Merge pull request #310 from t20100/update-dependencies

Updated embedded filters: LZ4 (commit 49e3b65), hdf5-blosc (v1.0.1), SZ (commit f466775); Updated library: Snappy (v1.2.1)

doc/information.rst

@@ -68,22 +68,22 @@ HDF5 filters and compression libraries
 HDF5 compression filters and compression libraries sources were obtained from:
 
 * `LZ4 plugin <https://github.com/nexusformat/HDF5-External-Filter-Plugins>`_ 
-  (commit `d48f960 <https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/d48f96064cb6e229ede4bf5e5c0e1935cf691036>`_)
+  (commit `49e3b65 <https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/49e3b65eca772bca77af13ba047d8b577673afba>`_)
   using LZ4.
 * `bitshuffle plugin <https://github.com/kiyo-masui/bitshuffle>`_ (v0.5.1) using LZ4 and ZStd.
 * bzip2 plugin (from `PyTables <https://github.com/PyTables/PyTables/>`_ v3.9.2)
   using `BZip2 <https://sourceware.org/git/bzip2.git>`_ (v1.0.8).
-* `hdf5-blosc plugin <https://github.com/Blosc/hdf5-blosc>`_ (v1.0.0)
+* `hdf5-blosc plugin <https://github.com/Blosc/hdf5-blosc>`_ (v1.0.1)
   using `c-blosc <https://github.com/Blosc/c-blosc>`_ (v1.21.5), LZ4, Snappy, ZLib and ZStd.
 * hdf5-blosc2 plugin (from `PyTables <https://github.com/PyTables/PyTables/>`_ v3.9.2)
   using `c-blosc2 <https://github.com/Blosc/c-blosc2>`_ (v2.13.2), LZ4, ZLib and ZStd.
 * `FCIDECOMP plugin <ftp://ftp.eumetsat.int/pub/OPS/out/test-data/Test-data-for-External-Users/MTG_FCI_Test-Data/FCI_Decompression_Software_V1.0.2>`_ (v1.0.2)
   using `CharLS <https://github.com/team-charls/charls>`_
   (1.x branch, commit `25160a4 <https://github.com/team-charls/charls/tree/25160a42fb62e71e4b0ce081f5cb3f8bb73938b5>`_).
 * `SZ plugin <https://github.com/szcompressor/SZ>`_
-  (commit `c25805c12b3 <https://github.com/szcompressor/SZ/commit/c25805c12b339d2cb2f406f95293b9a7313c4fb1>`_)
-* `H5Z-SPERR plugin <https://github.com/NCAR/H5Z-SPERR>`_ (v0.1.3) using `SPERR <https://github.com/NCAR/SPERR>`_ (v0.8.1).
+  (commit `f466775 <https://github.com/szcompressor/SZ/tree/f4667759ead6a902110e80ff838ccdfddbc8dcd7>`_)
   using `SZ <https://github.com/szcompressor/SZ>`_, ZLib and ZStd.
+* `H5Z-SPERR plugin <https://github.com/NCAR/H5Z-SPERR>`_ (v0.1.3) using `SPERR <https://github.com/NCAR/SPERR>`_ (v0.8.1).
 * `SZ3 plugin <https://github.com/szcompressor/SZ3>`_
   (commit `4bbe9df7e4bcb <https://github.com/szcompressor/SZ3/commit/4bbe9df7e4bcb6ae6339fcb3033100da07fe7434>`_)
   using `SZ3 <https://github.com/szcompressor/SZ3>`_ and ZStd.
@@ -95,7 +95,7 @@ HDF5 compression filters and compression libraries sources were obtained from:
 Sources of compression libraries shared accross multiple filters were obtained from:
 
 * `LZ4 v1.9.4 <https://github.com/Blosc/c-blosc2/tree/v2.13.2/internal-complibs/lz4-1.9.4>`_
-* `Snappy v1.1.10 <https://github.com/google/snappy>`_
+* `Snappy v1.2.1 <https://github.com/google/snappy>`_
 * `ZStd v1.5.5 <https://github.com/Blosc/c-blosc2/tree/v2.13.2/internal-complibs/zstd-1.5.5>`_
 * `ZLib v1.2.13 <https://github.com/Blosc/c-blosc/tree/v1.21.5/internal-complibs/zlib-1.2.13>`_
 

