Sync develop changes April 1 - April 3 to hdf5_1_14 (#4316)

* Fix divide-by-zero when page buf page size is 0 (#4296) If a corrupt file sets the page buffer size in the superblock to zero, the library could attempt to divide by zero when allocating space in the file. The library now checks for valid page buffer sizes when reading the superblock message. Fixes oss-fuzz issue 58762 * Fix typo - Cnversion (#4301) * Bump the github-actions group with 3 updates (#4300) Bumps the github-actions group with 3 updates: [actions/download-artifact](https://github.com/actions/download-artifact), [softprops/action-gh-release](https://github.com/softprops/action-gh-release) and [github/codeql-action](https://github.com/github/codeql-action). Updates `actions/download-artifact` from 4.1.1 to 4.1.4 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v4.1.1...c850b93) Updates `softprops/action-gh-release` from 1 to 2 - [Release notes](https://github.com/softprops/action-gh-release/releases) - [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md) - [Commits](softprops/action-gh-release@de2c0eb...9d7c94c) Updates `github/codeql-action` from 3.24.6 to 3.24.9 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@8a470fd...1b1aada) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: softprops/action-gh-release dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix typo - glueing (#4299) * Prepend MPI_TEST_ to parallel example test names (#4306) * Report build options of VFDs (#4304) * changed to if string contains instead * return status of VFDs in libhdf5.settings * use *_ENABLE_* settings instead to report the state * added map state * updated resetting status if cmake option fails * PR merge workflows (#4303) * Merge the Test Express workflows into the PR CI * Split merge request triggers into autotools vs cmake * Fix typo - differetly (#4311) * Fix README badges (#4313) * Remove old wait_H5Tinit.cmake file (#4314) * Update branch names: develop=>hdf5_1_14 in 2 new workflows merged from develop.
HDFGroup · Apr 3, 2024 · 45185da · 45185da
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diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
@@ -2,7 +2,23 @@ name: hdf5 1.14 autools CI
 
 # Controls when the action will run. Triggers the workflow on push or pull request
 on:
-  workflow_call:
+  workflow_dispatch:
+  push:
+  pull_request:
+    branches: [ hdf5_1_14 ]
+    paths-ignore:
+      - '.github/CODEOWNERS'
+      - '.github/FUNDING.yml'
+      - 'doc/**'
+      - 'release_docs/**'
+      - 'ACKNOWLEDGEMENTS'
+      - 'COPYING**'
+      - '**.md'
+
+# Using concurrency to cancel any in-progress job or run
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
+  cancel-in-progress: true
 
 permissions:
   contents: read
@@ -83,10 +99,21 @@ jobs:
       with:
             build_mode: "production"
 
-    call-release-cmake-julia:
+    call-release-auto-julia:
         name: "Autotools Julia Workflows"
         uses: ./.github/workflows/julia-auto.yml
         with:
             build_mode: "production"
-
-
+
+    call-release-auto-xpr:
+        name: "Autotools TestExpress Workflows"
+        uses: ./.github/workflows/testxpr-auto.yml
+
+#  workflow-msys2-autotools:
+#    name: "CMake msys2 Workflows"
+#    uses: ./.github/workflows/msys2-auto.yml
+#    with:
+#        build_mode: "production"
+#        build_option: "--enable-production"
+
+
diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -2,7 +2,23 @@ name: hdf5 1.14 cmake CI
 
 # Controls when the action will run. Triggers the workflow on push or pull request
 on:
-  workflow_call:
+  workflow_dispatch:
+  push:
+  pull_request:
+    branches: [ hdf5_1_14 ]
+    paths-ignore:
+      - '.github/CODEOWNERS'
+      - '.github/FUNDING.yml'
+      - 'doc/**'
+      - 'release_docs/**'
+      - 'ACKNOWLEDGEMENTS'
+      - 'COPYING**'
+      - '**.md'
+
+# Using concurrency to cancel any in-progress job or run
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
+  cancel-in-progress: true
 
 permissions:
   contents: read
@@ -91,4 +107,9 @@ jobs:
         uses: ./.github/workflows/julia-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/main.yml b/.github/workflows/main.yml
diff --git a/.github/workflows/release-files.yml b/.github/workflows/release-files.yml
@@ -167,7 +167,7 @@ jobs:
           echo "${{ steps.get-file-base.outputs.FILE_BASE }}" > ./last-file.txt
 
