Python: Series to DataFrame #538
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| name: 🐧 Linux | |
| on: [push, pull_request] | |
| concurrency: | |
| group: ${{ github.ref }}-${{ github.head_ref }}-linux | |
| cancel-in-progress: true | |
| jobs: | |
| clang7_nopy_nompi_h5_libcpp: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Spack Cache | |
| uses: actions/cache@v3 | |
| with: {path: /opt/spack, key: clang7_nopy_nompi_h5_libcpp_v2} | |
| - name: Install | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install clang-7 libc++-7-dev libc++abi-7-dev | |
| sudo .github/workflows/dependencies/install_spack | |
| - name: Build | |
| env: {CC: clang-7, CXX: clang++-7, CXXFLAGS: -stdlib=libc++ -Werror -Wno-ignored-attributes -Wno-unused-const-variable} | |
| # -Wno-ignored-attributes -Wno-unused-const-variable: clang-6 has a | |
| # false positive on src/auxiliary/Filesystem.cpp | |
| # [[maybe_unused]] MPI_Datatype const MPI_Types< unsigned >::value = MPI_UNSIGNED; | |
| run: | | |
| eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_nompi_h5_libcpp/) | |
| spack install | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=OFF \ | |
| -DopenPMD_USE_MPI=OFF \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON \ | |
| -DCMAKE_VERBOSE_MAKEFILE=ON | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| clang7_nopy_ompi_h5_ad2_libcpp: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Spack Cache | |
| uses: actions/cache@v3 | |
| with: {path: /opt/spack, key: clang7_nopy_ompi_h5_ad2_libcpp_v2} | |
| - name: Install | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install clang-7 libc++-7-dev libc++abi-7-dev gfortran libopenmpi-dev python3 | |
| sudo .github/workflows/dependencies/install_spack | |
| - name: Build | |
| env: {CC: clang-7, CXX: clang++-7, CXXFLAGS: -stdlib=libc++ -Werror -Wno-ignored-attributes -Wno-unused-const-variable} | |
| # -Wno-ignored-attributes -Wno-unused-const-variable: clang-6 has a | |
| # false positive on src/auxiliary/Filesystem.cpp | |
| # [[maybe_unused]] MPI_Datatype const MPI_Types< unsigned >::value = MPI_UNSIGNED; | |
| run: | | |
| cmake --version | |
| mpiexec --version | |
| perl --version | |
| python --version | |
| eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2_libcpp/) | |
| spack install | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=OFF \ | |
| -DopenPMD_USE_MPI=ON \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_ADIOS2=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON \ | |
| -DCMAKE_VERBOSE_MAKEFILE=ON | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| find . -name *.bp | xargs -n1 -P1 -I {} rm -rf {} | |
| find . -name *.bp.dir | xargs -n1 -P1 -I {} rm -rf {} | |
| ctest --test-dir build --output-on-failure | |
| clang7_nopy_ompi_h5_ad2: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Spack Cache | |
| uses: actions/cache@v3 | |
| with: {path: /opt/spack, key: clang7_nopy_ompi_h5_ad2_v2 } | |
| - name: Install | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install clang-7 gfortran libopenmpi-dev python3 | |
| sudo .github/workflows/dependencies/install_spack | |
| - name: Build | |
| env: {CC: clang-7, CXX: clang++-7, CXXFLAGS: -Werror} | |
| run: | | |
| eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2/) | |
| spack install | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=OFF \ | |
| -DopenPMD_USE_MPI=ON \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_ADIOS2=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON \ | |
| -DCMAKE_VERBOSE_MAKEFILE=ON | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| # TODO | |
| # clang7_py36_nompi_h5_ad2_libstdc++ | |
| clang14_py311_nompi_h5_ad2: | |
| runs-on: ubuntu-22.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Spack Cache | |
| uses: actions/cache@v3 | |
| with: {path: /opt/spack, key: clang14_py311_nompi_h5_ad2_v2 } | |
| - name: Install | |
| run: | | |
| sudo apt update | |
| sudo apt install clang-14 cmake gfortran libhdf5-dev python3.11 python3.11-dev wget | |
| wget https://bootstrap.pypa.io/get-pip.py | |
| python3.11 get-pip.py | |
| python3.11 -m pip install numpy pandas | |
| sudo .github/workflows/dependencies/install_spack | |
| - name: Build | |
| env: {CC: clang-14, CXX: clang++-14, CXXFLAGS: -Werror} | |
| run: | | |
| eval $(spack env activate --sh .github/ci/spack-envs/clang14_py311_nompi_h5_ad2/) | |
| spack install | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=ON \ | |
| -DopenPMD_USE_MPI=OFF \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_ADIOS2=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON \ | |
