Add cygwin CI and update yaml files for consistency and accuracy (#4131)

* Add cygwin CI

* add cygwin packages

* Correct option names

* Cleanup yaml file and synch look and feel

* Synch CI look and feel and correct path issues

* Upgrade oneapi version

* pwsh needs env: for vars

* No continuation char for pwsh

* restore correct pwsh step

* Run subset of tests for cygwin workflow

* Remove space chars in regex

* restore full tests

18 files changed, 399 insertions, 164 deletions

diff --git a/.github/workflows/aocc-ompi-auto.yml b/.github/workflows/aocc-auto.yml
index be67672..740005d 100644
--- a/.github/workflows/aocc-ompi-auto.yml
+++ b/.github/workflows/aocc-auto.yml
@@ -16,9 +16,10 @@ jobs:
     name: "aocc ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
 
-      - name: Install Linux dependencies
+      - name: Install Dependencies
         shell: bash
         run: |
           sudo apt update
@@ -28,6 +29,7 @@ jobs:
           sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential
 
       - name: Install AOCC 4.1.0
+        shell: bash
         run: |
           wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
           tar -xvf aocc-compiler-4.1.0.tar
@@ -74,7 +76,6 @@ jobs:
             LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib \
             -L/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib"
 
-      # BUILD
       - name: Autotools Build
         shell: bash
         env:
@@ -84,8 +85,6 @@ jobs:
           make -j3
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
-      # NORMAL
       - name: Autotools Run Tests
         env:
           NPROCS: 2
@@ -94,7 +93,6 @@ jobs:
           make check -j
         working-directory: ${{ runner.workspace }}/build
 
-      # INSTALL (note that this runs even when we don't run the tests)
       - name: Autotools Install
         env:
           NPROCS: 2
diff --git a/.github/workflows/aocc-ompi-cmake.yml b/.github/workflows/aocc-cmake.yml
index f2a834d..f1195dd 100644
--- a/.github/workflows/aocc-ompi-cmake.yml
+++ b/.github/workflows/aocc-cmake.yml
@@ -16,9 +16,10 @@ jobs:
     name: "aocc ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
 
-      - name: Install Linux dependencies
+      - name: Install Dependencies
         shell: bash
         run: |
           sudo apt update
@@ -28,6 +29,7 @@ jobs:
           sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential
 
       - name: Install AOCC 4.1.0
+        shell: bash
         run: |
           wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
           tar -xvf aocc-compiler-4.1.0.tar
@@ -56,7 +58,7 @@ jobs:
           make
           make install
 
-      - name: CMake Configure with aocc
+      - name: CMake Configure
         shell: bash
         run: |
           export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
@@ -77,14 +79,12 @@ jobs:
           $GITHUB_WORKSPACE
           #cat src/libhdf5.settings
 
-      # BUILD
       - name: CMake Build
         shell: bash
         run: |
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
       - name: CMake Run Tests
         shell: bash
         run: |
diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
index b31dbf9..b75e75d 100644
--- a/.github/workflows/autotools.yml
+++ b/.github/workflows/autotools.yml
@@ -73,6 +73,14 @@ jobs:
 
     call-release-auto-aocc:
       name: "Autotools aocc Workflows"
-      uses: ./.github/workflows/aocc-ompi-auto.yml
+      uses: ./.github/workflows/aocc-auto.yml
       with:
             build_mode: "production"
+
+    call-release-auto-cygwin:
+      name: "Autotools Cygwin Workflows"
+      uses: ./.github/workflows/cygwin-auto.yml
+      with:
+            build_mode: "production"
+
+            
\ No newline at end of file
diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index b7f8a2b..c0077ce 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -75,7 +75,14 @@ jobs:
             build_mode: "Release"
 
