sci-libs/gerris: Patch use of sci-libs/lis function prototypes

Gentoo-bug: 593282
* EAPI=6
* Made all PATCHES -p1 compliant
* Exchanged -D_BSD_SOURCE with -D_DEFAULT_SOURCE in order
  to silence deprecation from dev-libs/glib
* Add subslot operators for sci-libs/netcdf and sci-libs/gsl
* Add proper SLOT and operator for sci-libs/fftw
* Delete all .la files, as package provides .pc files

Package-Manager: portage-2.3.0

6 files changed, 111 insertions, 6 deletions

diff --git a/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch
index f05512efbddf..a52c78bf77c8 100644
--- a/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch
+++ b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch
@@ -1,7 +1,7 @@
 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
+--- a/configure.ac
++++ b/configure.ac
 @@ -336,7 +336,7 @@
  
  # Build hypre module if HYPRE 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
index 21d6810bbd2b..d4c7bfae15bb 100644
--- a/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch
+++ b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch
@@ -1,5 +1,5 @@
---- modules/lis.c.orig	2013-07-22 15:34:05.346631560 -0700
-+++ modules/lis.c	2013-07-22 15:33:28.621427315 -0700
+--- a/modules/lis.c
++++ b/modules/lis.c
 @@ -45,7 +45,7 @@
  			    g_array_index (stencil->coeff, double, j), 
  			    A);
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
index 4c8985ce5e77..1c25a8f516b6 100644
--- a/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch
+++ b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch
@@ -1,5 +1,5 @@
---- modules/Makefile.am.orig	2013-07-22 14:13:10.339130133 -0700
-+++ modules/Makefile.am	2013-07-22 14:15:10.770813929 -0700
+--- a/modules/Makefile.am
++++ b/modules/Makefile.am
 @@ -105,7 +105,7 @@
  libstokes2D_la_LIBADD = $(GFS2D_LIBS)
  
diff --git a/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch
new file mode 100644
index 000000000000..d20df635512c
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch
@@ -0,0 +1,16 @@
+Silence warnings due to _BSD_SOURCE being deprecated by glib:
+* /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and
+* _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
+* # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -108,7 +108,7 @@
+ AC_PROG_CC
+ 
+ # -D_GNU_SOURCE is only necessary for old (< 2.10) glibc implementations of open_memstream()
+-CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_BSD_SOURCE -D_GNU_SOURCE"
++CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_DEFAULT_SOURCE -D_GNU_SOURCE"
+ if test x$GCC = xyes ; then
+   CFLAGS="$CFLAGS -Wall -Werror-implicit-function-declaration -Wmissing-prototypes -Wmissing-declarations -pipe -std=c99"
+ fi
diff --git a/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch
new file mode 100644
index 000000000000..28892ddadedf
--- /dev/null
+++ b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch
@@ -0,0 +1,18 @@
+sci-libs/lis changed some of its function prototypes by renaming
+lis_solver_get_iters to lis_solver_get_iter in version 1.4.43 from 17 July 2014
+
+See also:
+http://www.ssisc.org/lis/ChangeLog.txt
+https://bugs.gentoo.org/show_bug.cgi?id=593282
+
+--- a/modules/lis.c
++++ b/modules/lis.c
+@@ -67,7 +67,7 @@
+ 
+   lis_solve (A, b, x, solver);
+   int iter;
+-  lis_solver_get_iters (solver, &iter);
++  lis_solver_get_iter (solver, &iter);
+   par->niter = iter;
+ 
+   lis_vector_get_values (x, 0, lp->lhs->len, (double *) lp->lhs->data);
diff --git a/sci-libs/gerris/gerris-20131206-r1.ebuild b/sci-libs/gerris/gerris-20131206-r1.ebuild
new file mode 100644
index 000000000000..464ca8ab0de8
--- /dev/null
+++ b/sci-libs/gerris/gerris-20131206-r1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools flag-o-matic toolchain-funcs
+
+MY_P=${P/-20/-snapshot-}
+
+DESCRIPTION="Gerris Flow Solver"
+HOMEPAGE="http://gfs.sourceforge.net/"
+SRC_URI="http://gerris.dalembert.upmc.fr/gerris/tarballs/${MY_P}.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:3.0=
+	virtual/lapack
+	mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+# buggy tests, need extra packages and require gerris to be installed
+RESTRICT=test
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-20130531-hypre-no-mpi.patch
+	"${FILESDIR}"/${PN}-20130531-lis-matrix-csr.patch
+	"${FILESDIR}"/${PN}-20130531-use-blas-lapack-system.patch
+	"${FILESDIR}"/${PN}-20131206-lis-api-change.patch
+	"${FILESDIR}"/${PN}-20131206-DEFAULT_SOURCE-replacement.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	append-cppflags "-I${EPREFIX}/usr/include/hypre"
+	econf \
+		--enable-shared \
+		$(use_enable static-libs static) \
+		$(use_enable mpi) \
+		LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
+}
+
+src_install() {
+	default
+	use examples && dodoc -r doc/examples
+
+	find "${D}" -name '*.la' -delete || die
+}