       - name: Get NEWSLETTER
-        uses: actions/download-artifact@6b208ae046db98c579e8a3aa621ab581ff575935 # v4.1.1
+        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
         with:
               name: NEWSLETTER
               path: ${{ github.workspace }}
@@ -179,7 +179,7 @@ jobs:
       - name: PreRelease tag
         id: create_prerelease
         if: ${{ (inputs.use_environ == 'snapshots') }}
-        uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 # v1
+        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: true
@@ -204,7 +204,7 @@ jobs:
       - name: Release tag
         id: create_release
         if: ${{ (inputs.use_environ == 'release') }}
-        uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 # v1
+        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: false

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -67,6 +67,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@8a470fddafa5cbb6266ee11b37ef4d8aae19c571 # v3.24.6
+        uses: github/codeql-action/upload-sarif@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/testxpr-auto.yml b/.github/workflows/testxpr-auto.yml
@@ -0,0 +1,68 @@
+name: hdf5 TestExpress Autotools CI
+
+on:
+  workflow_call:
+
+permissions:
+  contents: read
+
+jobs:
+  build_and_test:
+    strategy:
+      matrix:
+        build_mode: ["production", "debug"]
+        include:
+          - build_mode: "production"
+          - build_mode: "debug"
+
+    name: "Autotools ${{ matrix.build_mode }} Express Test Workflows"
+
+    # Don't run the action if the commit message says to skip CI
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Linux Dependencies
+        run: |
+           sudo apt-get update
+           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+           sudo apt install gcc-12 g++-12 gfortran-12
+           sudo apt install automake autoconf libtool libtool-bin
+           sudo apt install libaec0 libaec-dev
+           echo "CC=gcc-12" >> $GITHUB_ENV
+           echo "CXX=g++-12" >> $GITHUB_ENV
+           echo "FC=gfortran-12" >> $GITHUB_ENV
+
+      - name: Get Sources
+        uses: actions/[email protected]
+
+      - name: Autotools Configure
+        shell: bash
+        run: |
+           sh ./autogen.sh
+           mkdir "${{ runner.workspace }}/build"
+           cd "${{ runner.workspace }}/build"
+           $GITHUB_WORKSPACE/configure \
+                --enable-build-mode=${{ matrix.build_mode }} \
+                --enable-shared \
+                --disable-parallel \
+                --disable-cxx \
+                --disable-fortran \
+                --disable-java \
+                --with-szlib=yes
+
+      - name: Autotools Build
+        shell: bash
+        run:         |
+           make -j3
+        working-directory: ${{ runner.workspace }}/build
+
+      - name: Autotools Test
+        shell: bash
+        env:
+            HDF5TestExpress: 0
+        run: |
+           cd test
+           make -j3 check
+        working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/testxpr-cmake.yml b/.github/workflows/testxpr-cmake.yml
@@ -0,0 +1,66 @@
+name: hdf5 TestExpress CMake CI
+
+on:
+  workflow_call:
+
+permissions:
+  contents: read
+
+jobs:
+  build_and_test:
+    strategy:
+      matrix:
+        build_mode: ["Release", "Debug"]
+        include:
+          - build_mode: "Release"
+          - build_mode: "Debug"
+
+    name: "CMake ${{ matrix.build_mode }} Express Test Workflows"
+
+    # Don't run the action if the commit message says to skip CI
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Linux Dependencies
+        run: |
+           sudo apt-get update
+           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+           sudo apt install libaec0 libaec-dev
+           sudo apt install gcc-12 g++-12 gfortran-12
+           echo "CC=gcc-12" >> $GITHUB_ENV
+           echo "CXX=g++-12" >> $GITHUB_ENV
+           echo "FC=gfortran-12" >> $GITHUB_ENV
+
+      - name: Get Sources
+        uses: actions/[email protected]
+
+      - name: CMake Configure
+        shell: bash
+        run: |
+           mkdir "${{ runner.workspace }}/build"
+           cd "${{ runner.workspace }}/build"
+           cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+                -G Ninja \
+                -DCMAKE_BUILD_TYPE=${{ matrix.build_mode }} \
+                -DBUILD_SHARED_LIBS=ON \
+                -DHDF5_ENABLE_ALL_WARNINGS=ON \
+                -DHDF5_ENABLE_PARALLEL:BOOL=OFF \
+                -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
+                -DHDF5_BUILD_FORTRAN=OFF \
+                -DHDF5_BUILD_JAVA=OFF \
+                -DHDF5_BUILD_DOC=OFF \
+                -DLIBAEC_USE_LOCALCONTENT=OFF \
+                -DZLIB_USE_LOCALCONTENT=OFF \
+                -DHDF_TEST_EXPRESS=0 \
+                $GITHUB_WORKSPACE
+
+      - name: CMake Build
+        run: cmake --build . --parallel 3 --config ${{ matrix.build_mode }}
+        working-directory: ${{ runner.workspace }}/build
+
+      - name: CMake Run Tests
+        run: ctest . --parallel 2 -C ${{ matrix.build_mode }} -V -R H5TESTXPR
+        working-directory: ${{ runner.workspace }}/build
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -679,6 +679,7 @@ if (HDF5_ENABLE_HDFS)
       list (APPEND LINK_LIBS -pthread)
     endif ()
   else ()
+    set (HDF5_ENABLE_HDFS OFF CACHE BOOL "Enable HDFS" FORCE)
     message (FATAL_ERROR "Set to use libhdfs library, but could not find or use libhdfs. Please verify that the path to HADOOP_HOME is valid, and/or reconfigure without HDF5_ENABLE_HDFS")
   endif ()
 endif ()
@@ -806,11 +807,15 @@ if (HDF5_ENABLE_SUBFILING_VFD)
 
