gentoo resync : 29.12.2022

6 files changed, 283 insertions, 1 deletions

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index fca66049cd37..1b93996cac29 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1,5 +1,7 @@
 AUX hdf5-1.12.1-cmake_installdirs.patch 4313 BLAKE2B 78b894a3535c71dbd673e2061e09e1a57d57c1d65418ac87e51669e7cf8a77f023aac076686e978b89903fb0aa74f0511f779ceb149ab783e5624ec24bf5c6a6 SHA512 4a8fce1e3a5ae9d8cdca4fa377011fb7333de0b233e79c6eeed9a24154925eb8dededfe8cff4e28a7cedeb2fbfe194df1a5f18629d56de47b4ba3097824e6b7d
 AUX hdf5-1.12.2-cmake_installdirs.patch 7289 BLAKE2B 7a8846200194c93f014e1862165d153e3dc21df87f08458c827356051cb4e1ffc90df4f176063356347eea881153f48c791cf51fa209ec3b5ca883edc13c06b1 SHA512 3c0933d64207ddead06cd575d40d919402a94a5317f14da1a5ee3b06c88ac65b108754d698715618b87104d8d471eaa6131310b0077202eac0ed221b3da18c5b
+AUX hdf5-1.12.2-no-messing-ldpath.patch 1086 BLAKE2B 77aba02cd8f3663883fa5cf91b3f77067163f58ec4270d22e2c4e1a5b9b1cc138a2e9dd1c7a44331165c69d6c7a0427fe2708bae63958b416a9f26c799de7443 SHA512 8b8aa080cb6feded376900cf9f4b1f1bbe98550b37e9ae8ad660419f732e686aae2ff6eac37e7810ee438a0e9c1b7a37d24f5db8590cce0c91f482ec7b873527
+AUX hdf5-1.12.2-no-strip-symbols.patch 434 BLAKE2B c8d96cb95d3444c18349d72b7fd59f76b4af3d0c5422a7c31161b8f98afacb322b042b8f5751b581565b351148fd0f4003379349b6ca964f5957cd9e19ebdebc SHA512 6b593a8bbbd4a4e9b97e8b3324ad90024b2c09c669d2f6e21a0d23adb66bbbec34afc5961bf97bc6f913492e33610a4b5aeca6a7a4ef9f7605ce5b69fbba6527
 AUX hdf5-1.8.13-no-messing-ldpath.patch 1141 BLAKE2B d7d186e4c00acb9fd3d44beb1d8c3c4da0c373f88b3fdf21e1f89b169b747d49572239385228687cfc10380bdceb9ca6d1ac0d5f5154cb7a328f8a2d509fb28d SHA512 e43021ceb83909ab06ba378363c192aa0f1b34cc7c2b121f5000e215516dbdea1b825a53ac4023073bf4870a5c3452c22f5535391d95af45ad63a309e1ffa5a4
 AUX hdf5-1.8.9-mpicxx.patch 494 BLAKE2B 148d87af064e2ba28c918c8db39ece0782a179803e4c38c5cd5eaba81a673bb8aa3699a48e80a7ae2d4579ac0261cc21d5509e46661ada9a69f444a58eb45ecd SHA512 8b4c39e40591860652547ea8ff205230da7d67488233e911cbcb3416eab561f2529c65bc5e7c9c812bf4298812346f47f9209e5f69f7e8f66ad587306a5b477b
 AUX hdf5-1.8.9-static_libgfortran.patch 429 BLAKE2B 9e1c544a453c09b3498a7d9d3e8090c928571776934c4dd6b426cbdb2783ed8f47185d6ee0c73ede6b4f14e27459ef5e1412112e9d897daa2dc57f1ad5fb0b24 SHA512 af97c54469a90bf3b0e8ec1218d4ca95822ac0cbc7120114979fc467fe3114743c74f4d4e16f0c10b1cd82d40880ef482f6fd34e1effc7c621b981ad466204f9
@@ -10,5 +12,7 @@ EBUILD hdf5-1.10.5-r1.ebuild 2940 BLAKE2B 45e4cf6004cb70667829844ddf37f2c4f96d6b
 EBUILD hdf5-1.10.5.ebuild 2770 BLAKE2B 33a671a87978ba04e1b43cbc048093f12d6303841353124a0ba405fec1d32fdc2cb15ed627b968fc5c3feeba151e78525adf77be3f420993d02f793cf094b96d SHA512 3bb860418e226967b1a2b50ecbbeb6ca793790a7915d6cb6f9ea201816cbc555b455596e200fc2504084597ccbe4d1ae1f91cbc64d68c7a39d2eeae998194304
 EBUILD hdf5-1.12.1-r1.ebuild 3468 BLAKE2B da5ba395f8971076a6a3186332f94446dadc7be2817fbb488c612bf4f1b283fc927ea33b7eff23dfbe5b43c1c27a85d72d72ddd4fb617e37a79416fede96bd1b SHA512 96c6c2f95e13a7841f6a9fa63e838ad218819bd0c854c8994a382c15e2f3fff1ae11f099cd613c4b41efa726b1616ead0cf9c4a0d6aedf6d0c7b2d8ca0d8f7ea
 EBUILD hdf5-1.12.1.ebuild 3144 BLAKE2B 2bd023c0ade920fc795f4434260318095a34b200ddb6a458a6ee7d647fac79d4e31029f93a0d2aafede8682e515a9f9c9db46b5a976f07cd83d5086f77538079 SHA512 10ce8493fd3fa421d8c71267e7c57adaac490244742ed93166ce634f5b956b392efb3b86814c17ad8bfba3347c4e3be54b5688b8eec3af848f1d13c341bb8bcc