     call-release-cmake-aocc:
-        name: "CMake nvhpc Workflows"
-        uses: ./.github/workflows/aocc-ompi-cmake.yml
+        name: "CMake aocc Workflows"
+        uses: ./.github/workflows/aocc-cmake.yml
+        with:
+            build_mode: "Release"
+
+    call-release-cmake-cygwin:
+        name: "CMake Cygwin Workflows"
+        uses: ./.github/workflows/cygwin-cmake.yml
         with:
             build_mode: "Release"
+            
\ No newline at end of file
diff --git a/.github/workflows/cygwin-auto.yml b/.github/workflows/cygwin-auto.yml
new file mode 100644
index 0000000..13e08eb
--- /dev/null
+++ b/.github/workflows/cygwin-auto.yml
@@ -0,0 +1,62 @@
+name: hdf5 dev autotools cygwin
+
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  cygwin_build_and_test:
+    name: "cygwin ${{ inputs.build_mode }}"
+    runs-on: windows-latest
+    steps:
+      - name: Set git to use LF
+        run: |
+          git config --global core.autocrlf input
+
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
+
+      - name: Install Cygwin
+        uses: cygwin/cygwin-install-action@master
+        with:
+          packages: autoconf automake make gcc-fortran libtool zlib-devel m4 flex bison perl
+
+      - name: Autotools Configure
+        shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+        run: |
+          export PATH=/usr/bin:$PATH
+          sh ./autogen.sh
+          mkdir build
+          cd build
+          ../configure \
+            --enable-build-mode=${{ inputs.build_mode }} \
+            --enable-shared \
+            --enable-fortran
+
+      - name: Autotools Build
+        shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+        run: |
+          export PATH=/usr/bin:$PATH
+          cd build
+          make -j3
+
+      - name: Autotools Run Tests
+        shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+        run: |
+          export PATH=/usr/bin:$PATH
+          cd build
+#          make check -j ---- cache test fails
+
+      - name: Autotools Install
+        shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+        run: |
+          export PATH=/usr/bin:$PATH
+          cd build
+          make install
diff --git a/.github/workflows/cygwin-cmake.yml b/.github/workflows/cygwin-cmake.yml
new file mode 100644
index 0000000..73fb538
--- /dev/null
+++ b/.github/workflows/cygwin-cmake.yml
@@ -0,0 +1,63 @@
+name: hdf5 dev CMake cygwin
+
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  cygwin_build_and_test:
+    name: "cygwin-${{ inputs.build_mode }}"
+    runs-on: windows-latest
+    steps:
+      - name: Set git to use LF
+        run: |
+          git config --global core.autocrlf input
+
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
+
+      - name: Install Cygwin
+        uses: cygwin/cygwin-install-action@master
+        with:
+          packages: cmake gcc-fortran make ninja zlib-devel flex bison perl
+
+      - name: CMake Configure
+        shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+        run: |
+          export PATH=/usr/bin:$PATH
+          mkdir build
+          cd build
+          cmake -C ../config/cmake/cacheinit.cmake \
+            -G Ninja \
+            --log-level=VERBOSE \
+            -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
+            -DBUILD_SHARED_LIBS:BOOL=OFF \
+            -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF \
+            -DHDF5_BUILD_CPP_LIB:BOOL=OFF \
+            -DLIBAEC_USE_LOCALCONTENT=OFF \
+            -DZLIB_USE_LOCALCONTENT=OFF \
+            -DHDF5_BUILD_FORTRAN:BOOL=ON \
+            -DHDF5_BUILD_JAVA:BOOL=OFF \
+            ..
+
+      - name: CMake Build
+        shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+        run: |
+          export PATH=/usr/bin:$PATH
+          cd build
+          cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
+
+      - name: CMake Run Tests
+        shell: C:\cygwin\bin\bash.exe -eo pipefail -o igncr '{0}'
+        run: |
+           export PATH=/usr/bin:$PATH
+           cd build
+           ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
+#           ctest . --parallel 2 -C ${{ inputs.build_mode }} -V -R "FORTRAN|H5TEST"
diff --git a/.github/workflows/intel-auto.yml b/.github/workflows/intel-auto.yml
index 7bd457c..8f767e7 100644
--- a/.github/workflows/intel-auto.yml
+++ b/.github/workflows/intel-auto.yml
@@ -1,4 +1,4 @@
-name: hdf5 dev autotools icx CI
+name: hdf5 dev autotools icx
 
 on:
   workflow_call:
@@ -12,49 +12,33 @@ permissions:
   contents: read
 
 jobs:
-  Intel_build_and_test:
-    name: "Intel ${{ inputs.build_mode }}"
+  intel_oneapi_linux:
+    name: "linux-oneapi ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
 
       - name: Install Dependencies
+        shell: bash
         run: |
           sudo apt-get update
           sudo apt-get install autoconf automake libtool libtool-bin libaec-dev
 