   unset (CMAKE_EXTRA_INCLUDE_FILES)
   unset (CMAKE_REQUIRED_LIBRARIES)
+  if(NOT H5_HAVE_SUBFILING_VFD EQUAL 1)
+    set (HDF5_ENABLE_SUBFILING_VFD OFF CACHE BOOL "Build Parallel HDF5 Subfiling VFD" FORCE)
+  endif()
 endif()
 
 #option (DEFAULT_API_VERSION "Enable v1.14 API (v16, v18, v110, v112, v114)" "v114")
 set (DEFAULT_API_VERSION "v114" CACHE STRING "Enable v1.14 API (v16, v18, v110, v112, v114)")
 set_property (CACHE DEFAULT_API_VERSION PROPERTY STRINGS v16 v18 v110 v112 v114)
+
 #-----------------------------------------------------------------------------
 # Option to use 1.6.x API
 #-----------------------------------------------------------------------------
@@ -932,6 +937,8 @@ endif ()
 option (HDF5_ENABLE_MAP_API "Build the map API" OFF)
 if (HDF5_ENABLE_MAP_API)
   set (H5_HAVE_MAP_API 1)
+else ()
+  set (HDF5_ENABLE_MAP_API OFF CACHE BOOL "Build the map API" FORCE)
 endif ()
 