-EBUILD hdf5-1.12.2-r1.ebuild 3168 BLAKE2B cf26e034088a10e89f8130fc76e7f52395b5ad61e69b946afe53946d44d9c35c87452d39dd501e54c928e645482cf6543eae8d0d4c787d17843130aad10e4cf1 SHA512 b4a1b842d6adf407b9b9b86be1da8dcea61a0c26d9c8107a0331242b36ef5e2bbf3c1d8078f2ff6be2cbff56f1402c025961aa0be739dac5565eb2cc54e3cefb
+EBUILD hdf5-1.12.2-r1.ebuild 3389 BLAKE2B 536c7a51533849c8b19f2a086b35352a9a845d89417ba10464ef53b0ee444fcab2fec0e369d5bdf9a1aa4746c0f004726200db1b60b67b3876eb425504d6d173 SHA512 1ccc6ce4ca8712bdd39d79e5acd82886a592d0578f14162ed374675e9bfcd2e8fe838354acea030298b340c9fac22f250913e205a9e943a4919237c0603766cc
+EBUILD hdf5-1.12.2-r2.ebuild 3456 BLAKE2B d59c684d4494e7f7f484dc87297ef1465998a8f9d75c2cf268e1d689353fd5e092c27dd0a61907ffe11cb35c424e2f9e972a7e3770f0938808bd704cdeca7961 SHA512 4e0b609458298ab12214aa68bb298063d35f64c12c4eff0cc656546b930dce5cc5891e9cdd6d030f7d616aa4ca13386dbbb020970cbea6d939bbe2356fb310ed
+EBUILD hdf5-1.12.2-r4.ebuild 3139 BLAKE2B 7a307b26c007fdfdb84e2eda430093fed044854c40330b0d584dfce5fc51f17c6a73db07369ea4f002ced8634b00924d8a2e99ae8ed135aee870418d45cae456 SHA512 6036a8152dc08610784596c616acc72822f095daea25f90ed907ff1683f7b9d7e8e0449bc9f3b36a89cfaf6f63b9fe4ef621f5ec76367996a7df82adbf50e5f1
 MISC metadata.xml 935 BLAKE2B b9195ac707556cdb2ee2c4d032fabd88aad674ad4fa52a60fbeb31c47ae51b9511bb097d4271d19b05d1dbc3b59b3cafb3b7d407bd9b8095bfd449fa8728ab6a SHA512 57c4694ea2c024c7babdf34474a61b92165b6c322fa11ec7fefdf16d66b44f91f66d63eeb355311b121fbeec8da810e393e3e785a4c434ff658c7b4bd7baf22b
diff --git a/sci-libs/hdf5/files/hdf5-1.12.2-no-messing-ldpath.patch b/sci-libs/hdf5/files/hdf5-1.12.2-no-messing-ldpath.patch
new file mode 100644
index 000000000000..b8585fc647f6
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.12.2-no-messing-ldpath.patch
@@ -0,0 +1,20 @@
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -159,8 +159,6 @@ settings_DATA=libhdf5.settings
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5Tinit.c: H5detect$(EXEEXT)
+-	LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) |                  \
+-		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
+ 	$(RUNSERIAL) ./H5detect$(EXEEXT)  $@  ||                               \
+ 	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
+ 	    ($(RM) $@ ; exit 1)
+@@ -171,8 +169,6 @@ H5Tinit.c: H5detect$(EXEEXT)
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
+-	LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) |                  \
+-		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
+ 	$(RUNSERIAL) ./H5make_libsettings$(EXEEXT)  $@  ||                               \
+ 	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
+ 	    ($(RM) $@ ; exit 1)
diff --git a/sci-libs/hdf5/files/hdf5-1.12.2-no-strip-symbols.patch b/sci-libs/hdf5/files/hdf5-1.12.2-no-strip-symbols.patch
new file mode 100644
index 000000000000..0f3bf3981fa7
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.12.2-no-strip-symbols.patch
@@ -0,0 +1,16 @@
+https://bugs.gentoo.org/665378
+--- a/configure.ac
++++ b/configure.ac
+@@ -2368,9 +2368,9 @@ case "X-$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])
+     ;;
+   *)
diff --git a/sci-libs/hdf5/hdf5-1.12.2-r1.ebuild b/sci-libs/hdf5/hdf5-1.12.2-r1.ebuild
index d5390cee5762..325f24396b29 100644
--- a/sci-libs/hdf5/hdf5-1.12.2-r1.ebuild
