Merges from develop/1.14 (HDFGroup#3118)

* Fix release action that allows files to be uploaded.
Add autotools h5copy help test.
Update cmake tools.cmake file for clang-tidy.
CMake build is missing H5FDsubfiling.h
macros improved for configure output capture.
Remove obsolete files

* Revert parallel config with TS

* Fix doxygen warnings

.github/workflows/cmake-ctest.yml

@@ -96,7 +96,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install CMake Dependencies (Linux)
-        run: sudo apt-get install ninja-build
+        run: sudo apt-get install ninja-build doxygen graphviz
 
       - name: Set file base name (Linux)
         id: set-file-base
@@ -151,14 +151,22 @@ jobs:
               path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204.tar.gz
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
+      # Save doxygen files created by ctest script
+      - name: Save published doxygen (Linux)
+        uses: actions/upload-artifact@v3
+        with:
+              name: docs-doxygen
+              path: ${{ runner.workspace }}/hdf5/build/ci-StdShar-GNUC/hdf5lib_docs/html
+              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
+
   build_and_test_mac:
   # MacOS w/ Clang + CMake
   #
     name: "MacOS Clang CMake"
     runs-on: macos-11
     steps:
       - name: Install Dependencies (MacOS)
-        run: brew install ninja
+        run: brew install ninja doxygen
 
       - name: Set file base name (MacOS)
         id: set-file-base

.github/workflows/main.yml

@@ -81,13 +81,15 @@ jobs:
             cpp: ON
             fortran: OFF
             java: ON
+            docs: OFF
             libaecfc: ON
             localaec: OFF
             zlibfc: ON
             localzlib: OFF
             parallel: OFF
             mirror_vfd: OFF
             direct_vfd: OFF
+            ros3_vfd: OFF
             generator: "-G \"Visual Studio 17 2022\" -A x64"
             run_tests: true
 
@@ -100,13 +102,15 @@ jobs:
             cpp: ON
             fortran: ON
             java: ON
+            docs: ON
             libaecfc: ON
             localaec: OFF
             zlibfc: ON
             localzlib: OFF
             parallel: OFF
             mirror_vfd: ON
             direct_vfd: ON
+            ros3_vfd: OFF
             toolchain: "config/toolchain/gcc.cmake"
             generator: "-G Ninja"
             run_tests: true
@@ -120,9 +124,11 @@ jobs:
             cpp: enable
             fortran: enable
             java: enable
+            docs: disable
             parallel: disable
             mirror_vfd: enable
             direct_vfd: enable
+            ros3_vfd: enable
             deprec_sym: enable
             default_api: v112
             szip: yes
@@ -141,9 +147,11 @@ jobs:
             cpp: disable
             fortran: enable
             java: disable
+            docs: disable
             parallel: enable
             mirror_vfd: disable
             direct_vfd: disable
+            ros3_vfd: disable
             deprec_sym: enable
             default_api: v112
             szip: yes
@@ -161,13 +169,15 @@ jobs:
             cpp: ON
             fortran: OFF
             java: ON
+            docs: OFF
             libaecfc: ON
             localaec: OFF
             zlibfc: ON
             localzlib: OFF
             parallel: OFF
             mirror_vfd: ON
             direct_vfd: OFF
+            ros3_vfd: OFF
             toolchain: "config/toolchain/clang.cmake"
             generator: "-G Ninja"
             run_tests: true
@@ -186,9 +196,11 @@ jobs:
             cpp: enable
             fortran: enable
             java: enable
+            docs: disable
             parallel: disable
             mirror_vfd: enable
             direct_vfd: enable
+            ros3_vfd: enable
             deprec_sym: enable
             default_api: v16
             szip: yes
@@ -209,9 +221,11 @@ jobs:
             cpp: enable
             fortran: enable
             java: enable
+            docs: disable
             parallel: disable
             mirror_vfd: enable
             direct_vfd: enable
+            ros3_vfd: enable
             deprec_sym: enable
             default_api: v18
             szip: yes
@@ -232,9 +246,11 @@ jobs:
             cpp: enable
             fortran: enable
             java: enable
+            docs: disable
             parallel: disable
             mirror_vfd: enable
             direct_vfd: enable
+            ros3_vfd: enable
             deprec_sym: enable
             default_api: v110
             szip: yes
@@ -255,9 +271,11 @@ jobs:
             cpp: enable
             fortran: enable
             java: enable
+            docs: disable
             parallel: disable
             mirror_vfd: enable
             direct_vfd: enable
+            ros3_vfd: enable
             deprec_sym: enable
             default_api: v112
             szip: yes
@@ -278,9 +296,11 @@ jobs:
             cpp: enable
             fortran: enable
             java: enable
+            docs: disable
             parallel: disable
             mirror_vfd: enable
             direct_vfd: enable
+            ros3_vfd: enable
             deprec_sym: disable
             default_api: v112
             szip: yes
@@ -317,14 +337,15 @@ jobs:
         run: echo '${{ toJSON(matrix) }}'
 
