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Unidata · Oct 20, 2023 · dea0607 · dea0607
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diff --git a/.github/workflows/build_latest.yml b/.github/workflows/build_latest.yml
@@ -0,0 +1,104 @@
+name: Build and Test Linux with latest netcdf-c
+on: [push, pull_request]
+jobs:
+  build-linux:
+    name: Python (${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    env:
+      PNETCDF_VERSION: 1.12.1
+      NETCDF_VERSION: 4.9.2
+      NETCDF_DIR: ${{ github.workspace }}/..
+      NETCDF_EXTRA_CONFIG: --enable-pnetcdf
+      CC: mpicc.mpich
+      #NO_NET: 1
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Ubuntu Dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install mpich libmpich-dev libhdf5-mpich-dev libcurl4-openssl-dev bzip2 libsnappy-dev libblosc-dev libzstd-dev
+        echo "Download and build PnetCDF version ${PNETCDF_VERSION}"
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-${PNETCDF_VERSION}.tar.gz
+        tar -xzf pnetcdf-${PNETCDF_VERSION}.tar.gz
+        pushd pnetcdf-${PNETCDF_VERSION}
+        ./configure --prefix $NETCDF_DIR --enable-shared --disable-fortran --disable-cxx
+        make -j 2
+        make install
+        popd
+        echo "Download and build netCDF version ${NETCDF_VERSION}"
+        wget https://downloads.unidata.ucar.edu/netcdf-c/${NETCDF_VERSION}/netcdf-c-${NETCDF_VERSION}.tar.gz
+        tar -xzf netcdf-c-${NETCDF_VERSION}.tar.gz
+        pushd netcdf-c-${NETCDF_VERSION}
+        export CPPFLAGS="-I/usr/include/hdf5/mpich -I${NETCDF_DIR}/include"
+        export LDFLAGS="-L${NETCDF_DIR}/lib"
+        export LIBS="-lhdf5_mpich_hl -lhdf5_mpich -lm -lz"
+        ./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --enable-dap --enable-parallel4 $NETCDF_EXTRA_CONFIG
+        make -j 2
+        make install
+        popd
+
+#   - name: The job has failed
+#     if: ${{ failure() }}
+#     run: |
+#       cd netcdf-c-${NETCDF_VERSION}
+#       cat config.log 
+
+    - name: Install python dependencies via pip
+      run: |
+        python -m pip install --upgrade pip
+        pip install numpy cython cftime pytest twine wheel check-manifest mpi4py
+
+    - name: Install netcdf4-python
+      run: |
+        export PATH=${NETCDF_DIR}/bin:${PATH} 
+        export NETCDF_PLUGIN_DIR=${{ github.workspace }}/netcdf-c-${NETCDF_VERSION}/plugins/plugindir
+        python setup.py install
+    - name: Test
+      run: |
+        export PATH=${NETCDF_DIR}/bin:${PATH} 
+        python checkversion.py
+        # serial
+        cd test
+        python run_all.py
+        # parallel (hdf5 for netcdf4, pnetcdf for netcdf3)
+        cd ../examples
+        mpirun.mpich -np 4 python mpi_example.py
+        if [ $? -ne 0 ] ; then
+          echo "hdf5 mpi test failed!"
+          exit 1
+        else
+          echo "hdf5 mpi test passed!"
+        fi
+        mpirun.mpich -np 4 python mpi_example_compressed.py
+        if [ $? -ne 0 ] ; then
+          echo "hdf5 compressed mpi test failed!"
+          exit 1
+        else
+          echo "hdf5 compressed mpi test passed!"
+        fi
+        mpirun.mpich -np 4 python mpi_example.py NETCDF3_64BIT_DATA
+        if [ $? -ne 0 ] ; then
+          echo "pnetcdf mpi test failed!"
+          exit 1
+        else
+          echo "pnetcdf mpi test passed!"
+        fi
+
+#   - name: Tarball
+#     run: |
+#       export PATH=${NETCDF_DIR}/bin:${PATH} 
+#       python setup.py --version  
+#       check-manifest --version
+#       check-manifest --verbose 
+#       pip wheel . -w dist --no-deps 
+#       twine check dist/* 
diff --git a/.github/workflows/build_master.yml b/.github/workflows/build_master.yml
@@ -0,0 +1,78 @@
+name: Build and Test on Linux with netcdf-c github master
+on: [push, pull_request]
+jobs:
+  build-linux:
+    name: Python (${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    env:
+      NETCDF_DIR: ${{ github.workspace }}/..
