Merge remote-tracking branch 'origin/develop' into refactor_h5cx_stack

.github/workflows/cmake-script.yml

@@ -490,9 +490,7 @@ jobs:
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
           CC: ${{ steps.setup-fortran.outputs.cc }}
-          CXX: ${{ steps.setup-fortran.outputs.cxx }}
-          BINSIGN: ${{ needs.check-secret.outputs.sign-state }}
-          SIGNTOOLDIR: ${{ github.workspace }}/Microsoft.Windows.SDK.BuildTools/bin/10.0.22621.0/x64
+          CXX: ${{ steps.setup-fortran.outputs.cc }}
         run: |
           cd "${{ runner.workspace }}/hdf5"
           ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-Intel,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=VS202264,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
@@ -603,110 +601,6 @@ jobs:
           if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
 ####### clang builds
-  build_and_test_win_clang:
-  # Windows w/ clang + CMake
-  #
-    name: "Windows ClangCL CTest"
-    runs-on: windows-latest
-    steps:
-      - name: Install Dependencies (Windows_clang)
-        run: choco install ninja
-
-      - name: add clang to env
-        uses: KyleMayes/[email protected]
-        id: setup-clang
-        with:
-          env: true
-          version: '18'
-
-      - name: Set file base name (Windows_clang)
-        id: set-file-base
-        run: |
-          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
-          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-          if [[ '${{ inputs.use_environ }}' == 'release' ]]
-          then
-            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
-          else
-            SOURCE_NAME_BASE=$(echo "hdfsrc")
-          fi
-          echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
-        shell: bash
-
-      # Get files created by release script
-      - name: Get zip-tarball (Windows_clang)
-        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
-        with:
-          name: zip-tarball
-          path: ${{ github.workspace }}
-
-      - name: using powershell
-        shell: pwsh
-        run: Get-Location
-
-      - name: List files for the space (Windows_clang)
-        run: |
-          Get-ChildItem -Path ${{ github.workspace }}
-          Get-ChildItem -Path ${{ runner.workspace }}
-        shell: pwsh
-
-      - name: Uncompress source (Windows_clang)
-        working-directory: ${{ github.workspace }}
-        run: 7z x ${{ steps.set-file-base.outputs.FILE_BASE }}.zip
-        shell: bash
-
-      - name: Copy script files for the space (Windows_clang)
-        run: |
-          Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/config/cmake/scripts/CTestScript.cmake -Destination ${{ runner.workspace }}/hdf5/
-          Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/config/cmake/scripts/HDF5config.cmake -Destination ${{ runner.workspace }}/hdf5/
-        shell: pwsh
-
-      - name: List files for the hdf5 (Windows_clang)
-        run: |
-          Get-ChildItem -Path ${{ runner.workspace }}/hdf5
-        shell: pwsh
-
-      - name: Create options file (Windows_clang)
-        uses: "DamianReeves/write-file-action@master"
-        with:
-          path: ${{ runner.workspace }}/hdf5/HDF5options.cmake
-          write-mode: overwrite
-          contents: |
-              set (CTEST_DROP_SITE_INIT "my.cdash.org")
-              # Change following line to submit to your CDash dashboard to a different CDash project
-              #set (CTEST_DROP_LOCATION_INIT "/submit.php?project=HDF5")
-              set (SITE_BUILDNAME_SUFFIX "${{ steps.set-file-base.outputs.FILE_BASE }}")
-              #set (CMAKE_GENERATOR_TOOLSET "ClangCL")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
-              #set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/clang.cmake")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=ON")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=ON")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=ON")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
-              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
-
-      - name: Run ctest (Windows_clang) with clang
-        env:
-          BINSIGN: ${{ needs.check-secret.outputs.sign-state }}
-          SIGNTOOLDIR: ${{ github.workspace }}/Microsoft.Windows.SDK.BuildTools/bin/10.0.22621.0/x64
-        run: |
-          cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-Clang,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=VS202264,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
-        shell: pwsh
-        continue-on-error: true
-
-      # Save log files created by ctest script
-      - name: Save log (Windows_clang)
-        uses: actions/upload-artifact@v4
-        with:
-          name: clang-win-log
-          path: ${{ runner.workspace }}/hdf5/hdf5.log
-          if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
-
   build_and_test_linux_clang:
   # Linux (Ubuntu) w/ clang + CMake
   #