src/LZ4/COPYING

@@ -1,3 +1,4 @@
+
 Copyright Notice and License Terms for 
 HDF5 LZ4 compression filter plugin
 -----------------------------------------------------------------------------
@@ -56,4 +57,4 @@ Source code of the HDF5 LZ4 filter is based on h5py implementation found in
            Additional_Legal/h5py_Copyrights_and_Licenses.txt
       Original source:
            http://docs.h5py.org/en/latest/licenses.html
-License type: BSD-style license
+      License type: BSD-style license

src/LZ4/lz4_h5filter.h

@@ -17,7 +17,7 @@
 
 
 #ifndef LZ4_H5FILTER_H
-#define LZ5_H5FILTER_H
+#define LZ4_H5FILTER_H
 
 #define H5Z_class_t_vers 2
 #include "hdf5.h"

src/SZ/sz/CMakeLists.txt

@@ -92,11 +92,23 @@ set_target_properties (SZ PROPERTIES
     OUTPUT_NAME_RELWITHDEBINFO ${LIB_RELEASE_NAME}
   )
 
-target_link_libraries (SZ PUBLIC ${ZLIB_dep} ${ZSTD_dep} m)
+if (WIN32 AND NOT MINGW)
+    target_link_libraries (SZ PUBLIC ${ZLIB_dep} ${ZSTD_dep})
+else ()
+    target_link_libraries (SZ PUBLIC ${ZLIB_dep} ${ZSTD_dep} m)
+endif ()
 
-target_compile_options(SZ
-	PRIVATE $<$<CONFIG:Debug>:-Wall -Wextra -Wpedantic -Wno-unused-parameter>
-	)
+if (WIN32 AND NOT MINGW)
+    message(STATUS "Native windows compiler detected, adding compile flags")
+    target_compile_options(SZ
+        PRIVATE $<$<CONFIG:Debug>:-Wall>
+    )
+else ()
+    message(STATUS "GCC detected, adding compile flags")
+    target_compile_options(SZ
+        PRIVATE $<$<CONFIG:Debug>:-Wall -Wextra -Wpedantic -Wno-unused-parameter>
+    )
+endif()
 
 if(BUILD_OPENMP)
   target_link_libraries(SZ PRIVATE OpenMP::OpenMP_C)

src/SZ/sz/src/sz.c

@@ -485,7 +485,16 @@ unsigned char *SZ_compress_rev(int dataType, void *data, void *reservedValue, si
 
 void *SZ_decompress(int dataType, unsigned char *bytes, size_t byteLength, size_t r5, size_t r4, size_t r3, size_t r2, size_t r1)
 {
-	if(confparams_dec==NULL)
+    //correct dimension if needed
+    size_t _r[5];
+    filterDimension(r5, r4, r3, r2, r1, _r);
+    r5 = _r[4];
+    r4 = _r[3];
+    r3 = _r[2];
+    r2 = _r[1];
+    r1 = _r[0];
+
+    if(confparams_dec==NULL)
 		confparams_dec = (sz_params*)malloc(sizeof(sz_params));
 	memset(confparams_dec, 0, sizeof(sz_params));
 	if(exe_params==NULL)

src/SZ/zlib/CMakeLists.txt

@@ -4,6 +4,10 @@ else ()
   set (BUILD_EXT_LIBS_TYPE "STATIC")
 endif ()
 
+if (WIN32 AND NOT MINGW)
+  set (BUILD_EXT_LIBS_TYPE "STATIC")
+endif ()
+
 add_library(ZLIB ${BUILD_EXT_LIBS_TYPE} 
   ./gzclose.c
   ./uncompr.c

src/SZ/zstd/CMakeLists.txt

@@ -4,6 +4,10 @@ else ()
   set (BUILD_EXT_LIBS_TYPE "STATIC")
 endif ()
 
+if (WIN32 AND NOT MINGW)
+  set (BUILD_EXT_LIBS_TYPE "STATIC")
+endif ()
+
 add_library(zstd ${BUILD_EXT_LIBS_TYPE} 
   ./common/entropy_common.c
   ./common/pool.c

src/hdf5-blosc/CMakeLists.txt

@@ -1,6 +1,8 @@
 cmake_minimum_required(VERSION 2.8.10)
+cmake_policy(SET CMP0074 NEW)
 project(blosc_hdf5)
 include(ExternalProject)
+include(GNUInstallDirs)
 