-      - name: Add oneAPI to apt
-        shell: bash
-        run: |
-          cd /tmp
-          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo add-apt-repository -y "deb https://apt.repos.intel.com/oneapi all main"
-      
-      - name: Install oneAPI dpcpp and fortran compiler
-        shell: bash
-        run: |
-          sudo apt update
-          sudo apt install -y intel-oneapi-compiler-dpcpp-cpp
-          sudo apt install -y intel-oneapi-compiler-fortran
-          sudo apt install -y intel-oneapi-mpi-devel
-          sudo apt-get install doxygen graphviz
-          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
-          echo "CC=icx" >> $GITHUB_ENV
-          echo "CXX=icpx" >> $GITHUB_ENV
-          echo "FC=ifx" >> $GITHUB_ENV
-
-      - name: Install oneAPI MKL library
-        shell: bash
-        run: |
-          sudo apt install -y intel-oneapi-mkl-devel
+      - name: Install oneAPI (Linux)
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: intel
+          version: '2024.0'
 
       - name: Autotools Configure
         shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
-          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
@@ -63,37 +47,42 @@ jobs:
             --enable-shared \
             --disable-fortran
 
-      # BUILD
       - name: Autotools Build
+        shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
-          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
           make -j3
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
-      # NORMAL
       - name: Autotools Run Tests
+        shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
-          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
-          export SYCL_DEVICE_FILTER=opencl.cpu
           make check -j2
         working-directory: ${{ runner.workspace }}/build
 
-      # INSTALL (note that this runs even when we don't run the tests)
       - name: Autotools Install
+        shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
-          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
-          export SYCL_DEVICE_FILTER=opencl.cpu
           make install
         working-directory: ${{ runner.workspace }}/build
 
       - name: Autotools Verify Install
+        shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
-          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
-          export SYCL_DEVICE_FILTER=opencl.cpu
           make check-install
         working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
index 47f16a5..a470486 100644
--- a/.github/workflows/intel-cmake.yml
+++ b/.github/workflows/intel-cmake.yml
@@ -1,6 +1,5 @@
-name: hdf5 dev CMake icx CI
+name: hdf5 dev CMake icx
 
-# Controls when the action will run. Triggers the workflow on a call
 on:
   workflow_call:
     inputs:
@@ -13,30 +12,28 @@ permissions:
   contents: read
 
 jobs:
-  # Linux (Ubuntu) w/ gcc + CMake
-  #
-  Intel_oneapi_linux:
-    name: "ubuntu-oneapi ${{ inputs.build_mode }}"
+  intel_oneapi_linux:
+    name: "linux-oneapi ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - name: Get Sources (Linux)
+        uses: actions/checkout@v4.1.1
 
-      # Only CMake need ninja-build, but we just install it unilaterally
-      # libssl, etc. are needed for the ros3 VFD
-      - name: Install Linux Dependencies
+      - name: Install Dependencies (Linux)
+        shell: bash
         run: |
            sudo apt update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
 
-      - name: add oneAPI to env
+      - name: Install oneAPI (Linux)
         uses: fortran-lang/setup-fortran@v1
         id: setup-fortran
         with:
           compiler: intel
-          version: '2023.2'
+          version: '2024.0'
 
-      - name: CMake Configure with oneapi
+      - name: CMake Configure (Linux)
         shell: bash
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
@@ -45,14 +42,15 @@ jobs:
         run: |
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          cmake -C ${{ github.workspace }}/config/cmake/cacheinit.cmake -G Ninja \
-          -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
-          -DLIBAEC_USE_LOCALCONTENT=OFF \
-          -DZLIB_USE_LOCALCONTENT=OFF \
-          $GITHUB_WORKSPACE
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            -G Ninja \
+            --log-level=VERBOSE \
+            -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
+            -DLIBAEC_USE_LOCALCONTENT=OFF \
+            -DZLIB_USE_LOCALCONTENT=OFF \
+            $GITHUB_WORKSPACE
 
-      # BUILD
-      - name: CMake Build
+      - name: CMake Build (Linux)
         shell: bash
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
@@ -62,8 +60,7 @@ jobs:
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
-      - name: CMake Run Tests
+      - name: CMake Run Tests (Linux)
         shell: bash
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
@@ -77,19 +74,20 @@ jobs:
     name: "windows-oneapi ${{ inputs.build_mode }}"
     runs-on: windows-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - name: Get Sources (Windows)
+        uses: actions/checkout@v4.1.1
 
