Fix bug in run_newformat.sh #1360
Workflow file for this run
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| ### | |
| # Build hdf4, hdf5 dependencies and cache them in a combined directory. | |
| # See https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners | |
| # for information related to github runners. | |
| ### | |
| 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: | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2, 1.14.3 ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ### | |
| # libhdf5 | |
| ### | |
| - name: Cache libhdf5-${{ runner.os }}-${{ matrix.hdf5 }} | |
| id: cache-hdf5-osx | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }} | |
| - name: Build libhdf5-${{ runner.os}}-${{ matrix.hdf5 }} | |
| if: steps.cache-hdf5-osx.outputs.cache-hit != 'true' | |
| run: | | |
| set -x | |
| set -e | |
| wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(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/${{ matrix.hdf5 }} --enable-hl --with-szlib | |
| make -j | |
| make install -j | |
| popd | |
| nc-autotools-osx: | |
| needs: [ nc-cmake-tests-oneoff-osx-shared, nc-cmake-tests-oneoff-osx-static, nc-ac-tests-oneoff-osx ] | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2, 1.14.3 ] | |
| use_nc4: [ nc3, nc4 ] | |
| use_dap: [ dap_off, dap_on ] | |
| use_nczarr: [ nczarr_off, nczarr_on ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV | |
| - run: | | |
| echo "NETCDF_ENABLE_HDF4=--disable-hdf4" >> $GITHUB_ENV | |
| echo "NETCDF_ENABLE_HDF5=--disable-hdf5" >> $GITHUB_ENV | |
| if: matrix.use_nc4 == 'nc3' | |
| - run: | | |
| echo "NETCDF_ENABLE_HDF4=--enable-hdf4" >> $GITHUB_ENV | |
| echo "NETCDF_ENABLE_HDF5=--enable-hdf5" >> $GITHUB_ENV | |
| if: matrix.use_nc4 == 'nc4' | |
| - run: echo "NETCDF_ENABLE_DAP=--disable-dap" >> $GITHUB_ENV | |
| if: matrix.use_dap == 'dap_off' | |
| - run: echo "NETCDF_ENABLE_DAP=--enable-dap" >> $GITHUB_ENV | |
| if: matrix.use_dap == 'dap_on' | |
| - run: echo "NETCDF_ENABLE_NCZARR=--disable-nczarr" >> $GITHUB_ENV | |
| if: matrix.use_nczarr == 'nczarr_off' | |
| - run: echo "NETCDF_ENABLE_NCZARR=--enable-nczarr" >> $GITHUB_ENV | |
| if: matrix.use_nczarr == 'nczarr_on' | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf-osx | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }} | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Install autoconf | |
| shell: bash -l {0} | |
| run: brew install automake | |
| - name: Run autoconf | |
| shell: bash -l {0} | |
| run: autoreconf -if | |
| - name: Configure | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure ${NETCDF_ENABLE_HDF5} ${NETCDF_ENABLE_DAP} ${NETCDF_ENABLE_NCZARR} | |
| if: ${{ success() }} | |
| - name: Look at config.log if error | |
| shell: bash -l {0} | |
| run: cat config.log | |
| if: ${{ failure() }} | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: cat libnetcdf.settings | |
| - name: Build Library and Utilities | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j | |
| if: ${{ success() }} | |
| - name: Build Tests | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j | |
| if: ${{ success() }} | |
| # - name: Make Distcheck | |
| # shell: bash -l {0} | |
| # run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} DISTCHECK_CONFIGURE_FLAGS="${NETCDF_ENABLE_HDF4} ${NETCDF_ENABLE_HDF5} ${NETCDF_ENABLE_DAP} ${NETCDF_ENABLE_NCZARR}" make distcheck | |
| # if: ${{ success() }} | |
| #- name: Start SSH Debug | |
| # uses: luchihoratiu/debug-via-ssh@main | |
| # with: | |
| # NGROK_AUTH_TOKEN: ${{ secrets.NGROK_AUTH_TOKEN }} | |
| # SSH_PASS: ${{ secrets.SSH_PASS }} | |
| # if: ${{ failure() }} | |
| nc-cmake-osx: | |
| needs: [ nc-cmake-tests-oneoff-osx-shared, nc-cmake-tests-oneoff-osx-static, nc-ac-tests-oneoff-osx ] | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2, 1.14.3 ] | |
| use_nc4: [ nc3, nc4 ] | |
| use_dap: [ dap_off, dap_on ] | |
| use_nczarr: [ nczarr_off, nczarr_on ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV | |
| - run: | | |
| echo "NETCDF_ENABLE_HDF4=OFF" >> $GITHUB_ENV | |
| echo "NETCDF_ENABLE_HDF5=OFF" >> $GITHUB_ENV | |
| if: matrix.use_nc4 == 'nc3' | |
| - run: | | |
| echo "NETCDF_ENABLE_HDF4=ON" >> $GITHUB_ENV | |
| echo "NETCDF_ENABLE_HDF5=ON" >> $GITHUB_ENV | |
| if: matrix.use_nc4 == 'nc4' | |
| - run: echo "NETCDF_ENABLE_DAP=OFF" >> $GITHUB_ENV | |
| if: matrix.use_dap == 'dap_off' | |
| - run: echo "NETCDF_ENABLE_DAP=ON" >> $GITHUB_ENV | |
| if: matrix.use_dap == 'dap_on' | |
