sci-libs/silo: add 4.11.1

* Partially fix tests with GCC 14 (reported another issue on the upstream PR for that).
* Disable LTO and SA given the comments on a linked upstream bug wrt opimisation.

Closes: https://bugs.gentoo.org/862927
Signed-off-by: Sam James <sam@gentoo.org>

3 files changed, 109 insertions, 0 deletions

diff --git a/sci-libs/silo/Manifest b/sci-libs/silo/Manifest
index f860b2cafed1..a2470626ee06 100644
--- a/sci-libs/silo/Manifest
+++ b/sci-libs/silo/Manifest
@@ -1 +1,2 @@
 DIST silo-4.11-bsd.tgz 13298515 BLAKE2B fcf2e7912381e57d1a64644d3cee4dea50302c12704eaf0ee9e2569b7bc29b1d5c9df66878744ffc2cc04e16834fdf1cd4d677983af36005e4ecf0918c6283d5 SHA512 f642dd21dacffa147aea54d6f8669c704772d5640d6eb7eeff1d7e5e5d37ddbde250d78bad30e9478dcfec63a86863243d7a56cd9b692eaefdd7a89b34df35d0
+DIST silo-4.11.1-bsd.tar.xz 4581480 BLAKE2B 577bb9e367cae08496ec2062ce7b1fc6ebd04a8221bfb304585ea8b338502793a8ba43c14dbf8a7fd1f61b3c8a3a7886da1e9a7f9a1972d2a9cb69d5e36362e3 SHA512 e4ecfc434b43ea0bd2e3cda469f5e232b0bdfd25a44da04e77f2213ff20fd4158bc085d16b10de22d9a4be0ce822899e2b7f20c53b4d4bd941f92357a873c4a2
diff --git a/sci-libs/silo/files/silo-4.11.1-gcc14-tests.patch b/sci-libs/silo/files/silo-4.11.1-gcc14-tests.patch
new file mode 100644
index 000000000000..1e729ee74e32
--- /dev/null
+++ b/sci-libs/silo/files/silo-4.11.1-gcc14-tests.patch
@@ -0,0 +1,45 @@
+https://github.com/LLNL/Silo/pull/371
+
+From f0737787eb02093defc30de05a731ffe63c4c6f4 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 17 Mar 2024 07:35:36 +0000
+Subject: [PATCH] tests: add missing header for `difftime`
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+With GCC 14, which makes implicit function declarations an error by default:
+```
+TestReadMask.c: In function ‘ElapsedTime’:
+TestReadMask.c:746:15: error: implicit declaration of function ‘difftime’ [-Wimplicit-function-declaration]
+  746 |     ms = (int)difftime(end_time.tv_sec, start_time.tv_sec);
+      |               ^~~~~~~~
+TestReadMask.c:62:1: note: ‘difftime’ is defined in header ‘<time.h>’; this is probably fixable by adding ‘#include <time.h>’
+   61 | #include <std.c>
+  +++ |+#include <time.h>
+   62 |
+```
+
+Fix the include guards and include <time.h> unconditionally (for difftime) and <string.h>
+unconditionally too (for memcpy).
+
+Signed-off-by: Sam James <sam@gentoo.org>
+--- a/tests/TestReadMask.c
++++ b/tests/TestReadMask.c
+@@ -51,13 +51,12 @@ product endorsement purposes.
+ */
+ #include <stdio.h>
+ #include <silo.h>
++#include <string.h>
+ #ifndef WIN32
+ #include <sys/time.h>
+-#else
+-#include <string.h>
+-#include <time.h>
+ #endif
+ #include <sys/timeb.h>
++#include <time.h>
+ #include <std.c>
+ 
+ /* To compile this program on hyper, here is the command:
+
diff --git a/sci-libs/silo/silo-4.11.1.ebuild b/sci-libs/silo/silo-4.11.1.ebuild
new file mode 100644
index 000000000000..78b80eb13d33
--- /dev/null
+++ b/sci-libs/silo/silo-4.11.1.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic fortran-2 qmake-utils
+
+DESCRIPTION="A mesh and field I/O library and scientific database"
+HOMEPAGE="https://software.llnl.gov/Silo/"
+SRC_URI="https://github.com/LLNL/Silo/releases/download/${PV}/${P}-bsd.tar.xz"
+S="${WORKDIR}/${P}-bsd"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="browser +hdf5 +silex"
+
+# see bugs 656432 and 741741
+RDEPEND="
+	dev-qt/qtcore:5
+	dev-qt/qtgui:5
+	dev-qt/qtwidgets:5
+	net-dialup/lrzsz
+	virtual/szip
+	hdf5? ( sci-libs/hdf5 )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="dev-qt/linguist-tools:5"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.11-test-disable-largefile.patch
+	"${FILESDIR}"/${PN}-4.11-tests.patch
+	"${FILESDIR}"/${PN}-4.11-testsuite-python-write.patch
+	"${FILESDIR}"/${PN}-4.11-widgets.patch
+	"${FILESDIR}"/${PN}-4.11-qtbindir.patch
+	"${FILESDIR}"/${PN}-4.11.1-gcc14-tests.patch
+)
+
+src_configure() {
+	# bug #862927 and https://github.com/LLNL/Silo/issues/248
+	append-flags -fno-strict-aliasing
+	filter-lto
+
+	# add fflags for fixing test bug on matf77.f
+	# see https://github.com/LLNL/Silo/issues/234
+	append-fflags $(test-flags-F77 -fallow-argument-mismatch)
+
+	CONFIG_SHELL="${BROOT}"/bin/bash \
+	QMAKE=$(qt5_get_bindir)/qmake \
+	QT_BIN_DIR=$(qt5_get_bindir) \
+	econf \
+		--enable-install-lite-headers \
+		--enable-shared \
+		$(use_enable silex silex ) \
+		$(use_enable browser browser ) \
+		$(use_with hdf5 hdf5 "${EPREFIX}"/usr/include,"${EPREFIX}"/usr/$(get_libdir) )
+}
+
+src_test() {
+	# see https://github.com/LLNL/Silo/issues/236
+	# some tests are skipped by default so we are gonna drop them directly
+	emake ATARGS="1-34 36-44 50-51 66-76 78-81" -C tests check
+}