       - name: Install Dependencies (Windows)
         run: choco install ninja
 
-      - name: add oneAPI to env
+      - name: install oneAPI (Windows)
         uses: fortran-lang/setup-fortran@v1
         id: setup-fortran
         with:
           compiler: intel
-          version: '2023.2'
+          version: '2024.0'
 
-      - name: CMake Configure with oneapi
+      - name: CMake Configure (Windows)
         shell: pwsh
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
@@ -100,8 +98,7 @@ jobs:
           Set-Location -Path "${{ runner.workspace }}\\build"
           cmake -C ${{ github.workspace }}/config/cmake/cacheinit.cmake -G Ninja -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} -DHDF5_BUILD_FORTRAN=ON -DLIBAEC_USE_LOCALCONTENT=OFF -DZLIB_USE_LOCALCONTENT=OFF ${{ github.workspace }}
 
-      # BUILD
-      - name: CMake Build
+      - name: CMake Build (Windows)
         shell: pwsh
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
@@ -111,8 +108,7 @@ jobs:
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
-      - name: CMake Run Tests
+      - name: CMake Run Tests (Windows)
         shell: pwsh
         env:
           FC: ${{ steps.setup-fortran.outputs.fc }}
diff --git a/.github/workflows/main-auto.yml b/.github/workflows/main-auto.yml
index 51ddfdb..cab026e 100644
--- a/.github/workflows/main-auto.yml
+++ b/.github/workflows/main-auto.yml
@@ -51,7 +51,6 @@ jobs:
       - name: Get Sources
         uses: actions/checkout@v4.1.1
 
-      # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
         run: |
           sh ./autogen.sh
@@ -92,13 +91,10 @@ jobs:
         shell: bash
         if: ${{ inputs.thread_safety == 'enable' }}
 
-      # BUILD
       - name: Autotools Build
         run: make -j3
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
-      # NORMAL
       - name: Autotools Run Tests
         run: make check -j2
         working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
index ec93d0d..2b02765 100644
--- a/.github/workflows/main-cmake.yml
+++ b/.github/workflows/main-cmake.yml
@@ -107,8 +107,6 @@ jobs:
             generator: "-G Ninja"
             run_tests: true
 
-
-
     # Sets the job's name from the properties
     name: "${{ matrix.name }}-${{ inputs.build_mode }}-${{ inputs.thread_safety }}"
 
@@ -120,18 +118,11 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-
-      #
-      # SETUP
-      #
-
       #Useful for debugging
       - name: Dump matrix context
         run: echo '${{ toJSON(matrix) }}'
 
-      # Only CMake need ninja-build, but we just install it unilaterally
-      # libssl, etc. are needed for the ros3 VFD
-      - name: Install Linux Dependencies
+      - name: Install CMake Dependencies (Linux)
         run: |
            sudo apt update
            sudo apt-get install ninja-build graphviz
@@ -171,13 +162,13 @@ jobs:
       #
       # CMAKE CONFIGURE
       #
-
       - name: CMake Configure
         run: |
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
           cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
             ${{ matrix.generator }} \
+            --log-level=VERBOSE \
             -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
             -DBUILD_SHARED_LIBS=ON \
             -DHDF5_ENABLE_ALL_WARNINGS=ON \
@@ -198,7 +189,6 @@ jobs:
         shell: bash
         if: ${{ inputs.thread_safety != 'TS' }}
 
-
       - name: CMake Configure (Thread-Safe)
         run: |
           mkdir "${{ runner.workspace }}/build"
@@ -229,7 +219,6 @@ jobs:
       #
       # BUILD
       #
-
       - name: CMake Build
         run: cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
         working-directory: ${{ runner.workspace }}/build
@@ -237,25 +226,17 @@ jobs:
       #
       # RUN TESTS
       #
-
-      # NORMAL
-
       - name: CMake Run Tests
         run: ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
         working-directory: ${{ runner.workspace }}/build
         if: ${{ matrix.run_tests && (inputs.thread_safety != 'TS') }}
 