.github/workflows/daily-build.yml

@@ -1,6 +1,7 @@
 name: hdf5 dev daily build
 
-# Triggers the workflow on a schedule or on demand
+# Triggers the workflow on demand or on a call from another workflow
+# NOTE: inputs must be duplicated between triggers
 on:
   workflow_dispatch:
     inputs:
@@ -9,8 +10,13 @@ on:
         type: string
         required: false
         default: check
-  schedule:
-    - cron: "6 0 * * *"
+  workflow_call:
+    inputs:
+      use_ignore:
+        description: 'Ignore has_changes check'
+        type: string
+        required: false
+        default: check
 
 permissions:
   contents: read
@@ -61,6 +67,14 @@ jobs:
       use_environ: snapshots
     if: ${{ ((needs.call-workflow-tarball.outputs.has_changes == 'true') || (needs.get-old-names.outputs.run-ignore == 'ignore')) }}
 
+  call-workflow-sanitizers:
+    needs: [get-old-names, call-workflow-tarball]
+    uses: ./.github/workflows/cmake-analysis.yml
+    with:
+      file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
+      use_environ: snapshots
+    if: ${{ ((needs.call-workflow-tarball.outputs.has_changes == 'true') || (needs.get-old-names.outputs.run-ignore == 'ignore')) }}
+
   call-workflow-ctest:
     needs: [get-old-names, call-workflow-tarball]
     uses: ./.github/workflows/cmake-ctest.yml

.github/workflows/daily-schedule.yml

@@ -0,0 +1,16 @@
+name: hdf5 dev daily build on schedule
+
+# Triggers the workflow on a schedule or on demand
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "6 0 * * *"
+
+permissions:
+    contents: write # In order to allow tag creation and file deletion
+
+jobs:
+  daily-build:
+    uses: ./.github/workflows/daily-build.yml
+    with:
+      use_ignore: check

.github/workflows/main-cmake.yml

@@ -270,11 +270,3 @@ jobs:
               path: ${{ runner.workspace }}/build/HDF5-*-Darwin.tar.gz
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
         if: ${{ (matrix.os == 'macos-latest') && (inputs.thread_safety != 'TS') }}
-
-      - name: Save published dmg binary (Mac_latest)
-        uses: actions/upload-artifact@v4
-        with:
-              name: tgz-macos14_clang-${{ inputs.build_mode }}-dmg-binary
-              path: ${{ runner.workspace }}/build/HDF5-*-Darwin.dmg
-              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
-        if: ${{ (matrix.os == 'macos-latest') && (inputs.thread_safety != 'TS') }}

.github/workflows/release.yml

@@ -55,7 +55,7 @@ jobs:
     needs: [log-the-inputs, call-workflow-tarball, call-workflow-ctest]
     uses: ./.github/workflows/abi-report.yml
     with:
-      file_ref: '1.14.4.3'
+      file_ref: '1.14.5'
       file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
       use_tag: ${{ needs.log-the-inputs.outputs.rel_tag }}
       use_environ: release

CMakeLists.txt

@@ -600,8 +600,10 @@ option (HDF5_ENABLE_COVERAGE "Enable code coverage for Libraries and Programs" O
 if (HDF5_ENABLE_COVERAGE)
   include (${HDF5_SOURCE_DIR}/config/sanitizer/code-coverage.cmake)
   if(CODE_COVERAGE AND CODE_COVERAGE_ADDED)
+    message(VERBOSE "Add instrumentation to all targets")
     add_code_coverage () # Adds instrumentation to all targets
   else ()
+    message(VERBOSE "Use --coverage option")
     set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -O0 --coverage -fprofile-arcs -ftest-coverage")
     set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g --coverage -O0 -fprofile-arcs -ftest-coverage")
     if (CMAKE_C_COMPILER_ID STREQUAL "GNU")

README.md

@@ -90,12 +90,10 @@ are tentative.
 
 | Release | New Features |
 | ------- | ------------ |
-| 1.14.5 | oss-fuzz fixes, ros3 VFD improvements |
-| 1.14.6 | Last maintenance release of 1.14 |
-| 1.16.0 | Complex number support, updated library defaults (cache sizes, etc.) |
-| 2.0.0 | Multi-threaded HDF5, crashproofing / metadata journaling, Full (VFD) SWMR, encryption, digital signatures, sparse datasets, improved storage for variable-length datatypes, better Unicode support (especially on Windows), semantic versioning |
+| 2.0.0 | Drop Autotools support, complex number support, updated library defaults (cache sizes, etc.), semantic versioning |
+| FUTURE | Multi-threaded HDF5, crashproofing / metadata journaling, Full (VFD) SWMR, encryption, digital signatures, sparse datasets, improved storage for variable-length datatypes, better Unicode support (especially on Windows) |
 
-Some HDF5 2.0.0 features listed here may be released in a 1.16.x release.
+NOTE: In the March 2025 release we will begin using semantic versioning (https://semver.org/) and the previously announced 1.16.0 version will instead be numbered 2.0.0.
 
