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Sync develop changes May 6 - May 20 to hdf5_1_14 (#4503)
* win32defs: Fix Wundef warning (#4467) * Refactor error handling code to eliminate internal ID calls (#4453) All calls to the H5I routines are now made in API routines (sometimes in FUNC_ENTER/LEAVE_* macros), except for some calls to H5E_clear_stack() within the library, but I'm planning to remove those over time. Also, made all the library internal error messages into static const variables, instead of malloc'ing them, which means that they can just be referenced and not copied. Several new and updated auto-generated header files were necessary to enable this. * CMake: Fix mingw/fortran build (#4466) * Update for blosc2 in plugins and prefix hdf5 cmake varnames (#4468) * Fix an issue where compound datatype member IDs can be leaked during conversion (#4459) Also fixes issues with handling of partially initialized datatypes during library shutdown * H5Group: Fix operator= (#4473) Closes #4472 * Fix github issue #2523: doxygen -- fix grammatically incorrect sentence alias (#4474) * Remove env step not used by CI in testing (#4476) * Add H5fortkit dependecy for H5Rff.F90 (#4482) * Properly clean up cache when failing to load an object header (#4477) * Properly clean up cache when failing to load an object header * Don't check message type a second time in H5G__open_oid if the first attempt returns error * Add more asserts to H5O__assert() to avoid segfaults --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add a missing image from the original document (#4490) * Disable EOF checks for SWMR readers in more cases. (#4489) Fixes a race condition where the reader opens the file and sets its EOF from the file's size (from the stat() call in the driver open callback). Then, before the reader can read the file's superblock, a SWMR writer races in, extends the file, and closes the file, writing an updated superblock with the 'writer' and 'SWMR writer' flags in the superblock off (appropriately). Then the reader proceeds to read the superblock, and flags the EOF as wrong. Taking out the check for the 'writer' and 'SWMR writer' flags will cause SWMR readers to avoid flagging the file as incorrect. * Remove unnecessary fortran install (#4498) * Only one version of binaries is produced for platforms (#4496) * Fix for github issue #2220. (#4497) Document the limitation in the Passthrough Conncector section of the VOL Connector Author Guide. The limitation is posted by Neil in the github issue on Dec 22, 2022. * Release asset tarballs with no version filenames (#4494) * Improve spec. reading superblock into cache (a little) by using v2 size (#4491) * Improve spec. reading superblock into cache (a little) by using v2 size Instead of reading the absolute minimal possible, use the likely value of a v2+ superblock w/8-byte addresses & lengths. * Fix for github Issue #1388 can't delete renamed dense attribute with corder tracking enabled (#4462) * Fix for github issue #1388: can't delete renamed dense attribute with corder tracking enabled The problem occurs in step 3(b) below which will delete the attribute with corder x from the creation order index v2 B-tree. The rename sequence in H5A__dense_rename() occurs in the following order: 1) The old attribute with corder x was removed from the creation order index v2 B-tree 2) The new renamed attribute was inserted via H5A__dense_insert(): (a) insert the attribute with new name j into the name index v2 B-tree (b) insert the attribute with corder x into the creation order index v2 B-tree 3) The old attribute was removed via H5A__dense_remove(): (a) remove the attribute with old name k from the name index v2 B-tree (b) remove the attribute with coorder x from the creation order index v2 B-tree Fix: deactivate the "corder_bt2_addr" field so that H5A__dense_remove() won't delete the attribute with corder x from the creation order index v2 B-tree. * Fix/revert a libtool sed hack (#4501) * Revert "Remove Autotools sed hack (#3848)" This reverts commit 8b3ffde. * Fix libtool sed cleanup on MacOS Convert sed -i line to sed > libtool.bak && mv libtool.bak libtool to avoid non-portable -i option. * Update src/H5public.h * Set H5 specific vars immediately if legacy find (#4512) * Correct find process vars (vs in-line build) * Correct SZIP find * Everything is libaec 1.0.6 or newer * Correct option help text
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -308,7 +308,7 @@ jobs: | |
| cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Clang/README.md ${{ runner.workspace }}/build114/hdf5 | ||
| cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Clang/*.tar.gz ${{ runner.workspace }}/build114/hdf5 | ||
| cd "${{ runner.workspace }}/build114" | ||
| tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx12.tar.gz hdf5 | ||
| tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx.tar.gz hdf5 | ||
| shell: bash | ||
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| - name: List files in the space (MacOS) | ||
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@@ -320,8 +320,8 @@ jobs: | |
| - name: Save published binary (MacOS) | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: tgz-osx12-binary | ||
| path: ${{ runner.workspace }}/build114/${{ steps.set-file-base.outputs.FILE_BASE }}-osx12.tar.gz | ||
| name: tgz-osx-binary | ||
| path: ${{ runner.workspace }}/build114/${{ steps.set-file-base.outputs.FILE_BASE }}-osx.tar.gz | ||
| if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn` | ||
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| build_and_test_S3_linux: | ||
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@@ -413,9 +413,6 @@ jobs: | |
| compiler: intel | ||
| version: '2024.1' | ||
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| - name: Enable Developer Command Prompt | ||
| uses: ilammy/[email protected] | ||
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| - name: Set file base name (Windows_intel) | ||
| id: set-file-base | ||
| run: | | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -9,9 +9,9 @@ | |
| # If you do not have access to either file, you may request a copy from | ||
| # [email protected]. | ||
| # | ||
| option (USE_LIBAEC_STATIC "Use static AEC library " OFF) | ||
| option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" OFF) | ||
| option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" OFF) | ||
| option (USE_LIBAEC_STATIC "Use static AEC library" OFF) | ||
| option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB else search" OFF) | ||
| option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP else search" OFF) | ||
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| if (NOT ZLIB_USE_LOCALCONTENT) | ||
| set (ZLIB_URL ${ZLIB_TGZ_ORIGPATH}/${ZLIB_TGZ_NAME}) | ||
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@@ -32,8 +32,8 @@ include (ExternalProject) | |
| set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)") | ||
| set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) | ||
| if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") | ||
| set (ZLIB_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for ZLIB" FORCE) | ||
| set (SZIP_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for SZIP" FORCE) | ||
| set (ZLIB_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for ZLIB else search" FORCE) | ||
| set (SZIP_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for SZIP else search" FORCE) | ||
| if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT") | ||
| set (ZLIB_URL ${ZLIB_GIT_URL} CACHE STRING "Path to zlib git repository") | ||
| set (ZLIB_BRANCH ${ZLIB_GIT_BRANCH}) | ||
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@@ -57,9 +57,9 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT | |
| endif () | ||
| else () | ||
| set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE) | ||
| set (ZLIB_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for ZLIB") | ||
| set (ZLIB_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for ZLIB else search") | ||
| set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE) | ||
| set (SZIP_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for SZIP") | ||
| set (SZIP_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for SZIP else search") | ||
| endif () | ||
| endif () | ||
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@@ -71,20 +71,20 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT) | |
| if (NOT H5_ZLIB_HEADER) | ||
| if (NOT ZLIB_USE_EXTERNAL) | ||
| find_package (ZLIB NAMES ${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared) | ||
| if (NOT ZLIB_FOUND) | ||
| if (NOT H5_ZLIB_FOUND) | ||
| find_package (ZLIB) # Legacy find | ||
| endif () | ||
| if (ZLIB_FOUND) | ||
| if (H5_ZLIB_FOUND) | ||
| set (H5_ZLIB_HEADER "zlib.h") | ||
| set (ZLIB_INCLUDE_DIR_GEN ${ZLIB_INCLUDE_DIR}) | ||
| set (ZLIB_INCLUDE_DIRS ${ZLIB_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIR}) | ||
| set (H5_ZLIB_INCLUDE_DIR_GEN ${ZLIB_INCLUDE_DIR}) | ||
| set (H5_ZLIB_INCLUDE_DIRS ${H5_ZLIB_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIR}) | ||
| set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_LIBRARIES}) | ||
| endif () | ||
| else () | ||
| if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") | ||
| EXTERNAL_ZLIB_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT}) | ||
| message (VERBOSE "Filter HDF5_ZLIB is built") | ||
| set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY}) | ||
| set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${H5_ZLIB_STATIC_LIBRARY}) | ||
| endif () | ||
| endif () | ||
| else () | ||
