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added documentation about reading an unknown netCDF/HDF5 file in tutorial, and some other documentation fixes #1419

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added documentation about reading an unknown netCDF/HDF5 file in tutorial, and some other documentation fixes

added documentation about reading an unknown netCDF/HDF5 file in tutorial, and some other documentation fixes #1419

Workflow file for this run

.github/workflows/run_tests_ubuntu.yml at 7eeb055
###
# Build hdf5 dependencies and cache them in a combined directory.
###
name: Run Ubuntu/Linux netCDF Tests
on: [pull_request,workflow_dispatch]
env:
REMOTETESTDOWN: ${{ vars.REMOTETESTDOWN }}
concurrency:
group: ${{ github.workflow}}-${{ github.head_ref }}
cancel-in-progress: true
jobs:
build-deps-serial:
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.10.8, 1.12.2, 1.14.3 ]
steps:
- uses: actions/checkout@v4
- 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-${{ matrix.hdf5 }}
id: cache-hdf5
uses: actions/cache@v4
with:
path: ~/environments/${{ 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/${{ matrix.hdf5 }} --enable-hl --with-szlib
make -j
make install -j
popd
build-deps-parallel:
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.14.3 ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev
###
# Installing libhdf5
###
- name: Cache libhdf5-parallel-${{ matrix.hdf5 }}
id: cache-hdf5
uses: actions/cache@v4
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/${{ matrix.hdf5 }}
make -j
make install -j
popd
#####
# One-Off Autotools-based tests.
#####
##
# Serial, Shared
##
nc-ac-tests-oneoff-serial-shared:
needs: build-deps-serial
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.14.3 ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen valgrind
###
# Set Environmental Variables
###
- run: echo "CFLAGS=-I${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" >> $GITHUB_ENV
###
# Fetch Cache
###
- name: Fetch HDF Cache
id: cache-hdf
uses: actions/cache@v4
with:
path: ~/environments/${{ 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: 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 --enable-doxygen --enable-external-server-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: ${{ success() }}
- name: Run Tests
shell: bash -l {0}
run: |
LD_LIBRARY_PATH="/home/runner/work/netcdf-c/netcdf-c/liblib/.libs:${LD_LIBRARY_PATH}"
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
if: ${{ success() }}
- name: Create source distribution
shell: bash -l {0}
if: ${{ success() }}
run: make dist -j
- uses: actions/upload-artifact@v3
with:
name: netcdf-c-autotools-source-distribution
path: |
*.tar*
*.zip
*.tgz
##
#
## Serial, Static
nc-ac-tests-oneoff-serial-static:
needs: build-deps-serial
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.14.3 ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen valgrind
###
# Set Environmental Variables
###
- run: echo "CFLAGS=-I${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" >> $GITHUB_ENV
###
# Fetch Cache
###
- name: Fetch HDF Cache
id: cache-hdf
uses: actions/cache@v4
with:
path: ~/environments/${{ 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: 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 --enable-doxygen --enable-external-server-tests --disable-libxml2 --disable-shared --enable-static
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: ${{ success() }}
- name: Run Tests
shell: bash -l {0}
run: |
LD_LIBRARY_PATH="/home/runner/work/netcdf-c/netcdf-c/liblib/.libs:${LD_LIBRARY_PATH}"
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
if: ${{ success() }}
- name: Create source distribution
shell: bash -l {0}
if: ${{ success() }}
run: make dist -j
- uses: actions/upload-artifact@v3
with:
name: netcdf-c-autotools-source-distribution
path: |
*.tar*
*.zip
*.tgz
##
# Parallel
##
nc-ac-tests-oneoff-parallel:
needs: build-deps-parallel
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.14.3 ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev
###
# Set Environmental Variables
###
- run: echo "CFLAGS=-I${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" >> $GITHUB_ENV
- name: Fetch HDF Cache
id: cache-hdf
uses: actions/cache@v4
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-parallel-${{ runner.os }}-${{ 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: 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} CC=mpicc ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-parallel-tests --enable-pnetcdf
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} CC=mpicc make -j
if: ${{ success() }}
- name: Build Tests
shell: bash -l {0}
run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc make check TESTS="" -j
if: ${{ success() }}
- name: Run Tests
shell: bash -l {0}
run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc make check -j
if: ${{ success() }}
#####
# One-Off CMake-based tests.
#####
##
# Serial, Shared
##
nc-cmake-tests-oneoff-serial-shared:
needs: build-deps-serial
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.14.3 ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen
###
# Set Environmental Variables
###
- run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV
- run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
###
# Fetch Cache
###
- name: Fetch HDF Cache
id: cache-hdf5
uses: actions/cache@v4
with:
path: ~/environments/${{ 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 -DNETCDF_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: ${{ failure() }}
##
# Serial, Shared
##
nc-cmake-tests-oneoff-serial-static:
needs: build-deps-serial
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.14.3 ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen
###
# Set Environmental Variables
###
- run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV
- run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
- run: echo "CMAKE_C_FLAGS=-fPIC" >> $GITHUB_ENV
###
# Fetch Cache
###
- name: Fetch HDF Cache
id: cache-hdf5
uses: actions/cache@v4
with:
path: ~/environments/${{ 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 -DNETCDF_ENABLE_DAP_LONG_TESTS=TRUE -DNETCDF_ENABLE_LIBXML2=FALSE -DBUILD_SHARED_LIBS=FALSE -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: ${{ failure() }}
##
# Parallel
##
nc-cmake-tests-oneoff-parallel:
needs: build-deps-parallel
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.14.3 ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen mpich libmpich-dev
###
# Set Environmental Variables
###
- run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV
- run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
###
# Fetch Cache
###
- name: Fetch HDF Cache
id: cache-hdf5
uses: actions/cache@v4
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-parallel-${{ runner.os }}-${{ 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=${LD_LIBRARY_PATH} cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DNETCDF_ENABLE_DAP=TRUE -DNETCDF_ENABLE_HDF5=TRUE -DNETCDF_ENABLE_NCZARR=TRUE -D NETCDF_ENABLE_DAP_LONG_TESTS=TRUE -DNETCDF_ENABLE_PNETCDF=TRUE
- 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-autotools:
needs: [ nc-cmake-tests-oneoff-serial-shared, nc-cmake-tests-oneoff-serial-static, nc-ac-tests-oneoff-serial-shared, nc-ac-tests-oneoff-serial-static, nc-cmake-tests-oneoff-parallel, nc-ac-tests-oneoff-parallel ]
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [1.10.8, 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/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 ${name}
break
fi
done
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev
###
# Set Environmental Variables
###
- run: echo "CFLAGS=-I${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_HDF5=--disable-hdf5" >> $GITHUB_ENV
if: matrix.use_nc4 == 'nc3'
- run: |
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" >> $GITHUB_ENV
if: matrix.use_nczarr == 'nczarr_on'
###
# Fetch Cache
###
- name: Fetch HDF Cache
id: cache-hdf
uses: actions/cache@v4
with:
path: ~/environments/${{ 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: Run autoconf
shell: bash -l {0}
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" ${NETCDF_ENABLE_HDF5} ${NETCDF_ENABLE_DAP} ${NETCDF_ENABLE_NCZARR}
if: ${{ success() }}
- name: Look at config.log if error
shell: bash -l {0}
run: |
if [ -d ../build ];
then
cd ../build
else
cd build
fi && cat config.log
if: ${{ failure() }}
- name: Print Summary
shell: bash -l {0}
run: |
if [ -d ../build ];
then
cd ../build
else
cd build
fi && cat libnetcdf.settings
- name: Build Library and Utilities
shell: bash -l {0}
run: |
if [ -d ../build ];
then
cd ../build
else
cd build
fi && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j
if: ${{ success() }}
- name: Build Tests
shell: bash -l {0}
run: |
if [ -d ../build ];
then
cd ../build
else
cd build
fi && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j
if: ${{ success() }}
- name: Run Tests
shell: bash -l {0}
run: |
if [ -d ../build ];
then
cd ../build
else
cd build
fi && CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j
if: ${{ success() }}
nc-cmake:
needs: [ nc-cmake-tests-oneoff-serial-shared, nc-cmake-tests-oneoff-serial-static, nc-ac-tests-oneoff-serial-shared, nc-ac-tests-oneoff-serial-static, nc-cmake-tests-oneoff-parallel, nc-ac-tests-oneoff-parallel ]
runs-on: ubuntu-latest
strategy:
matrix:
hdf5: [ 1.10.8, 1.12.2, 1.14.3 ]
use_nc4: [ nc3, nc4 ]
use_dap: [ dap_off, dap_on ]
use_nczarr: [ nczarr_off, nczarr_on ]
steps:
- uses: actions/checkout@v4
- name: Install System dependencies
shell: bash -l {0}
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev
###
# Set Environmental Variables
###
- run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV
- run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
- run: |
echo "NETCDF_ENABLE_HDF5=OFF" >> $GITHUB_ENV
if: matrix.use_nc4 == 'nc3'
- run: |
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" >> $GITHUB_ENV
###
# Fetch Cache
###
- name: Fetch HDF Cache
id: cache-hdf5
uses: actions/cache@v4
with:
path: ~/environments/${{ matrix.hdf5 }}
key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
- name: Check Cache
shell: bash -l {0}
run: ls ${HOME}/environments/${{ 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() }}