| -DCMAKE_VERBOSE_MAKEFILE=ON \ | |
| -DPython_EXECUTABLE=$(which python3.11) | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| # ADIOS2 v2.7.1 | |
| clang8_py38_mpich_h5_ad2: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Spack Cache | |
| uses: actions/cache@v3 | |
| with: {path: /opt/spack, key: clang8_py38_mpich_h5_ad2_newLayout_v2 } | |
| - name: Install | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install clang-8 gfortran libmpich-dev python3 | |
| sudo .github/workflows/dependencies/install_spack | |
| - name: Build | |
| env: {CC: clang-8, CXX: clang++-8, CXXFLAGS: -Werror} | |
| run: | | |
| cmake --version | |
| mpiexec --version | |
| perl --version | |
| python --version | |
| eval $(spack env activate --sh .github/ci/spack-envs/clang8_py38_mpich_h5_ad2/) | |
| spack install | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=OFF \ | |
| -DopenPMD_USE_MPI=ON \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_ADIOS2=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| # TODO: (old Travis-CI coverage) | |
| # clang10_py38_ompi_h5_1-10-6_ad2_release | |
| # ..._h5coll with OPENPMD_HDF5_INDEPENDENT: OFF | |
| # TODO: (old Travis-CI coverage) | |
| # gcc-4.9.4_nopy_nompi_h5_ad2 | |
| # gcc-4.9.4_nopy_ompi_h5_ad2 | |
| # gcc-9.3.0_nopy_nompi_h5_ad2-2.6.0 | |
| # gcc-7.4.0_nopy_ompi_h5_h5coll | |
| # gcc-6.5.0_py35_nompi_h5-1.13.1 | |
| # gcc-8.1.0_py37_nompi_h5_static | |
| # gcc-6.5.0_py36_nompi_h5-1.8.13 | |
| # gcc-4.8.5_py35_nompi_h5 | |
| # gcc-7.4.0_py_ompi_h5_ad2_coveralls | |
| gcc7_py36_pd_dd_ompi_h5_ad2: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Spack Cache | |
| uses: actions/cache@v3 | |
| with: {path: /opt/spack, key: gcc7_py36_ompi_h5_ad2_v2 } | |
| - name: Install | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install g++-7 gfortran libopenmpi-dev python3 python3-setuptools | |
| sudo .github/workflows/dependencies/install_spack | |
| python3 -m pip install -U pip | |
| python3 -m pip install -U numpy | |
| python3 -m pip install -U mpi4py | |
| python3 -m pip install -U pandas | |
| python3 -m pip install -U dask | |
| python3 -m pip install -U pyarrow | |
| - name: Build | |
| env: {CC: gcc-7, CXX: g++-7, CXXFLAGS: -Werror} | |
| run: | | |
| eval $(spack env activate --sh .github/ci/spack-envs/gcc7_py36_ompi_h5_ad2/) | |
| spack install | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=ON \ | |
| -DopenPMD_USE_MPI=ON \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_ADIOS2=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| gcc9_py38_pd_nompi_h5_ad2_libcpp: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev python3 python3-numpy python3-mpi4py python3-pandas | |
| # TODO ADIOS2 | |
| - name: Build | |
| env: {CXXFLAGS: -Werror, PKG_CONFIG_PATH: /usr/lib/x86_64-linux-gnu/pkgconfig} | |
| run: | | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=ON \ | |
| -DopenPMD_USE_MPI=ON \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| musllinux_py10: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| container: | |
| image: quay.io/pypa/musllinux_1_1_x86_64 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install | |
| run: | | |
| apk update | |
| apk add hdf5-dev | |
| python3.10 -m pip install numpy | |
| - name: Build | |
| env: {CXXFLAGS: -Werror} | |
| run: | | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=ON \ | |
| -DopenPMD_USE_MPI=OFF \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON \ | |
| -DPython_EXECUTABLE=$(which python3.10) | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure | |
| conda_ompi_all: | |
| runs-on: ubuntu-20.04 | |
| if: github.event.pull_request.draft == false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| name: Setup conda | |
| with: | |
| auto-update-conda: true | |
| activate-environment: testing | |
| auto-activate-base: false | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| - name: Install | |
| shell: bash -eo pipefail -l {0} | |
| run: | | |
| conda install -c conda-forge -y mamba | |
| mamba env create --file conda.yml | |
| - name: Build | |
| shell: bash -eo pipefail -l {0} | |
| env: {CXXFLAGS: -Werror} | |
| run: | | |
| source activate openpmd-api-dev | |
| share/openPMD/download_samples.sh build | |
| cmake -S . -B build \ | |
| -DopenPMD_USE_PYTHON=ON \ | |
| -DopenPMD_USE_MPI=ON \ | |
| -DopenPMD_USE_HDF5=ON \ | |
| -DopenPMD_USE_ADIOS2=ON \ | |
| -DopenPMD_USE_INVASIVE_TESTS=ON | |
| cmake --build build --parallel 2 | |
| ctest --test-dir build --output-on-failure |