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@@ -93,14 +93,14 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT) | |
| set (H5_HAVE_ZLIB_H 1) | ||
| set (H5_HAVE_LIBZ 1) | ||
| endif () | ||
| if (ZLIB_FOUND) | ||
| if (H5_ZLIB_FOUND) | ||
| set (H5_HAVE_FILTER_DEFLATE 1) | ||
| set (H5_HAVE_ZLIB_H 1) | ||
| set (H5_HAVE_LIBZ 1) | ||
| if (H5_HAVE_FILTER_DEFLATE) | ||
| set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DEFLATE") | ||
| endif () | ||
| set (HDF5_COMP_INCLUDE_DIRECTORIES "${HDF5_COMP_INCLUDE_DIRECTORIES};${ZLIB_INCLUDE_DIRS}") | ||
| set (HDF5_COMP_INCLUDE_DIRECTORIES "${HDF5_COMP_INCLUDE_DIRECTORIES};${H5_ZLIB_INCLUDE_DIRS}") | ||
| message (VERBOSE "Filter HDF5_ZLIB is ON") | ||
| else () | ||
| set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE) | ||
|
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@@ -115,36 +115,30 @@ option (HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" ON) | |
| if (HDF5_ENABLE_SZIP_SUPPORT) | ||
| option (HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" ON) | ||
| if (NOT SZIP_USE_EXTERNAL) | ||
| set(libaec_USE_STATIC_LIBS ${HDF5_USE_LIBAEC_STATIC}) | ||
| set(SZIP_FOUND FALSE) | ||
| set(libaec_USE_STATIC_LIBS ${USE_LIBAEC_STATIC}) | ||
| find_package (libaec 1.0.5 CONFIG) | ||
| if (SZIP_FOUND) | ||
| set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES}) | ||
| endif () | ||
| find_package (SZIP NAMES ${LIBAEC_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared) | ||
| if (NOT SZIP_FOUND) | ||
| find_package (SZIP NAMES ${LIBAEC_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared) | ||
| if (NOT SZIP_FOUND) | ||
| find_package (SZIP) # Legacy find | ||
| endif () | ||
| find_package (SZIP) # Legacy find | ||
| endif () | ||
| if (SZIP_FOUND) | ||
| set (SZIP_INCLUDE_DIR_GEN ${SZIP_INCLUDE_DIR}) | ||
| set (SZIP_INCLUDE_DIRS ${SZIP_INCLUDE_DIRS} ${SZIP_INCLUDE_DIR}) | ||
| if (H5_SZIP_FOUND) | ||
| set (H5_SZIP_INCLUDE_DIR_GEN ${SZIP_INCLUDE_DIR}) | ||
| set (H5_SZIP_INCLUDE_DIRS ${H5_SZIP_INCLUDE_DIRS} ${SZIP_INCLUDE_DIR}) | ||
| set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_LIBRARIES}) | ||
| endif () | ||
| else () | ||
| if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") | ||
| EXTERNAL_SZIP_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT} ${HDF5_ENABLE_SZIP_ENCODING}) | ||
| message (VERBOSE "Filter SZIP is built") | ||
| message (VERBOSE "... with library AEC") | ||
| set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_STATIC_LIBRARY}) | ||
| set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${H5_SZIP_STATIC_LIBRARY}) | ||
| endif () | ||
| endif () | ||
| if (SZIP_FOUND) | ||
| if (H5_SZIP_FOUND) | ||
| set (H5_HAVE_FILTER_SZIP 1) | ||
| set (H5_HAVE_SZLIB_H 1) | ||
| set (H5_HAVE_LIBSZ 1) | ||
| set (HDF5_COMP_INCLUDE_DIRECTORIES "${HDF5_COMP_INCLUDE_DIRECTORIES};${SZIP_INCLUDE_DIRS}") | ||
| set (HDF5_COMP_INCLUDE_DIRECTORIES "${HDF5_COMP_INCLUDE_DIRECTORIES};${H5_SZIP_INCLUDE_DIRS}") | ||
| message (VERBOSE "Filter SZIP is ON") | ||
| if (H5_HAVE_FILTER_SZIP) | ||
| set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DECODE") | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,7 +9,7 @@ | |
| # If you do not have access to either file, you may request a copy from | ||
| # [email protected]. | ||
| # | ||
| option (PLUGIN_USE_EXTERNAL "Use External Library Building for filter PLUGIN" OFF) | ||
| option (PLUGIN_USE_EXTERNAL "Use External Library Building for filter PLUGIN else search" OFF) | ||
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| if (NOT PLUGIN_USE_LOCALCONTENT) | ||
| set (PLUGIN_URL ${PLUGIN_TGZ_ORIGPATH}/${PLUGIN_TGZ_NAME}) | ||
|
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@@ -26,7 +26,7 @@ include (ExternalProject) | |
| set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)") | ||
| set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) | ||
| if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") | ||
| set (PLUGIN_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for PLUGIN" FORCE) | ||
| set (PLUGIN_USE_EXTERNAL ON CACHE BOOL "Use External Library Building for PLUGIN else search" FORCE) | ||
| if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT") | ||
| set (PLUGIN_URL ${PLUGIN_GIT_URL} CACHE STRING "Path to PLUGIN git repository") | ||
| set (PLUGIN_BRANCH ${PLUGIN_GIT_BRANCH}) | ||
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@@ -41,7 +41,7 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT | |
| endif () | ||
| endif () | ||
| else () | ||
| set (PLUGIN_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for PLUGIN") | ||
| set (PLUGIN_USE_EXTERNAL OFF CACHE BOOL "Use External Library Building for PLUGIN else search") | ||
| message (VERBOSE "Filter PLUGIN not built") | ||
| endif () | ||
| endif () | ||
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