 # options
 option(BUILD_TESTS
@@ -9,7 +11,7 @@ option(BUILD_TESTS
 option(BUILD_PLUGIN
     "Build dynamically loadable plugin for HDF5 version > 1.8.11" ON)
 if(BUILD_PLUGIN)
-    set(PLUGIN_INSTALL_PATH "/usr/local/hdf5/lib/plugin" CACHE PATH 
+    set(PLUGIN_INSTALL_PATH "/usr/local/hdf5/lib/plugin" CACHE PATH
       "Where to install the dynamic HDF5-plugin")
 endif(BUILD_PLUGIN)
 
@@ -25,6 +27,7 @@ message("GIT_EXECUTABLE='${GIT_EXECUTABLE}'")
 ExternalProject_Add(project_blosc
   PREFIX ${BLOSC_PREFIX}
   GIT_REPOSITORY https://github.com/Blosc/c-blosc.git
+  GIT_TAG main
   INSTALL_DIR ${BLOSC_INSTALL_DIR}
   CMAKE_ARGS ${BLOSC_CMAKE_ARGS}
 )
@@ -52,7 +55,7 @@ include_directories(${HDF5_INCLUDE_DIRS})
 
 # add blosc libraries
 add_library(blosc_shared SHARED IMPORTED)
-set_property(TARGET blosc_shared PROPERTY IMPORTED_LOCATION ${BLOSC_INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}blosc${CMAKE_SHARED_LIBRARY_SUFFIX})
+set_property(TARGET blosc_shared PROPERTY IMPORTED_LOCATION ${BLOSC_INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}blosc${CMAKE_SHARED_LIBRARY_SUFFIX})
 add_dependencies(blosc_shared project_blosc)
 include_directories(${BLOSC_INSTALL_DIR}/include)
 

src/hdf5-blosc/README.rst

@@ -26,7 +26,7 @@ Instead of just linking this Blosc filter into your HDF5 application, it is poss
 it as a system-wide HDF5 plugin (with HDF5 1.8.11 or later).  This is useful because it allows
 *every* HDF5-using program on your system to transparently read Blosc-compressed HDF5 files.
 
-As described in the `HDF5 plugin documentation <https://www.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf>`_, you just need to compile the Blosc plugin into a shared library and
+As described in the `HDF5 plugin documentation <https://portal.hdfgroup.org/display/HDF5/HDF5+Dynamically+Loaded+Filters>`_, you just need to compile the Blosc plugin into a shared library and
 copy it to the plugin directory (which defaults to ``/usr/local/hdf5/lib/plugin`` on non-Windows systems).
 
 Following the ``cmake`` instructions below produces a ``libH5Zblosc.so`` shared library 

src/hdf5-blosc/RELEASE_NOTES.txt

@@ -6,6 +6,15 @@
 :Contact: [email protected]
 :URL: http://www.blosc.org
 
+Changes from 1.0.0 to 1.0.1
+===========================
+
+- Fix warnings related to const for blosc_filter.c.  Thanks to
+  @matchy233.  Closes #34.
+
+- Fix build on systems where the libdir is lib64 instead of lib.  Thanks to
+  Lehman Garrison.
+
 
 Changes from 0.0.1 to 1.0.0
 ===========================

src/hdf5-blosc/src/blosc_filter.c

@@ -155,8 +155,8 @@ size_t blosc_filter(unsigned flags, size_t cd_nelmts,
   int doshuffle = 1;             /* Shuffle default */
   int compcode;                  /* Blosc compressor */
   int code;
-  char* compname = "blosclz";    /* The compressor by default */
-  char* complist;
+  const char* compname = "blosclz";    /* The compressor by default */
+  const char* complist;
   char errmsg[256];
 
   /* Filter params that are always set */

src/hdf5-blosc/src/example.c

@@ -56,6 +56,8 @@ int main(){
     /* Register the filter with the library */
     r = register_blosc(&version, &date);
     printf("Blosc version info: %s (%s)\n", version, date);
+    free(version);
+    free(date);
 
     if(r<0) goto failed;
 

src/snappy/.bazelrc

@@ -0,0 +1,2 @@
+# googletest requires C++14 or above
+build --cxxopt='-std=c++17'

src/snappy/.gitignore

@@ -5,4 +5,5 @@
 
 # Build directory.
 build/
+/bazel-*
 out/