Merge branch 'develop' of https://github.com/HDFGroup/hdf5 into develop

7 files changed, 13 insertions, 106 deletions

diff --git a/config/cmake/HDF5PluginMacros.cmake b/config/cmake/HDF5PluginMacros.cmake
index 3cded02..2c9e5e6 100644
--- a/config/cmake/HDF5PluginMacros.cmake
+++ b/config/cmake/HDF5PluginMacros.cmake
@@ -49,8 +49,8 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type)
             -DLZ4_PACKAGE_NAME:STRING=${LZ4_PACKAGE_NAME}
             -DLZF_TGZ_NAME:STRING=${LZF_TGZ_NAME}
             -DLZF_PACKAGE_NAME:STRING=${LZF_PACKAGE_NAME}
-            #-DSZ_TGZ_NAME:STRING=${SZ_TGZ_NAME}
-            #-DSZ_PACKAGE_NAME:STRING=${SZ_PACKAGE_NAME}
+            -DSZF_TGZ_NAME:STRING=${SZF_TGZ_NAME}
+            -DSZF_PACKAGE_NAME:STRING=${SZF_PACKAGE_NAME}
             -DZFP_TGZ_NAME:STRING=${ZFP_TGZ_NAME}
             -DZFP_PACKAGE_NAME:STRING=${ZFP_PACKAGE_NAME}
     )
@@ -101,8 +101,8 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type)
             -DLZ4_PACKAGE_NAME:STRING=${LZ4_PACKAGE_NAME}
             -DLZF_TGZ_NAME:STRING=${LZF_TGZ_NAME}
             -DLZF_PACKAGE_NAME:STRING=${LZF_PACKAGE_NAME}
-            #-DSZ_TGZ_NAME:STRING=${SZ_TGZ_NAME}
-            #-DSZ_PACKAGE_NAME:STRING=${SZ_PACKAGE_NAME}
+            -DSZF_TGZ_NAME:STRING=${SZF_TGZ_NAME}
+            -DSZF_PACKAGE_NAME:STRING=${SZF_PACKAGE_NAME}
             -DZFP_TGZ_NAME:STRING=${ZFP_TGZ_NAME}
             -DZFP_PACKAGE_NAME:STRING=${ZFP_PACKAGE_NAME}
     )
diff --git a/config/cmake/HDF5_Process_Flex_Files.cmake b/config/cmake/HDF5_Process_Flex_Files.cmake
deleted file mode 100644
index 2595c39..0000000
--- a/config/cmake/HDF5_Process_Flex_Files.cmake
+++ /dev/null
@@ -1,95 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-# post process flex/bison files
-
-message (STATUS "File: ${GEN_DIR} ${FILE_PARSE} ${FILE_ANALYZE}")
-
-if (FILE_PARSE)
-  # fix H5LTparse.c to declare H5LTyyparse return type as an hid_t
-  # instead of int.  Currently the generated function H5LTyyparse is
-  # generated with a return value of type int, which is a mapping to the
-  # flex yyparse function.  The return value in the HL library should be
-  # an hid_t.
-  # I propose to not use flex to generate this function, but for now I am
-  # adding a perl command to find and replace this function declaration in
-  # H5LTparse.c.
-    file (READ ${GEN_DIR}/${FILE_PARSE}.c TEST_STREAM)
-    string (REGEX REPLACE "int yyparse" "hid_t yyparse" TEST_STREAM "${TEST_STREAM}")
-    string (REGEX REPLACE "int\nyyparse" "hid_t\nyyparse" TEST_STREAM "${TEST_STREAM}")
-    string (REGEX REPLACE "int H5LTyyparse" "hid_t H5LTyyparse" TEST_STREAM "${TEST_STREAM}")
-    file (WRITE ${FILE_PARSE}.c "${TEST_STREAM}")
-    message (STATUS "replacing signature in H5LTparse.c")
-
-  # Add code that disables warnings in the flex/bison-generated code.
-  #
-  # Note that the GCC pragmas did not exist until gcc 4.2. Earlier versions
-  # will simply ignore them, but we want to avoid those warnings.
-    file (READ ${FILE_PARSE}.c TEST_STREAM)
-    file (WRITE ${FILE_PARSE}.c "
-#if __GNUC__ >= 4 && __GNUC_MINOR__ >=2\n
-#pragma GCC diagnostic ignored \"-Wconversion\"\n
-#pragma GCC diagnostic ignored \"-Wimplicit-function-declaration\"\n
-#pragma GCC diagnostic ignored \"-Wlarger-than=\"\n
-#pragma GCC diagnostic ignored \"-Wmissing-prototypes\"\n
-#pragma GCC diagnostic ignored \"-Wnested-externs\"\n
-#pragma GCC diagnostic ignored \"-Wold-style-definition\"\n
-#pragma GCC diagnostic ignored \"-Wsign-compare\"\n
-#pragma GCC diagnostic ignored \"-Wsign-conversion\"\n
-#pragma GCC diagnostic ignored \"-Wstrict-prototypes\"\n
-#pragma GCC diagnostic ignored \"-Wswitch-default\"\n
-#pragma GCC diagnostic ignored \"-Wunused-function\"\n
-#pragma GCC diagnostic ignored \"-Wunused-macros\"\n
-#pragma GCC diagnostic ignored \"-Wunused-parameter\"\n
-#pragma GCC diagnostic ignored \"-Wredundant-decls\"\n
-#elif defined __SUNPRO_CC\n
-#pragma disable_warn\n
-#elif defined _MSC_VER\n
-#pragma warning(push, 1)\n
-#endif\n
-    ")
-    file (APPEND ${FILE_PARSE}.c "${TEST_STREAM}")
-    message (STATUS "processed pragma in ${FILE_PARSE}")
-    file (READ ${GEN_DIR}/${FILE_PARSE}.h TEST_STREAM)
-    file (WRITE ${FILE_PARSE}.h "${TEST_STREAM}")
-endif ()
-
-if (FILE_ANALYZE)
-  # Add code that disables warnings in the flex/bison-generated code.
-  #
-  # Note that the GCC pragmas did not exist until gcc 4.2. Earlier versions
-  # will simply ignore them, but we want to avoid those warnings.
-    file (READ ${GEN_DIR}/${FILE_ANALYZE} TEST_STREAM)
-    file (WRITE ${FILE_ANALYZE} "
-#if __GNUC__ >= 4 && __GNUC_MINOR__ >=2\n
-#pragma GCC diagnostic ignored \"-Wconversion\"\n
-#pragma GCC diagnostic ignored \"-Wimplicit-function-declaration\"\n
-#pragma GCC diagnostic ignored \"-Wlarger-than=\"\n
-#pragma GCC diagnostic ignored \"-Wmissing-prototypes\"\n
-#pragma GCC diagnostic ignored \"-Wnested-externs\"\n
-#pragma GCC diagnostic ignored \"-Wold-style-definition\"\n
-#pragma GCC diagnostic ignored \"-Wsign-compare\"\n
-#pragma GCC diagnostic ignored \"-Wsign-conversion\"\n
-#pragma GCC diagnostic ignored \"-Wstrict-prototypes\"\n
-#pragma GCC diagnostic ignored \"-Wswitch-default\"\n
-#pragma GCC diagnostic ignored \"-Wunused-function\"\n
-#pragma GCC diagnostic ignored \"-Wunused-macros\"\n
-#pragma GCC diagnostic ignored \"-Wunused-parameter\"\n
-#pragma GCC diagnostic ignored \"-Wredundant-decls\"\n
-#elif defined __SUNPRO_CC\n
-#pragma disable_warn\n
-#elif defined _MSC_VER\n
-#pragma warning(push, 1)\n
-#endif\n
-    ")
-    file (APPEND ${FILE_ANALYZE} "${TEST_STREAM}")
-    message (STATUS "processed pragma in ${FILE_ANALYZE}")
-endif ()
diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake
index 926e230..f8ab3a2 100644
--- a/config/cmake/cacheinit.cmake
+++ b/config/cmake/cacheinit.cmake
@@ -155,15 +155,15 @@ set (LZF_PACKAGE_NAME "lzf" CACHE STRING "Name of LZF package" FORCE)
 #set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE)
 
