Try installing h5py from nightly-wheels #1514
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| name: Linux/Mac build | |
| on: | |
| push: | |
| paths: | |
| - '**' | |
| - '!*' | |
| - '*.py' | |
| - '!doc/**' | |
| - '!.github/**' | |
| - '.github/workflows/build.yml' | |
| pull_request: | |
| paths-ignore: | |
| - 'doc/**' | |
| schedule: | |
| - cron: '0 20 * * 2' | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| if: "!contains(github.event.head_commit.message, 'ci skip')" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_actionAngle.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_sphericaldf.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: true | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_actionAngleTorus.py tests/test_conversion.py tests/test_galpypaper.py tests/test_import.py tests/test_interp_potential.py tests/test_kuzminkutuzov.py tests/test_util.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_SpiralArmsPotential.py tests/test_potential.py tests/test_scf.py tests/test_snapshotpotential.py | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_quantity.py tests/test_coords.py | |
| REQUIRES_PYNBODY: false | |
| # needs to be separate for different config | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_orbit.py -k test_energy_jacobi_conservation | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_orbit.py tests/test_orbits.py -k 'not test_energy_jacobi_conservation' | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_evolveddiskdf.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_jeans.py tests/test_dynamfric.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_qdf.py tests/test_pv2qdf.py tests/test_streamgapdf_impulse.py tests/test_noninertial.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: true | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_streamgapdf.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_diskdf.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_streamdf.py tests/test_streamspraydf.py | |
| REQUIRES_PYNBODY: false | |
| REQUIRES_ASTROPY: false | |
| REQUIRES_ASTROQUERY: false | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.12" | |
| TEST_FILES: tests/test_orbit.py -k test_energy_jacobi_conservation | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.12" | |
| TEST_FILES: tests/test_orbit.py tests/test_orbits.py -k 'not test_energy_jacobi_conservation' | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| TEST_FILES: tests/test_orbit.py -k test_energy_jacobi_conservation | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| TEST_FILES: tests/test_orbit.py tests/test_orbits.py -k 'not test_energy_jacobi_conservation' | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| TEST_FILES: tests/test_orbit.py -k test_energy_jacobi_conservation | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| TEST_FILES: tests/test_orbit.py tests/test_orbits.py -k 'not test_energy_jacobi_conservation' | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: 3.9 | |
| TEST_FILES: tests/test_orbit.py -k test_energy_jacobi_conservation | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: 3.9 | |
| TEST_FILES: tests/test_orbit.py tests/test_orbits.py -k 'not test_energy_jacobi_conservation' | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: 3.8 | |
| TEST_FILES: tests/test_orbit.py -k test_energy_jacobi_conservation | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: ubuntu-latest | |
| python-version: 3.8 | |
| TEST_FILES: tests/test_orbit.py tests/test_orbits.py -k 'not test_energy_jacobi_conservation' | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: macos-12 | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_orbit.py -k test_energy_jacobi_conservation | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| - os: macos-12 | |
| python-version: "3.13" | |
| TEST_FILES: tests/test_orbit.py tests/test_orbits.py -k 'not test_energy_jacobi_conservation' | |
| REQUIRES_PYNBODY: true | |
| REQUIRES_ASTROPY: true | |
| REQUIRES_ASTROQUERY: true | |
| REQUIRES_NUMBA: false | |
| REQUIRES_JAX: false | |
| env: | |
| PYTHON_COVREPORTS_VERSION: "3.13" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| allow-prereleases: true | |
| - name: Install lcov | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| wget https://github.com/linux-test-project/lcov/releases/download/v1.15/lcov-1.15.tar.gz | |
| tar xf lcov-1.15.tar.gz | |
| sudo make -C lcov-1.15/ install | |
| - name: Install the GSL | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get install libgsl-dev | |
| - name: Install the GSL and OpenMP | |
| if: matrix.os == 'macos-12' | |
| run: | | |
| brew install gsl libomp | |
| brew info libomp | |
| echo "CFLAGS=-I$(brew --prefix)/include -I/usr/local/opt/libomp/include" >> $GITHUB_ENV | |