 This list of feature release versions is also tentative, and the specific release
 in which a feature is introduced may change.

c++/test/tfile.cpp

@@ -759,7 +759,7 @@ test_libver_bounds()
 
     /* Run the tests */
     test_libver_bounds_real(H5F_LIBVER_EARLIEST, H5O_VERSION_1, H5F_LIBVER_LATEST, H5O_VERSION_2);
-    test_libver_bounds_real(H5F_LIBVER_LATEST, H5O_VERSION_2, H5F_LIBVER_EARLIEST, H5O_VERSION_2);
+    test_libver_bounds_real(H5F_LIBVER_LATEST, H5O_VERSION_2, H5F_LIBVER_EARLIEST, H5O_VERSION_1);
     PASSED();
 } /* end test_libver_bounds() */
 

config/cmake/ConfigureChecks.cmake

@@ -67,6 +67,8 @@ if (WIN32 AND NOT MINGW)
       set (${HDF_PREFIX}_HAVE_VISUAL_STUDIO 1)
     endif ()
   endif ()
+  message (TRACE "MSVC=${MSVC}")
+  message (TRACE "HAVE_VISUAL_STUDIO=${${HDF_PREFIX}_HAVE_VISUAL_STUDIO}")
 endif ()
 
 if (WINDOWS)
@@ -79,13 +81,12 @@ if (WINDOWS)
   endif ()
   if (NOT UNIX AND NOT CYGWIN)
     set (${HDF_PREFIX}_HAVE_GETCONSOLESCREENBUFFERINFO 1)
-    if (MSVC_VERSION GREATER_EQUAL 1900)
-      set (${HDF_PREFIX}_HAVE_TIMEZONE 1)
-    endif ()
+    set (${HDF_PREFIX}_HAVE_TIMEZONE 1)
     set (${HDF_PREFIX}_HAVE_GETTIMEOFDAY 1)
     set (${HDF_PREFIX}_HAVE_LIBWS2_32 1)
     set (${HDF_PREFIX}_HAVE_LIBWSOCK32 1)
   endif ()
+  message (TRACE "HAVE_TIMEZONE=${${HDF_PREFIX}_HAVE_TIMEZONE}")
 endif ()
 
 # ----------------------------------------------------------------------

config/sanitizer/code-coverage.cmake

@@ -81,9 +81,13 @@ option(
 
 # Programs
 find_program(LLVM_COV_PATH llvm-cov)
+message(VERBOSE "program llvm-cov=${LLVM_COV_PATH}")
 find_program(LLVM_PROFDATA_PATH llvm-profdata)
+message(VERBOSE "program llvm-profdata=${LLVM_PROFDATA_PATH}")
 find_program(LCOV_PATH lcov)
+message(VERBOSE "program lcov=${LCOV_PATH}")
 find_program(GENHTML_PATH genhtml)
+message(VERBOSE "program genhtml=${GENHTML_PATH}")
 # Hide behind the 'advanced' mode flag for GUI/ccmake
 mark_as_advanced(FORCE LLVM_COV_PATH LLVM_PROFDATA_PATH LCOV_PATH GENHTML_PATH)
 

config/toolchain/intel.cmake

@@ -4,7 +4,11 @@
 set(CMAKE_COMPILER_VENDOR "intel")
 
 set(CMAKE_C_COMPILER icx)
-set(CMAKE_CXX_COMPILER icpx)
+if(WIN32)
+ set(CMAKE_CXX_COMPILER icx)
+else()
+  set(CMAKE_CXX_COMPILER icpx)
+endif()
 set(CMAKE_Fortran_COMPILER ifx)
 
 # the following is used if cross-compiling

doc/img/release-schedule.plantuml

@@ -23,26 +23,24 @@ Project starts 2023-01-01
 [1.12.3] happens 2023-11-30
 [1.12] is colored in #88CCEE
 
