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

HDFGroup · Oct 26, 2024 · affe3a2 · affe3a2
2 parents a2e0f5b + b8a06b5
commit affe3a2
Show file tree

Hide file tree

Showing 40 changed files with 1,540 additions and 934 deletions.
diff --git a/.github/workflows/cmake-analysis.yml b/.github/workflows/cmake-analysis.yml
@@ -106,7 +106,7 @@ jobs:
     - name: Run ctest (Linux_coverage)
       run: |
         cd "${{ runner.workspace }}/hdf5"
-        ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH_COV,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
+        ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}_COV,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
       shell: bash
       continue-on-error: true
 
@@ -206,7 +206,7 @@ jobs:
       - name: Run ctest (Linux_Leak)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-LEAK,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-LEAK,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -306,7 +306,7 @@ jobs:
       - name: Run ctest (Linux_Address)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-ADDR,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-ADDR,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -406,7 +406,7 @@ jobs:
       - name: Run ctest (Linux_UndefinedBehavior)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-UNDEF,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-UNDEF,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Debug -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 

diff --git a/.github/workflows/cmake-script.yml b/.github/workflows/cmake-script.yml
@@ -111,7 +111,7 @@ jobs:
       - name: Run ctest script (Windows)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=VS202264,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }},LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=VS202264,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -200,7 +200,7 @@ jobs:
       - name: Run ctest (Linux)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-GCC,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-GCC,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -302,7 +302,7 @@ jobs:
         id: run-ctest
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-Clang,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-Clang,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -387,7 +387,7 @@ jobs:
       - name: Run ctest (Linux S3)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-S3,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-S3,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -493,7 +493,7 @@ jobs:
           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=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-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
         shell: pwsh
         continue-on-error: true
 
@@ -588,7 +588,7 @@ jobs:
           CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-Intel,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-Intel,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -682,7 +682,7 @@ jobs:
       - name: Run ctest (Linux_clang)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-Clang,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=${{ github.event.repository.full_name }}-Clang,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -125,12 +125,6 @@ jobs:
         with:
             build_mode: "Release"
 
-    call-release-cmake-cygwin:
-        name: "CMake Cygwin Workflows"
-        uses: ./.github/workflows/cygwin-cmake.yml
-        with:
-            build_mode: "Release"
-
     call-release-cmake-xpr:
         name: "CMake TestExpress Workflows"
         uses: ./.github/workflows/testxpr-cmake.yml

diff --git a/.github/workflows/cygwin-cmake.yml b/.github/workflows/cygwin-cmake.yml
@@ -4,10 +4,20 @@ name: hdf5 dev CMake cygwin
 on:
   workflow_call:
     inputs:
-      build_mode:
-        description: "release vs. debug build"
+      snap_name:
+        description: 'The name in the source tarballs'
+        type: string
+        required: false
+        default: hdfsrc
+      file_base:
+        description: "The common base name of the source tarballs"
         required: true
         type: string
+      use_environ:
+        description: 'Environment to locate files'
+        type: string
+        required: true
+        default: snapshots
 
 permissions:
   contents: read
@@ -30,36 +40,80 @@ jobs:
         with:
           packages: cmake gcc-fortran make ninja zlib-devel flex bison perl
 
-      - name: CMake Configure
+      - name: Set file base name (Cygwin)
+        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: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+
+      # Get files created by release script
+      - name: Get zip-tarball (Cygwin)
+        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
+        with:
+              name: zip-tarball
+              path: ${{ github.workspace }}
+
+      - name: List files for the space (Cygwin)
         run: |
-          export PATH=/usr/bin:$PATH
-          mkdir build
-          cd build
-          cmake -C ../config/cmake/cacheinit.cmake \
-            -G Ninja \
-            --log-level=VERBOSE \
-            -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
-            -DBUILD_SHARED_LIBS:BOOL=OFF \
-            -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF \
-            -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
-            -DLIBAEC_USE_LOCALCONTENT=OFF \
-            -DZLIB_USE_LOCALCONTENT=OFF \
-            -DHDF5_BUILD_FORTRAN:BOOL=ON \
-            -DHDF5_BUILD_JAVA:BOOL=OFF \
-            ..
+            ls -l ${{ github.workspace }}
+            ls ${{ runner.workspace }}
 
