Fixes the "multiple @param documentation sections" doxygen warnings (#6195)

Addresses the "multiple @ param documentation sections" warnings are caused by the interaction of three things: 1. MACRO_EXPANSION = YES with EXPAND_ONLY_PREDEF = NO in Doxyfile.in 2. Versioned API macros in H5version.h like: \def documentation in APIVersions.dox like: 3. \def H5Tarray_create \api_vers_2{H5Tarray_create,H5Tarray_create1,H5Tarray_create2} Because Doxygen expands all macros, it sees H5Tarray_create as an alias for H5Tarray_create1. It then associates documentation from both the \def block (for the macro) and the function's own doc block (with \param entries) with the same function — resulting in "multiple @ param documentation sections." * Update Doxygen version from 1.16.0 to 1.16.1 Use Doxygen 1.16.1 for all platforms. This version includes the latest bug fixes and improvements while maintaining compatibility with our documentation format. * Fix Windows Doxygen installation for version 1.16.1 Handle different Windows binary naming conventions across Doxygen versions: - 1.16.1 uses: doxygen-VERSION.windows.x64.bin.zip - 1.16.0 uses: doxygen-VERSION.x64.bin.zip Try the newer naming convention first, then fall back to the older one if the download fails. This ensures compatibility across versions. * Use ssciwr/doxygen-install in setup-doxygen action Replace direct installation of official Doxygen binaries with ssciwr/doxygen-install action. This avoids Java documentation parsing errors that occur with official binaries but not with distribution builds. The setup-doxygen action now serves as a thin wrapper around ssciwr/doxygen-install@f13be16c83 (v1), using commit hash for security and reproducibility. * Remove redundant version specification from workflows The setup-doxygen action already has a default version (1.16.1), so explicit version specification in workflows is unnecessary. This follows DRY principles and makes version updates simpler.
2026-09-25 04:09:44 +03:00 · 2026-02-12 10:45:17 -06:00
parent 58eaa31b6e
commit a46a399230
41 changed files with 626 additions and 487 deletions
@@ -0,0 +1,14 @@
 name: 'Setup Doxygen'
 description: 'Install Doxygen with version that supports Fortran cross-references'
 inputs:
  version:
    description: 'Doxygen version to install'
    required: false
    default: '1.16.1'
 runs:
  using: 'composite'
  steps:
    - name: Install Doxygen
      uses: ssciwr/doxygen-install@f13be1686235deee0aeb6cdf56640170691dc96b # v1
      with:
        version: ${{ inputs.version }}
@@ -37,10 +37,13 @@ jobs:
      with:
        sparse-checkout: .github/actions
    - name: Setup Doxygen
      uses: ./.github/actions/setup-doxygen
    - name: Install Dependencies (Linux_coverage)
      run: |
        sudo apt update
-        sudo apt-get install ninja-build doxygen graphviz curl build-essential
+        sudo apt-get install ninja-build graphviz curl build-essential
        sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
        sudo apt-get install lcov -q -y
@@ -138,10 +141,13 @@ jobs:
        with:
          sparse-checkout: .github/actions
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (Linux_Leak)
        run: |
          sudo apt update
-          sudo apt-get install ninja-build doxygen graphviz curl
+          sudo apt-get install ninja-build graphviz curl
      - name: Set file base name (Linux_Leak)
        id: set-file-base
@@ -239,10 +245,13 @@ jobs:
        with:
          sparse-checkout: .github/actions
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (Linux_Address)
        run: |
          sudo apt update
-          sudo apt-get install ninja-build doxygen graphviz curl
+          sudo apt-get install ninja-build graphviz curl
      - name: Set file base name (Linux_Address)
        id: set-file-base
@@ -340,10 +349,13 @@ jobs:
        with:
          sparse-checkout: .github/actions
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (Linux_UndefinedBehavior)
        run: |
          sudo apt update
-          sudo apt-get install ninja-build doxygen graphviz curl
+          sudo apt-get install ninja-build graphviz curl
      - name: Set file base name (Linux_UndefinedBehavior)
        id: set-file-base
@@ -38,10 +38,11 @@ jobs:
    runs-on: windows-11-arm
    if: ${{ inputs.build_mode != 'Debug' }}
    steps:
-      - name: Install Dependencies
+      - name: Get Sources
-        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
-        with:
+
-          version: "1.13.2"
+      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
@@ -67,10 +68,6 @@ jobs:
          echo "CXX=cl.exe" >> $GITHUB_ENV
          echo "CC=cl.exe" >> $GITHUB_ENV
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -172,21 +169,19 @@ jobs:
    name: "Ubuntu gcc-${{ inputs.build_mode }}-${{ inputs.thread_safety }}-${{ inputs.concurrent }}"
    runs-on: ubuntu-24.04-arm
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (Linux)
        run: |
          sudo apt-get update
          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -283,14 +278,16 @@ jobs:
    name: "MacOS Clang-${{ inputs.build_mode }}-${{ inputs.thread_safety }}-${{ inputs.concurrent }}"
    runs-on: macos-15
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (macOS)
        run: brew install ninja curl
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -303,10 +300,6 @@ jobs:
          which cmake
          cmake --version
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -116,7 +116,7 @@ jobs:
      - name: Install Dependencies (Linux)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
      - name: Set up JDK ${{ inputs.java_version }}
        uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
@@ -173,7 +173,7 @@ jobs:
    runs-on: macos-latest
    steps:
      - name: Install Dependencies (MacOS_latest)
-        run: brew install ninja doxygen
+        run: brew install ninja
      - name: Set up JDK ${{ inputs.java_version }}
        uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
@@ -241,7 +241,7 @@ jobs:
      - name: Install Dependencies (Linux)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
      - name: Set up JDK ${{ inputs.java_version }}
        uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
@@ -34,21 +34,19 @@ jobs:
 #      - name: Verify Wine64 installation
 #        run: wine64 --version
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install MinGW64 Cross-Compiler
        run: |
          sudo apt update
          sudo apt-get install -y mingw-w64
          sudo apt-get install gfortran-mingw-w64-x86-64-win32
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CMAKE CONFIGURE
      - name: CMake Configure
        run: |
@@ -90,11 +90,6 @@ jobs:
      - name: Install Dependencies (Windows)
        run: choco install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Enable Developer Command Prompt
        uses: ilammy/msvc-dev-cmd@0b201ec74fa43914dc39ae48a89fd1d8cb592756 # v1.13.0
@@ -246,11 +241,6 @@ jobs:
          sudo apt-get update
          sudo apt-get install ninja-build graphviz
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -419,11 +409,6 @@ jobs:
      - name: Install Dependencies (MacOS_latest)
        run: brew install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: check clang version
        shell: bash
        run: |
@@ -650,7 +635,7 @@ jobs:
      - name: Install Dependencies (Linux S3)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen
+          sudo apt-get install ninja-build
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
@@ -891,7 +876,7 @@ jobs:
      - name: Install Dependencies (Linux_intel)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
      - name: add oneAPI to env
        uses: fortran-lang/setup-fortran@47809fdb6e637da656ce9ada436527b240c1287f # v1
@@ -29,10 +29,18 @@ jobs:
           FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
           echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
      - name: Get Actions
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          sparse-checkout: .github/actions
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build 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
@@ -100,14 +108,17 @@ jobs:
    runs-on: windows-latest
    steps:
      - name: Get Actions
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          sparse-checkout: .github/actions
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (Windows)
        run: choco install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Enable Developer Command Prompt
        uses: ilammy/msvc-dev-cmd@0b201ec74fa43914dc39ae48a89fd1d8cb592756 # v1.13.0
@@ -176,14 +187,17 @@ jobs:
    name: "MacOS Clang"
    runs-on: macos-latest
    steps:
      - name: Get Actions
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          sparse-checkout: .github/actions
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (MacOS_latest)
        run: brew install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Check Clang Version
        shell: bash
        run: |
@@ -263,10 +277,18 @@ jobs:
    name: "Ubuntu Clang"
    runs-on: ubuntu-latest
    steps:
      - name: Get Actions
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          sparse-checkout: .github/actions
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (Linux_clang)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz curl
+          sudo apt-get install ninja-build graphviz curl
      - name: Check Clang Version
        shell: bash
@@ -27,7 +27,7 @@ jobs:
        shell: bash
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
      - name: Install oneAPI (Linux)
@@ -23,7 +23,7 @@ jobs:
        shell: bash
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
          sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential
@@ -31,7 +31,7 @@ jobs:
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
           sudo apt install gcc-12 g++-12 gfortran-12
           sudo apt install libaec0 libaec-dev
@@ -31,7 +31,7 @@ jobs:
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
           sudo apt install gcc-12 g++-12 gfortran-12
           sudo apt install libaec0 libaec-dev