 ######
-# sz
+# szf
 ######
 
-set (SZ_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE)
-set (SZ_GIT_BRANCH "master" CACHE STRING "" FORCE)
+set (SZF_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE)
+set (SZF_GIT_BRANCH "master" CACHE STRING "" FORCE)
 
-set (SZ_TGZ_NAME "sz.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE)
+set (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE)
 
-set (SZ_PACKAGE_NAME "sz" CACHE STRING "Name of SZ package" FORCE)
+set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE)
 
 ######
 # zfp
diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake
index 3a8d5b7..61c535e 100644
--- a/config/cmake/scripts/HDF5config.cmake
+++ b/config/cmake/scripts/HDF5config.cmake
@@ -204,7 +204,7 @@ endif ()
 #set (LOCAL_NO_PACKAGE "TRUE")
 #####       Following controls source update                  #####
 #set (LOCAL_UPDATE "TRUE")
-set (REPOSITORY_URL "https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git")
+set (REPOSITORY_URL "https://github.com/HDFGroup/hdf5.git")
 set (REPOSITORY_BRANCH "develop")
 
 #uncomment to use a compressed source file: *.tar on linux or mac *.zip on windows
diff --git a/config/cmake/scripts/HDF5options.cmake b/config/cmake/scripts/HDF5options.cmake
index f132234..33ec74b 100644
--- a/config/cmake/scripts/HDF5options.cmake
+++ b/config/cmake/scripts/HDF5options.cmake
@@ -57,7 +57,9 @@ set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRIN
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT")
 ### ext libs on system
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO")
+#set(ENV{ZLIB_ROOT} "some_location")
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include")
+#set(ENV{SZIP_ROOT} "some_location")
 #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include")
 
 ### disable using ext zlib
diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake
index 0ddb6d0..7988772 100644
--- a/config/cmake_ext_mod/ConfigureChecks.cmake
+++ b/config/cmake_ext_mod/ConfigureChecks.cmake
@@ -69,6 +69,7 @@ if (MINGW)
   set (WINDOWS 1) # MinGW tries to imitate Windows
   set (CMAKE_REQUIRED_FLAGS "-DWIN32_LEAN_AND_MEAN=1 -DNOGDI=1")
   set (${HDF_PREFIX}_HAVE_WINSOCK2_H 1)
+  set (__USE_MINGW_ANSI_STDIO 1)
 endif ()
 
 if (WIN32 AND NOT MINGW)
diff --git a/config/gnu-warnings/7 b/config/gnu-warnings/7
index 266f5c1..9d5b44d 100644
--- a/config/gnu-warnings/7
+++ b/config/gnu-warnings/7
@@ -3,5 +3,4 @@
 -Wduplicated-branches
 -Wformat-overflow=2
 -Wformat-truncation=1
--Wimplicit-fallthrough=5
 -Wrestrict