update to master

Unidata · Dec 16, 2023 · 6aaafd5 · 6aaafd5
2 parents a73a5c1 + e993b1e
commit 6aaafd5
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diff --git a/.github/workflows/run_tests_cdash.yml b/.github/workflows/run_tests_cdash.yml
@@ -0,0 +1,179 @@
+###
+# Build hdf5 dependencies and cache them in a combined directory.
+###
+
+name: Run CDash Ubuntu/Linux netCDF Tests
+
+on: workflow_dispatch
+
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
+jobs:
+
+  build-deps-cdash:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        hdf5: [ 1.10.8, 1.12.2, 1.14.0 ]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install System dependencies
+        shell: bash -l {0}
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen openssl
+
+        ###
+        # Installing libhdf5
+        ###
+      - name: Cache libhdf5-${{ matrix.hdf5 }}
+        id: cache-hdf5
+        uses: actions/cache@v3
+        with:
+          path: ~/environments/${{ matrix.hdf5 }}
+          key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
+
+
+      - name: Build libhdf5-${{ matrix.hdf5 }}
+        if: steps.cache-hdf5.outputs.cache-hit != 'true'
+        run: |
+          set -x
+
+          wget https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.15/src/hdf-4.2.15.tar.bz2
+          tar -jxf hdf-4.2.15.tar.bz2
+          pushd hdf-4.2.15
+          ./configure --prefix=${HOME}/environments/${{ matrix.hdf5 }} --disable-static --enable-shared --disable-fortran --disable-netcdf --with-szlib --enable-hdf4-xdr
+          make -j
+          make install -j
+          popd
+
+          wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2
+          tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2
+          pushd hdf5-${{ matrix.hdf5 }}
+          ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} --enable-hl --with-szlib
+          make -j
+          make install -j
+          popd
+          
+
+  build-deps-parallel:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        hdf5: [ 1.14.0 ]
+
+    steps:
+
+      - uses: actions/checkout@v3
+
+      - name: Install System dependencies
+        shell: bash -l {0}
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev 
+
+        ###
+        # Installing libhdf5
+        ###
+      - name: Cache libhdf5-parallel-${{ matrix.hdf5 }}
+        id: cache-hdf5
+        uses: actions/cache@v3
+        with:
+          path: ~/environments/${{ matrix.hdf5 }}
+          key: hdf5-parallel-${{ runner.os }}-${{ matrix.hdf5 }}
+
+
+      - name: Build libhdf5-${{ matrix.hdf5 }}-pnetcdf-1.12.3
+        if: steps.cache-hdf5.outputs.cache-hit != 'true'
+        run: |
+          set -x
+
+          wget https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.15/src/hdf-4.2.15.tar.bz2
+          tar -jxf hdf-4.2.15.tar.bz2
+          pushd hdf-4.2.15
+          CC=mpicc ./configure --prefix=${HOME}/environments/${{ matrix.hdf5 }} --disable-static --enable-shared --disable-fortran --disable-netcdf --with-szlib --enable-parallel --enable-hdf4-xdr
+          make -j
+          make install -j
+          popd
+
+          wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2
+          tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2
+          pushd hdf5-${{ matrix.hdf5 }}
+          CC=mpicc ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} --enable-hl --with-szlib --enable-parallel
+          make -j
+          make install -j
+          popd
+          wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
+          tar -zxf pnetcdf-1.12.3.tar.gz
+          pushd pnetcdf-1.12.3
+          CC=mpicc ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} 
+          make -j
+          make install -j
+          popd
+
+
+      ###
+      # Run CTest Serial Script
+      ###
+  nc-ctest-serial:
+      needs: build-deps-cdash
+      runs-on: ubuntu-latest
+      environment: CDashCI
+
+      strategy:
+        matrix:
+          hdf5: [ 1.10.8, 1.12.2, 1.14.0 ]
+
+      steps:          
+        - uses: actions/checkout@v3
+          with:
+            CDASH_TOKEN: ${{ secrets.CDASH_TOKEN }}
+          env:
+            CDASH_TOKEN: ${{ secrets.CDASH_TOKEN }}
+
+        - name: Install System dependencies
+          shell: bash -l {0}
+          run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev
+
+        ###
+        # Set Environmental Variables
+        ###
+
+        - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV
+        - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
+        - run: echo "CTEST_OUTPUT_ON_FAILURE=1" >> $GITHUB_ENV
+
+        ###
+        # Fetch Cache
+        ###
+
+        - name: Fetch HDF Cache
+          id: cache-hdf5
+          uses: actions/cache@v3
+          with:
+            path: ~/environments/${{ matrix.hdf5 }}
+            key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
+
+        - name: Check Cache
+          shell: bash -l {0}
+          run: ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib
+
+        - name: Run ctest serial script
+          shell: bash -l {0}
+          env: 
+            CDASH_TOKEN: ${{ secrets.CDASH_TOKEN }}
+          run: |
+            mkdir build
+            cd build
+            LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 -V -S ../ctest_scripts/ctest_serial.ctest
+
+        - name: Verbose Output if CTest Failure
+          shell: bash -l {0}
+          run: |
+            cd build
+            LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 --rerun-failed --output-on-failure -VV
+          if: ${{ failure() }}
diff --git a/.github/workflows/run_tests_osx.yml b/.github/workflows/run_tests_osx.yml
@@ -6,9 +6,12 @@
 
 name: Run macOS-based netCDF Tests
 
-
 on: [pull_request,workflow_dispatch]
 
