ebbd 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -2,9 +2,7 @@
- 
- AUTOMAKE_OPTIONS = 1.6
- 
--AM_CPPFLAGS = -DGFS_MODULES_DIR=\"$(libdir)/gerris\"
--
--INCLUDES = -I$(top_srcdir) -I$(includedir) \
-+AM_CPPFLAGS = -DGFS_MODULES_DIR=\"$(libdir)/gerris\" \
-            -DG_LOG_DOMAIN=\"Gfs\" $(GTS_CFLAGS)
- 
- bin_SCRIPTS = gfs-config
-@@ -114,12 +112,14 @@ libgfs3D_la_LDFLAGS = $(NO_UNDEFINED)\
-         -version-info $(LT_CURRENT):$(LT_REVISION):$(LT_AGE)\
- 	-release $(LT_RELEASE) -export-dynamic
- libgfs3D_la_SOURCES = $(SRC)
-+libgfs3D_la_LIBADD = $(GTS_LIBS)
- 
- libgfs2D_la_LDFLAGS = $(NO_UNDEFINED)\
-         -version-info $(LT_CURRENT):$(LT_REVISION):$(LT_AGE)\
- 	-release $(LT_RELEASE) -export-dynamic
- libgfs2D_la_SOURCES = $(SRC)
--libgfs2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
-+libgfs2D_la_CPPFLAGS = $(AM_CPPFLAGS) -DFTT_2D=1
-+libgfs2D_la_LIBADD = $(GTS_LIBS)
- 
- CLEANFILES = $(BUILT_SOURCES)
- 
-@@ -131,12 +131,12 @@ EXTRA_DIST = \
- bin_PROGRAMS = gerris2D gerris3D
- 
- gerris2D_SOURCES = gerris.c
--gerris2D_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
--gerris2D_LDADD = $(GFS2D_LIBS)
-+gerris2D_CPPFLAGS = $(AM_CPPFLAGS) -DFTT_2D=1
-+gerris2D_LDADD = libgfs2D.la
- gerris2D_DEPENDENCIES = libgfs2D.la
- 
- gerris3D_SOURCES = gerris.c
--gerris3D_LDADD = $(GFS3D_LIBS)
-+gerris3D_LDADD = libgfs3D.la
- gerris3D_DEPENDENCIES = libgfs3D.la
- 
- if DARCS_CONTROLLED
diff --git a/sci-libs/gerris/files/gerris-20111123-autotools.patch b/sci-libs/gerris/files/gerris-20111123-autotools.patch
deleted file mode 100644
index 05bd3b5a9bed..000000000000
--- a/sci-libs/gerris/files/gerris-20111123-autotools.patch
+++ /dev/null
@@ -1,96 +0,0 @@
---- Makefile.am.orig	2012-01-20 19:59:56.000000000 +0000
-+++ Makefile.am	2012-01-21 04:35:19.000000000 +0000
-@@ -28,7 +28,7 @@
- DARCS_CHANGELOG = 
- endif
- 
--pkglib_SCRIPTS = build_function libtool
-+noinst_SCRIPTS = build_function libtool
- 
- ChangeLog: $(DARCS_CHANGELOG)
- 
---- src/Makefile.am.orig	2012-01-20 19:59:56.000000000 +0000
-+++ src/Makefile.am	2012-01-21 05:13:31.000000000 +0000
-@@ -1,10 +1,9 @@
--## Process this file with automake to produce Makefile.in
-+## Process this file with automake to produce Makefile.in
- 
- AUTOMAKE_OPTIONS = 1.6
- 
--AM_CPPFLAGS = -DGFS_MODULES_DIR=\"$(libdir)/gerris\"
--
--INCLUDES = -I$(top_srcdir) -I$(includedir) \
-+AM_CPPFLAGS = -DGFS_MODULES_DIR=\"$(libdir)/gerris\" \
-+	 -I$(top_srcdir) -I$(includedir) \
-            -DG_LOG_DOMAIN=\"Gfs\" $(GTS_CFLAGS)
- 
- bin_SCRIPTS = gfs-config
-@@ -15,7 +14,8 @@
- 
- pkgconfigdir = $(libdir)/pkgconfig
- pkgconfig_DATA = gerris2D.pc gerris3D.pc
--pkglib_DATA = m4.awk
-+pkgawkdir = $(datadir)/gerris
-+pkgawk_DATA = m4.awk
- 
- lib_LTLIBRARIES = libgfs2D.la libgfs3D.la
- 
-@@ -119,7 +119,7 @@
-         -version-info $(LT_CURRENT):$(LT_REVISION):$(LT_AGE)\
- 	-release $(LT_RELEASE) -export-dynamic
- libgfs2D_la_SOURCES = $(SRC)