+++ b/sci-libs/hdf5/hdf5-1.12.2-r1.ebuild
@@ -64,6 +64,10 @@ pkg_setup() {
 src_configure() {
 	use sparc && tc-is-gcc && append-flags -fno-tree-ccp # bug 686620
 	local mycmakeargs=(
+		# Workaround needed to allow build with USE=fortran when an older
+		# version is installed. See bug #808633 and
+		# https://github.com/HDFGroup/hdf5/issues/1027 upstream.
+		-DCMAKE_INCLUDE_DIRECTORIES_PROJECT_BEFORE=ON
 		-DBUILD_STATIC_LIBS=OFF
 		-DONLY_SHARED_LIBS=ON
 		-DFETCHCONTENT_FULLY_DISCONNECTED=ON
diff --git a/sci-libs/hdf5/hdf5-1.12.2-r2.ebuild b/sci-libs/hdf5/hdf5-1.12.2-r2.ebuild
new file mode 100644
index 000000000000..12d13c181a04
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.12.2-r2.ebuild
@@ -0,0 +1,125 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+FORTRAN_NEEDED="fortran"
+
+inherit cmake flag-o-matic fortran-2 toolchain-funcs
+
+MY_P="${PN}-${PV/_p/-patch}"
+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://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2"
+
+LICENSE="NCSA-HDF"
+SLOT="0/${PV%%_p*}"
+KEYWORDS="~alpha amd64 arm arm64 ~hppa ~ia64 ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux"
+IUSE="cxx debug doc examples fortran +hl mpi szip test threads unsupported zlib"
+
+REQUIRED_USE="
+	!unsupported? (
+		mpi? ( !cxx !threads )
+		threads? ( !cxx !fortran !hl )
+	)"
+
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	mpi? ( virtual/mpi[romio] )
+	szip? ( virtual/szip )
+	zlib? ( sys-libs/zlib:0= )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="doc? (
+	app-doc/doxygen
+	virtual/latex-base
+)"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.12.2-cmake_installdirs.patch
+)
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	use fortran && fortran-2_pkg_setup
+
+	if use mpi; then
+		if has_version 'sci-libs/hdf5[-mpi]'; then
+			ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
+			ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
+		fi
+		export CC="mpicc"
+		use fortran && export FC="mpif90"
+		append-libs -lmpi
+	elif has_version 'sci-libs/hdf5[mpi]'; then
+		ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
+		ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
+	fi
+}
+
+src_configure() {
+	use sparc && tc-is-gcc && append-flags -fno-tree-ccp # bug 686620
+	local mycmakeargs=(
+		# Workaround needed to allow build with USE=fortran when an older
+		# version is installed. See bug #808633 and
+		# https://github.com/HDFGroup/hdf5/issues/1027 upstream.
+		-DCMAKE_INCLUDE_DIRECTORIES_PROJECT_BEFORE=ON
+		-DBUILD_STATIC_LIBS=OFF
+		-DONLY_SHARED_LIBS=ON
+		-DFETCHCONTENT_FULLY_DISCONNECTED=ON
+		-DHDF5_BUILD_EXAMPLES=OFF
+		-DH5_DEFAULT_PLUGINDIR="${EPREFIX}/usr/$(get_libdir)/hdf5/plugin"
+		-DALLOW_UNSUPPORTED=$(usex unsupported)
+		-DBUILD_TESTING=$(usex test)
+		-DHDF5_BUILD_CPP_LIB=$(usex cxx)
+		-DHDF5_BUILD_DOC=$(usex doc)
+		-DHDF5_BUILD_FORTRAN=$(usex fortran)
+		-DHDF5_BUILD_HL_LIB=$(usex hl)
+		-DHDF5_ENABLE_CODESTACK=$(usex debug)
+		-DHDF5_ENABLE_PARALLEL=$(usex mpi)
+		-DHDF5_ENABLE_SZIP_ENCODING=$(usex szip)
+		-DHDF5_ENABLE_SZIP_SUPPORT=$(usex szip)
+		-DHDF5_ENABLE_THREADSAFE=$(usex threads)
+		-DHDF5_ENABLE_Z_LIB_SUPPORT=$(usex zlib)
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	# TODO: generate functioning example runners from their respective
+	# .in files - as of version 1.12.1 upstream only has it implemented
+	# for autoconf.