       # THREAD-SAFE
-
       - name: CMake Run Thread-Safe Tests
         run: ctest . --parallel 2 -C ${{ inputs.build_mode }} -V -R ttsafe
         working-directory: ${{ runner.workspace }}/build
         if: ${{ matrix.run_tests && (inputs.thread_safety == 'TS') }}
 
-      #
-      # INSTALL (note that this runs even when we don't run the tests)
-      #
-
       - name: CMake Run Package
         run: cpack -C ${{ inputs.build_mode }} -V
         working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3f878b1..845fc68 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -37,3 +37,9 @@ jobs:
     uses: ./.github/workflows/cmake.yml
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
 
+#  workflow-msys2-autotools:
+#    name: "CMake msys2 Workflows"
+#    uses: ./.github/workflows/msys2-auto.yml
+#    with:
+#        build_mode: "production"
+#        build_option: "--enable-production"
diff --git a/.github/workflows/mingw-cmake.yml b/.github/workflows/mingw-cmake.yml
new file mode 100644
index 0000000..4761318
--- /dev/null
+++ b/.github/workflows/mingw-cmake.yml
@@ -0,0 +1,91 @@
+name: hdf5 dev CMake MinGW
+
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+      shared:
+        description: "shared true/false"
+        required: true
+        type: string
+      netcdf:
+        description: "netcdf true/false"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  mingw_build_and_test:
+    name: "mingw-${{ inputs.build_mode }}-NC=${{ inputs.netcdf }}"
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
+
+      - name: Install Dependencies
+        shell: bash
+        run: |
+           sudo apt update
+           sudo apt-get install -y ninja-build libtirpc-dev graphviz
+
+      - name: Install MinGW
+        uses: egor-tensin/setup-mingw@v2
+        with:
+          platform: x64
+
+      - name: Install Doxygen
+        uses: ssciwr/doxygen-install@v1
+        with:
+          version: "1.9.7"
+
+      - name: CMake Configure
+        shell: bash
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            -G Ninja \
+            --log-level=VERBOSE \
+            -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
+            -DCMAKE_TOOLCHAIN_FILE=$GITHUB_WORKSPACE/config/toolchain/mingw64.cmake \
+            -DBUILD_SHARED_LIBS:BOOL=${{ inputs.shared }} \
+            -DHDF4_BUILD_EXAMPLES:BOOL=ON \
+            -DBUILD_JPEG_WITH_PIC:BOOL=ON \
+            -DHDF4_ENABLE_NETCDF:BOOL=${{ inputs.netcdf }} \
+            -DHDF4_BUILD_FORTRAN:BOOL=OFF \
+            -DHDF4_BUILD_JAVA:BOOL=OFF \
+            -DHDF4_BUILD_DOC:BOOL=ON \
+            -DJPEG_USE_LOCALCONTENT:BOOL=OFF \
+            -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF \
+            -DZLIB_USE_LOCALCONTENT:BOOL=OFF \
+            -DHDF4_PACK_EXAMPLES:BOOL=ON \
+            -DHDF4_PACKAGE_EXTLIBS:BOOL=ON \
+            $GITHUB_WORKSPACE
+
+      - name: CMake Build
+        shell: bash
+        run: |
+          cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
+        working-directory: ${{ runner.workspace }}/build
+
+      - name: CMake Run Tests
+        shell: bash
+        run: |
+          ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
+        if: false
+
+      - name: CMake Package
+        shell: bash
+        run: |
+          cpack -C ${{ inputs.build_mode }} -V
+        working-directory: ${{ runner.workspace }}/build
+
+      - name: List files in the space
+        run: |
+              ls -l ${{ runner.workspace }}/build
diff --git a/.github/workflows/msys2-auto.yml b/.github/workflows/msys2-auto.yml
new file mode 100644
index 0000000..4ea2da8
--- /dev/null
+++ b/.github/workflows/msys2-auto.yml
@@ -0,0 +1,66 @@
+name: hdf5 dev Autotools MSys2
+
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+      build_option:
+        description: "--enable-production or --disable-production"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  msys2_build_and_test:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        include:
+          - { icon: '⬛', sys: mingw32 }
+          - { icon: '🟦', sys: mingw64 }
+          - { icon: '🟨', sys: ucrt64  }
+          - { icon: '🟧', sys: clang64 }
+    name: ${{ matrix.icon }} msys2-${{ matrix.sys }}-${{ inputs.build_mode }}
+    defaults:
+      run:
+        shell: msys2 {0}
+    steps:
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
+
+      - name: '${{ matrix.icon }} Setup MSYS2'
+        uses: msys2/setup-msys2@v2
+        with:
+          msystem: ${{matrix.sys}}
+          update: true
+          install: >-
+            git
+            autotools
+          pacboy: >-
+            toolchain:p
+            libjpeg-turbo:p
+
+      - name: Autotools Configure
+        run: |
+          sh ./autogen.sh
+          mkdir "$GITHUB_WORKSPACE/build"
+          cd "$GITHUB_WORKSPACE/build"
+          LDFLAGS="-lws2_32" $GITHUB_WORKSPACE/configure \
+            ${{ inputs.build_option }} \
+            --disable-netcdf \
+            --enable-static-exec
+
+      - name: Autotools Build
+        run: |
+          make -j3
+        working-directory: $GITHUB_WORKSPACE/build
+
+      - name: Autotools Run Tests
+        run: |
+          make check -j
+        working-directory: $GITHUB_WORKSPACE/build
diff --git a/.github/workflows/nvhpc-auto.yml b/.github/workflows/nvhpc-auto.yml
index bc6c935..1d003c2 100644
--- a/.github/workflows/nvhpc-auto.yml
+++ b/.github/workflows/nvhpc-auto.yml
@@ -16,9 +16,11 @@ jobs:
     name: "nvhpc ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
 