+      CC: mpicc.mpich
+      #NO_NET: 1
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Ubuntu Dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install mpich libmpich-dev libhdf5-mpich-dev libcurl4-openssl-dev bzip2 libsnappy-dev libblosc-dev libzstd-dev
+        echo "Download and build netCDF github master"
+        git clone https://github.com/Unidata/netcdf-c
+        pushd netcdf-c
+        export CPPFLAGS="-I/usr/include/hdf5/mpich -I${NETCDF_DIR}/include"
+        export LDFLAGS="-L${NETCDF_DIR}/lib"
+        export LIBS="-lhdf5_mpich_hl -lhdf5_mpich -lm -lz"
+        autoreconf -i
+        ./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --enable-dap --enable-parallel4 
+        make -j 2
+        make install
+        popd
+
+#   - name: The job has failed
+#     if: ${{ failure() }}
+#     run: |
+#       cd netcdf-c-${NETCDF_VERSION}
+#       cat config.log 
+
+    - name: Install python dependencies via pip
+      run: |
+        python -m pip install --upgrade pip
+        pip install numpy cython cftime pytest twine wheel check-manifest mpi4py
+
+    - name: Install netcdf4-python
+      run: |
+        export PATH=${NETCDF_DIR}/bin:${PATH} 
+        export NETCDF_PLUGIN_DIR=${{ github.workspace }}/netcdf-c/plugins/plugindir
+        python setup.py install
+    - name: Test
+      run: |
+        export PATH=${NETCDF_DIR}/bin:${PATH} 
+        #export HDF5_PLUGIN_PATH=${NETCDF_DIR}/plugins/plugindir
+        python checkversion.py
+        # serial
+        cd test
+        python run_all.py
+        # parallel
+        cd ../examples
+        mpirun.mpich -np 4 python mpi_example.py
+        if [ $? -ne 0 ] ; then
+          echo "hdf5 mpi test failed!"
+          exit 1
+        else
+          echo "hdf5 mpi test passed!"
+        fi
+        mpirun.mpich -np 4 python mpi_example_compressed.py
+        if [ $? -ne 0 ] ; then
+          echo "hdf5 compressed mpi test failed!"
+          exit 1
+        else
+          echo "hdf5 compressed mpi test passed!"
+        fi
diff --git a/.github/workflows/build_old.yml b/.github/workflows/build_old.yml
@@ -0,0 +1,104 @@
+name: Build and Test Linux with older netcdf-c
+on: [push, pull_request]
+jobs:
+  build-linux:
+    name: Python (${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    env:
+      PNETCDF_VERSION: 1.12.1
+      NETCDF_VERSION: 4.8.1
+      NETCDF_DIR: ${{ github.workspace }}/..
+      NETCDF_EXTRA_CONFIG: --enable-pnetcdf
+      CC: mpicc.mpich
+      #NO_NET: 1
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Ubuntu Dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install mpich libmpich-dev libhdf5-mpich-dev libcurl4-openssl-dev bzip2 libsnappy-dev libblosc-dev libzstd-dev
+        echo "Download and build PnetCDF version ${PNETCDF_VERSION}"
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-${PNETCDF_VERSION}.tar.gz
+        tar -xzf pnetcdf-${PNETCDF_VERSION}.tar.gz
+        pushd pnetcdf-${PNETCDF_VERSION}
+        ./configure --prefix $NETCDF_DIR --enable-shared --disable-fortran --disable-cxx
+        make -j 2
+        make install
+        popd
+        echo "Download and build netCDF version ${NETCDF_VERSION}"
+        wget https://downloads.unidata.ucar.edu/netcdf-c/${NETCDF_VERSION}/netcdf-c-${NETCDF_VERSION}.tar.gz
+        tar -xzf netcdf-c-${NETCDF_VERSION}.tar.gz
+        pushd netcdf-c-${NETCDF_VERSION}
+        export CPPFLAGS="-I/usr/include/hdf5/mpich -I${NETCDF_DIR}/include"
+        export LDFLAGS="-L${NETCDF_DIR}/lib"
+        export LIBS="-lhdf5_mpich_hl -lhdf5_mpich -lm -lz"
+        ./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --enable-dap --enable-parallel4 $NETCDF_EXTRA_CONFIG
+        make -j 2
+        make install
+        popd
+
+#   - name: The job has failed
+#     if: ${{ failure() }}
+#     run: |
+#       cd netcdf-c-${NETCDF_VERSION}
+#       cat config.log 
+
+    - name: Install python dependencies via pip
+      run: |
+        python -m pip install --upgrade pip
+        pip install numpy cython cftime pytest twine wheel check-manifest mpi4py
+
+    - name: Install netcdf4-python
+      run: |
+        export PATH=${NETCDF_DIR}/bin:${PATH} 
+        export NETCDF_PLUGIN_DIR=${{ github.workspace }}/netcdf-c-${NETCDF_VERSION}/plugins/plugindir
+        python setup.py install
+    - name: Test
+      run: |
+        export PATH=${NETCDF_DIR}/bin:${PATH} 
+        python checkversion.py
+        # serial
+        cd test
+        python run_all.py
+        # parallel (hdf5 for netcdf4, pnetcdf for netcdf3)
+        cd ../examples
+        mpirun.mpich -np 4 python mpi_example.py
+        if [ $? -ne 0 ] ; then
+          echo "hdf5 mpi test failed!"