| - run: echo "NETCDF_ENABLE_NCZARR=OFF" >> $GITHUB_ENV | |
| if: matrix.use_nczarr == 'nczarr_off' | |
| - run: echo "NETCDF_ENABLE_NCZARR=ON" >> $GITHUB_ENV | |
| if: matrix.use_nczarr == 'nczarr_on' | |
| - run: echo "CTEST_OUTPUT_ON_FAILURE=1" >> $GITHUB_ENV | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf5-osx | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }} | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Perform out-of-directory build | |
| shell: bash -l {0} | |
| run: | | |
| mkdir build | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DNETCDF_ENABLE_DAP=${NETCDF_ENABLE_DAP} -DNETCDF_ENABLE_HDF5=${NETCDF_ENABLE_HDF5} -DNETCDF_ENABLE_NCZARR=${NETCDF_ENABLE_NCZARR} | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| cat libnetcdf.settings | |
| - name: Build All | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12 | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest --verbose -j 12 . | |
| if: ${{ success() }} | |
| - name: Verbose Output if CTest Failure | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 --rerun-failed --output-on-failure -VV | |
| if: ${{ failure() }} | |
| ##### | |
| # One-Off Autotools-based tests. | |
| ##### | |
| nc-ac-tests-oneoff-osx: | |
| needs: build-deps-osx | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2, 1.14.3 ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf-osx | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }} | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Install autoconf | |
| shell: bash -l {0} | |
| run: brew install automake | |
| - name: Run autoconf | |
| shell: bash -l {0} | |
| run: autoreconf -if | |
| - name: Configure | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests --disable-libxml2 | |
| if: ${{ success() }} | |
| - name: Look at config.log if error | |
| shell: bash -l {0} | |
| run: cat config.log | |
| if: ${{ failure() }} | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: cat libnetcdf.settings | |
| - name: Build Library and Utilities | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j | |
| if: ${{ success() }} | |
| - name: Build Tests | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j | |
| if: ${{ success() }} | |
| ##### | |
| # One-Off CMake-based tests. | |
| ##### | |
| nc-cmake-tests-oneoff-osx-shared: | |
| needs: build-deps-osx | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2, 1.14.3 ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf5-osx | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }} | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Perform out-of-directory build | |
| shell: bash -l {0} | |
| run: | | |
| mkdir build | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DNETCDF_ENABLE_DAP=TRUE -DNETCDF_ENABLE_HDF5=TRUE -DNETCDF_ENABLE_NCZARR=TRUE -D NETCDF_ENABLE_DAP_LONG_TESTS=TRUE -DNETCDF_ENABLE_LIBXML2=FALSE | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| cat libnetcdf.settings | |
| - name: Build All | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12 | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest --output-on-failure -j 12 . | |
| if: ${{ success() }} | |
| - name: Verbose Output if CTest Failure | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 --rerun-failed --output-on-failure -VV | |
| if: ${{ failure() }} | |
| nc-cmake-tests-oneoff-osx-static: | |
| needs: build-deps-osx | |
| runs-on: macos-12 | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2, 1.14.3 ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV | |
| - run: echo "CMAKE_C_FLAGS=-fPIC" >> $GITHUB_ENV | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf5-osx | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }} | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Perform out-of-directory build | |
| shell: bash -l {0} | |
| run: | | |
| mkdir build | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DNETCDF_ENABLE_DAP=TRUE -DNETCDF_ENABLE_HDF5=TRUE -DNETCDF_ENABLE_NCZARR=TRUE -D NETCDF_ENABLE_DAP_LONG_TESTS=TRUE -DNETCDF_ENABLE_LIBXML2=FALSE -DBUILD_SHARED_LIBS=OFF -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| cat libnetcdf.settings | |
| - name: Build All | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12 | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest --output-on-failure -j 12 . | |
| if: ${{ success() }} | |
| - name: Verbose Output if CTest Failure | |
| shell: bash -l {0} | |
| run: | | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 --rerun-failed --output-on-failure -VV | |
| if: ${{ failure() }} |