@@ -27,20 +27,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -86,20 +89,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -140,20 +146,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -194,20 +203,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -246,20 +258,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -298,20 +313,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -351,14 +369,16 @@ jobs:
    runs-on: windows-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Dependencies (Windows)
        run: choco install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: install oneAPI (Windows)
        uses: fortran-lang/setup-fortran@47809fdb6e637da656ce9ada436527b240c1287f # v1
        id: setup-fortran
@@ -366,10 +386,6 @@ jobs:
          compiler: intel
          version: '2025.0'
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Configure (Windows)
        shell: pwsh
        env:
@@ -403,20 +419,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
          sudo apt install gcc-12 g++-12 gfortran-12 zlib1g-dev
          echo "CC=gcc-12" >> $GITHUB_ENV
          echo "CXX=g++-12" >> $GITHUB_ENV
          echo "FC=gfortran-12" >> $GITHUB_ENV
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -460,20 +479,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -513,20 +535,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -566,20 +591,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -614,20 +642,23 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      # SETUP
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-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
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -121,6 +121,13 @@ jobs:
  # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      #Useful for debugging
      - name: Dump matrix context
        run: echo '${{ toJSON(matrix) }}'
@@ -138,11 +145,6 @@ jobs:
        run: brew install ninja curl
        if: ${{ matrix.ostype == 'macos' }}
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -162,10 +164,6 @@ jobs:
          echo "CC=cl.exe" >> $GITHUB_ENV
        if:  matrix.ostype == 'windows'
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      # CONFIGURE
      - name: Configure
        run: |
@@ -138,6 +138,13 @@ jobs:
    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      #Useful for debugging
      - name: Dump matrix context
        run: echo '${{ toJSON(matrix) }}'
@@ -155,11 +162,6 @@ jobs:
        run: brew install ninja curl
        if: ${{ matrix.ostype == 'macos' }}
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -198,10 +200,6 @@ jobs:
          echo "CC=cl.exe" >> $GITHUB_ENV
        if:  matrix.ostype == 'windows'
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup jextract (FFM builds only)
        if: ${{ inputs.force_java_implementation == 'ffm' }}
        uses: ./.github/actions/setup-jextract
@@ -239,18 +239,17 @@ jobs:
        if: ${{ runner.os == 'Linux' }}
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
      - name: Install Dependencies (macOS)
        if: ${{ runner.os == 'macOS' }}
        run: |
-          brew install ninja doxygen graphviz
+          brew install ninja graphviz
      - name: Install Dependencies (Windows)
        if: ${{ runner.os == 'Windows' }}
        run: |
          choco install ninja
          choco install doxygen.install
          choco install graphviz
      - name: Enable Developer Command Prompt (Windows)
@@ -42,7 +42,7 @@ jobs:
        shell: bash
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt-get install ninja-build graphviz
          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
          sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential
@@ -46,11 +46,6 @@ jobs:
      - name: Install Dependencies (Windows)
        run: choco install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -182,11 +177,6 @@ jobs:
          sudo apt install gcc-12 g++-12 gfortran-12
          sudo apt install libaec0 libaec-dev
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -299,11 +289,6 @@ jobs:
      - name: Install Dependencies (MacOS_latest)
        run: brew install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Setup MPI (${{ matrix.mpi }})
        id: setup-mpi
        uses: mpi4py/setup-mpi@8ac56ec7ab12f2dffdcf55ffaf50f1920ebcc004 # v1
@@ -79,11 +79,6 @@ jobs:
          echo "CC=${{ runner.workspace }}/openmpi/bin/mpicc" >> $GITHUB_ENV
          echo "FC=${{ runner.workspace }}/openmpi/bin/mpif90" >> $GITHUB_ENV
      - name: Install Doxygen
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -201,11 +196,6 @@ jobs:
          echo "CC=${{ runner.workspace }}/mpich/bin/mpicc" >> $GITHUB_ENV
          echo "FC=${{ runner.workspace }}/mpich/bin/mpif90" >> $GITHUB_ENV
      - name: Install Doxygen
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -44,11 +44,6 @@ jobs:
      - name: Install Dependencies (Windows)
        run: choco install ninja
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Enable Developer Command Prompt
        uses: ilammy/msvc-dev-cmd@0b201ec74fa43914dc39ae48a89fd1d8cb592756 # v1.13.0
@@ -165,11 +160,6 @@ jobs:
          sudo apt-get update
          sudo apt-get install ninja-build graphviz curl
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
        with:
@@ -266,11 +256,6 @@ jobs:
      - name: Install Dependencies (MacOS_latest)
        run: brew install ninja curl
      - name: Install Dependencies
        uses: ssciwr/doxygen-install@501e53b879da7648ab392ee226f5b90e42148449 # v1
        with:
          version: "1.13.2"
      - name: check clang version
        shell: bash
        run: |
@@ -394,7 +379,7 @@ jobs:
      - name: Install Dependencies (Linux S3)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen
+          sudo apt-get install ninja-build
      - name: Install CMake
        uses: lukka/get-cmake@9e07ecdcee1b12e5037e42f410b67f03e2f626e1 # latest
@@ -629,7 +614,7 @@ jobs:
      - name: Install Dependencies (Linux_intel)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz curl
+          sudo apt-get install ninja-build graphviz curl
      - name: add oneAPI to env
        uses: fortran-lang/setup-fortran@47809fdb6e637da656ce9ada436527b240c1287f # v1
@@ -738,7 +723,7 @@ jobs:
      - name: Install Dependencies (Linux_clang)
        run: |
          sudo apt-get update
-          sudo apt-get install ninja-build doxygen graphviz curl
+          sudo apt-get install ninja-build graphviz curl
      - name: check clang version
        shell: bash
@@ -25,10 +25,16 @@ jobs:
    runs-on: ubuntu-latest
    steps:
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Setup Doxygen
        uses: ./.github/actions/setup-doxygen
      - name: Install Linux Dependencies
        run: |
           sudo apt-get update
-           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt-get install ninja-build 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
@@ -36,9 +42,6 @@ jobs:
           echo "CXX=g++-12" >> $GITHUB_ENV
           echo "FC=gfortran-12" >> $GITHUB_ENV
      - name: Get Sources
        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
      - name: Configure
        shell: bash
        run: |
@@ -20,3 +20,8 @@ src/H5config.h.in
 /CMakeUserPresets.json
 HDF5Examples/CMakeUserPresets.json
 /CLAUDE.md
 # Emacs temporary and lock files
 *~
 \#*\#
 .\#*
@@ -1147,7 +1147,7 @@ if (HDF5_BUILD_DOC AND EXISTS "${HDF5_DOXYGEN_DIR}" AND IS_DIRECTORY "${HDF5_DOX
    else ()
      set (HDF5_DOXY_WARNINGS "NO")
    endif ()
-    message (VERBOSE "Doxygen version: ${DOXYGEN_VERSION}")
+    message (STATUS "Found Doxygen version: ${DOXYGEN_VERSION}")
    # Set the default directory for the Java sources for doxygen
    if (Java_VERSION_STRING VERSION_GREATER_EQUAL "25.0.0")
@@ -478,6 +478,47 @@ sub create_public ($) {
    close HEADER;
 }
 ##############################################################################
 # Create the generated CMake file for Doxygen PREDEFINED macros
 #
 sub create_doxygen_cmake ($) {
    my $prefix = shift;         # Get the prefix for the source file (e.g., "src/")
    my $file = "H5version_doxygen.cmake";   # Name of file to generate
    # Output to doxygen directory (relative to src/)
    my $doxygen_dir = $prefix;
    $doxygen_dir =~ s/src\/?$/doxygen\//;   # Replace "src/" with "doxygen/"
    # Create doxygen directory if it doesn't exist
    if ($doxygen_dir ne "" && ! -d $doxygen_dir) {
        mkdir $doxygen_dir or die "unable to create directory: $doxygen_dir";
    }
    # Open new cmake file in doxygen directory
    open CMAKE, ">${doxygen_dir}${file}" or die "unable to create doxygen cmake file: ${doxygen_dir}${file}";
    # Create file contents
    print CMAKE "# Generated automatically by bin/make_vers -- do not edit\n";
    print CMAKE "# Add new versioned symbols to H5vers.txt file\n";
    print CMAKE "#\n";
    print CMAKE "# Doxygen PREDEFINED entries for versioned APIs\n";
    print CMAKE "# These macros tell Doxygen which version each API name maps to,\n";
    print CMAKE "# preventing \"multiple \@param documentation sections\" warnings\n";
    print CMAKE "\n";
    print CMAKE "list (APPEND _doxygen_predefined_entries\n";
    # Add function version macros (sorted for consistency)
    for my $name (sort keys %functions) {
        my $vers = $functions{$name};
        print CMAKE "  \"$name=$name$vers\"\n";
    }
    print CMAKE ")\n";
    # Close cmake file
    close CMAKE;
 }
 ##############################################################################
 # Read symbol version file (given as command-line argument) in and process it
 # into internal data structures, then create header files.
@@ -508,5 +549,7 @@ for $file (@ARGV) {
    # Create header files
    print "Generating 'H5version.h'\n";
    create_public($prefix);
    print "Generating 'doxygen/H5version_doxygen.cmake'\n";
    create_doxygen_cmake($prefix);
 }
@@ -32,7 +32,32 @@ if (DOXYGEN_FOUND)
  set (DOXYGEN_SEARCHENGINE_URL)
  set (DOXYGEN_STRIP_FROM_PATH ${HDF5_SOURCE_DIR})
  set (DOXYGEN_STRIP_FROM_INC_PATH ${HDF5_SOURCE_DIR})
-  set (DOXYGEN_PREDEFINED "H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_DOXYGEN H5_HAVE_SUBFILING_VFD H5_HAVE_IOC_VFD H5_HAVE_MIRROR_VFD H5std_string=std::string H5G_link_t=H5L_type_t")