       - name: Install CMake Dependencies (Linux)
-        run: sudo apt-get install ninja-build
+        run: sudo apt-get install ninja-build doxygen graphviz
         if: matrix.os == 'ubuntu-latest'
 
       - name: Install Autotools Dependencies (Linux, serial)
         run: |
            sudo apt update
            sudo apt install automake autoconf libtool libtool-bin
            sudo apt install gcc-12 g++-12 gfortran-12
+           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            echo "CC=gcc-12" >> $GITHUB_ENV
            echo "CXX=g++-12" >> $GITHUB_ENV
            echo "FC=gfortran-12" >> $GITHUB_ENV
@@ -346,7 +367,7 @@ jobs:
         if: matrix.os == 'windows-latest'
 
       - name: Install Dependencies (macOS)
-        run: brew install ninja
+        run: brew install ninja doxygen
         if: matrix.os == 'macos-13'
 
       - name: Set environment for MSVC (Windows)
@@ -369,7 +390,7 @@ jobs:
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --${{ matrix.deprec_sym }}-deprecated-symbols --with-default-api-version=${{ matrix.default_api }} --enable-shared --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --with-szlib=${{ matrix.szip }}
+          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --${{ matrix.deprec_sym }}-deprecated-symbols --with-default-api-version=${{ matrix.default_api }} --enable-shared --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --${{ matrix.ros3_vfd }}-ros3-vfd --with-szlib=${{ matrix.szip }}
         shell: bash
         if: (matrix.generator == 'autogen') && ! (matrix.thread_safety.enabled)
 
@@ -378,7 +399,7 @@ jobs:
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --enable-shared --enable-threadsafe --disable-hl --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --with-szlib=${{ matrix.szip }}
+          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --enable-shared --enable-threadsafe --disable-hl --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd --${{ matrix.ros3_vfd }}-ros3-vfd --with-szlib=${{ matrix.szip }}
         shell: bash
         if: (matrix.generator == 'autogen') && (matrix.thread_safety.enabled)
 
@@ -390,7 +411,7 @@ jobs:
         run: |
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} -DHDF5_BUILD_DOC=${{ matrix.docs }} -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} -DHDF5_ENABLE_ROS3_VFD:BOOL=${{ matrix.ros3_vfd }} $GITHUB_WORKSPACE
         shell: bash
         if: (matrix.generator != 'autogen') && ! (matrix.thread_safety.enabled)
 
@@ -399,7 +420,7 @@ jobs:
         run: |
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_FORTRAN:BOOL=OFF -DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=OFF -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_FORTRAN:BOOL=OFF -DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=OFF -DHDF5_BUILD_DOC=OFF -DBUILD_SZIP_WITH_FETCHCONTENT=${{ matrix.libaecfc }} -DLIBAEC_USE_LOCALCONTENT=${{ matrix.localaec }} -DBUILD_ZLIB_WITH_FETCHCONTENT=${{ matrix.zlibfc }} -DZLIB_USE_LOCALCONTENT=${{ matrix.localzlib }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} -DHDF5_ENABLE_ROS3_VFD:BOOL=${{ matrix.ros3_vfd }} $GITHUB_WORKSPACE
         shell: bash
         if: (matrix.generator != 'autogen') && (matrix.thread_safety.enabled)
 