--libgfs2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
-+libgfs2D_la_CPPFLAGS = $(AM_CPPFLAGS) -DFTT_2D=1
- libgfs2D_la_LIBADD = $(GTS_LIBS)
- 
- CLEANFILES = $(BUILT_SOURCES)
-@@ -132,13 +132,11 @@
- bin_PROGRAMS = gerris2D gerris3D
- 
- gerris2D_SOURCES = gerris.c
--gerris2D_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
--gerris2D_LDADD = $(GFS2D_LIBS)
--gerris2D_DEPENDENCIES = libgfs2D.la
-+gerris2D_CPPFLAGS = $(AM_CPPFLAGS) -DFTT_2D=1
-+gerris2D_LDADD = libgfs2D.la
- 
- gerris3D_SOURCES = gerris.c
--gerris3D_LDADD = $(GFS3D_LIBS)
--gerris3D_DEPENDENCIES = libgfs3D.la
-+gerris3D_LDADD = libgfs3D.la
- 
- if DARCS_CONTROLLED
- DARCS_VERSION = darcsversion
---- configure.in.orig	2012-01-20 19:59:56.000000000 +0000
-+++ configure.in	2012-01-23 01:10:36.000000000 +0000
-@@ -348,10 +350,14 @@
- 
- # AGMG module requires the gfortran compiler and lapack/blas
- if test x$with_agmg != xno; then
--   AC_PROG_FC([gfortran f90 xlf90],90)
--   AC_CHECK_LIB(lapack, sorg2l_, lapack="true", lapack="false", [-lblas -lm])
-+   AC_PROG_FC
-+   if [ -z "$LAPACK_LIBS" ]; then
-+      AC_CHECK_LIB(lapack, sorg2l_,lapack="true", lapack="false", [-lblas -lm])
-+   else
-+      LIBS="${LIBS} ${LAPACK_LIBS}"
-+   fi
- fi
--AM_CONDITIONAL(BUILD_AGMG, test x$FC = xgfortran -a x$lapack = xtrue -a x$with_agmg != xno)
-+AM_CONDITIONAL(BUILD_AGMG, test x$with_agmg != xno)
- 
- # Build wavewatch module if wavewatch is installed
- AM_CONDITIONAL(BUILD_WAVEWATCH, test -r $HOME/.wwatch3.env)
---- doc/examples/Makefile.am.orig	2012-01-20 19:59:56.000000000 +0000
-+++ doc/examples/Makefile.am	2012-01-23 02:02:38.000000000 +0000
-@@ -48,7 +48,6 @@
- 
- CLEANFILES = $(BUILT_SOURCES) Makefile.deps
- 
--pkglib_DATA = gfs2tex.py
--pkgdata_DATA = gfs.lang gerris.dic gfs-keywords.el gfs-mode.el gfs.sty gfs.hva kaltura.sh gfs.php
-+pkgdata_DATA = gfs2tex.py gfs.lang gerris.dic gfs-keywords.el gfs-mode.el gfs.sty gfs.hva kaltura.sh gfs.php
- 
- gerris.dic: classes modulesyms.sh $(top_srcdir)/modules/Makefile.am modules.list
-	($(srcdir)/classes && sh $(srcdir)/modulesyms.sh $(top_srcdir)/modules $(pkglibdir)) | sort > gerris.dic
- 
diff --git a/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch
new file mode 100644
index 000000000000..f05512efbddf
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch
@@ -0,0 +1,22 @@
+patch to allow gerris to use hypre without mpi
+
+--- configure.ac	2013-05-30 23:57:18.000000000 -0700
++++ configure.ac.new	2013-07-22 13:52:36.083974663 -0700
+@@ -336,7 +336,7 @@
+ 
+ # Build hypre module if HYPRE is installed
+ hypre=no
+-if test "x$use_mpicc" = "xyes" ; then # HYPRE needs MPI
++# hypre does not need mpi
+    AC_CHECK_LIB(HYPRE, HYPRE_IJMatrixCreate, hypre="yes", hypre="no", [-lm])
+    if test x$hypre = xyes; then
+       AC_CHECK_HEADERS(HYPRE.h, hypre="yes", hypre="no")
+@@ -344,7 +344,7 @@
+    if test x$hypre = xno; then
+       AC_MSG_WARN([HYPRE not found. hypre Module won't be available.])
