Various merges from develop (#3135)

* Merges from develop/1.14
* Fix doxygen warnings
* Fix spelling
* Fix doxygen ref
* Add braces
* Fix format
* Remove unused file

1 files changed, 47 insertions, 15 deletions

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 258c5ea..226d1ed 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -81,6 +81,7 @@ jobs:
             cpp: ON
             fortran: OFF
             java: ON
+            docs: OFF
             libaecfc: ON
             localaec: OFF
             zlibfc: ON
@@ -88,6 +89,7 @@ jobs:
             parallel: OFF
             mirror_vfd: OFF
             direct_vfd: OFF
+            ros3_vfd: OFF
             generator: "-G \"Visual Studio 17 2022\" -A x64"
             run_tests: true
 
@@ -100,6 +102,7 @@ jobs:
             cpp: ON
             fortran: ON
             java: ON
+            docs: ON
             libaecfc: ON
             localaec: OFF
             zlibfc: ON
@@ -107,6 +110,7 @@ jobs:
             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: v110
             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: v110
             szip: yes
@@ -157,10 +165,11 @@ jobs:
           # We could also build with the Autotools via brew installing them,
           # but that seems unnecessary
           - name: "MacOS Clang CMake"
-            os: macos-11
+            os: macos-13
             cpp: ON
             fortran: OFF
             java: ON
+            docs: OFF
             libaecfc: ON
             localaec: OFF
             zlibfc: ON
@@ -168,6 +177,7 @@ jobs:
             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: disable
             default_api: default
             szip: yes
@@ -294,17 +312,18 @@ 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-11 g++-11 gfortran-11
-           echo "CC=gcc-11" >> $GITHUB_ENV
-           echo "CXX=g++-11" >> $GITHUB_ENV
-           echo "FC=gfortran-11" >> $GITHUB_ENV
+           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
            sudo apt install libaec0 libaec-dev
         if: (matrix.generator == 'autogen') && (matrix.parallel != 'enable')
 
@@ -323,8 +342,8 @@ jobs:
         if: matrix.os == 'windows-latest'
 
       - name: Install Dependencies (macOS)
-        run: brew install ninja
-        if: matrix.os == 'macos-11'
+        run: brew install ninja doxygen
+        if: matrix.os == 'macos-13'
 
       - name: Set environment for MSVC (Windows)
         run: |
@@ -346,7 +365,7 @@ 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)
 
@@ -355,7 +374,7 @@ 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)
 
@@ -367,7 +386,7 @@ 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)
 
@@ -376,7 +395,7 @@ 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)
 
@@ -406,10 +425,23 @@ jobs:
         if: (matrix.generator == 'autogen') && (matrix.run_tests) && ! (matrix.thread_safety.enabled)
 
       - name: CMake Run Tests
-        run: ctest --build . --parallel 2 -C ${{ matrix.build_mode.cmake }} -V
+        run: ctest . --parallel 2 -C ${{ matrix.build_mode.cmake }} -V
         working-directory: ${{ runner.workspace }}/build
-        # Skip Debug MSVC while we investigate H5L Java test timeouts
-        if: (matrix.generator != 'autogen') && (matrix.run_tests) && ! ((matrix.name == 'Windows MSVC CMake') && (matrix.build_mode.cmake == 'Debug'))
+        if: (matrix.generator != 'autogen') && (matrix.run_tests) && ! (matrix.thread_safety.enabled)
+
+      # THREAD-SAFE
+
+      - name: Autotools Run Thread-Safe Tests
+        run: |
+          cd test
+          ./ttsafe
+        working-directory: ${{ runner.workspace }}/build
+        if: (matrix.generator == 'autogen') && (matrix.run_tests) && (matrix.thread_safety.enabled)
+
+      - name: CMake Run Thread-Safe Tests
+        run: ctest . --parallel 2 -C ${{ matrix.build_mode.cmake }} -V -R ttsafe
+        working-directory: ${{ runner.workspace }}/build
+        if: (matrix.generator != 'autogen') && (matrix.run_tests) && (matrix.thread_safety.enabled)
 
       #
       # INSTALL (note that this runs even when we don't run the tests)