+  # Versioned API macros are added to PREDEFINED to give Doxygen a fixed
  # expansion and prevent it from discovering the #defines in H5version.h,
  # which otherwise causes "multiple @param documentation sections" warnings
  # when the macro documentation (\def) and the function documentation both
  # get associated with the same underlying function.
  #
  # The versioned API macros are auto-generated from src/H5vers.txt by the
  # bin/make_vers script, which creates doxygen/H5version_doxygen.cmake.
  # This ensures the Doxygen configuration stays synchronized with the
  # actual default versions defined in src/H5version.h.
  set (_doxygen_predefined_entries
    H5_HAVE_DIRECT
    H5_HAVE_LIBHDFS
    H5_HAVE_MAP_API
    H5_HAVE_PARALLEL
    H5_HAVE_ROS3_VFD
    H5_DOXYGEN
    H5_HAVE_SUBFILING_VFD
    H5_HAVE_IOC_VFD
    H5_HAVE_MIRROR_VFD
    "H5std_string=std::string"
    "H5G_link_t=H5L_type_t"
  )
  # Load auto-generated versioned API macros from doxygen/H5version_doxygen.cmake
  include(${HDF5_DOXYGEN_DIR}/H5version_doxygen.cmake)
  list (JOIN _doxygen_predefined_entries " " DOXYGEN_PREDEFINED)
  set (DOXYGEN_WARN_AS_ERROR ${HDF5_DOXY_WARNINGS})
 # This configure and individual custom targets work together
@@ -719,7 +719,11 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
-INPUT                  = @DOXYGEN_INPUT_DIRECTORY@
+INPUT                  = @DOXYGEN_INPUT_DIRECTORY@ \
                         @DOXYGEN_DIR@/examples/menus/core_menu.md \
                         @DOXYGEN_DIR@/examples/menus/fortran_menu.md \
                         @DOXYGEN_DIR@/examples/menus/high_level_menu.md \
                         @DOXYGEN_DIR@/examples/menus/java_menu.md
 # This tag can be used to specify the character encoding of the source files
 # that Doxygen parses. Internally Doxygen uses the UTF-8 encoding. Doxygen uses
@@ -758,7 +762,6 @@ FILE_PATTERNS  = H5*public.h H5*module.h H5*develop.h H5FD*.h \
                 @DOXYGEN_JAVA_DIR@/hdf/hdf5lib/exceptions/HDF*.java \
                 *.F90 \
                 *.dox \
                 *.md \
                 h5copy.h h5diff_main.h h5dump.h h5format_convert.h h5import.h h5jam.h h5ls.h h5repack.h h5stat.h \
                 h5watch.h h5clear.h h5debug.h h5delete.h h5mkgrp.h h5repart.h \
                 @HDF5_CPP_SRC_DIR@/*.h \
@@ -777,7 +780,8 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which Doxygen is
 # run.
-EXCLUDE                = jsrc
+EXCLUDE                = jsrc \
                         @DOXYGEN_DIR@/../config/toolchain
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -804,10 +808,7 @@ EXCLUDE_PATTERNS       = */fortran/test/* \
                         */hl/fortran/src/*.h \
                         */HDF5Examples/FORTRAN/* \
                         */sanitizer/* \
-                         */README.md \
+                         */H5fortran_types.F90
                         */CONTRIBUTING.md \
                         */CHANGELOG.md \
                         */HISTORY-*.md
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -0,0 +1,48 @@
 # Generated automatically by bin/make_vers -- do not edit
 # Add new versioned symbols to H5vers.txt file
 #
 # Doxygen PREDEFINED entries for versioned APIs
 # These macros tell Doxygen which version each API name maps to,
 # preventing "multiple @param documentation sections" warnings
 list (APPEND _doxygen_predefined_entries
  "H5Acreate=H5Acreate2"
  "H5Aiterate=H5Aiterate2"
  "H5Dcreate=H5Dcreate2"
  "H5Dopen=H5Dopen2"
  "H5Dread_chunk=H5Dread_chunk2"
  "H5Eclear=H5Eclear2"
  "H5Eget_auto=H5Eget_auto2"
  "H5Eprint=H5Eprint2"
  "H5Epush=H5Epush2"
  "H5Eset_auto=H5Eset_auto2"
  "H5Ewalk=H5Ewalk2"
  "H5Fget_info=H5Fget_info2"
  "H5Gcreate=H5Gcreate2"
  "H5Gopen=H5Gopen2"
  "H5Iregister_type=H5Iregister_type2"
  "H5Lget_info=H5Lget_info2"
  "H5Lget_info_by_idx=H5Lget_info_by_idx2"
  "H5Literate=H5Literate2"
  "H5Literate_by_name=H5Literate_by_name2"
  "H5Lvisit=H5Lvisit2"
  "H5Lvisit_by_name=H5Lvisit_by_name2"
  "H5Oget_info=H5Oget_info3"
  "H5Oget_info_by_idx=H5Oget_info_by_idx3"
  "H5Oget_info_by_name=H5Oget_info_by_name3"
  "H5Ovisit=H5Ovisit3"
  "H5Ovisit_by_name=H5Ovisit_by_name3"
  "H5Pencode=H5Pencode2"
  "H5Pget_filter=H5Pget_filter2"
  "H5Pget_filter_by_id=H5Pget_filter_by_id2"
  "H5Pinsert=H5Pinsert2"
  "H5Pregister=H5Pregister2"
  "H5Rdereference=H5Rdereference2"
  "H5Rget_obj_type=H5Rget_obj_type2"
  "H5Sencode=H5Sencode2"
  "H5Tarray_create=H5Tarray_create2"
  "H5Tcommit=H5Tcommit2"
  "H5Tdecode=H5Tdecode2"
  "H5Tget_array_dims=H5Tget_array_dims2"
  "H5Topen=H5Topen2"
 )
@@ -268,13 +268,13 @@ are usually similar, see @ref HDF5LIB
 For example:
 <ul>
 <li>
-File Interface:<ul><li>#H5Fopen (C)</li><li>#h5f.h5fopen_f (FORTRAN)</li><li>H5.H5Fopen (Java)</li></ul>
+File Interface:<ul><li>#H5Fopen (C)</li><li>\ref h5f::h5fopen_f (FORTRAN)</li><li>H5.H5Fopen (Java)</li></ul>
 </li>
 <li>
-Dataset Interface:<ul><li>#H5Dopen (C)</li><li>#h5d.h5dopen_f (FORTRAN)</li><li>H5.H5Dopen (Java)</li></ul>
+Dataset Interface:<ul><li>#H5Dopen (C)</li><li>\ref h5d::h5dopen_f (FORTRAN)</li><li>H5.H5Dopen (Java)</li></ul>
 </li>
 <li>
-Dataspace interface:<ul><li>#H5Sclose (C)</li><li>#h5s.h5sclose_f (FORTRAN)</li><li>H5.H5Sclose (Java)</li></ul>
+Dataspace interface:<ul><li>#H5Sclose (C)</li><li>\ref h5s::h5sclose_f (FORTRAN)</li><li>H5.H5Sclose (Java)</li></ul>
 </li>
 </ul>
 The HDF5 Python APIs use methods associated with specific objects.
@@ -311,7 +311,7 @@ import numpy
 <li>
 <strong>FORTRAN</strong>:<br />
 <code>USE HDF5</code><br />
-and call #h5lib.h5open_f and #h5lib.h5close_f to initialize and close the HDF5 FORTRAN interface
+and call \ref h5lib::h5open_f and `h5close_f` to initialize and close the HDF5 FORTRAN interface
 </li>
 <li>
 <strong>Java</strong>:<br />
@@ -166,10 +166,10 @@ Keep the following in mind when looking at the example programs included in this
 <table>
 <tr>
 <td>File Interface: </td>
-<td>#h5f.h5fopen_f</td>
+<td>\ref h5f::h5fopen_f</td>
 </tr><tr>
 <td>Dataset Interface:</td>
-<td>#h5d.h5dopen_f</td>
+<td>\ref h5d::h5dopen_f</td>
 </tr>
 </table>
@@ -208,7 +208,7 @@ import numpy
 <li>
 <strong>FORTRAN</strong>:<br />
 <code>USE HDF5</code><br />
-and call #h5lib.h5open_f and #h5lib.h5close_f to initialize and close the HDF5 FORTRAN interface
+and call \ref h5lib::h5open_f and `h5close_f` to initialize and close the HDF5 FORTRAN interface
 </li>
 <li>
 <strong>Java</strong>:<br />
@@ -155,14 +155,14 @@ For details on compiling an HDF5 application:
 #H5Gcreate creates a group at the location specified by a location identifier and a name. The location identifier
 can be a file identifier or a group identifier and the name can be relative or absolute.
-The first #H5Gcreate/#h5g.h5gcreate_f creates the group <code style="background-color:whitesmoke;">MyGroup</code>
+The first #H5Gcreate/\ref h5g::h5gcreate_f creates the group <code style="background-color:whitesmoke;">MyGroup</code>
 in the root group of the specified file.
-The second #H5Gcreate/#h5g.h5gcreate_f creates the group <code style="background-color:whitesmoke;">Group_A</code>
+The second #H5Gcreate/\ref h5g::h5gcreate_f creates the group <code style="background-color:whitesmoke;">Group_A</code>
 in the group <code style="background-color:whitesmoke;">MyGroup</code> in the root group of the specified
 file. Note that the parent group (<code style="background-color:whitesmoke;">MyGroup</code>) already exists.
-The third #H5Gcreate/#h5g.h5gcreate_f creates the group <code style="background-color:whitesmoke;">Group_B</code> in the specified group.
+The third #H5Gcreate/\ref h5g::h5gcreate_f creates the group <code style="background-color:whitesmoke;">Group_B</code> in the specified group.
 \subsection secLBGrpCreateNamesExCont File Contents
@@ -390,7 +390,7 @@ Release 1.8.17 if their removal causes no problems.
 <h4>In the Fortran Interface</h4>
 The following Fortran 2003 API has been added:
-\li #h5t.h5tenum_insert_f
+\li \ref h5t::h5tenum_insert_f
 Operation of the new Fortran 2003 version of this API is more consistent with the operation of
 the C API than was the Fortran 90 version.
@@ -566,12 +566,12 @@ Additional overloads to the class Attribute to get an attribute's name for conve
 The following new Fortran subroutines have been added:
 Fortran2003 subroutines:
-\li #h5p.h5pset_file_image_f
+\li \ref h5p::h5pset_file_image_f
-\li #h5p.h5pget_file_image_f
+\li \ref h5p::h5pget_file_image_f
-\li #h5f.h5fget_file_image_f (Added in Release 1.8.11, but not documented at that time.)
+\li \ref h5f::h5fget_file_image_f (Added in Release 1.8.11, but not documented at that time.)
 The following Fortran subroutine has been changed:
-\li #h5p.h5pset_chunk_cache_f - The values of the constants H5D_CHUNK_CACHE_NSLOTS_DFLT_F
+\li \ref h5p::h5pset_chunk_cache_f - The values of the constants H5D_CHUNK_CACHE_NSLOTS_DFLT_F
    and H5D_CHUNK_CACHE_NBYTES_DFLT_F have been changed to INTEGER(KIND=size_t).
 <h4>Other New Features</h4>
@@ -752,21 +752,21 @@ transition from HDF5 Release 1.8.10 to Release 1.8.11.