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
 jobs:
 
   build-deps-osx:

diff --git a/.github/workflows/run_tests_s3.yml b/.github/workflows/run_tests_s3.yml
@@ -11,6 +11,10 @@ name: Run S3 netCDF Tests (under Ubuntu Linux)
 
 on: [workflow_dispatch]
 
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
 jobs:
 
   build-deps-serial:

diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml
@@ -6,6 +6,10 @@ name: Run Ubuntu/Linux netCDF Tests
 
 on: [pull_request, workflow_dispatch]
 
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
 jobs:
 
   build-deps-serial:
@@ -196,6 +200,19 @@ jobs:
           CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
         if: ${{ success() }}
 
+      - name: Create source distribution
+        shell: bash -l {0}
+        if: ${{ success() }}
+        run: make dist -j
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: netcdf-c-autotools-source-distribution
+          path: |
+            *.tar*
+            *.zip
+            *.tgz
+
   ##
   # Parallel
   ##
@@ -449,7 +466,28 @@ jobs:
         use_nczarr: [ nczarr_off, nczarr_on ]
     steps:
 
-      - uses: actions/checkout@v3
+      - uses: actions/download-artifact@v3
+        with:
+          name: netcdf-c-autotools-source-distribution
+
+      - name: Unpack source distribution
+        shell: bash -l {0}
+        run: |
+          if [ -f *.zip ];
+          then
+            unzip *.zip
+          else
+            tar xvzf $(ls *.tar* *.tgz *.zip | head -1)
+          fi
+          ls -d netcdf-c*
+          for name in netcdf-c*;
+          do
+              if [ -d ${name} ];
+              then
+                  cd ${name}
+                  break
+              fi
+          done
 
       - name: Install System dependencies
         shell: bash -l {0}
@@ -498,41 +536,85 @@ jobs:
 
       - name: Run autoconf
         shell: bash -l {0}
-        run: autoreconf -if
+        run: |
+          for name in netcdf-c*;
+          do
+              if [ -d ${name} ];
+              then
+                  cd ${name}
+                  break
+              fi
+          done
+          autoreconf -if
 
       - name: Configure
         shell: bash -l {0}
         run: |
+          for name in netcdf-c*;
+          do
+              if [ -d ${name} ];
+              then
+                  cd ${name}
+                  break
+              fi
+          done
           current_directory="$(pwd)"
           mkdir ../build
           cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} "${current_directory}/configure" ${ENABLE_HDF5} ${ENABLE_DAP} ${ENABLE_NCZARR}
         if: ${{ success() }}
 
       - name: Look at config.log if error
         shell: bash -l {0}
-        run: cd ../build && cat config.log
+        run: |
+          if [ -d ../build ];
+          then
+              cd ../build
+          else
+              cd build
+          fi && cat config.log
         if: ${{ failure() }}
 
       - name: Print Summary
         shell: bash -l {0}
-        run: cd ../build && cat libnetcdf.settings
+        run: |
+          if [ -d ../build ];
+          then
+              cd ../build
+          else
+              cd build
+          fi && cat libnetcdf.settings
 
       - name: Build Library and Utilities
         shell: bash -l {0}
         run: |
-          cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j
+          if [ -d ../build ];
+          then
+              cd ../build
+          else
+              cd build
+          fi && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j
         if: ${{ success() }}
 
       - name: Build Tests
         shell: bash -l {0}
         run: |
-          cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j
+          if [ -d ../build ];
+          then
+              cd ../build
+          else
+              cd build
+          fi && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j
         if: ${{ success() }}
 
       - name: Run Tests
         shell: bash -l {0}
         run: |
-          cd ../build && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
+          if [ -d ../build ];
+          then
+              cd ../build
+          else
+              cd build
+          fi && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
         if: ${{ success() }}
 
   nc-cmake:

diff --git a/.github/workflows/run_tests_win_cygwin.yml b/.github/workflows/run_tests_win_cygwin.yml
@@ -2,6 +2,10 @@ name: Run Cygwin-based tests
 
 on: [pull_request,workflow_dispatch]
 
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
 env:
   SHELLOPTS: igncr
   CHERE_INVOKING: 1

diff --git a/.github/workflows/run_tests_win_mingw.yml b/.github/workflows/run_tests_win_mingw.yml
@@ -4,13 +4,17 @@
 # for information related to github runners.
 ###
 
-name: Run MSYS2, MinGW64-based Tests
+name: Run MSYS2, MinGW64-based Tests (Not Visual Studio)
 
 env:
   CPPFLAGS: "-D_BSD_SOURCE"
 
 on: [pull_request,workflow_dispatch]
 
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
 jobs:
 
   build-and-test-autotools:

diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
@@ -74,7 +74,7 @@ FIND_PROGRAM(NC_DPKG NAMES dpkg)
 IF(NC_DPKG)
   # Define a macro for getting the dpkg architecture.
   MACRO(getdpkg_arch arch)
-    exec_program("${NC_DPKG}" ARGS "--print-architecture" OUTPUT_VARIABLE "${arch}")
+    execute_process(COMMAND "${NC_DPKG}" "--print-architecture" OUTPUT_VARIABLE "${arch}" OUTPUT_STRIP_TRAILING_WHITESPACE)
   ENDMACRO(getdpkg_arch)
   getdpkg_arch(dpkg_arch)