takeover from hdf5-openmpi (community package)

5 files changed, 157 insertions, 99 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 6d6669cb7aad..8617f12d22e3 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,31 +1,32 @@
 pkgbase = hdf5-openmpi-java
-	pkgdesc = General purpose library and file format for storing scientific data (openmpi version) (full version including its Java Native Interfaces)
-	pkgver = 1.10.5
+	pkgdesc = General purpose library and file format for storing scientific data (openmpi version including Java Native Interfaces)
+	pkgver = 1.12.0
 	pkgrel = 1
-	url = https://portal.hdfgroup.org/display/support
+	url = https://www.hdfgroup.org/hdf5
 	arch = x86_64
 	license = custom
 	makedepends = cmake
 	makedepends = time
-	makedepends = java-environment
 	makedepends = gcc-fortran
-	depends = bash
+	makedepends = java-environment
+	depends = zlib
 	depends = libaec
+	depends = bash
 	depends = openmpi
-	provides = hdf5-java
-	provides = hdf5-openmpi
 	provides = hdf5
 	provides = hdf5-cpp-fortran
 	provides = hdf5-fortran-openmpi
-	conflicts = hdf5-java
+	provides = hdf5-openmpi
+	provides = hdf5-java
 	conflicts = hdf5
 	conflicts = hdf5-openmpi
+	conflicts = hdf5-java
 	replaces = hdf5-fortran-openmpi
 	options = staticlibs
-	source = https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.bz2
-	source = mpi.patch
-	md5sums = 7c19d6b81ee2a3ba7d36f6922b2f90d3
-	md5sums = 63b43e3d4a5bbea4bcecc84874e08913
+	source = https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.bz2
+	source = hdf5-1.12.0-compat-1.6.patch
+	sha256sums = 97906268640a6e9ce0cde703d5a71c9ac3092eded729591279bf2e3ca9765f61
+	sha256sums = 72ad497c56760bb3af8193c88d3fa264125829850b843697de55d934c56f7f44
 
 pkgname = hdf5-openmpi-java
 
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 000000000000..44f27c04b1e5
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+pkg
+src
+*.tar.*
diff --git a/PKGBUILD b/PKGBUILD
index c9e3e9d5b742..2d5bbf7c4fef 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,8 +1,7 @@
-# Maintainer : George Eleftheriou <eleftg>
-# Contributor: Martin Diehl <MartinDiehl>
-# Contributor: Jingbei Li <petronny>
+# Maintainer: Martin Diehl <https://martin-diehl.net>
 # Contributor: Ronald van Haren <ronald.archlinux.org>
-# Contributor: Bruno Pagani (a.k.a. ArchangeGabriel) <archange@archlinux.org>
+# Contributor: Bruno Pagani <archange@archlinux.org>
+# Contributor: George Eleftheriou <eleftg>
 # Contributor: Stefan Husmann <stefan-husmann@t-online.de>
 # Contributor: damir <damir@archlinux.org>
 # Contributor: Tom K <tomk@runbox.com>
@@ -12,74 +11,57 @@
 _pkgname=hdf5
 _mpi=openmpi
 pkgname=${_pkgname}-${_mpi}-java
-_prefix=/usr
-pkgver=1.10.5
+pkgver=1.12.0
 pkgrel=1
-pkgdesc="General purpose library and file format for storing scientific data (${_mpi} version) (full version including its Java Native Interfaces)"
-arch=('x86_64')
-url="https://portal.hdfgroup.org/display/support"
-license=('custom')
