sci-libs/hdf5: add 1.14.4_p2

Drop LTO filtering as it's fixed upstream.

Bug: https://bugs.gentoo.org/922800
Bug: https://bugs.gentoo.org/930089
Signed-off-by: Sam James <sam@gentoo.org>

5 files changed, 243 insertions, 0 deletions

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index cef49f76a841..f07fe2e1a3ad 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -3,3 +3,4 @@ DIST hdf5-1.12.2.tar.bz2 10494264 BLAKE2B 99ca5b57f6f54fa044c909f0773de62b218c1f
 DIST hdf5-1.14.1.tar.bz2 16257319 BLAKE2B fbabbe2a61fca3f841d0206e3918390001ec1ec713696b69845eb6390595794a63740db9a7b48fd132814268e216d8fea6288cd23b04b2fa981058b557113e73 SHA512 b4dd3fca88547fdcbb2afcc22cb11bb45b7b15c3c01d9e11b7f06030ffff1a9d5c4995abb6cf27b0c4e748f1a7ca497a7f2d995ba00586f447fcd2fa537e0e16
 DIST hdf5-1.14.2.tar.bz2 16070491 BLAKE2B 04acdc5352f7f0455bf6304ef07ddf51b99125bb585984bd3e27a521a784a6ad6723d64aa3b4179e4bd382334b7e68d06650404d7d4617a696d3f64917487dbc SHA512 1e1bfdff50c2e0e172d399c2d5b79b9ad0c7c72b9b30c4849aad7c5656393e8cf2af788cdf62b51fbe596023483fbc7fa23fdebf37bfe3109dae7f0783ea590f
 DIST hdf5-1.14.3.tar.bz2 16320137 BLAKE2B 4c58edc04788db739c5c74d6edbfb9277011e2d6776862404fc29b30bb2c06a4314eb317393c230ebd2617a9a362ff78183d39ae80ce08f8963bdf6c02e8a865 SHA512 06d51638a56f387f6d0ef484b72e182509c15ab639315052be9821adeed6ad08551c50d7fe84d2b550b64211f68484cf3022a4660c8004cd0afd90eaa83c1bb1
+DIST hdf5-1.14.4-2.tar.gz 37033062 BLAKE2B cd75e0fec1ccea8622bb93839c4898e07093b298612cd3ba5aaa48178eba33f49e6a6492df779f0cc36ee263a107a3fa3e592caec35576d0e637b9e457da3965 SHA512 f1714b7999468d580b7cae2e575d3d7f31cea2fb81bfa4e37abd248d7223476b2351d1714197ace04eee970b451cf1f6971f5a291fd7426398737b8d7eb26924
diff --git a/sci-libs/hdf5/files/hdf5-1.14.4-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch b/sci-libs/hdf5/files/hdf5-1.14.4-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch
new file mode 100644
index 000000000000..5b3a5f85f2ce
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.14.4-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch
@@ -0,0 +1,28 @@
+From dcfab0f9f0c41cb61a25b11cd61eac7204365693 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 17 Dec 2023 09:25:43 +0000
+Subject: [PATCH 1/3] Make sure that during runtime we'll use the same
+ libgfortran as during linking
+
+Bug: https://bugs.gentoo.org/419991
+Bug: https://bugs.gentoo.org/419895
+Signed-off-by: Sam James <sam@gentoo.org>
+---
+ fortran/src/Makefile.am | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/fortran/src/Makefile.am b/fortran/src/Makefile.am
+index 8d8396f..de03df9 100644
+--- a/fortran/src/Makefile.am
++++ b/fortran/src/Makefile.am
+@@ -98,6 +98,7 @@ if BUILD_PARALLEL_CONDITIONAL
+ else
+   H5FC_NAME = h5fc
+ endif
++H5test_kind_LDFLAGS=-static-libgfortran
+ 
+ # Rules for automatically detecting which fortran types are present
+ # and matching them to C types.  This is accomplished using helper
+-- 
+2.44.0
+
diff --git a/sci-libs/hdf5/files/hdf5-1.14.4-0002-Disable-forced-stripping.patch b/sci-libs/hdf5/files/hdf5-1.14.4-0002-Disable-forced-stripping.patch
new file mode 100644
index 000000000000..25a3088dc031
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.14.4-0002-Disable-forced-stripping.patch