 <h4>The following new Fortran subroutines have been added</h4>
 <strong>Fortran90 subroutines</strong>:
-\li #h5o.h5odecr_refcount_f
+\li \ref h5o::h5odecr_refcount_f
-\li #h5o.h5oexists_by_name_f
+\li \ref h5o::h5oexists_by_name_f
-\li #h5o.h5oget_comment_f
+\li \ref h5o::h5oget_comment_f
-\li #h5o.h5oget_comment_by_name_f
+\li \ref h5o::h5oget_comment_by_name_f
-\li #h5o.h5oincr_refcount_f
+\li \ref h5o::h5oincr_refcount_f
-\li #h5o.h5oopen_by_idx_f
+\li \ref h5o::h5oopen_by_idx_f
-\li #h5o.h5oset_comment_f
+\li \ref h5o::h5oset_comment_f
-\li #h5o.h5oset_comment_by_name_f
+\li \ref h5o::h5oset_comment_by_name_f
 h5oclose_f was introduced in HDF5 Release 1.8.8 but remained undocumented until this release.
 Fortran2003 subroutines:
-\li #h5o.h5oget_info_f
+\li \ref h5o::h5oget_info_f
-\li #h5o.h5oget_info_by_idx_f
+\li \ref h5o::h5oget_info_by_idx_f
-\li #h5o.h5ovisit_by_name_f
+\li \ref h5o::h5ovisit_by_name_f
 <h4>New Feature: Dynamically Loaded Filters</h4>
 HDF5 now detects and dynamically loads external filters, reducing the need for an application to
@@ -797,7 +797,7 @@ The return value of the following high-level C function has changed:
    returned size of of the dimension scale name (bug fix).
 <h4>In the Fortran subroutines</h4>
-\li #h5p.h5pset_external_f and #h5p.h5pget_external_f - the type of the offset parameter has changed to
+\li \ref h5p::h5pset_external_f and \ref h5p::h5pget_external_f - the type of the offset parameter has changed to
    INTEGER(KIND=OFF_T) to support 8-byte integers, matching the C type definition of off_t.
 \li The HDF5 Library now supports data conversion from enumeration to integer and floating-point
    numeric datatypes.
@@ -828,7 +828,7 @@ transition from HDF5 Release 1.8.9 to Release 1.8.10.
 \li H5Pget_mpio_no_collective_cause
 <strong>The following new Fortran subroutine has been added</strong>:
-\li #h5p.h5pget_mpio_actual_io_mode_f
+\li \ref h5p::h5pget_mpio_actual_io_mode_f
 The syntax of the following high-level C function has changed:
 \li H5TBAget_fill - This function's return type has been changed to h5tri_t. A return value of 1
@@ -848,7 +848,7 @@ the transition from HDF5 Release 1.8.8 to Release 1.8.9.
 A new high level C function and Fortran subroutine were added to HDF5 Lite (H5LT) to determine
 whether an HDF5 path is correct and resolves to a valid HDF5 object:
 \li h5LTpath_valid
-\li #h5lt.h5ltpath_valid_f
+\li `h5ltpath_valid_f`
 The new file image operations feature consists of the following functions and their associated
 callbacks, struct, and ENUM. This feature enables an application to load a file into memory
@@ -896,8 +896,8 @@ for those who may have missed its introduction:
 <h4>New Fortran Subroutines</h4>
 The following Fortran subroutines have been added in this release:
-\li #h5lt.h5ltpath_valid_f
+\li `h5ltpath_valid_f`
-\li #h5o.h5ocopy_f
+\li \ref h5o::h5ocopy_f
 \li h5fset_mpi_atomicity_f
 \li h5fget_mpi_atomicity_f
@@ -905,7 +905,7 @@ Where a subroutine is part of a new HDF5 feature, that feature is described abov
 <h4>Fortran Subroutine with Changed Behavior</h4>
 The content of the buffer returned by the following Fortran subroutine has changed as noted:
-\li #h5lt.h5ltget_attribute_string_f - If the returned buffer requires padding, #h5lt.h5ltget_attribute_string_f
+\li `h5ltget_attribute_string_f` - If the returned buffer requires padding, `h5ltget_attribute_string_f`
    now employs space padding; this buffer was previously returned with a C NULL terminator.
 <h4>Command-line Utilities with New Options and/or Changed Behavior</h4>
@@ -957,13 +957,13 @@ Terminology:
 <h4>New Fortran 2003-only subroutines</h4>
 New subroutines available only in Fortran 2003 environments:
-\li #h5d.h5dvlen_reclaim_f
+\li \ref h5d::h5dvlen_reclaim_f
-\li #h5e.h5eset_auto_f
+\li \ref h5e::h5eset_auto_f
-\li #h5l.h5literate_by_name_f
+\li \ref h5l::h5literate_by_name_f
-\li #h5l.h5literate_f
+\li \ref h5l::h5literate_f
-\li #h5o.h5ovisit_f
+\li \ref h5o::h5ovisit_f
-\li #h5o.h5oget_info_by_name_f
+\li \ref h5o::h5oget_info_by_name_f
-\li #h5t.h5tconvert_f
+\li \ref h5t::h5tconvert_f
 <h4>Subroutines with Fortran 90 versions and extended features in Fortran 2003 environments</h4>
 Subroutines in this section have extended support in Fortran 2003 environments, but are new or unchanged in Fortran 90 environments.
@@ -971,44 +971,44 @@ Subroutines in this section have extended support in Fortran 2003 environments,
 All existing Fortran 90 subroutines, including those not mentioned below, are available in both Fortran 90 and Fortran 2003 environments.
 Subroutines with support for the derived type C_PTR in Fortran 2003 environments:
-\li #h5p.h5pget_f
+\li \ref h5p::h5pget_f
-\li #h5p.h5pget_fill_value_f
+\li \ref h5p::h5pget_fill_value_f
-\li #h5p.h5pinsert_f
+\li \ref h5p::h5pinsert_f
-\li #h5p.h5pregister_f
+\li \ref h5p::h5pregister_f
-\li #h5p.h5pset_f
+\li \ref h5p::h5pset_f
-\li #h5p.h5pset_fill_value_f
+\li \ref h5p::h5pset_fill_value_f
-\li #h5r.h5rcreate_f
+\li \ref h5r::h5rcreate_f
 \li h5rdereference_f
-\li #h5r.h5rget_name_f
+\li \ref h5r::h5rget_name_f
-\li #h5r.h5rget_object_type_f
+\li \ref h5r::h5rget_object_type_f
 Subroutines with support for the derived type C_PTR and a changed signature in Fortran 2003 environments:
-\li #h5a.h5aread_f
+\li \ref h5a::h5aread_f
-\li #h5a.h5awrite_f
+\li \ref h5a::h5awrite_f
-\li #h5d.h5dread_f
+\li \ref h5d::h5dread_f
-\li #h5d.h5dwrite_f
+\li \ref h5d::h5dwrite_f
 Subroutine with additional optional parameters in Fortran 2003 environments:
-\li #h5p.h5pcreate_class_f
+\li \ref h5p::h5pcreate_class_f
 <h4>New and updated Fortran 90 subroutines</h4>
 New Fortran 90 subroutines:
-\li #h5p.h5pset_nbit_f
+\li \ref h5p::h5pset_nbit_f
-\li #h5p.h5pset_scaleoffset_f
+\li \ref h5p::h5pset_scaleoffset_f
 Updated Fortran 90 subroutines:
-\li #h5lib.h5open_f
+\li \ref h5lib::h5open_f
-\li #h5lib.h5close_f - has been modified in this release to close only the HDF5 Fortran
+\li `h5close_f` - has been modified in this release to close only the HDF5 Fortran
    Library interface; it no longer closes the underlying HDF5 Library.
-\li #h5lib.h5check_version_f
+\li `h5check_version_f`
-\li #h5lib.h5get_libversion_f
+\li \ref h5lib::h5get_libversion_f
-\li #h5lib.h5garbage_collect_f
+\li \ref h5lib::h5garbage_collect_f
-\li #h5lib.h5dont_atexit_f
+\li \ref h5lib::h5dont_atexit_f
 <h4>New Fortran utility functions and derived types</h4>
 New Fortran utility functions:
-\li #h5lib.h5offsetof         Available only in Fortran 2003 environments.
+\li <code>h5offsetof</code>         Available only in Fortran 2003 environments.
-\li #h5lib.h5kind_to_type     Available in either Fortran environment.
+\li `h5kind_to_type`     Available in either Fortran environment.
 New Fortran derived types in Fortran 2003 environments:
 \li hvl_t              Described in New Features.
@@ -1016,15 +1016,15 @@ New Fortran derived types in Fortran 2003 environments:
 <h4>New high level Fortran interface</h4>
 New Fortran subroutines in the HDF5 Dimension Scale high-level interface, H5DS:
-\li #h5ds.h5dsset_scale_f
+\li `h5dsset_scale_f`
-\li #h5ds.h5dsattach_scale_f
+\li `h5dsattach_scale_f`
-\li #h5ds.h5dsdetach_scale_f
+\li `h5dsdetach_scale_f`
-\li #h5ds.h5dsis_attached_f
+\li `h5dsis_attached_f`
-\li #h5ds.h5dsis_scale_f
+\li `h5dsis_scale_f`
-\li #h5ds.h5dsset_label_f
+\li `h5dsset_label_f`
-\li #h5ds.h5dsget_label_f
+\li `h5dsget_label_f`
-\li #h5ds.h5dsget_scale_name_f
+\li `h5dsget_scale_name_f`
-\li #h5ds.h5dsget_num_scales_f
+\li `h5dsget_num_scales_f`
 These subtroutines are available in both Fortran 90 and Fortran 2003 environments.
@@ -1123,15 +1123,15 @@ Two new flags have been added:
 Several <code>h5ltmake_dataset\*\_f</code> and <code>h5ltread_dataset\*\_f</code> subroutines have
 been modified to allow them to create or read arrays of up to seven dimensions. They had previously
 been limited to three dimensions.