-[1.14] starts at 2023-01-01 and lasts 118 weeks
+[1.14] starts at 2023-01-01 and lasts 92 weeks
 [1.14.1] happens at 2023-04-30
 [1.14.2] happens at 2023-08-31
 [1.14.3] happens at 2023-10-31
 [1.14.4.2] happens at 2024-04-15
 [1.14.4.3] happens at 2024-05-22
 [1.14.5] happens at 2024-09-30
-[1.14.6] happens at 2025-03-31
 [1.14.1] displays on same row as [1.14.1]
 [1.14.2] displays on same row as [1.14.1]
 [1.14.3] displays on same row as [1.14.1]
 [1.14.4.2] displays on same row as [1.14.1]
 [1.14.5] displays on same row as [1.14.1]
-[1.14.6] displays on same row as [1.14.1]
 [1.14] is colored in #B187CF
 
-[1.16] starts at 2025-03-31 and lasts 35 weeks
-[1.16.0] happens at 2025-03-31
-[1.16.1] happens at 2025-09-30
-[1.16.1] displays on same row as [1.16.0]
-[1.16] is colored in #02BFA0
+[2.0] starts at 2024-09-30 and lasts 53 weeks
+[2.0.0] happens at 2025-03-31
+[2.1.0] happens at 2025-09-30
+[2.1.0] displays on same row as [2.0.0]
+[2.0] is colored in #02BFA0
 
 @endgantt

fortran/src/H5Rff.F90

@@ -856,13 +856,13 @@ INTEGER(C_INT) FUNCTION H5Requal(ref1_ptr, ref2_ptr) &
        END FUNCTION H5Requal
     END INTERFACE
 
-    c_equal = INT(H5Requal(ref1_ptr, ref2_ptr))
+    c_equal = INT(H5Requal(ref1_ptr, ref2_ptr), C_INT)
 
     hdferr = 0
     equal = .FALSE.
-    IF(c_equal .EQ. 1)THEN
+    IF(c_equal .EQ. 1_C_INT)THEN
        equal = .TRUE.
-    ELSE IF(c_equal .LT. 0)THEN
+    ELSE IF(c_equal .LT. 0_C_INT)THEN
        hdferr = -1
     ENDIF
 

fortran/src/H5VLff.F90

@@ -419,7 +419,8 @@ SUBROUTINE H5VLcmp_connector_cls_f(are_same, conn_id1, conn_id2, hdferr)
     INTEGER(HID_T), INTENT(IN) :: conn_id1
     INTEGER(HID_T), INTENT(IN) :: conn_id2
     INTEGER, INTENT(OUT) :: hdferr
-    INTEGER :: are_same_c
+
+    INTEGER(C_INT) :: are_same_c
 
     INTERFACE
        INTEGER(C_INT) FUNCTION H5VLcmp_connector_cls(cmp_value, conn_id1, conn_id2) BIND(C, NAME='H5VLcmp_connector_cls')
@@ -432,7 +433,7 @@ END FUNCTION H5VLcmp_connector_cls
 
     are_same = .FALSE.
     hdferr = INT(H5VLcmp_connector_cls(are_same_c, conn_id1, conn_id2))
-    IF(are_same_c .EQ. 0) are_same = .TRUE.
+    IF(are_same_c .EQ. 0_C_INT) are_same = .TRUE.
 
   END SUBROUTINE H5VLcmp_connector_cls_f
 

release_docs/RELEASE.txt

@@ -132,7 +132,19 @@ Bug Fixes since HDF5-1.16.0 release
 ===================================
     Library
     -------
-    -
+    - Only clear FE_INVALID when that symbol is present on the system
+
+      When we initialize the floating-point types at library startup, it's
+      possible to raise floating-point exceptions when we check which things
+      are supported. Normally, we clear these floating-point exceptions via
+      feclearexcept(FE_INVALID), but FE_INVALID may not be present on all
+      systems. Specifically, this was reported as being a problem when using
+      Emscripten 3.1.68 to compile HDF5 1.14.5 to WebAssembly.
+
+      We've added an #ifdef FE_INVALID block around the exception clearing
+      code to correct this.
+
+      Fixes GitHub issue #4952
 
 
     Java Library
@@ -191,14 +203,6 @@ Bug Fixes since HDF5-1.16.0 release
 
     Testing
     -------
-    - Disabled running of MPI Atomicity tests for OpenMPI major versions < 5
-
-      Support for MPI atomicity operations is not implemented for major
-      versions of OpenMPI less than version 5. This would cause the MPI
-      atomicity tests for parallel HDF5 to sporadically fail when run
-      with OpenMPI. Testphdf5 now checks if OpenMPI is being used and will
-      skip running the atomicity tests if the major version of OpenMPI is
-      < 5.
 
 
 Platforms Tested