+          exit 1
+        else
+          echo "hdf5 mpi test passed!"
+        fi
+        mpirun.mpich -np 4 python mpi_example_compressed.py
+        if [ $? -ne 0 ] ; then
+          echo "hdf5 compressed mpi test failed!"
+          exit 1
+        else
+          echo "hdf5 compressed mpi test passed!"
+        fi
+        mpirun.mpich -np 4 python mpi_example.py NETCDF3_64BIT_DATA
+        if [ $? -ne 0 ] ; then
+          echo "pnetcdf mpi test failed!"
+          exit 1
+        else
+          echo "pnetcdf mpi test passed!"
+        fi
+
+#   - name: Tarball
+#     run: |
+#       export PATH=${NETCDF_DIR}/bin:${PATH} 
+#       python setup.py --version  
+#       check-manifest --version
+#       check-manifest --verbose 
+#       pip wheel . -w dist --no-deps 
+#       twine check dist/* 
diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
@@ -19,9 +19,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          submodules: true
 
       - uses: actions/setup-python@v4
         name: Install Python
@@ -82,8 +79,59 @@ jobs:
         name: pypi-artifacts
         path: ${{ github.workspace }}/wheelhouse/*.whl
 
+
+  build_wheels_windows:
+    name: Build wheels for ${{matrix.arch}} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest]
+        arch: [win_amd64]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: 3.x
+
+      - name: Setup Micromamba Python ${{ matrix.python-version }}
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: build
+          init-shell: bash
+          create-args: >-
+            python=${{ matrix.python-version }} hdf5 libnetcdf --channel conda-forge
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install --upgrade cibuildwheel
+
+      - name: Build wheels for Windows (${{ matrix.arch }})
+        run: cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BUILD: "cp39-${{ matrix.arch }} cp310-${{ matrix.arch }} cp311-${{ matrix.arch }} cp312-${{ matrix.arch }}"
+          CIBW_ENVIRONMENT_WINDOWS: >
+            HDF5_DIR="C:\\Users\\runneradmin\\micromamba\\envs\\build\\Library"
+            netCDF4_DIR="C:\\Users\\runneradmin\\micromamba\\envs\\build\\Library"
+            PATH="C:\\Users\\runneradmin\\micromamba\\envs\\build\\Library\\bin;${PATH}"
+          CIBW_BEFORE_BUILD: "python -m pip install delvewheel"
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
+          CIBW_TEST_COMMAND: >
+            python -c "import netCDF4; print(f'netCDF4 v{netCDF4.__version__}')"
+            && xcopy {project}\\test . /E/H
+            && python -m pip install --upgrade numpy cython packaging
+            && python run_all.py
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: pypi-artifacts
+          path: ${{ github.workspace }}/wheelhouse/*.whl
+
+
   show-artifacts:
-    needs: [build_bdist, build_sdist]
+    needs: [build_bdist, build_sdist, build_wheels_windows]
     name: "Show artifacts"
     runs-on: ubuntu-latest
     steps:
@@ -98,7 +146,7 @@ jobs:
 
 
   publish-artifacts-pypi:
-    needs: [build_bdist, build_sdist]
+    needs: [build_bdist, build_sdist, build_wheels_windows]
     name: "Publish to PyPI"
     runs-on: ubuntu-latest
     # upload to PyPI for every tag starting with 'v'