Fix doxygen and actions - merge from develop (#3109)

* Update the workflows to changes in develop
* Disable java for error only action
* Fix Fortran doxygen
* add fortran alias
* Merge changes from develop to fix actions

3 files changed, 77 insertions, 20 deletions

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
index 083b595..a113dfa 100644
--- a/.github/workflows/cmake-ctest.yml
+++ b/.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
@@ -151,6 +151,14 @@ 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
   #
@@ -158,7 +166,7 @@ jobs:
     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
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index da65941..5dee711 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: v114
             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: v114
             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: 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: default
             szip: yes
@@ -302,9 +322,11 @@ jobs:
             cpp: enable
             fortran: disable
             java: disable
+            docs: disable
             parallel: disable
             mirror_vfd: disable
             direct_vfd: enable
+            ros3_vfd: disable
             deprec_sym: enable
             default_api: v114
             szip: yes
@@ -326,9 +348,11 @@ jobs:
             cpp: enable
             fortran: disable
             java: disable
+            docs: disable
             parallel: disable
             mirror_vfd: disable
             direct_vfd: enable
+            ros3_vfd: disable
             deprec_sym: enable
             default_api: v114
             szip: yes
@@ -350,9 +374,11 @@ jobs:
             cpp: disable
             fortran: disable
             java: disable
+            docs: disable
             parallel: enable
             mirror_vfd: disable
             direct_vfd: enable
+            ros3_vfd: disable
             deprec_sym: enable
             default_api: v114
             toolchain: ""
@@ -373,9 +399,11 @@ jobs:
             cpp: disable
             fortran: disable
             java: disable
+            docs: disable
             parallel: enable
             mirror_vfd: disable
             direct_vfd: enable
+            ros3_vfd: disable
             deprec_sym: enable
             default_api: v114
             toolchain: ""
@@ -411,17 +439,18 @@ 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')
 
@@ -440,8 +469,8 @@ 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: |
@@ -463,7 +492,7 @@ 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)
 
@@ -472,7 +501,7 @@ 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 --${{ matrix.parallel }}-parallel --${{ 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 --${{ matrix.parallel }}-parallel --${{ 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)
 
@@ -484,7 +513,7 @@ 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)
 
@@ -493,7 +522,7 @@ 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)
 
@@ -523,10 +552,23 @@ 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)
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 16285d6..ac22bdd 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -48,13 +48,19 @@ jobs:
   getfiles:
     runs-on: ubuntu-latest
     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:
@@ -95,7 +101,7 @@ jobs:
     permissions:
         contents: write
     steps:
-      - name: Set file base name
+      - name: Get file base name
         id: get-file-base
         run: |
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
@@ -107,6 +113,7 @@ jobs:
           tag_name: "snapshot"
           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