Merge pull request #5243 from fortnern/feature/sparse_data

Sync Feature/sparse data with develop
HDFGroup · Jan 16, 2025 · 47ed97a · 47ed97a
2 parents 1caf8b0 + 2dac89c
commit 47ed97a
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diff --git a/.clang-format b/.clang-format
@@ -58,8 +58,8 @@ IndentCaseLabels: true
 IndentGotoLabels: false
 #llvm11: IndentExternBlock: AfterExternBlock
 #llvm11: InsertTrailingCommas: None
-MacroBlockBegin: "^BEGIN_FUNC"
-MacroBlockEnd: "^END_FUNC"
+MacroBlockBegin: "^H5_BEFORE_USER_CB*|^H5E_PAUSE_ERRORS"
+MacroBlockEnd: "^H5_AFTER_USER_CB*|^H5E_RESUME_ERRORS"
 ObjCBlockIndentWidth: 4
 #llvm11: ObjCBreakBeforeNestedBlockParam: true
 ReflowComments:  true
@@ -81,9 +81,8 @@ StatementMacros:
   - FUNC_LEAVE_NOAPI_NAMECHECK_ONLY
   - FUNC_LEAVE_NOAPI_VOID_NAMECHECK_ONLY
   - FUNC_LEAVE_NOAPI_NOFS
+  - H5E_BEGIN_TRY
   - H5E_END_TRY
-  - H5E_PRINTF
-  - H5E_THROW
   - H5_BEGIN_TAG
   - H5_END_TAG
   - H5_GCC_DIAG_OFF

diff --git a/.gitattributes b/.gitattributes
@@ -204,7 +204,7 @@ java/src/hdf/hdf5lib/H5.java -text
 java/src/hdf/hdf5lib/HDF5Constants.java -text
 java/src/hdf/hdf5lib/HDFArray.java -text
 java/src/hdf/hdf5lib/HDFNativeData.java -text
-java/src/hdf/hdf5lib/callbacks/Callbacks.java -text
+java/src/hdf/hdf5lib/callbacks/H5Callbacks.java -text
 java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java -text
 java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java -text
 java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java -text

diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -1,3 +1,3 @@
 # These are supported funding model platforms
 
-custom: "https://www.hdfgroup.org/donate"
+github: hdfgroup
diff --git a/.github/workflows/aocc-cmake.yml b/.github/workflows/aocc-cmake.yml
@@ -70,6 +70,7 @@ jobs:
           CC=mpicc cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \
           -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
           -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF \
+          -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF \
           -DHDF5_ENABLE_PARALLEL:BOOL=ON \
           -DHDF5_ENABLE_SUBFILING_VFD:BOOL=ON \
           -DHDF5_BUILD_CPP_LIB:BOOL=OFF \

diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
@@ -44,31 +44,51 @@ jobs:
       with:
             build_mode: "production"
 
+    call-debug-concurrent-autotools:
+      name: "Autotools Debug Concurrency Workflows"
+      uses: ./.github/workflows/main-auto.yml
+      with:
+            concurrent: enable
+            thread_safety: disable
+            build_mode: "debug"
+
+    call-release-concurrent-autotools:
+      name: "Autotools Release Concurrency Workflows"
+      uses: ./.github/workflows/main-auto.yml
+      with:
+            concurrent: enable
+            thread_safety: disable
+            build_mode: "production"
+
     call-debug-thread-autotools:
       name: "Autotools Debug Thread-Safety Workflows"
       uses: ./.github/workflows/main-auto.yml
       with:
+            concurrent: disable
             thread_safety: enable
             build_mode: "debug"
 
     call-release-thread-autotools:
       name: "Autotools Release Thread-Safety Workflows"
       uses: ./.github/workflows/main-auto.yml
       with:
+            concurrent: disable
             thread_safety: enable
             build_mode: "production"
 
     call-debug-autotools:
       name: "Autotools Debug Workflows"
       uses: ./.github/workflows/main-auto.yml
       with:
+            concurrent: disable
             thread_safety: disable
             build_mode: "debug"
 
     call-release-autotools:
       name: "Autotools Release Workflows"
       uses: ./.github/workflows/main-auto.yml
       with:
+            concurrent: disable
             thread_safety: disable
             build_mode: "production"
 

diff --git a/.github/workflows/cmake-analysis.yml b/.github/workflows/cmake-analysis.yml
@@ -27,12 +27,12 @@ jobs:
   # Linux (Ubuntu) w/ gcc + coverage
   #
     name: "Ubuntu GCC Coverage"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - name: Install CMake Dependencies (Linux_coverage)
       run: |
         sudo apt update
-        sudo apt-get install ninja-build doxygen graphviz curl libncurses5 build-essential
+        sudo apt-get install ninja-build doxygen graphviz curl build-essential
         sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
         sudo apt-get install lcov -q -y
 