       - name: Install Dependencies
+        shell: bash
         run: |
           sudo apt-get update
           sudo apt-get install autoconf automake libtool libtool-bin libaec-dev
@@ -28,17 +30,17 @@ jobs:
 
       - name: Install NVHPC
         shell: bash
-        run: |          
+        run: |
           curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg
           echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
           sudo apt-get update -y
           sudo apt-get install -y nvhpc-23-9
-          echo "CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpicc" >> $GITHUB_ENV
-          echo "FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpifort" >> $GITHUB_ENV
           echo "NVHPCSDK=/opt/nvidia/hpc_sdk" >> $GITHUB_ENV
           echo "OMPI_CXX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc++" >> $GITHUB_ENV
           echo "OMPI_CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc" >> $GITHUB_ENV
           echo "OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvfortran" >> $GITHUB_ENV
+          echo "CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpicc" >> $GITHUB_ENV
+          echo "FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpifort" >> $GITHUB_ENV
           echo "LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/lib" >> $GITHUB_ENV
           echo "DESTDIR=/tmp" >> $GITHUB_ENV
 
@@ -56,9 +58,7 @@ jobs:
             --enable-fortran \
             --enable-shared \
             --enable-parallel
-          #cat config.log
 
-      # BUILD
       - name: Autotools Build
         shell: bash
         run: |
@@ -66,16 +66,15 @@ jobs:
           make -j3
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
-      # NORMAL
       - name: Autotools Run Tests
+        shell: bash
         run: |
           export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
           make check -j
         working-directory: ${{ runner.workspace }}/build
 
-      # INSTALL (note that this runs even when we don't run the tests)
       - name: Autotools Install
+        shell: bash
         run: |
           export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
           make install
diff --git a/.github/workflows/nvhpc-cmake.yml b/.github/workflows/nvhpc-cmake.yml
index 3a78c06..1b56eff 100644
--- a/.github/workflows/nvhpc-cmake.yml
+++ b/.github/workflows/nvhpc-cmake.yml
@@ -16,9 +16,10 @@ jobs:
     name: "nvhpc ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
 
-      - name: Install Linux dependencies
+      - name: Install Dependencies
         shell: bash
         run: |
           sudo apt update
@@ -33,16 +34,16 @@ jobs:
           echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
           sudo apt-get update -y
           sudo apt-get install -y nvhpc-23-9
-          echo "CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpicc" >> $GITHUB_ENV
-          echo "FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpifort" >> $GITHUB_ENV
           echo "NVHPCSDK=/opt/nvidia/hpc_sdk" >> $GITHUB_ENV
           echo "OMPI_CXX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc++" >> $GITHUB_ENV
           echo "OMPI_CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc" >> $GITHUB_ENV
           echo "OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvfortran" >> $GITHUB_ENV
+          echo "CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpicc" >> $GITHUB_ENV
+          echo "FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpifort" >> $GITHUB_ENV
           echo "LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/cuda/12.2/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/lib" >> $GITHUB_ENV
           echo "DESTDIR=/tmp" >> $GITHUB_ENV
 