-depends=('bash' 'libaec' "${_mpi}")
-makedepends=('cmake' 'time' 'java-environment' 'gcc-fortran')
-options=('staticlibs')
-provides=('hdf5-java' 'hdf5-openmpi' 'hdf5' 'hdf5-cpp-fortran' "hdf5-fortran-${_mpi}")
-conflicts=('hdf5-java' 'hdf5' 'hdf5-openmpi')
-replaces=("hdf5-fortran-${_mpi}")
-source=("https://support.hdfgroup.org/ftp/HDF5/releases/${_pkgname}-${pkgver:0:4}/${_pkgname}-${pkgver}/src/${_pkgname}-${pkgver}.tar.bz2"
-        'mpi.patch')
-md5sums=('7c19d6b81ee2a3ba7d36f6922b2f90d3'
-         '63b43e3d4a5bbea4bcecc84874e08913')
-
-prepare() {
-    mkdir -p build
-    cd "${_pkgname}-${pkgver}"
-
-    # FS#33343
-    patch -p1 -i ../mpi.patch
-}
+pkgdesc="General purpose library and file format for storing scientific data (${_mpi} version including Java Native Interfaces)"
+arch=(x86_64)
+url="https://www.hdfgroup.org/hdf5"
+license=(custom)
+depends=(zlib libaec bash ${_mpi})
+makedepends=(cmake time gcc-fortran java-environment)
+provides=(hdf5 hdf5-cpp-fortran hdf5-fortran-${_mpi} hdf5-${_mpi} hdf5-java)
+conflicts=(hdf5 hdf5-openmpi hdf5-java)
+replaces=(hdf5-fortran-${_mpi})
+options=(staticlibs)
+source=("https://support.hdfgroup.org/ftp/HDF5/releases/${_pkgname}-${pkgver:0:4}/${_pkgname}-${pkgver/_/-}/src/${_pkgname}-${pkgver/_/-}.tar.bz2"
+        hdf5-1.12.0-compat-1.6.patch)
+sha256sums=('97906268640a6e9ce0cde703d5a71c9ac3092eded729591279bf2e3ca9765f61'
+            '72ad497c56760bb3af8193c88d3fa264125829850b843697de55d934c56f7f44')
 
 build() {
-    cd build
-
     # Crazy workaround: run CMake to generate pkg-config file
+    mkdir -p build && cd build
+    CXX="mpicxx" \
+    CC="mpicc" \
+    FC="mpif90" \
+    F9X="mpif90" \
     RUNPARALLEL="mpirun" \
     OMPI_MCA_disable_memory_allocator=1 \
-    JAVADOC='javadoc -Xdoclint:none' \
-    cmake ../${_pkgname}-${pkgver}  \
-        -DCMAKE_CXX_COMPILER=mpicxx \
-        -DCMAKE_C_COMPILER=mpicc \
-        -DCMAKE_Fortran_COMPILER=mpif90 \
-        -DCMAKE_C_FLAGS="${CPPFLAGS} ${CFLAGS}" \
-        -DCMAKE_CXX_FLAGS="${CPPFLAGS} ${CXXFLAGS}" \
-        -DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \
-        -DCMAKE_SHARED_LINKER_FLAGS="${LDFLAGS}" \
-        -DCMAKE_MODULE_LINKER_FLAGS="${LDFLAGS}" \
-        -DCMAKE_INSTALL_RPATH="" \
+    cmake ../${_pkgname}-${pkgver/_/-} \
+        -DCMAKE_INSTALL_PREFIX=/usr \
         -DBUILD_SHARED_LIBS=ON \
         -DCMAKE_BUILD_TYPE=Release \
-        -DCMAKE_INSTALL_PREFIX="${_prefix}" \
         -DALLOW_UNSUPPORTED=ON \
         -DHDF5_BUILD_HL_LIB=ON \
         -DHDF5_BUILD_CPP_LIB=ON \
         -DHDF5_BUILD_FORTRAN=ON \
         -DHDF5_BUILD_JAVA=ON \
+        -DHDF5_ENABLE_PARALLEL=ON \
         -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
         -DHDF5_ENABLE_SZIP_SUPPORT=ON \
-        -DHDF5_ENABLE_SZIP_ENCODING=ON \
-        -DHDF5_ENABLE_PARALLEL=ON \
-        -DBUILD_TESTING=OFF
-
+        -DHDF5_ENABLE_SZIP_ENCODING=ON
     # But don’t build with it, it’s quite broken