-\li #h5lt.h5ltmake_dataset_f
+\li `h5ltmake_dataset_f`
 \li .h5ltmake_dataset_int_f
 \li .h5ltmake_dataset_float_f
 \li h5ltmake_dataset_double_f
-\li #h5lt.h5ltread_dataset_f
+\li `h5ltread_dataset_f`
 \li h5ltread_dataset_int_f
 \li h5ltread_dataset_float_f
 \li h5ltread_dataset_double_f
-\li #h5tb.h5tbget_field_info_f has a new maxlen_out parameter. This parameter is optional.
+\li `h5tbget_field_info_f` has a new maxlen_out parameter. This parameter is optional.
 <h4>Command-line Utilities with New Options</h4>
 \ref sec_cltools_h5diff has a new verbose with levels option to display additional attribute information:
@@ -1281,8 +1281,8 @@ The overloaded forms of the following C++ member functions are new in this relea
 <h4>Fortran Subroutines with Changed Interface</h4>
 The link type parameter values associated with the following Fortran subroutines have changed in this release:
-\li #h5l.h5lget_info_f
+\li \ref h5l::h5lget_info_f
-\li #h5l.h5lget_info_by_idx_f
+\li \ref h5l::h5lget_info_by_idx_f
 Valid values for the parameter link_type have changed to the following:
 \li     H5L_TYPE_HARD_F
@@ -1334,9 +1334,9 @@ The function has also been changed to suppress the warning message entirely if
 <h4>Fortran Subroutines with Changed Syntax</h4>
 The following Fortran subroutines have changed syntax in this release:
-\li #h5l.h5lget_info_f - The type of the parameter address has changed from INTEGER to INTEGER(HADDR_T).
+\li \ref h5l::h5lget_info_f - The type of the parameter address has changed from INTEGER to INTEGER(HADDR_T).
    (This note added on 13 January 2010.)
-\li #h5l.h5lget_info_by_idx_f - <code>h5lget_info_by_idx_f (loc_id, group_name, index_field, order, n,
+\li \ref h5l::h5lget_info_by_idx_f - <code>h5lget_info_by_idx_f (loc_id, group_name, index_field, order, n,
    &link_type, f_corder_valid, corder, cset, address, val_size, &hdferr, lapl_id)</code> - The
    parameters link_type, address, and val_size have been added; the parameter data_size has been removed.
@@ -1378,10 +1378,10 @@ The following C functions are new for this release and are documented in the HDF
 <h4>Fortran Subroutines</h4>
 The following subroutines are new in this release:
-\li #h5d.h5dget_access_plist_f
+\li \ref h5d::h5dget_access_plist_f
-\li #h5i.h5iis_valid_f
+\li \ref h5i::h5iis_valid_f
-\li #h5p.h5pset_chunk_cache_f
+\li \ref h5p::h5pset_chunk_cache_f
-\li #h5p.h5pget_chunk_cache_f
+\li \ref h5p::h5pget_chunk_cache_f
 <h4>Function with Changed Behavior</h4>
 \li H5set_free_list_limits
@@ -1422,7 +1422,7 @@ The following C functions are new for this release and are documented in the \re
 <h4>Fortran Subroutine</h4>
 The following subroutine is new in this release:
-\li #h5t.h5tget_native_type_f
+\li \ref h5t::h5tget_native_type_f
 <h4>New C++ Wrappers</h4>
 A number of C++ wrappers were added/removed.  See RELEASE.txt for details.
@@ -1436,9 +1436,9 @@ The following function syntaxes have changed; the affected return values and par
 <h4>Changed Fortran Subroutines</h4>
 The optional parameter mounted has been added to the following subroutines:
-\li #h5g.h5gget_info_f
+\li \ref h5g::h5gget_info_f
-\li #h5g.h5gget_info_by_idx_f
+\li \ref h5g::h5gget_info_by_idx_f
-\li #h5g.h5gget_info_by_name_f
+\li \ref h5g::h5gget_info_by_name_f
 <strong>Changed Data Structure</strong>
 \li H5G_info_t - A mounted filed has been added to the H5G_info_t struct.
@@ -1519,108 +1519,108 @@ There are no new C functions for Release 1.8.1.
 <h4>Fortran subroutines</h4>
 The following Fortran subroutines are new for Release 1.8.1 and are documented in the HDF5 Reference Manual.
 \b H5A
-\li #h5a.h5acreate_f
+\li \ref h5a::h5acreate_f
-\li #h5a.h5acreate_by_name_f
+\li \ref h5a::h5acreate_by_name_f
-\li #h5a.h5adelete_by_idx_f
+\li \ref h5a::h5adelete_by_idx_f
-\li #h5a.h5adelete_by_name_f
+\li \ref h5a::h5adelete_by_name_f
-\li #h5a.h5aexists_f
+\li \ref h5a::h5aexists_f
-\li #h5a.h5aexists_by_name_f
+\li \ref h5a::h5aexists_by_name_f
-\li #h5a.h5aget_create_plist_f
+\li \ref h5a::h5aget_create_plist_f
-\li #h5a.h5aget_info_f
+\li \ref h5a::h5aget_info_f
-\li #h5a.h5aget_info_by_idx_f
+\li \ref h5a::h5aget_info_by_idx_f
-\li #h5a.h5aget_info_by_name_f
+\li \ref h5a::h5aget_info_by_name_f
-\li #h5a.h5aget_name_by_idx_f
+\li \ref h5a::h5aget_name_by_idx_f
-\li #h5a.h5aget_storage_size_f
+\li \ref h5a::h5aget_storage_size_f
-\li #h5a.h5aopen_f
+\li \ref h5a::h5aopen_f
-\li #h5a.h5aopen_by_idx_f
+\li \ref h5a::h5aopen_by_idx_f
-\li #h5a.h5aopen_by_name_f
+\li \ref h5a::h5aopen_by_name_f
-\li #h5a.h5arename_f
+\li \ref h5a::h5arename_f
-\li #h5a.h5arename_by_name_f
+\li \ref h5a::h5arename_by_name_f
 \b H5D
-\li #h5d.h5dcreate_anon_f
+\li \ref h5d::h5dcreate_anon_f
-\li #h5d.h5dcreate_f
+\li \ref h5d::h5dcreate_f
-\li #h5d.h5dopen_f
+\li \ref h5d::h5dopen_f
-\li #h5d.h5dset_extent_f
+\li `h5dset_extent_f`
 \b H5G
-\li #h5g.h5gcreate_anon_f
+\li \ref h5g::h5gcreate_anon_f
-\li #h5g.h5gcreate_f
+\li \ref h5g::h5gcreate_f
-\li #h5g.h5gget_create_plist_f
+\li \ref h5g::h5gget_create_plist_f
-\li #h5g.h5gget_info_f
+\li \ref h5g::h5gget_info_f
-\li #h5g.h5gget_info_by_idx_f
+\li \ref h5g::h5gget_info_by_idx_f
-\li #h5g.h5gget_info_by_name_f
+\li \ref h5g::h5gget_info_by_name_f
-\li #h5g.h5gopen_f
+\li \ref h5g::h5gopen_f
 \b H5L
-\li #h5l.h5lcopy_f
+\li \ref h5l::h5lcopy_f
-\li #h5l.h5lcreate_external_f
+\li \ref h5l::h5lcreate_external_f
-\li #h5l.h5lcreate_hard_f
+\li \ref h5l::h5lcreate_hard_f
-\li #h5l.h5lcreate_soft_f
+\li \ref h5l::h5lcreate_soft_f
-\li #h5l.h5ldelete_f
+\li \ref h5l::h5ldelete_f
-\li #h5l.h5ldelete_by_idx_f
+\li \ref h5l::h5ldelete_by_idx_f
-\li #h5l.h5lexists_f
+\li \ref h5l::h5lexists_f
-\li #h5l.h5lget_info_f
+\li \ref h5l::h5lget_info_f
-\li #h5l.h5lget_info_by_idx_f
+\li \ref h5l::h5lget_info_by_idx_f
-\li #h5l.h5lget_name_by_idx_f
+\li \ref h5l::h5lget_name_by_idx_f
-\li #h5l.h5lmove_f
+\li \ref h5l::h5lmove_f
 \b H5O
-\li #h5o.h5olink_f
+\li \ref h5o::h5olink_f
-\li #h5o.h5oopen_f
+\li \ref h5o::h5oopen_f
 \b H5P
-\li #h5p.h5pget_attr_creation_order_f
+\li \ref h5p::h5pget_attr_creation_order_f
-\li #h5p.h5pget_attr_phase_change_f
+\li \ref h5p::h5pget_attr_phase_change_f
-\li #h5p.h5pget_char_encoding_f
+\li \ref h5p::h5pget_char_encoding_f
-\li #h5p.h5pget_copy_object_f
+\li \ref h5p::h5pget_copy_object_f
-\li #h5p.h5pget_create_inter_group_f
+\li \ref h5p::h5pget_create_inter_group_f
-\li #h5p.h5pget_data_transform_f
+\li \ref h5p::h5pget_data_transform_f
 \li h5pget_elink_prefix_f
-\li #h5p.h5pget_est_link_info_f
+\li \ref h5p::h5pget_est_link_info_f
-\li #h5p.h5pget_fapl_direct_f
+\li \ref h5p::h5pget_fapl_direct_f
-\li #h5p.h5pget_link_creation_order_f
+\li \ref h5p::h5pget_link_creation_order_f
-\li #h5p.h5pget_link_phase_change_f
+\li \ref h5p::h5pget_link_phase_change_f
-\li #h5p.h5pget_local_heap_size_hint_f
+\li \ref h5p::h5pget_local_heap_size_hint_f
-\li #h5p.h5pget_nlinks_f
+\li \ref h5p::h5pget_nlinks_f
-\li #h5p.h5pget_obj_track_times_f
+\li \ref h5p::h5pget_obj_track_times_f
 \li h5pget_shared_mesg_index_f
 \li h5pget_shared_mesg_nindexes_f
-\li #h5p.h5pset_attr_creation_order_f
+\li \ref h5p::h5pset_attr_creation_order_f
-\li #h5p.h5pset_attr_phase_change_f
+\li \ref h5p::h5pset_attr_phase_change_f
-\li #h5p.h5pset_char_encoding_f
+\li \ref h5p::h5pset_char_encoding_f
-\li #h5p.h5pset_copy_object_f
+\li \ref h5p::h5pset_copy_object_f
-\li #h5p.h5pset_create_inter_group_f
+\li \ref h5p::h5pset_create_inter_group_f
-\li #h5p.h5pset_data_transform_f
+\li \ref h5p::h5pset_data_transform_f
 \li h5pset_elink_prefix_f
-\li #h5p.h5pset_est_link_info_f
+\li \ref h5p::h5pset_est_link_info_f
-\li #h5p.h5pset_fapl_direct_f
+\li \ref h5p::h5pset_fapl_direct_f
-\li #h5p.h5pset_libver_bounds_f
+\li \ref h5p::h5pset_libver_bounds_f
-\li #h5p.h5pset_link_creation_order_f
+\li \ref h5p::h5pset_link_creation_order_f
-\li #h5p.h5pset_link_phase_change_f
+\li \ref h5p::h5pset_link_phase_change_f
-\li #h5p.h5pset_local_heap_size_hint_f
+\li \ref h5p::h5pset_local_heap_size_hint_f
-\li #h5p.h5pset_obj_track_times_f
+\li \ref h5p::h5pset_obj_track_times_f
-\li #h5p.h5pset_nbit_f
+\li \ref h5p::h5pset_nbit_f
-\li #h5p.h5pset_nlinks_f
+\li \ref h5p::h5pset_nlinks_f
-\li #h5p.h5pset_scaleoffset_f
+\li \ref h5p::h5pset_scaleoffset_f
 \b H5R
-\li #h5r.h5rget_name_f
+\li \ref h5r::h5rget_name_f
 \b H5S
-\li #h5s.h5sdecode_f
+\li \ref h5s::h5sdecode_f
-\li #h5s.h5sencode_f
+\li \ref h5s::h5sencode_f
-\li #h5s.h5sextent_equal_f
+\li \ref h5s::h5sextent_equal_f
 \b H5T
-\li #h5t.h5tcommit_anon_f
+\li \ref h5t::h5tcommit_anon_f
-\li #h5t.h5tcommit_f
+\li \ref h5t::h5tcommit_f
-\li #h5t.h5tcommitted_f
+\li \ref h5t::h5tcommitted_f
-\li #h5t.h5tcompiler_conv_f
+\li \ref h5t::h5tcompiler_conv_f
-\li #h5t.h5tdecode_f
+\li \ref h5t::h5tdecode_f
-\li #h5t.h5tencode_f
+\li \ref h5t::h5tencode_f
-\li #h5t.h5tget_create_plist_f
+\li \ref h5t::h5tget_create_plist_f
-\li #h5t.h5topen_f
+\li \ref h5t::h5topen_f
 <h4>C++ wrappers</h4>
 There are no new C++ wrappers for Release 1.8.1.