-      - name: CMake Build
+      - name: Uncompress source (Cygwin)
+        working-directory: ${{ github.workspace }}
+        run: 7z x ${{ steps.set-file-base.outputs.FILE_BASE }}.zip
         shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+
+      - name: Copy script files for the space (Cygwin)
         run: |
-          export PATH=/usr/bin:$PATH
-          cd build
-          cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
+          cp ${{ github.workspace }}/${{ steps.set-file-base.outputs.SOURCE_BASE }}/config/cmake/scripts/CTestScript.cmake ${{ runner.workspace }}/hdf5
+          cp ${{ github.workspace }}/${{ steps.set-file-base.outputs.SOURCE_BASE }}/config/cmake/scripts/HDF5config.cmake ${{ runner.workspace }}/hdf5
+
+      - name: List files for the hdf5 (Cygwin)
+        run: |
+            ls ${{ runner.workspace }}/hdf5
+
+      - name: Create options file (Cygwin)
+        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 (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_GENERATE_HEADERS=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
+            set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
+            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: CMake Run Tests
+      - name: Run ctest (Cygwin)
         shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
         run: |
-           export PATH=/usr/bin:$PATH
-           cd build
-           ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
-#           ctest . --parallel 2 -C ${{ inputs.build_mode }} -V -R "FORTRAN|H5TEST"
+          export PATH=/usr/bin:$PATH
+          cd "${{ runner.workspace }}/hdf5"
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-CYG,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C Release -VV -O hdf5.log
+        continue-on-error: true
+
+      # Save log files created by ctest script
+      - name: Save log (Cygwin)
+        uses: actions/upload-artifact@v4
+        with:
+            name: gcc-cygwin-log
+            path: ${{ runner.workspace }}/hdf5/hdf5.log
+            if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
diff --git a/.github/workflows/daily-build.yml b/.github/workflows/daily-build.yml
@@ -59,6 +59,15 @@ jobs:
       use_tag: snapshot
       use_environ: snapshots
 
+  call-release-cmake-cygwin:
+    needs: [get-old-names, call-workflow-tarball]
+    name: "CMake Cygwin Workflows"
+    uses: ./.github/workflows/cygwin-cmake.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-c-script:
     needs: [get-old-names, call-workflow-tarball]
     uses: ./.github/workflows/cmake-script.yml

diff --git a/.github/workflows/h5py.yml b/.github/workflows/h5py.yml
@@ -21,7 +21,7 @@ jobs:
 
     - name: Run a multi-line script
       run: |
-        sed -i 's/[email protected].4:1.14/[email protected].4:/g' \
+        sed -i 's/[email protected].6:1.14/[email protected].6:/g' \
         ./spack/var/spack/repos/builtin/packages/py-h5py/package.py
         . ./spack/share/spack/setup-env.sh
         ./spack/bin/spack spec py-h5py@master+mpi ^[email protected]

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1186,7 +1186,7 @@ if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/for
   option (HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF)
   if (HDF5_BUILD_FORTRAN)
     message (VERBOSE "Fortran compiler ID is ${CMAKE_Fortran_COMPILER_ID}")
-    include (${HDF_RESOURCES_DIR}/HDFFortranCompilerFlags.cmake)
+    include (${HDF_RESOURCES_DIR}/HDFCompilerFortranFlags.cmake)
     include (${HDF_RESOURCES_DIR}/HDF5UseFortran.cmake)
     set (LINK_Fortran_LIBS ${LINK_LIBS})
 
@@ -1246,7 +1246,7 @@ if (EXISTS "${HDF5_SOURCE_DIR}/c++" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/c++")
       endif ()
     endif ()
 
-    include (${HDF_RESOURCES_DIR}/HDFCXXCompilerFlags.cmake)
+    include (${HDF_RESOURCES_DIR}/HDFCompilerCXXFlags.cmake)
 
     add_subdirectory (c++)
     if (HDF5_BUILD_HL_LIB)

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-HDF5 version 1.17.0 currently under development
+HDF5 version 2.0.0 currently under development
 
 ![HDF5 Logo](doxygen/img/HDF5.png)
 
@@ -10,8 +10,6 @@ HDF5 version 1.17.0 currently under development
 [![CVE regression](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/cve.yml?branch=develop&label=CVE)](https://github.com/HDFGroup/hdf5/actions/workflows/cve.yml?query=branch%3Adevelop)
 [![HDF5 VOL connectors build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/vol.yml?branch=develop&label=HDF5-VOL)](https://github.com/HDFGroup/hdf5/actions/workflows/vol.yml?query=branch%3Adevelop)
 [![HDF5 VFD build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/vfd.yml?branch=develop&label=HDF5-VFD)](https://github.com/HDFGroup/hdf5/actions/workflows/vfd.yml?query=branch%3Adevelop)
-[![1.14 cmake build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/cmake.yml?branch=hdf5_1_14&label=HDF5%201.14%20CMake%20CI)](https://github.com/HDFGroup/hdf5/actions/workflows/cmake.yml?query=branch%3Ahdf5_1_14)
-[![1.14 autotools build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/autotools.yml?branch=hdf5_1_14&label=HDF5%201.14%20Autotools%20CI)](https://github.com/HDFGroup/hdf5/actions/workflows/autotools.yml?query=branch%3Ahdf5_1_14)
 [![BSD](https://img.shields.io/badge/License-BSD-blue.svg)](https://github.com/HDFGroup/hdf5/blob/develop/LICENSE)
 
 [HPC configure/build/test results](https://my.cdash.org/index.php?project=HDF5)
@@ -90,7 +88,7 @@ are tentative.
 
 | Release | New Features |
 | ------- | ------------ |
-| 2.0.0 | Drop Autotools support, complex number support, updated library defaults (cache sizes, etc.), semantic versioning |
+| 2.0.0 | Drop Autotools support, drop the C++ API, drop the HDF5 <--> GIF tools, add complex number support, update library defaults (cache sizes, etc.), use 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) |
 
 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.