-    "${srcdir}/${_pkgname}-${pkgver}"/configure \
+    cd ../${_pkgname}-${pkgver/_/-}
+    ./configure \
         CXX="mpicxx" \
         CC="mpicc" \
         FC="mpif90" \
         F9X="mpif90" \
         RUNPARALLEL="mpirun" \
         OMPI_MCA_disable_memory_allocator=1 \
-        JAVADOC='javadoc -Xdoclint:none' \
-        --prefix="${_prefix}" \
-        --docdir="${_prefix}/share/doc/${_pkgname}" \
+        --prefix=/usr \
+        --docdir=/usr/share/doc/hdf5/ \
+        --with-examplesdir='${DESTDIR}/${prefix}/share/doc/hdf5/examples' \
         --enable-static \
         --disable-sharedlib-rpath \
         --enable-build-mode=production \
@@ -92,22 +74,29 @@ build() {
         --with-pic \
         --with-zlib \
         --with-szlib
-
     make
 }
 
-package() {
-    cd build
+check() {
+    cd ${_pkgname}-${pkgver/_/-}
+    # Without this, checks are failing with messages like “error while loading shared libraries: libhdf5.so.101: cannot open shared object file: No such file or directory”
+    export LD_LIBRARY_PATH="${srcdir}"/${pkgname}-${pkgver/_/-}/src/.libs/
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/c++/src/.libs/
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/fortran/src/.libs/
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/hl/src/.libs/
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/hl/c++/src/.libs/
+    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/hl/fortran/src/.libs/
+    # This is a parallel build, they are always OpenMPI bugs
+    make check || warning "Tests failed"
+}
 
+package() {
+    cd ${_pkgname}-${pkgver/_/-}
     make DESTDIR="${pkgdir}" install
-
-    # Move examples to a proper place
-    install -dm755 "${pkgdir}${_prefix}/share/doc/${_pkgname}"
-    mv "${pkgdir}${_prefix}"/share/{hdf5_examples,doc/${_pkgname}/examples}
-
-    install -Dm644 "${srcdir}/${_pkgname}-${pkgver}/COPYING" \
-        "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
-
-    install -Dm644 CMakeFiles/hdf5{,_hl}{,_cpp}-${pkgver}.pc \
-        -t "${pkgdir}${_prefix}"/lib/pkgconfig
+    install -Dm644 COPYING -t "${pkgdir}"/usr/share/licenses/${_pkgname}
+    # Install pkg-config files from CMake tree
+    install -Dm644 ../build/CMakeFiles/hdf5{,_hl}{,_cpp}-${pkgver}.pc -t "${pkgdir}"/usr/lib/pkgconfig/
+    # Fix 1.6 compatibility for h5py
+    cd "${pkgdir}"/usr/include/
+    patch -p1 -i "${srcdir}"/hdf5-1.12.0-compat-1.6.patch
 }
diff --git a/hdf5-1.12.0-compat-1.6.patch b/hdf5-1.12.0-compat-1.6.patch
new file mode 100644
index 000000000000..eda1919dc94b
--- /dev/null
+++ b/hdf5-1.12.0-compat-1.6.patch
@@ -0,0 +1,89 @@
+--- a/H5version.h
++++ b/H5version.h
+@@ -97,6 +97,10 @@
+   #define H5Ewalk_vers 1
+ #endif /* !defined(H5Ewalk_vers) */
+ 
++#if !defined(H5Fget_info_vers)
++  #define H5Fget_info_vers 1
++#endif /* !defined(H5Fget_info_vers) */
++
+ #if !defined(H5Gcreate_vers)
+   #define H5Gcreate_vers 1
+ #endif /* !defined(H5Gcreate_vers) */
+@@ -105,6 +109,38 @@