@@ -2131,13 +2131,13 @@ Symbols and preset values associated with the following functions, subroutines o
        <li>#H5Z_FILTER_SCALEOFFSET</li></ul>
 Fortran90 subroutines:
-\li     #h5p.h5pget_filter_f
+\li     \ref h5p::h5pget_filter_f
-\li     #h5p.h5pget_filter_by_id_f
+\li     \ref h5p::h5pget_filter_by_id_f
-\li     #h5p.h5pmodify_filter_f
+\li     \ref h5p::h5pmodify_filter_f
-\li     #h5p.h5premove_filter_f
+\li     \ref h5p::h5premove_filter_f
-\li     #h5p.h5pset_filter_f
+\li     \ref h5p::h5pset_filter_f
-\li     #h5z.h5zfilter_avail_f
+\li     \ref h5z::h5zfilter_avail_f
-\li     #h5z.h5zget_filter_info_f - Two new filter identifiers are available for the filter or filter_id parameters:<ul>
+\li     \ref h5z::h5zget_filter_info_f - Two new filter identifiers are available for the filter or filter_id parameters:<ul>
        <li>H5Z_FILTER_NBIT_F</li>
        <li>H5Z_FILTER_SCALEOFFSET_F</li></ul>
@@ -168,19 +168,19 @@ The following C++ wrapper was added:
 <h4>In the Fortran API</h4>
 The following Fortran wrappers were added or changed:
-\li #h5f.h5fget_dset_no_attrs_hint_f - Wrappers for the dataset object header minimization calls. See #H5Fget_dset_no_attrs_hint.
+\li `h5fget_dset_no_attrs_hint_f` - Wrappers for the dataset object header minimization calls. See #H5Fget_dset_no_attrs_hint.
-\li #h5f.h5fset_dset_no_attrs_hint_f - Wrappers for the dataset object header minimization calls. See #H5Fset_dset_no_attrs_hint.
+\li `h5fset_dset_no_attrs_hint_f` - Wrappers for the dataset object header minimization calls. See #H5Fset_dset_no_attrs_hint.
-\li #h5p.h5pget_dset_no_attrs_hint_f - Wrappers for the dataset object header minimization calls. See #H5Pget_dset_no_attrs_hint.
+\li `h5pget_dset_no_attrs_hint_f` - Wrappers for the dataset object header minimization calls. See #H5Pget_dset_no_attrs_hint.
-\li #h5p.h5pset_dset_no_attrs_hint_f - Wrappers for the dataset object header minimization calls. See #H5Pset_dset_no_attrs_hint.
+\li `h5pset_dset_no_attrs_hint_f` - Wrappers for the dataset object header minimization calls. See #H5Pset_dset_no_attrs_hint.
-\li #h5o.h5ovisit_f - Added new Fortran 'fields' optional parameter. See #H5Ovisit2.
+\li \ref h5o::h5ovisit_f - Added new Fortran 'fields' optional parameter. See #H5Ovisit2.
-\li #h5o.h5oget_info_by_name_f - Added new Fortran 'fields' optional parameter. See #H5Oget_info_by_name2.
+\li \ref h5o::h5oget_info_by_name_f - Added new Fortran 'fields' optional parameter. See #H5Oget_info_by_name2.
-\li #h5o.h5oget_info_f - Added new Fortran 'fields' optional parameter. See #H5Oget_info2.
+\li \ref h5o::h5oget_info_f - Added new Fortran 'fields' optional parameter. See #H5Oget_info2.
-\li #h5o.h5oget_info_by_idx_f - Added new Fortran 'fields' optional parameter. See #H5Oget_info_by_idx2.
+\li \ref h5o::h5oget_info_by_idx_f - Added new Fortran 'fields' optional parameter. See #H5Oget_info_by_idx2.
-\li #h5o.h5ovisit_by_name_f - Added new Fortran 'fields' optional parameter. See #H5Ovisit_by_name2.
+\li \ref h5o::h5ovisit_by_name_f - Added new Fortran 'fields' optional parameter. See #H5Ovisit_by_name2.
 The following Fortran utility function was added:
-\li #h5lib.h5gmtime - converts (C) <code>time_t</code> structure to Fortran DATE AND TIME storage format
+\li `h5gmtime` - converts (C) <code>time_t</code> structure to Fortran DATE AND TIME storage format
 A new Fortran derived type was added:
 \li c_h5o_info_t - This is interoperable with C's h5o_info_t. This is needed for callback functions which
@@ -442,13 +442,13 @@ page, we list each feature and its associated C functions and Fortran wrappers.
    raw data, but it does rewrite HDF5 metadata.
 <h4>Collective Metadata I/O:</h4>
-\li #H5Pset_coll_metadata_write and #h5p.h5pset_coll_metadata_write_f - Establishes I/O mode property setting,
+\li #H5Pset_coll_metadata_write and `h5pset_coll_metadata_write_f` - Establishes I/O mode property setting,
    collective or independent, for metadata writes.
-\li #H5Pget_coll_metadata_write and #h5p.h5pget_coll_metadata_write_f - Retrieves I/O mode property setting
+\li #H5Pget_coll_metadata_write and `h5pget_coll_metadata_write_f` - Retrieves I/O mode property setting
    for metadata writes.
-\li #H5Pset_all_coll_metadata_ops and #h5p.h5pset_all_coll_metadata_ops_f - Establishes I/O mode, collective
+\li #H5Pset_all_coll_metadata_ops and `h5pset_all_coll_metadata_ops_f` - Establishes I/O mode, collective
    or independent, for metadata read operations.
-\li #H5Pget_all_coll_metadata_ops and #h5p.h5pget_all_coll_metadata_ops_f - Retrieves I/O mode for metadata
+\li #H5Pget_all_coll_metadata_ops and `h5pget_all_coll_metadata_ops_f` - Retrieves I/O mode for metadata
    read operations.
 <h4>Fine-tuning the Metadata Cache:</h4>
@@ -486,34 +486,34 @@ when processing files employing the VDS feature:
    and handles the file and metadata appropriately.
 <h4>Virtual Dataset or VDS:</h4>
-\li #H5Pset_virtual and #h5p.h5pset_virtual_f - Sets the mapping between virtual and source datasets.
+\li #H5Pset_virtual and `h5pset_virtual_f` - Sets the mapping between virtual and source datasets.
-\li #H5Pget_virtual_count and #h5p.h5pget_virtual_count_f - Retrieves the number of mappings for the
+\li #H5Pget_virtual_count and `h5pget_virtual_count_f` - Retrieves the number of mappings for the
    virtual dataset.
-\li #H5Pget_virtual_vspace and #h5p.h5pget_virtual_vspace_f - Retrieves a dataspace identifier for the
+\li #H5Pget_virtual_vspace and `h5pget_virtual_vspace_f` - Retrieves a dataspace identifier for the
    selection within the virtual dataset used in the mapping.
-\li #H5Pget_virtual_srcspace and #h5p.h5pget_virtual_srcspace_f - Retrieves a dataspace identifier
+\li #H5Pget_virtual_srcspace and `h5pget_virtual_srcspace_f` - Retrieves a dataspace identifier
    for the selection within the source dataset used in the mapping.
