commit: b11b637c1a4593fd66fd89d2fce77c57664b54e8
Author: Marek Szuba <marecki <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 16 16:10:28 2021 +0000
Commit: Marek Szuba <marecki <AT> gentoo <DOT> org>
CommitDate: Mon Aug 16 16:12:32 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b11b637c
sci-libs/hdf5: add 1.12.1
Signed-off-by: Marek Szuba <marecki <AT> gentoo.org>
profiles/base/package.use.mask | 5 +
sci-libs/hdf5/Manifest | 1 +
.../hdf5/files/hdf5-1.12.1-cmake_installdirs.patch | 103 ++++++++++++++++++
sci-libs/hdf5/hdf5-1.12.1.ebuild | 118 +++++++++++++++++++++
4 files changed, 227 insertions(+)
diff --git a/profiles/base/package.use.mask b/profiles/base/package.use.mask
index 82a710c7c50..52fdfc5312f 100644
--- a/profiles/base/package.use.mask
+++ b/profiles/base/package.use.mask
@@ -6,6 +6,11 @@
# This file is only for generic masks. For arch-specific masks (i.e.
# mask everywhere, unmask on arch/*) use arch/base.
+# Marek Szuba <mare...@gentoo.org> (2021-07-14)
+# Even on a clean install, 8 phdf5 tests fail (Bug #808612)
+# Mask for further study.
+>=sci-libs/hdf5-1.12.1 mpi
+
# James Le Cuirot <ch...@gentoo.org> (2021-08-07)
# The ORBlite scanner plugin only works on amd64 and x86.
net-print/hplip-plugin orblite
diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index 64df5831a55..bd0243d2494 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1 +1,2 @@
DIST hdf5-1.10.5.tar.bz2 8706317 BLAKE2B
ac326be8fe4ccc4b0153f15bc7d65aa8f1adc2ae279d3980f57ed46722b754d3f36ecf1d6273c75e80ed1afd4bbf10c6b1c5d9408e1f83a4b2e397e7902a7d3c
SHA512
769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4
+DIST hdf5-1.12.1.tar.bz2 9724309 BLAKE2B
cc75ba497188b33972218d02a7601acad1a0443bdb934ecd1641ef5996076fe120e3b72dba3a99d99f919fb4e478d1e531414448de9a7b97a0afde58a4c7c23f
SHA512
158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd
diff --git a/sci-libs/hdf5/files/hdf5-1.12.1-cmake_installdirs.patch
b/sci-libs/hdf5/files/hdf5-1.12.1-cmake_installdirs.patch
new file mode 100644
index 00000000000..8c4dc34cb80
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.12.1-cmake_installdirs.patch
@@ -0,0 +1,103 @@
+--- a/c++/src/CMakeLists.txt
++++ b/c++/src/CMakeLists.txt
+@@ -180,8 +180,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_CPP_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -46,6 +46,13 @@
+ endif()
+ endif ()
+
++include (GNUInstallDirs)
++set (HDF5_INSTALL_BIN_DIR "${CMAKE_INSTALL_FULL_BINDIR}")
++set (HDF5_INSTALL_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}")
++set (HDF5_INSTALL_DOC_DIR "${CMAKE_INSTALL_FULL_DOCDIR}")
++set (HDF5_INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_FULL_INCLUDEDIR}")
++set (HDF5_INSTALL_LIB_DIR "${CMAKE_INSTALL_FULL_LIBDIR}")
++
+ #-----------------------------------------------------------------------------
+ # Instructions for use : Sub-Project Build
+ #
+--- a/fortran/src/CMakeLists.txt
++++ b/fortran/src/CMakeLists.txt
+@@ -537,8 +537,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_F90_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+
+--- a/hl/c++/src/CMakeLists.txt
++++ b/hl/c++/src/CMakeLists.txt
+@@ -91,8 +91,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_HL_CPP_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+
+--- a/hl/fortran/src/CMakeLists.txt
++++ b/hl/fortran/src/CMakeLists.txt
+@@ -324,8 +324,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_HL_F90_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+
+--- a/hl/src/CMakeLists.txt
++++ b/hl/src/CMakeLists.txt
+@@ -123,8 +123,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_HL_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -1311,8 +1311,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+
+@@ -1419,7 +1419,7 @@
+ # )
+ install (
+ DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html
+- DESTINATION ${HDF5_INSTALL_DATA_DIR}
++ DESTINATION ${HDF5_INSTALL_DOC_DIR}
+ COMPONENT Documents
+ )
+
diff --git a/sci-libs/hdf5/hdf5-1.12.1.ebuild b/sci-libs/hdf5/hdf5-1.12.1.ebuild
new file mode 100644
index 00000000000..c5ef043111b
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.12.1.ebuild
@@ -0,0 +1,118 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+FORTRAN_NEEDED="fortran"
+
+inherit cmake flag-o-matic fortran-2
+
+MY_P="${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/${PV%%_p*}"
+KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86
~amd64-linux ~x86-linux"
+IUSE="cxx debug doc examples fortran +hl mpi szip test threads unsupported
zlib"
+
+REQUIRED_USE="
+ !unsupported? (
+ mpi? ( !cxx !threads )
+ threads? ( !cxx !fortran !hl )
+ )"
+
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ mpi? ( virtual/mpi[romio] )
+ szip? ( virtual/szip )
+ zlib? ( sys-libs/zlib:0= )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="doc? (
+ app-doc/doxygen
+ virtual/latex-base
+)"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.12.1-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() {
+ local mycmakeargs=(
+ -DBUILD_STATIC_LIBS=OFF
+ -DFETCHCONTENT_FULLY_DISCONNECTED=ON
+ -DHDF5_BUILD_EXAMPLES=OFF
+ -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
+}