@@ -99,6 +99,7 @@ jobs:
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON")
@@ -122,19 +123,19 @@ jobs:
   # Linux (Ubuntu) w/ clang + LeakSanitizer
   #
     name: "Ubuntu Clang LeakSanitizer"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Install CMake Dependencies (Linux_Leak)
         run: |
           sudo apt update
-          sudo apt-get install ninja-build doxygen graphviz curl libncurses5
+          sudo apt-get install ninja-build doxygen graphviz curl libtinfo5
 
       - name: add clang to env
         uses: KyleMayes/[email protected]
         id: setup-clang
         with:
           env: true
-          version: '18'
+          version: '18.1'
 
       - name: Set file base name (Linux_Leak)
         id: set-file-base
@@ -202,6 +203,7 @@ jobs:
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=OFF")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest (Linux_Leak)
         run: |
@@ -222,19 +224,19 @@ jobs:
   # Linux (Ubuntu) w/ clang + AddressSanitizer
   #
     name: "Ubuntu Clang AddressSanitizer"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Install CMake Dependencies (Linux_Address)
         run: |
           sudo apt update
-          sudo apt-get install ninja-build doxygen graphviz curl libncurses5
+          sudo apt-get install ninja-build doxygen graphviz curl libtinfo5
 
       - name: add clang to env
         uses: KyleMayes/[email protected]
         id: setup-clang
         with:
           env: true
-          version: '18'
+          version: '18.1'
 
       - name: Set file base name (Linux_Address)
         id: set-file-base
@@ -302,6 +304,7 @@ jobs:
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=OFF")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest (Linux_Address)
         run: |
@@ -322,19 +325,19 @@ jobs:
   # Linux (Ubuntu) w/ clang + UndefinedBehaviorSanitizer
   #
     name: "Ubuntu Clang UndefinedBehaviorSanitizer"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Install CMake Dependencies (Linux_UndefinedBehavior)
         run: |
           sudo apt update
-          sudo apt-get install ninja-build doxygen graphviz curl libncurses5
+          sudo apt-get install ninja-build doxygen graphviz curl libtinfo5
 
       - name: add clang to env
         uses: KyleMayes/[email protected]
         id: setup-clang
         with:
           env: true
-          version: '18'
+          version: '18.1'
 
       - name: Set file base name (Linux_UndefinedBehavior)
         id: set-file-base
@@ -402,6 +405,7 @@ jobs:
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=OFF")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+              set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest (Linux_UndefinedBehavior)
         run: |

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -333,6 +333,12 @@ jobs:
         with:
           version: "1.9.7"
 
+      - name: check clang version
+        shell: bash
+        run: |
+          which clang
+          clang -v
+
       - name: Install the Apple certificate and provisioning profile
         shell: bash
         env:
@@ -680,7 +686,7 @@ 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
         run: |
@@ -796,7 +802,6 @@ jobs:
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
           CC: ${{ steps.setup-fortran.outputs.cc }}
-          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
           cd "${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}"
           cmake --workflow --preset=${{ inputs.preset_name }}-Intel --fresh

diff --git a/.github/workflows/cmake-par-script.yml b/.github/workflows/cmake-par-script.yml
@@ -131,9 +131,10 @@ jobs:
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
-            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=ON")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest script (${{ matrix.mpi }})
         run: |
@@ -244,9 +245,10 @@ jobs:
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
-            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=ON")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest script (${{ matrix.mpi }})
         run: |
@@ -353,9 +355,10 @@ jobs:
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
-            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=ON")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PLUGIN_SUPPORT:BOOL=OF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest script (${{ matrix.mpi }})
         run: |

diff --git a/.github/workflows/cmake-par-source.yml b/.github/workflows/cmake-par-source.yml
@@ -136,6 +136,7 @@ jobs:
             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 "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest script (OpenMPI)
         run: |
@@ -251,6 +252,7 @@ jobs:
             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 "${ADD_BUILD_OPTIONS} -DZLIB_USE_LOCALCONTENT:BOOL=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DPLUGIN_USE_LOCALCONTENT:BOOL=OFF")
 
       - name: Run ctest script (MPICH)
         run: |