@@ -0,0 +1,31 @@
+From 9bcb00e44ce2442db9dcd173e70f8635d7e22c1d Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 17 Dec 2023 09:26:33 +0000
+Subject: [PATCH 2/3] Disable forced stripping
+
+Bug: https://bugs.gentoo.org/665378
+Signed-off-by: Sam James <sam@gentoo.org>
+---
+ configure.ac | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 6a3beee..fc44a39 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -2512,9 +2512,9 @@ case "X-$SYMBOLS" in
+     AC_MSG_RESULT([yes])
+     ;;
+   X-no)
+-    H5_CFLAGS="$H5_CFLAGS $NO_SYMBOLS_CFLAGS"
+-    H5_CXXFLAGS="$H5_CXXFLAGS $NO_SYMBOLS_CXXFLAGS"
+-    H5_FCFLAGS="$H5_FCFLAGS $NO_SYMBOLS_FCFLAGS"
++    H5_CFLAGS="$H5_CFLAGS"
++    H5_CXXFLAGS="$H5_CXXFLAGS"
++    H5_FCFLAGS="$H5_FCFLAGS"
+     AC_MSG_RESULT([no])
+     ;;
+   *)
+-- 
+2.44.0
+
diff --git a/sci-libs/hdf5/files/hdf5-1.14.4-0003-Drop-broken-Werror-stripping.patch b/sci-libs/hdf5/files/hdf5-1.14.4-0003-Drop-broken-Werror-stripping.patch
new file mode 100644
index 000000000000..3b8a628b0384
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.14.4-0003-Drop-broken-Werror-stripping.patch
@@ -0,0 +1,65 @@
+From 014f4857dc0e5883cb07393d5875412806855d28 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 17 Dec 2023 09:27:18 +0000
+Subject: [PATCH 3/3] Drop broken -Werror stripping
+
+The stripping is broken and mangles -Werror=x -> -x [0].
+
+[0] https://github.com/HDFGroup/hdf5/commit/41526f68f3482f2b3a7aa581288bc86e9c6dcb43#r100076265
+
+Bug: https://bugs.gentoo.org/917448
+Signed-off-by: Sam James <sam@gentoo.org>
+---
+ configure.ac | 36 ------------------------------------
+ 1 file changed, 36 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index fc44a39..2117303 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -193,42 +193,6 @@ saved_user_JAVAFLAGS="$JAVAFLAGS"
+ saved_user_LDFLAGS="$LDFLAGS"
+ saved_user_CPPFLAGS="$CPPFLAGS"
+ 
+-## Strip out -Werror from CFLAGS since that can cause checks to fail when
+-## compiling test programs fails due to warnings
+-##
+-##  Regex:
+-##
+-##      -Werror        Literal -Werror
+-##      \(             Start optional capturing group
+-##      =              Literal equals sign
+-##      [^[:space:]]   Non-space characters
+-##      \+             1 or more of the above
+-##      \)             End optional capturing group
+-##      \?             0 or 1 capturing group matches
+-##
+-## Note that the outer pair of '[]' ends up getting removed
+-WERROR_SED='s/-Werror\(=[[^[:space:]]]\+\)\?//g'
+-CFLAGS_SED="`echo $CFLAGS | sed -e $WERROR_SED`"
+-if test $? -eq 0; then
+-  CFLAGS="$CFLAGS_SED"
+-fi
+-CXXFLAGS_SED="`echo $CXXFLAGS | sed -e $WERROR_SED`"
+-if test $? -eq 0; then
+-  CXXFLAGS="$CXXFLAGS_SED"
+-fi
+-FCFLAGS_SED="`echo $FCFLAGS | sed -e $WERROR_SED`"
+-if test $? -eq 0; then
+-  FCFLAGS="$FCFLAGS_SED"
+-fi
+-JAVACFLAGS_SED="`echo $JAVACFLAGS | sed -e $WERROR_SED`"
+-if test $? -eq 0; then
+-  JAVACFLAGS="$JAVACFLAGS_SED"
+-fi
+-CPPFLAGS_SED="`echo $CPPFLAGS | sed -e $WERROR_SED`"
+-if test $? -eq 0; then
+-  CPPFLAGS="$CPPFLAGS_SED"
+-fi
+-
+ ## Support F9X variable to define Fortran compiler if FC variable is
+ ## not used.  This should be deprecated in the future.