 #-----------------------------------------------------------------------------

diff --git a/HDF5Examples/C/H5PAR/CMakeLists.txt b/HDF5Examples/C/H5PAR/CMakeLists.txt
@@ -32,7 +32,7 @@ if (H5EX_BUILD_TESTING)
     if (last_test)
       set_tests_properties (${EXAMPLE_VARNAME}_${testname}-clearall PROPERTIES DEPENDS ${last_test})
     endif ()
-    add_test (NAME ${EXAMPLE_VARNAME}_${testname} COMMAND "${CMAKE_COMMAND}"
+    add_test (NAME MPI_TEST_${EXAMPLE_VARNAME}_${testname} COMMAND "${CMAKE_COMMAND}"
         -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${mumprocs};${MPIEXEC_PREFLAGS};$<TARGET_FILE:${EXAMPLE_VARNAME}_${testname}>;${MPIEXEC_POSTFLAGS}"
         -D "TEST_ARGS:STRING="
         -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
@@ -43,8 +43,8 @@ if (H5EX_BUILD_TESTING)
         -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}"
         -P "${H5EX_RESOURCES_DIR}/grepTest.cmake"
     )
-    set_tests_properties (${EXAMPLE_VARNAME}_${testname} PROPERTIES DEPENDS ${EXAMPLE_VARNAME}_${testname}-clearall)
-    set (last_test "${EXAMPLE_VARNAME}_${testname}")
+    set_tests_properties (MPI_TEST_${EXAMPLE_VARNAME}_${testname} PROPERTIES DEPENDS ${EXAMPLE_VARNAME}_${testname}-clearall)
+    set (last_test "MPI_TEST_${EXAMPLE_VARNAME}_${testname}")
   endmacro ()
 
   # Ensure that 24 is a multiple of the number of processes.

diff --git a/HDF5Examples/FORTRAN/H5PAR/CMakeLists.txt b/HDF5Examples/FORTRAN/H5PAR/CMakeLists.txt
@@ -46,7 +46,7 @@ if (H5EX_BUILD_TESTING)
     if (last_test)
       set_tests_properties (${EXAMPLE_VARNAME}_f90_${testname}-clearall PROPERTIES DEPENDS ${last_test})
     endif ()
-    add_test (NAME ${EXAMPLE_VARNAME}_f90_${testname} COMMAND "${CMAKE_COMMAND}"
+    add_test (NAME MPI_TEST_${EXAMPLE_VARNAME}_f90_${testname} COMMAND "${CMAKE_COMMAND}"
         -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${mumprocs};${MPIEXEC_PREFLAGS};$<TARGET_FILE:${EXAMPLE_VARNAME}_f90_${testname}>;${MPIEXEC_POSTFLAGS}"
         -D "TEST_ARGS:STRING="
         -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
@@ -57,8 +57,8 @@ if (H5EX_BUILD_TESTING)
         -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}"
         -P "${H5EX_RESOURCES_DIR}/grepTest.cmake"
     )
-    set_tests_properties (${EXAMPLE_VARNAME}_f90_${testname} PROPERTIES DEPENDS ${EXAMPLE_VARNAME}_f90_${testname}-clearall)
-    set (last_test "${EXAMPLE_VARNAME}_f90_${testname}")
+    set_tests_properties (MPI_TEST_${EXAMPLE_VARNAME}_f90_${testname} PROPERTIES DEPENDS ${EXAMPLE_VARNAME}_f90_${testname}-clearall)
+    set (last_test "MPI_TEST_${EXAMPLE_VARNAME}_f90_${testname}")
   endmacro ()
 
   # Ensure that 24 is a multiple of the number of processes.

diff --git a/README.md b/README.md
@@ -2,7 +2,8 @@ HDF5 version 1.14.4-1 currently under development
 
 ![HDF5 Logo](doxygen/img/HDF5.png)
 
-[![1.14 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_14&label=1.14)](https://github.com/HDFGroup/hdf5/actions/workflows/main.yml?query=branch%3Ahdf5_1_14)
+[![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/hdf5_1_14/COPYING)
 
 *Please refer to the release_docs/INSTALL file for installation instructions.*