+    fi
+-fi
++
+ AM_CONDITIONAL(BUILD_HYPRE, test x$hypre = xyes)
+ 
+ # Build lis module if lis is installed
diff --git a/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch
new file mode 100644
index 000000000000..21d6810bbd2b
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch
@@ -0,0 +1,11 @@
+--- modules/lis.c.orig	2013-07-22 15:34:05.346631560 -0700
++++ modules/lis.c	2013-07-22 15:33:28.621427315 -0700
+@@ -45,7 +45,7 @@
+ 			    g_array_index (stencil->coeff, double, j), 
+ 			    A);
+   }
+-  lis_matrix_set_type (A, LIS_MATRIX_CRS);
++  lis_matrix_set_type (A, LIS_MATRIX_CSR);
+   lis_matrix_assemble (A);
+ 
+   LIS_VECTOR b, x;
diff --git a/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch
new file mode 100644
index 000000000000..4c8985ce5e77
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch
@@ -0,0 +1,33 @@
+--- modules/Makefile.am.orig	2013-07-22 14:13:10.339130133 -0700
++++ modules/Makefile.am	2013-07-22 14:15:10.770813929 -0700
+@@ -105,7 +105,7 @@
+ libstokes2D_la_LIBADD = $(GFS2D_LIBS)
+ 
+ libwavewatch2D_la_SOURCES = wavewatch.c
+-libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran
++libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch
+ libwavewatch2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 \
+   -DW3SRCE=`nm wavewatch/libwavewatch.a | grep w3srce | awk '{ if ($$2 == "T") print $$3; }'` \
+   -DGFSW3INIT=`nm wavewatch/libwavewatch.a | grep gfsw3_init | awk '{ if ($$2 == "T") print $$3; }'`
+@@ -164,17 +164,17 @@
+ 
+ liblis3D_la_SOURCES = lis.c
+ liblis3D_la_CFLAGS = $(AM_CFLAGS)
+-liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lgfortran -lm
++liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lm
+ liblis2D_la_SOURCES = lis.c
+ liblis2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
+-liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lgfortran -lm
++liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lm
+ 
+ libagmg3D_la_SOURCES = agmg.c dagmg.f90
+ libagmg3D_la_CFLAGS = $(AM_CFLAGS)
+-libagmg3D_la_LIBADD = $(GFS3D_LIBS) -llapack -lblas -lgfortran -lm
++libagmg3D_la_LIBADD = $(GFS3D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm
+ libagmg2D_la_SOURCES = agmg.c dagmg.f90
+ libagmg2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1
+-libagmg2D_la_LIBADD = $(GFS2D_LIBS) -llapack -lblas -lgfortran -lm
++libagmg2D_la_LIBADD = $(GFS2D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm
+ 
+ libokada3D_la_SOURCES = okada.c
+ libokada3D_la_CFLAGS = $(AM_CFLAGS)
diff --git a/sci-libs/gerris/gerris-20130531.ebuild b/sci-libs/gerris/gerris-20130531.ebuild
new file mode 100644
index 000000000000..96db6435084b
--- /dev/null
+++ b/sci-libs/gerris/gerris-20130531.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/gerris/gerris-20130531.ebuild,v 1.1 2013/07/22 22:42:13 bicatali Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils eutils flag-o-matic toolchain-funcs
+
+MYP=${P/-20/-snapshot-}
+
+DESCRIPTION="Gerris Flow Solver"
+HOMEPAGE="http://gfs.sourceforge.net/"
+SRC_URI="http://gerris.dalembert.upmc.fr/gerris/tarballs/${MYP}.tar.gz"
+
+LICENSE="GPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples mpi static-libs"
+
+# all these deps could be optional
+# but the configure.in would have to be modified
+# heavily for the automagic
+RDEPEND="
+	dev-libs/glib:2
+	dev-games/ode
+	sci-libs/netcdf
+	sci-libs/gsl
+	sci-libs/gts
+	sci-libs/hypre[mpi?]
+	sci-libs/lis[mpi?]
+	sci-libs/proj
+	>=sci-libs/fftw-3
+	virtual/lapack
+	mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${MYP}"
+
+# buggy tests, need extra packages and require gerris to be installed
+RESTRICT=test
+
+PATCHES=(
+	"${FILESDIR}"/${P}-hypre-no-mpi.patch
+	"${FILESDIR}"/${P}-lis-matrix-csr.patch
+	"${FILESDIR}"/${P}-use-blas-lapack-system.patch
+)
+
+src_configure() {
+	append-cppflags "-I${EPREFIX}/usr/include/hypre"
+	local myeconfargs=(
+		$(use_enable mpi)
+	)
+	autotools-utils_src_configure \
+		LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
+}
+
+src_install() {
+	autotools-utils_src_install
+	if use examples; then
+		insinto /usr/share/doc/${PF}/examples
+		doins -r doc/examples/*
+	fi
+}
diff --git a/sci-libs/gerris/metadata.xml b/sci-libs/gerris/metadata.xml
index 2406d4e01ce8..430d5d021bdf 100644
--- a/sci-libs/gerris/metadata.xml
+++ b/sci-libs/gerris/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci</herd>
-  <longdescription lang="en">
+<herd>sci</herd>
+<longdescription lang="en">
   Gerris Flow Solver is a software program for the solution of the partial
   differential equations describing fluid flow.
 </longdescription>