+   #define H5Gopen_vers 1
+ #endif /* !defined(H5Gopen_vers) */
+ 
++#if !defined(H5Lget_info_vers)
++  #define H5Lget_info_vers 1
++#endif /* !defined(H5Lget_info_vers) */
++
++#if !defined(H5Lget_info_by_idx_vers)
++  #define H5Lget_info_by_idx_vers 1
++#endif /* !defined(H5Lget_info_by_idx_vers) */
++
++#if !defined(H5Oget_info_vers)
++  #define H5Oget_info_vers 1
++#endif /* !defined(H5Oget_info_vers) */
++
++#if !defined(H5Oget_info_by_idx_vers)
++  #define H5Oget_info_by_idx_vers 1
++#endif /* !defined(H5Oget_info_by_idx_vers) */
++
++#if !defined(H5Oget_info_by_name_vers)
++  #define H5Oget_info_by_name_vers 1
++#endif /* !defined(H5Oget_info_by_name_vers) */
++
++#if !defined(H5Ovisit_vers)
++  #define H5Ovisit_vers 1
++#endif /* !defined(H5Ovisit_vers) */
++
++#if !defined(H5Ovisit_by_name_vers)
++  #define H5Ovisit_by_name_vers 1
++#endif /* !defined(H5Ovisit_by_name_vers) */
++
++#if !defined(H5Pencode_vers)
++  #define H5Pencode_vers 1
++#endif /* !defined(H5Pencode_vers) */
++
+ #if !defined(H5Pget_filter_vers)
+   #define H5Pget_filter_vers 1
+ #endif /* !defined(H5Pget_filter_vers) */
+@@ -133,6 +169,10 @@
+   #define H5Tarray_create_vers 1
+ #endif /* !defined(H5Tarray_create_vers) */
+ 
++#if !defined(H5Sencode_vers)
++  #define H5Sencode_vers 1
++#endif /* !defined(H5Sencode_vers) */
++
+ #if !defined(H5Tcommit_vers)
+   #define H5Tcommit_vers 1
+ #endif /* !defined(H5Tcommit_vers) */
+@@ -153,6 +193,14 @@
+   #define H5E_auto_t_vers 1
+ #endif /* !defined(H5E_auto_t_vers) */
+ 
++#if !defined(H5O_info_t_vers)
++  #define H5O_info_t_vers 1
++#endif /* !defined(H5O_info_t_vers) */
++
++#if !defined(H5O_iterate_t_vers)
++  #define H5O_iterate_t_vers 1
++#endif /* !defined(H5O_iterate_t_vers) */
++
+ #if !defined(H5Z_class_t_vers)
+   #define H5Z_class_t_vers 1
+ #endif /* !defined(H5Z_class_t_vers) */
+@@ -261,6 +309,10 @@
+   #define H5Ovisit_by_name_vers 1
+ #endif /* !defined(H5Ovisit_by_name_vers) */
+ 
++#if !defined(H5Pencode_vers)
++  #define H5Pencode_vers 1
++#endif /* !defined(H5Pencode_vers) */
++
+ #if !defined(H5Pget_filter_vers)
+   #define H5Pget_filter_vers 2
+ #endif /* !defined(H5Pget_filter_vers) */
diff --git a/mpi.patch b/mpi.patch
deleted file mode 100644
index e435f9be3ff5..000000000000
--- a/mpi.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Prevent accidental inclusion of mpi c++ headers 
-when hdf5.h is included third party library
-
-https://bugs.gentoo.org/show_bug.cgi?id=420777
-https://bugs.archlinux.org/task/33343
-
---- a/src/H5public.h
-+++ b/src/H5public.h
-@@ -57,6 +57,15 @@
- #   include <stddef.h>
- #endif
- #ifdef H5_HAVE_PARALLEL
-+#   ifndef OMPI_SKIP_MPICXX
-+#      define OMPI_SKIP_MPICXX
-+#   endif
-+#   ifndef MPICH_IGNORE_CXX_SEEK
-+#      define MPICH_IGNORE_CXX_SEEK
-+#   endif
-+#   ifndef MPICH_SKIP_MPICXX
-+#      define MPICH_SKIP_MPICXX
-+#   endif
- #   include <mpi.h>
- #ifndef MPI_FILE_NULL		/*MPIO may be defined in mpi.h already       */
- #   include <mpio.h>