+	if use examples; then
+		# These are all useless outside the source tree
+		rm -f {examples,c++/examples,fortran/examples}/{Makefile*,CMake*}
+		rm -f hl/{examples,c++/examples,fortran/examples}/{Makefile*,CMake*}
+
+		dodoc -r examples
+		if use cxx; then
+			docinto c++
+			dodoc -r c++/examples
+		fi
+		if use fortran; then
+			docinto fortran
+			dodoc -r fortran/examples
+		fi
+		if use hl; then
+			docinto hl
+			dodoc -r hl/examples
+			if use cxx; then
+				docinto hl/c++
+				dodoc -r hl/c++/examples
+			fi
+			if use fortran; then
+				docinto hl/fortran
+				dodoc -r hl/fortran/examples
+			fi
+		fi
+	fi
+}
diff --git a/sci-libs/hdf5/hdf5-1.12.2-r4.ebuild b/sci-libs/hdf5/hdf5-1.12.2-r4.ebuild
new file mode 100644
index 000000000000..7cb1b8716025
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.12.2-r4.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+FORTRAN_NEEDED=fortran
+
+# We've reverted *back* to autotools from CMake because of
+# https://github.com/HDFGroup/hdf5/issues/1814.
+inherit autotools fortran-2 flag-o-matic toolchain-funcs prefix
+
+MY_P=${PN}-${PV/_p/-patch}
+MAJOR_P=${PN}-$(ver_cut 1-2)
+
+DESCRIPTION="General purpose library and file format for storing scientific data"
+HOMEPAGE="https://www.hdfgroup.org/HDF5/"
+SRC_URI="https://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="NCSA-HDF"
+SLOT="0/${PV%%_p*}"
+KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="cxx debug examples fortran +hl mpi szip threads zlib"
+REQUIRED_USE="
+	cxx? ( !mpi ) mpi? ( !cxx )
+	threads? ( !cxx !mpi !fortran !hl )"
+
+RDEPEND="
+	mpi? ( virtual/mpi[romio] )
+	szip? ( virtual/szip )
+	zlib? ( sys-libs/zlib:0= )"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
+	"${FILESDIR}"/${PN}-1.12.2-no-messing-ldpath.patch
+	"${FILESDIR}"/${PN}-1.12.2-no-strip-symbols.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
+
+	# Respect Gentoo examples directory
+	sed \
+		-e "s:hdf5_examples:doc/${PF}/examples:g" \
+		-i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die
+	sed \
+		-e '/docdir/d' \
+		-i config/commence.am || die
+
+	if ! use examples; then
+		# bug #409091
+		sed -e '/^install:/ s/install-examples//' \
+			-i Makefile.am || die
+	fi
+
+	# Enable shared libs by default for h5cc config utility
+	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" bin/h5cc.in || die
+	hprefixify m4/libtool.m4
+
+	eautoreconf
+}
+
+src_configure() {
+	# bug #686620
+	use sparc && tc-is-gcc && append-flags -fno-tree-ccp
+
+	econf \
+		--disable-static \
+		--enable-deprecated-symbols \
+		--enable-build-mode=$(usex debug debug production) \
+		$(use_enable cxx) \
+		$(use_enable debug codestack) \
+		$(use_enable fortran) \
+		$(use_enable hl) \
+		$(use_enable mpi parallel) \
+		$(use_enable threads threadsafe) \
+		$(use_with szip szlib) \
+		$(use_with threads pthread) \
+		$(use_with zlib)
+}
+
+src_install() {
+	emake DESTDIR="${D}" EPREFIX="${EPREFIX}" install
+
+	# No static archives
+	find "${ED}" -name '*.la' -delete || die
+
+	# Remove "perf" executable due to file collisions with dev-util/perf.
+	# Previously with the CMake build system we only installed h5perf, so
+	# let's simply remove the file for now.
+	use mpi && { rm "${ED}"/usr/bin/perf || die "rm failed" ; }
+}