diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog new file mode 100644 index 0000000..e3ade83 --- /dev/null +++ b/sci-libs/hdf5/ChangeLog @@ -0,0 +1,6 @@ +*hdf5-1.12.1 (01 Oct 2021) + + 01 Oct 2021; +files/hdf5-1.12.1-cmake_installdirs.patch, + +hdf5-1.12.1.ebuild, +metadata.xml: + sci-libs/hdf5: added ROS3 support (DANDI stack) Pending: + https://github.com/gentoo/gentoo/pull/22455 diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest new file mode 100644 index 0000000..9c78b4a --- /dev/null +++ b/sci-libs/hdf5/Manifest @@ -0,0 +1 @@ +DIST hdf5-1.12.1.tar.bz2 9724309 SHA256 aaf9f532b3eda83d3d3adc9f8b40a9b763152218fa45349c3bc77502ca1f8f1c SHA512 158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd WHIRLPOOL 1fa4d86b495652d48a662a955a8d0b384d6d996f83a86e8f23e6f3597fa5795294b10302913a771250ebc1dbc5b5a5619268a549cba594b75bd5d7bc9cad52c3 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 0000000..8c4dc34 --- /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 ${HDF5_INSTALL_DOC_DIR} + COMPONENT Documents + ) + diff --git a/sci-libs/hdf5/hdf5-1.12.1.ebuild b/sci-libs/hdf5/hdf5-1.12.1.ebuild new file mode 100644 index 0000000..2075608 --- /dev/null +++ b/sci-libs/hdf5/hdf5-1.12.1.ebuild @@ -0,0 +1,123 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +FORTRAN_NEEDED="fortran" + +inherit cmake flag-o-matic fortran-2 + +MY_P="${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/${PV%%_p*}" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="cxx debug doc examples fortran +hl mpi ros3 szip test threads unsupported zlib" + +REQUIRED_USE=" + !unsupported? ( + mpi? ( !cxx !threads ) + threads? ( !cxx !fortran !hl ) + )" + +RESTRICT="!test? ( test )" + +RDEPEND=" + mpi? ( virtual/mpi[romio] ) + ros3? ( + net-misc/curl + dev-libs/openssl + ) + szip? ( virtual/szip ) + zlib? ( sys-libs/zlib:0= ) +" +DEPEND="${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) + -DHDF5_ENABLE_ROS3_VFD:BOOL=$(usex ros3) + ) + 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/metadata.xml b/sci-libs/hdf5/metadata.xml new file mode 100644 index 0000000..042059b --- /dev/null +++ b/sci-libs/hdf5/metadata.xml @@ -0,0 +1,19 @@ + + + + + sci@gentoo.org + Gentoo Science Project + + + HDF5 is a file format and library for storing scientific data. HDF5 + was designed and implemented to address the deficiencies of HDF4.x. It + has a more powerful and flexible data model, supports files larger + than 2 GB, and supports parallel I/O. + + + Enable high level API (https://support.hdfgroup.org/HDF5/doc/HL/index.html) + Enable support for read-only S3 access (https://portal.hdfgroup.org/display/HDF5/Configuration+and+Setup+for+HDF5+Read+Only+S3+VFD) + Enable unsupported combinations of configuration options + +