-\li #H5Pget_virtual_dsetname and #h5p.h5pget_virtual_dsetname_f - Retrieves the name of a source
+\li #H5Pget_virtual_dsetname and `h5pget_virtual_dsetname_f` - Retrieves the name of a source
    dataset used in the mapping.
-\li #H5Pget_virtual_filename and #h5p.h5pget_virtual_filename_f - Retrieves the filename of a source
+\li #H5Pget_virtual_filename and `h5pget_virtual_filename_f` - Retrieves the filename of a source
    dataset used in the mapping.
-\li #H5Pset_virtual_printf_gap and #h5p.h5pset_virtual_printf_gap_f - Sets maximum number of missing
+\li #H5Pset_virtual_printf_gap and `h5pset_virtual_printf_gap_f` - Sets maximum number of missing
    source files and/or datasets with printf-style names when getting the extent of an unlimited virtual dataset.
-\li #H5Pget_virtual_printf_gap and #h5p.h5pget_virtual_printf_gap_f - Returns maximum number of missing
+\li #H5Pget_virtual_printf_gap and `h5pget_virtual_printf_gap_f` - Returns maximum number of missing
    source files and/or datasets with printf-style names when getting the extent for an unlimited virtual dataset.
-\li #H5Pset_virtual_view and #h5p.h5pset_virtual_view_f - Sets the view of the virtual dataset to include
+\li #H5Pset_virtual_view and `h5pset_virtual_view_f` - Sets the view of the virtual dataset to include
    or exclude missing mapped elements.
-\li #H5Pget_virtual_view and #h5p.h5pget_virtual_view_f - Retrieves the view of a virtual dataset.
+\li #H5Pget_virtual_view and `h5pget_virtual_view_f` - Retrieves the view of a virtual dataset.
 <h4>Supporting Functions:</h4>
-\li #H5Sis_regular_hyperslab and #h5s.h5sis_regular_hyperslab_f - Determines whether a hyperslab selection is regular.
+\li #H5Sis_regular_hyperslab and `h5sis_regular_hyperslab_f` - Determines whether a hyperslab selection is regular.
-\li #H5Sget_regular_hyperslab and #h5s.h5sget_regular_hyperslab_f - Retrieves a regular hyperslab selection.
+\li #H5Sget_regular_hyperslab and `h5sget_regular_hyperslab_f` - Retrieves a regular hyperslab selection.
 <h4>Modified Functions:</h4>
 The following pre-exising functions have been modified to understand virtual datasets.
-\li #H5Pset_layout and #h5p.h5pset_layout_f - Specifies the layout to be used for a dataset.
+\li #H5Pset_layout and `h5pset_layout_f` - Specifies the layout to be used for a dataset.
    Virtual dataset, #H5D_VIRTUAL, has been added to the list of layouts available through this function.
-\li #H5Pget_layout and #h5p.h5pget_layout_f - Retrieves the layout in use for a dataset.
+\li #H5Pget_layout and `h5pget_layout_f` - Retrieves the layout in use for a dataset.
    Virtual dataset, #H5D_VIRTUAL, has been added to the list of layouts.
 <h4>Partial Edge Chunks:</h4>
@@ -176,26 +176,26 @@ list the specific new feature that they were added for.
 <strong>In the Fortran Interface (main library)</strong><br />
 Following are the new or changed APIs introduced in HDF5-1.12.0. Those introduced with a new feature
 list the specific new feature that they were added for.
-\li #h5f.h5fget_fileno_f - Retrieves a file's file number that uniquely identifies the open file
+\li \ref h5f::h5fget_fileno_f - Retrieves a file's file number that uniquely identifies the open file
-\li #h5f.h5fis_accessible_f - Determines if a file can be opened with a given fapl
+\li \ref h5f::h5fis_accessible_f - Determines if a file can be opened with a given fapl
-\li #h5l.h5lget_info_f - The function h5lget_info_f is mapped to #H5Lget_info2.
+\li <code>h5lget_info_f</code> - The function h5lget_info_f is mapped to #H5Lget_info2.
-\li #h5l.h5lget_info_by_idx_f - The function h5lget_info_by_idx_f is mapped to #H5Lget_info_by_idx2.
+\li <code>h5lget_info_by_idx_f</code> - The function h5lget_info_by_idx_f is mapped to #H5Lget_info_by_idx2.
-\li #h5l.h5literate_f - The function h5literate_f  is mapped to #H5Literate2.
+\li \ref h5l::h5literate_f - The function h5literate_f  is mapped to #H5Literate2.
-\li #h5l.h5literate_by_name_f - The function h5literate_by_name_f is mapped to #H5Literate_by_name2.
+\li \ref h5l::h5literate_by_name_f - The function h5literate_by_name_f is mapped to #H5Literate_by_name2.
-\li #h5o.h5oopen_by_token_f - Opens an object in an HDF5 file using its VOL independent token
+\li <code>h5oopen_by_token_f</code> - Opens an object in an HDF5 file using its VOL independent token
-\li #h5o.h5otoken_cmp_f - Compares two VOL connector object tokens
+\li <code>h5otoken_cmp_f</code> - Compares two VOL connector object tokens
-\li #h5p.h5pget_vol_id_f - Returns the identifier of the current VOL connector
+\li \ref h5p::h5pget_vol_id_f - Returns the identifier of the current VOL connector
-\li #h5p.h5pset_vol_f - Set the file VOL connector for a file access property list
+\li \ref h5p::h5pset_vol_f - Set the file VOL connector for a file access property list
-\li #h5vl.h5vlclose_f - Closes a VOL connector identifier
+\li \ref h5vl::h5vlclose_f - Closes a VOL connector identifier
-\li #h5vl.h5vlget_connector_id_f - Retrieves the VOL connector identifier for a given object identifier
+\li \ref h5vl::h5vlget_connector_id_f - Retrieves the VOL connector identifier for a given object identifier
-\li #h5vl.h5vlget_connector_id_by_name_f - Retrieves the identifier for a registered VOL connector name
+\li \ref h5vl::h5vlget_connector_id_by_name_f - Retrieves the identifier for a registered VOL connector name
-\li #h5vl.h5vlget_connector_id_by_value_f - Retrieves the identifier for a registered VOL connector value
+\li \ref h5vl::h5vlget_connector_id_by_value_f - Retrieves the identifier for a registered VOL connector value
-\li #h5vl.h5vlget_connector_name_f - Retrieves the connector name for the VOL associated with the object or file identifier
+\li \ref h5vl::h5vlget_connector_name_f - Retrieves the connector name for the VOL associated with the object or file identifier
-\li #h5vl.h5vlis_connector_registered_by_name_f - Tests whether a VOL class has been registered or not for a connector name
+\li \ref h5vl::h5vlis_connector_registered_by_name_f - Tests whether a VOL class has been registered or not for a connector name
-\li #h5vl.h5vlis_connector_registered_by_value_f - Tests whether a VOL class has been registered or not for a connector value
+\li \ref h5vl::h5vlis_connector_registered_by_value_f - Tests whether a VOL class has been registered or not for a connector value
-\li #h5vl.h5vlregister_connector_by_name_f - Registers a new VOL connector by name
+\li \ref h5vl::h5vlregister_connector_by_name_f - Registers a new VOL connector by name
-\li #h5vl.h5vlregister_connector_by_value_f - Registers a new VOL connector by connector value
+\li \ref h5vl::h5vlregister_connector_by_value_f - Registers a new VOL connector by connector value
-\li #h5vl.h5vlunregister_connector_f - Removes a VOL connector identifier from the library
+\li \ref h5vl::h5vlunregister_connector_f - Removes a VOL connector identifier from the library
 <h4>In the C++ Wrapper</h4>
 \li <code>H5File::getFileNum</code> - See #H5Fget_fileno
@@ -94,20 +94,20 @@ Following are the new APIs introduced in HDF5-1.14.3.
 \li #H5Pget_actual_selection_io_mode - Retrieves the type(s) of I/O performed on raw data
 <h4>In the Fortran Interface</h4>
-\li #h5lib.h5get_free_list_sizes_f - Gets the current size of the free lists used to manage memory
+\li `h5get_free_list_sizes_f` - Gets the current size of the free lists used to manage memory
-\li #h5d.h5dwrite_chunk_f - Writes a raw data chunk from a buffer directly to a dataset in a file
+\li \ref h5d::h5dwrite_chunk_f - Writes a raw data chunk from a buffer directly to a dataset in a file
-\li #h5d.h5dread_chunk_f - Reads a raw data chunk directly from a dataset in a file into a buffer
+\li \ref h5d::h5dread_chunk_f - Reads a raw data chunk directly from a dataset in a file into a buffer
-\li #h5f.h5fget_info_f - Retrieves global file information
+\li `h5fget_info_f` - Retrieves global file information
-\li #h5l.h5lvisit_f - Recursively visits all links starting from a specified group
+\li \ref h5l::h5lvisit_f - Recursively visits all links starting from a specified group
-\li #h5l.h5lvisit_by_name_f - Recursively visits all links starting from a specified group
+\li `h5lvisit_by_name_f` - Recursively visits all links starting from a specified group
-\li #h5p.h5pget_no_selection_io_cause_f - Retrieves the cause for not performing selection or vector I/O on the last parallel I/O call
+\li \ref h5p::h5pget_no_selection_io_cause_f - Retrieves the cause for not performing selection or vector I/O on the last parallel I/O call
-\li #h5p.h5pget_mpio_no_collective_cause_f - Retrieves local and global causes that broke collective I/O on the last parallel I/O call
+\li \ref h5p::h5pget_mpio_no_collective_cause_f - Retrieves local and global causes that broke collective I/O on the last parallel I/O call
-\li #h5s.h5sselect_shape_same_f - Checks if two selections are the same shape
+\li `h5sselect_shape_same_f` - Checks if two selections are the same shape
-\li #h5s.h5sselect_intersect_block_f - Checks if current selection intersects with a block
+\li `h5sselect_intersect_block_f` - Checks if current selection intersects with a block
-\li #h5p.h5pget_file_space_page_size_f - Gets the file space page size for a file creation property list
+\li \ref h5p::h5pget_file_space_page_size_f - Gets the file space page size for a file creation property list
-\li #h5p.h5pset_file_space_page_size_f - Sets the file space page size for a file creation property list
+\li \ref h5p::h5pset_file_space_page_size_f - Sets the file space page size for a file creation property list
-\li #h5p.h5pget_file_space_strategy_f - Gets the file space handling strategy and persisting free-space values for a file creation property list
+\li \ref h5p::h5pget_file_space_strategy_f - Gets the file space handling strategy and persisting free-space values for a file creation property list
-\li #h5p.h5pset_file_space_strategy_f - Sets the file space handling strategy and persisting free-space values for a file creation property list
+\li `h5pset_file_space_strategy_f` - Sets the file space handling strategy and persisting free-space values for a file creation property list
 In addition, there are other new Fortran functions including the Fortran async APIs
 and the Fortran VOL capability definitions.