+ if test "x" = "x$FC"; then
+-- 
+2.44.0
+
diff --git a/sci-libs/hdf5/hdf5-1.14.4_p2.ebuild b/sci-libs/hdf5/hdf5-1.14.4_p2.ebuild
new file mode 100644
index 000000000000..b71c204edfea
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.14.4_p2.ebuild
@@ -0,0 +1,118 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+FORTRAN_NEEDED=fortran
+
+# We've reverted *back* to autotools from CMake because of
+# https://github.com/HDFGroup/hdf5/issues/1814.
+inherit autotools fortran-2 flag-o-matic toolchain-funcs prefix
+
+MY_PV=${PV/_p/-}
+MY_P=${PN}-${MY_PV}
+MAJOR_P=${PN}-$(ver_cut 1-2)
+
+DESCRIPTION="General purpose library and file format for storing scientific data"
+HOMEPAGE="https://www.hdfgroup.org/HDF5/"
+SRC_URI="https://github.com/HDFGroup/hdf5/releases/download/${PN}_${MY_PV/-/.}/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="NCSA-HDF"
+SLOT="0/${PV%%_p*}"
+KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~loong ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~x64-macos"
+IUSE="cxx debug examples fortran +hl mpi szip test threads unsupported zlib"
+RESTRICT="!test? ( test )"
+REQUIRED_USE="
+	!unsupported? (
+		cxx? ( !mpi ) mpi? ( !cxx )
+		threads? ( !cxx !mpi !fortran !hl )
+	)
+"
+
+RDEPEND="
+	mpi? ( virtual/mpi[romio] )
+	szip? ( virtual/szip )
+	zlib? ( sys-libs/zlib:= )
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/hdf5-1.14.4-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch
+	"${FILESDIR}"/hdf5-1.14.4-0002-Disable-forced-stripping.patch
+	"${FILESDIR}"/hdf5-1.14.4-0003-Drop-broken-Werror-stripping.patch
+)
+
+pkg_setup() {
+	# Workaround for bug 285148
+	tc-export CXX CC AR
+
+	use fortran && fortran-2_pkg_setup
+
+	if use mpi; then
+		if has_version 'sci-libs/hdf5[-mpi]'; then
+			ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
+			ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
+		fi
+
+		export CC=mpicc
+		use fortran && export FC=mpif90
+	elif has_version 'sci-libs/hdf5[mpi]'; then
+		ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
+		ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
+	fi
+}
+
+src_prepare() {
+	default
+
+	sed \
+		-e '/docdir/d' \
+		-i config/commence.am || die
+
+	if ! use examples; then
+		# bug #409091
+		sed -e '/^install:/ s/install-examples//' \
+			-i Makefile.am || die
+	fi
+
+	# Enable shared libs by default for h5cc config utility
+	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" bin/h5cc.in || die
+	hprefixify m4/libtool.m4
+
+	eautoreconf
+}
+
+src_configure() {
+	# bug #686620
+	use sparc && tc-is-gcc && append-flags -fno-tree-ccp
+
+	local myeconfargs=(
+		--disable-static
+		--disable-doxygen-errors
+		--enable-deprecated-symbols
+		--enable-build-mode=$(usex debug debug production)
+		--with-default-plugindir="${EPREFIX}/usr/$(get_libdir)/${PN}/plugin"
+		--with-examplesdir="\${datarootdir}/doc/${PF}/examples" \
+		$(use_enable cxx)
+		$(use_enable debug codestack)
+		$(use_enable fortran)
+		$(use_enable hl)
+		$(use_enable mpi parallel)
+		$(use_enable test tests)
+		$(use_enable threads threadsafe)
+		$(use_enable unsupported)
+		$(use_with szip szlib)
+		$(use_with threads pthread)
+		$(use_with zlib)
+	)
+
+	econf "${myeconfargs[@]}"
+}
+
+src_install() {
+	emake DESTDIR="${D}" EPREFIX="${EPREFIX}" install
+
+	# No static archives
+	find "${ED}" -name '*.la' -delete || die
+}