sys-cluster/singularity: Version Bump

Closes: https://github.com/gentoo/gentoo/pull/5005

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=621248
Package-Manager: Portage-2.3.6, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec@gentoo.org>

4 files changed, 108 insertions, 0 deletions

diff --git a/sys-cluster/singularity/Manifest b/sys-cluster/singularity/Manifest
index 8ac63cfcb319..a5f4dc4fadc9 100644
--- a/sys-cluster/singularity/Manifest
+++ b/sys-cluster/singularity/Manifest
@@ -1 +1,2 @@
 DIST singularity-2.2.1.tar.gz 493368 SHA256 0e2a0b0cf6c8d4dc041365f715b2df157e0d8d89986e4eb111c61716df031c8a SHA512 b1195e98254957cd8d80b35b13d4f11060c5836f05ed450d242544fc30f8c298b837ba8986b1184288bc9a5ff2ebb5b1f56dc55a0686b540242b0042a152f902 WHIRLPOOL 3d3c5cb0928bd5beb683c4075c88453d076795c0e41ad30676f7169ccbd6d71a70ad64104833925913138f47b8fc318e90366af79259a05bad41bb0a42703b05
+DIST singularity-2.3.1.tar.gz 643021 SHA256 dcccae9ff67a550d142c94e932c0fb59442dd59ae69ce1deeb7ba45829ef2cd7 SHA512 36c581e8dba57d133013c2fcfea26886b54a1a9a9165b011d2cebacb2a6249fe0f8e5aa91ed90f7a18855c658300682436c431a226629408f31422cc8a036600 WHIRLPOOL d9bb8604ce2afb6bb2b5b257eb88276a93987916cd4c08ecc800d98761f5d1ae54e48ed615d77b1c992bcc8bb6202e9bf5e04637d10d1126fba6d1c2619cb98c
diff --git a/sys-cluster/singularity/files/singularity-2.3.1-slurm.patch b/sys-cluster/singularity/files/singularity-2.3.1-slurm.patch
new file mode 100644
index 000000000000..71a8d9972b75
--- /dev/null
+++ b/sys-cluster/singularity/files/singularity-2.3.1-slurm.patch
@@ -0,0 +1,54 @@
+From e858cfaf73eadb4cf4076a754c4836816c908d44 Mon Sep 17 00:00:00 2001
+From: Petr Votava <votava.petr@gene.com>
+Date: Thu, 29 Jun 2017 16:53:48 +0000
+Subject: [PATCH] A patch for slurm plugin build
+
+---
+ src/slurm/Makefile.am   | 2 +-
+ src/slurm/singularity.c | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/src/slurm/Makefile.am b/src/slurm/Makefile.am
+index 860c7667d..152e41450 100644
+--- a/src/slurm/Makefile.am
++++ b/src/slurm/Makefile.am
+@@ -4,7 +4,7 @@ plugindir = $(libdir)/slurm
+ if WITH_SLURM
+ plugin_LTLIBRARIES = singularity_spank.la
+ singularity_spank_la_SOURCES = singularity.c
+-singularity_spank_la_LIBADD = ../lib/libsingularity_internal.la
++singularity_spank_la_LIBADD = ../lib/runtime/libinternal.la
+ singularity_spank_la_LDFLAGS = -module -no-undefined -avoid-version -export-symbols-regex '^slurm_spank_|^plugin_'
+ endif
+ 
+diff --git a/src/slurm/singularity.c b/src/slurm/singularity.c
+index acddddfd1..3509f4d8e 100644
+--- a/src/slurm/singularity.c
++++ b/src/slurm/singularity.c
+@@ -22,6 +22,7 @@
+ 
+ #define _GNU_SOURCE 1
+ 
++#include <stdio.h>
+ #include <stdlib.h>
+ #include <unistd.h>
+ #include <sys/types.h>
+@@ -29,9 +30,9 @@
+ #include <string.h>
+ 
+ #include "config.h"
+-#include "lib/singularity.h"
+ #include "util/util.h"
+ #include "util/file.h"
++#include "util/registry.h"
+ 
+ #include "slurm/spank.h"
+ 
+@@ -169,7 +170,6 @@ static int setup_container(spank_t spank)
+     }
+ 
+ 
+-    char *image;
+     if ( ( image = singularity_registry_get("IMAGE") ) == NULL ) {
+         singularity_message(ERROR, "SINGULARITY_CONTAINER not defined!\n");
+     }
diff --git a/sys-cluster/singularity/metadata.xml b/sys-cluster/singularity/metadata.xml
index f47500258195..bb97aa8832e8 100644
--- a/sys-cluster/singularity/metadata.xml
+++ b/sys-cluster/singularity/metadata.xml
@@ -8,4 +8,9 @@
 	<upstream>
 		<remote-id type="github">singularityware/singularity</remote-id>
 	</upstream>
+	<use>
+		<flag name="slurm">
+			Compile spank plugin for <pkg>sys-cluster/slurm</pkg>
+		</flag>
+	</use>
 </pkgmetadata>
diff --git a/sys-cluster/singularity/singularity-2.3.1.ebuild b/sys-cluster/singularity/singularity-2.3.1.ebuild
new file mode 100644
index 000000000000..235fb8923437
--- /dev/null
+++ b/sys-cluster/singularity/singularity-2.3.1.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_{4,5,6}} )
+
+inherit autotools eutils python-single-r1
+
+DESCRIPTION="Application containers for Linux"
+HOMEPAGE="http://singularity.lbl.gov/"
+SRC_URI="https://github.com/${PN}ware/${PN}/releases/download/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="cctbx-2.0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples slurm static-libs +suid"
+
+RDEPEND="
+	sys-cluster/slurm
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-slurm.patch
+)
+
+src_prepare() {
+	default
+	# automake version hardcoding
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--with-userns \
+		$(use_with slurm) \
+		$(usex suid "" "--disable-suid") \
+		$(use_enable static-libs static)
+}
+
+src_install() {
+	MAKEOPTS+=" -j1"
+	default
+	prune_libtool_files
+	dodoc ChangeLog AUTHORS.md CONTRIBUTING.md
+	use examples && dodoc -r examples
+}