.github/workflows/release.yml

@@ -45,16 +45,26 @@ jobs:
       - run: |
           echo "Tag already present: ${{ steps.tag_create.outputs.tag_exists }}"
 
-  getfiles:
+  PreRelease-getfiles:
     runs-on: ubuntu-latest
+    needs: create-tag
+    environment: snapshots_1_12
+    permissions:
+        contents: write
     steps:
-      - name: Set file base name
-        id: set-file-base
+      - name: Get file base name
+        id: get-file-base
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
 
       # Get files created by tarball script
+      - name: Get doxygen (Linux)
+        uses: actions/download-artifact@v3
+        with:
+              name: docs-doxygen
+              path: ${{ github.workspace }}/${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen
+
       - name: Get tgz-tarball (Linux)
         uses: actions/download-artifact@v3
         with:
@@ -86,27 +96,13 @@ jobs:
               name: tgz-ubuntu-2204-binary
               path: ${{ github.workspace }}
 
-      # Get files used by release script
-
-  PreRelease:
-    runs-on: ubuntu-latest
-    needs: [create-tag, getfiles]
-    environment: snapshots_1_12
-    permissions:
-        contents: write
-    steps:
-      - name: Set file base name
-        id: get-file-base
-        run: |
-          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
-          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
-
       - name: PreRelease tag
         uses: softprops/action-gh-release@v1
         with:
-          tag_name: "snapshot"
+          tag_name: "snapshot_1_12"
           prerelease: true
           files: |
+              ${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen
               ${{ steps.get-file-base.outputs.FILE_BASE }}.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}.zip
               ${{ steps.get-file-base.outputs.FILE_BASE }}-osx12.tar.gz

config/cmake/ConfigureChecks.cmake

@@ -272,6 +272,7 @@ if (MINGW OR NOT WINDOWS)
     set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE)
 
     option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON)
+    mark_as_advanced (HDF_ENABLE_LARGE_FILE)
     if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN)
       set (msg "Performing TEST_LFS_WORKS")
       try_run (TEST_LFS_WORKS_RUN   TEST_LFS_WORKS_COMPILE
@@ -702,6 +703,7 @@ endif ()
 # Option for --enable-strict-format-checks
 #-----------------------------------------------------------------------------
 option (HDF5_STRICT_FORMAT_CHECKS "Whether to perform strict file format checks" OFF)
+mark_as_advanced (HDF5_STRICT_FORMAT_CHECKS)
 if (HDF5_STRICT_FORMAT_CHECKS)
   set (${HDF_PREFIX}_STRICT_FORMAT_CHECKS 1)
 endif ()
@@ -714,6 +716,7 @@ MARK_AS_ADVANCED (HDF5_STRICT_FORMAT_CHECKS)
 # support denormalized floating values) to maximize speed.
 #-----------------------------------------------------------------------------
 option (HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conversions" ON)
+mark_as_advanced (HDF5_WANT_DATA_ACCURACY)
 if (HDF5_WANT_DATA_ACCURACY)
   set (${HDF_PREFIX}_WANT_DATA_ACCURACY 1)
 endif ()
@@ -726,6 +729,7 @@ MARK_AS_ADVANCED (HDF5_WANT_DATA_ACCURACY)
 # actually benefit little.
 #-----------------------------------------------------------------------------
 option (HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON)
+mark_as_advanced (HDF5_WANT_DCONV_EXCEPTION)
 if (HDF5_WANT_DCONV_EXCEPTION)
   set (${HDF_PREFIX}_WANT_DCONV_EXCEPTION 1)
 endif ()
@@ -735,6 +739,7 @@ MARK_AS_ADVANCED (HDF5_WANT_DCONV_EXCEPTION)
 # Check if they would like the function stack support compiled in
 #-----------------------------------------------------------------------------
 option (HDF5_ENABLE_CODESTACK "Enable the function stack tracing (for developer debugging)." OFF)
+mark_as_advanced (HDF5_ENABLE_CODESTACK)
 if (HDF5_ENABLE_CODESTACK)
   set (${HDF_PREFIX}_HAVE_CODESTACK 1)
 endif ()