@@ -148,10 +148,10 @@ Following are the new APIs introduced in HDF5-1.14.1.
 \li #H5Pset_selection_io - Sets the selection I/O mode
 <h4>In the Fortran Interface</h4>
-\li #h5p.h5pget_modify_write_buf_f - Retrieves the "modify write buffer" property
+\li \ref h5p::h5pget_modify_write_buf_f - Retrieves the "modify write buffer" property
-\li #h5p.h5pget_selection_io_f - Retrieves the selection I/O mode
+\li \ref h5p::h5pget_selection_io_f - Retrieves the selection I/O mode
-\li #h5p.h5pset_modify_write_buf_f - Allows the library to modify the contents of the write buffer
+\li \ref h5p::h5pset_modify_write_buf_f - Allows the library to modify the contents of the write buffer
-\li #h5p.h5pset_selection_io_f - Sets the selection I/O mode
+\li \ref h5p::h5pset_selection_io_f - Sets the selection I/O mode
 \subsection subsec_rel_spec_114_change_0versus12_2 Release 1.14.0 versus Release 1.12.2
@@ -151,7 +151,9 @@ CONTAINS
 SUBROUTINE h5fdsubfiling_get_file_mapping_f(file_id, filenames, num_files, hdferr)
  IMPLICIT NONE
  INTEGER(HID_T), INTENT(IN) :: file_id
-#ifdef H5_FORTRAN_HAVE_CHAR_ALLOC
+#ifdef H5_DOXYGEN
  CHARACTER(LEN=:), ALLOCATABLE, DIMENSION(:), INTENT(OUT) :: filenames
 #elif defined(H5_FORTRAN_HAVE_CHAR_ALLOC)
  CHARACTER(LEN=:), ALLOCATABLE, DIMENSION(:), INTENT(OUT) :: filenames
 #else
  INTEGER, PARAMETER :: DEFAULT_MAX_LEN = 8192
@@ -160,6 +162,7 @@ SUBROUTINE h5fdsubfiling_get_file_mapping_f(file_id, filenames, num_files, hdfer
  INTEGER(SIZE_T), INTENT(OUT) :: num_files
  INTEGER, INTENT(OUT) :: hdferr
 #ifndef H5_DOXYGEN
  TYPE(C_PTR) :: filenames_ptr
  INTEGER(C_SIZE_T) :: c_num_files
  INTEGER(C_INT) :: ret_val
@@ -275,6 +278,7 @@ SUBROUTINE h5fdsubfiling_get_file_mapping_f(file_id, filenames, num_files, hdfer
  ! Free the C memory allocated by H5FDsubfiling_get_file_mapping
  ret_val = h5free_string_array_memory_c(filenames_ptr, c_num_files)
  ! Note: We ignore the return value of the free function since the main operation succeeded
 #endif
 END SUBROUTINE h5fdsubfiling_get_file_mapping_f
@@ -133,7 +133,7 @@ import org.slf4j.LoggerFactory;
 * </tr>
 * <tr>
 * <td>void * <br />
- * (i.e., pointer to `Any')</td>
+ * (i.e., pointer to Any)</td>
 * <td>Special -- see @ref HDFARRAY</td>
 * </tr>
 * </table>
@@ -194,11 +194,11 @@ import org.slf4j.LoggerFactory;
 * @endcode
 *
 * <p>
- * where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of bytes that
+ * where "void *" means that the data may be any valid numeric type, and is a contiguous block of bytes that
 * is the data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype
 * of the array ondisk (source) and in memory (destination).
 * <p>
- * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore,
+ * For Java, this "ANY" is a problem, as the type of data must always be declared. Furthermore,
 * multidimensional arrays are definitely <i>not</i> laid out contiguously in memory. It would be infeasible
 * to declare a separate routine for every combination of number type and dimensionality. For that reason, the
 * @ref HDFARRAY <b>HDFArray</b> class is used to discover the type, shape, and
@@ -206,7 +206,7 @@ import org.slf4j.LoggerFactory;
 * static  C order.
 * <p>
 * The upshot is that any Java array of numbers (either primitive or sub-classes of type <b>Number</b>) can be
- * passed as an ``Object'', and the Java API will translate to and from the appropriate packed array of bytes
+ * passed as an "Object", and the Java API will translate to and from the appropriate packed array of bytes
 * needed by the C library. So the function above would be declared:
 *
 * @code
@@ -108,7 +108,7 @@ import org.slf4j.LoggerFactory;
 * </tr>
 * <tr>
 * <td>void * <br />
- * (i.e., pointer to `Any')</td>
+ * (i.e., pointer to `Any`)</td>
 * <td>Special -- see @ref HDFARRAY</td>
 * </tr>
 * </table>
@@ -181,7 +181,7 @@ import org.slf4j.LoggerFactory;
 * static native C order.
 * <p>
 * The upshot is that any Java array of numbers (either primitive or sub-classes of type <b>Number</b>) can be
- * passed as an ``Object'', and the Java API will translate to and from the appropriate packed array of bytes
+ * passed as an `Object`, and the Java API will translate to and from the appropriate packed array of bytes
 * needed by the C library. So the function above would be declared:
 *
 * @code
@@ -544,7 +544,7 @@ H5_DLL herr_t H5Gclose_async(hid_t group_id, hid_t es_id);
 * An object has a certain type. The first few numbers are reserved for use
 * internally by HDF5. Users may add their own types with higher values.  The
 * values are never stored in the file -- they only exist while an application
- * is running.  An object may satisfy the `isa' function for more than one type.
+ * is running.  An object may satisfy the `isa` function for more than one type.
 *
 * \deprecated
 */
@@ -639,7 +639,7 @@ H5_DLL ssize_t H5Rget_attr_name(const H5R_ref_t *ref_ptr, char *name, size_t siz
 * \param[in] ref Reference to query
 *
 * \return Returns a valid object type if successful; otherwise returns a
- *         negative value (#H5G_UNKNOWN).
+ *         negative value (\c H5G_UNKNOWN).
 *
 * \deprecated This function has been renamed from H5Rget_obj_type() and is
 *             deprecated in favor of the macro H5Rget_obj_type() or the
@@ -39,7 +39,7 @@ typedef enum H5T_cmd_t {
 } H5T_cmd_t;
 /**
- * How is the `bkg' buffer used by the conversion function?
+ * How is the `bkg` buffer used by the conversion function?
 */
 typedef enum H5T_bkg_t {
    H5T_BKG_NO   = 0, /**< background buffer is not needed, send NULL */
@@ -2011,7 +2011,7 @@ filled according to the value of this property. The padding can be:
 * calculates the offset of member \Emph{m} within struct \Emph{s}. Alternatively, the
 * `offsetof(s, m)` macro, defined in \Emph{stddef.h}, serves the same purpose as the
 * `HOFFSET` macro. For Fortran users, the HDF5 library provides the function
- * \ref h5lib.h5offsetof to determine the offset of a member. To find the size of a
+ * \ref h5lib::h5offsetof to determine the offset of a member. To find the size of a
 * scalar derived type, the Fortran function equivalent of the \Emph{sizeof} can be used.
 * Note, in the past, the HDF5 Fortran applications had to calculate offsets by using sizes of
 * members datatypes and by considering the order of members in the Fortran derived type, thus
@@ -555,19 +555,19 @@
 * so the h5o_info_t, etc. structs no longer contain native file format information
 * and the callbacks will need to match the non-deprecated, token-enabled versions.
 * <ul>
- * <li>@ref h5l.h5lget_info_f</li>
+ * <li>\ref h5l::h5lget_info_f</li>
- * <li>@ref h5l.h5lget_info_by_idx_f</li>
+ * <li>\ref h5l::h5lget_info_by_idx_f</li>
- * <li>@ref h5l.h5literate_f</li>
+ * <li>\ref h5l::h5literate_f</li>
- * <li>@ref h5l.h5literate_by_name_f</li>
+ * <li>\ref h5l::h5literate_by_name_f</li>
- * <li>@ref h5o.h5oget_info_f</li>
+ * <li>\ref h5o::h5oget_info_f</li>
- * <li>@ref h5o.h5oget_info_by_idx_f</li>
+ * <li>\ref h5o::h5oget_info_by_idx_f</li>
- * <li>@ref h5o.h5oget_info_by_name_f</li>
+ * <li>\ref h5o::h5oget_info_by_name_f</li>
- * <li>@ref h5o.h5oopen_by_token_f</li>
+ * <li>\ref h5o::h5oopen_by_token_f</li>
- * <li>@ref h5o.h5ovisit_f</li>
+ * <li>\ref h5o::h5ovisit_f</li>
- * <li>@ref h5o.h5ovisit_by_name_f</li>
+ * <li>\ref h5o::h5ovisit_by_name_f</li>
 * </ul>
 *
- * Additionally, \ref h5f.h5fis_hdf5_f was updated to use \ref H5Fis_accessible internally,
+ * Additionally, \ref h5f::h5fis_hdf5_f was updated to use \ref H5Fis_accessible internally,
 * though with the same caveat as the C++ implementation: the default fapl is
 * always passed in so arbitrary VOL connectors will only work if the default VOL
 * connector is changed via the environment variable.