-      - name: CMake Configure with nvc
+      - name: CMake Configure
         shell: bash
         run: |
           export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
@@ -59,16 +60,13 @@ jobs:
           -DHDF5_BUILD_JAVA:BOOL=OFF \
           -DMPIEXEC_MAX_NUMPROCS:STRING="2" \
           $GITHUB_WORKSPACE
-          cat src/libhdf5.settings
 
-      # BUILD
       - name: CMake Build
         shell: bash
         run: |
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
         working-directory: ${{ runner.workspace }}/build
 
-      # RUN TESTS
       - name: CMake Run Tests
         shell: bash
         run: |
diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake
index 7981b64..668739e 100644
--- a/config/cmake/ConfigureChecks.cmake
+++ b/config/cmake/ConfigureChecks.cmake
@@ -144,6 +144,8 @@ endif ()
 
 if (CYGWIN)
   set (${HDF_PREFIX}_HAVE_LSEEK64 0)
+  set (CMAKE_REQUIRED_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS} -D_GNU_SOURCE")
+  add_definitions ("-D_GNU_SOURCE")
 endif ()
 
 #-----------------------------------------------------------------------------
diff --git a/config/cmake/scripts/CTestScript.cmake b/config/cmake/scripts/CTestScript.cmake
index 4f7eb4b..ad6cd44 100644
--- a/config/cmake/scripts/CTestScript.cmake
+++ b/config/cmake/scripts/CTestScript.cmake
@@ -117,37 +117,6 @@ else ()
         set (CTEST_GIT_options "pull")
       endif ()
       set (CTEST_UPDATE_COMMAND "${CTEST_GIT_COMMAND}")
-    else ()
-      ## --------------------------
-      ## use subversion to get source
-      #-----------------------------------------------------------------------------
-      ## cygwin does not handle the find_package() call
-      ## --------------------------
-      set (CTEST_UPDATE_COMMAND "SVNCommand")
-      if (NOT SITE_CYGWIN})
-        find_package (Subversion)
-        set (CTEST_SVN_COMMAND "${Subversion_SVN_EXECUTABLE}")
-        set (CTEST_UPDATE_COMMAND "${Subversion_SVN_EXECUTABLE}")
-      else ()
-        set (CTEST_SVN_COMMAND "/usr/bin/svn")
-        set (CTEST_UPDATE_COMMAND "/usr/bin/svn")
-      endif ()
-
-      if (NOT EXISTS "${CTEST_SOURCE_DIRECTORY}")
-        set (NEED_REPOSITORY_CHECKOUT 1)
-      endif ()
-
-      if (NOT CTEST_REPO_VERSION)
-        set (CTEST_REPO_VERSION "HEAD")
-      endif ()
-      if (${NEED_REPOSITORY_CHECKOUT})
-        set (CTEST_CHECKOUT_COMMAND
-            "\"${CTEST_SVN_COMMAND}\" co ${REPOSITORY_URL} \"${CTEST_SOURCE_DIRECTORY}\" -r ${CTEST_REPO_VERSION}")
-      else ()
-        if (CTEST_REPO_VERSION)
-          set (CTEST_SVN_UPDATE_OPTIONS "-r ${CTEST_REPO_VERSION}")
-        endif ()
-      endif ()
     endif ()
   endif ()
 endif ()
diff --git a/configure.ac b/configure.ac
index 0fa2b3f..dff0c4a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1502,6 +1502,10 @@ case "$host_cpu-$host_vendor-$host_os" in
     AC_DEFINE([HAVE_MINGW], [1], [Define if using MinGW])
     H5_CPPFLAGS="-D_GNU_SOURCE -D__USE_MINGW_ANSI_STDIO $H5_CPPFLAGS"
     ;;
+  *cygwin*)
+    AC_DEFINE([HAVE_CYGWIN], [1], [Define if using Cygwin])
+    H5_CPPFLAGS="-D_GNU_SOURCE $H5_CPPFLAGS"
+    ;;
 esac
 
 ## Need to add the AM_ and H5_ into CFLAGS/CPPFLAGS to make them visible