| echo "CPPFLAGS=-I$(brew --prefix)/include -I/usr/local/opt/libomp/include" >> $GITHUB_ENV | |
| echo "LDFLAGS=-L$(brew --prefix)/lib -L/usr/local/opt/libomp/lib" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=$(brew --prefix)/lib:/usr/local/opt/libomp/lib" >> $GITHUB_ENV | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('.github/workflows/build.yml') }}-${{ matrix.REQUIRES_PYNBODY }}-${{ matrix.REQUIRES_ASTROPY }}-${{ matrix.REQUIRES_ASTROQUERY }}-${{ matrix.REQUIRES_NUMBA }}-${{ matrix.REQUIRES_JAX }} | |
| - name: Install Python dependencies | |
| run: | | |
| pip install --upgrade --upgrade-strategy eager numpy scipy matplotlib numexpr setuptools cython pytest tqdm | |
| - name: Install pynbody (3.13; ubuntu) | |
| if: ${{ matrix.os == 'ubuntu-latest' && matrix.REQUIRES_PYNBODY && matrix.python-version == '3.13' }} | |
| run: | | |
| pip install --upgrade --upgrade-strategy eager --pre pytz tzdata posix_ipc | |
| pip install --upgrade --upgrade-strategy eager --no-deps --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple "pandas==3.0.0.dev0+1466.g715585de0d" h5py | |
| pip install --upgrade --upgrade-strategy eager wheel | |
| pip install --upgrade --upgrade-strategy eager --no-deps --pre git+https://github.com/pynbody/pynbody.git | |
| - name: Install pynbody (3.13; macos) | |
| if: ${{ matrix.os == 'macos-12' && matrix.REQUIRES_PYNBODY && matrix.python-version == '3.13' }} | |
| run: | | |
| pip install --upgrade --upgrade-strategy eager --pre pytz tzdata posix_ipc | |
| pip install --upgrade --upgrade-strategy eager --no-deps --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple "pandas==3.0.0.dev0+1451.g352289b3b6" | |
| brew install hdf5 | |
| export HDF5_DIR=$(brew --prefix hdf5) | |
| pip install --upgrade --upgrade-strategy eager wheel | |
| pip install --upgrade --upgrade-strategy eager --pre --no-deps --no-build-isolation --no-binary=h5py git+https://github.com/h5py/h5py.git | |
| pip install --upgrade --upgrade-strategy eager --no-deps --pre git+https://github.com/pynbody/pynbody.git | |
| - name: Install pynbody | |
| if: ${{ matrix.REQUIRES_PYNBODY && matrix.python-version != '3.13' }} | |
| run: | | |
| pip install --upgrade --upgrade-strategy eager h5py pandas pytz | |
| pip install --upgrade --upgrade-strategy eager wheel | |
| pip install --upgrade --upgrade-strategy eager pynbody | |
| - name: Install astropy | |
| if: ${{ matrix.REQUIRES_ASTROPY }} | |
| run: pip install astropy pyerfa | |
| - name: Install astroquery | |
| if: ${{ matrix.REQUIRES_ASTROQUERY }} | |
| run: pip install astroquery | |
| - name: Install numba | |
| if: ${{ matrix.REQUIRES_NUMBA }} | |
| run: | | |
| pip install numba | |
| # numba may force install an older version of setuptools, | |
| # but it isn't actually a *runtime* requirement numba/numba#8366 | |
| pip install --upgrade --force-reinstall setuptools | |
| - name: Install JAX | |
| if: ${{ matrix.REQUIRES_JAX }} | |
| run: pip install jax jaxlib | |
| - name: Install torus code | |
| env: | |
| TEST_FILES: ${{ matrix.TEST_FILES }} | |
| run: | | |
| if [[ $TEST_FILES != 'tests/test_evolveddiskdf.py' ]]; then | |
| git clone https://github.com/jobovy/Torus.git galpy/actionAngle/actionAngleTorus_c_ext/torus | |
| cd galpy/actionAngle/actionAngleTorus_c_ext/torus | |
| git checkout galpy | |
| cd - | |
| fi | |
| - name: Install package | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| python setup.py build_ext --no-openmp --coverage --single_ext --inplace | |
| python setup.py develop --single_ext | |
| - name: Install package | |
| if: matrix.os == 'macos-12' | |
| run: | | |
| python -m pip install -v . | |
| - name: Special config | |
| env: | |
| TEST_FILES: ${{ matrix.TEST_FILES }} | |
| run: | | |
| if [[ $TEST_FILES == 'tests/test_evolveddiskdf.py' ]]; then echo -e '[normalization]' > $HOME/.galpyrc && echo -e 'ro = 8.' >> $HOME/.galpyrc && echo -e 'vo = 220.' >> $HOME/.galpyrc; fi | |
| if [[ $TEST_FILES == 'tests/test_diskdf.py' ]]; then echo -e '[normalization]' > $HOME/.galpyrc && echo -e 'ro = 8.' >> $HOME/.galpyrc && echo -e '[astropy]' >> $HOME/.galpyrc && echo -e 'astropy-units = False' >> $HOME/.galpyrc && echo -e '[plot]' >> $HOME/.galpyrc && echo -e 'seaborn-bovy-defaults = True' >> $HOME/.galpyrc && echo -e '[warnings]' >> $HOME/.galpyrc && echo -e 'verbose = True' >> $HOME/.galpyrc; fi | |
| - name: Print debug info | |
| env: | |
| REQUIRES_ASTROPY : ${{ matrix.REQUIRES_ASTROPY }} | |
| REQUIRES_ASTROQUERY : ${{ matrix.REQUIRES_ASTROQUERY }} | |
| REQUIRES_PYNBODY : ${{ matrix.REQUIRES_PYNBODY }} | |
| run: | | |
| python -c "import numpy; print('numpy: {}'.format(numpy.__version__))" | |
| python -c "import scipy; print('scipy: {}'.format(scipy.__version__))" | |
| python -c "import matplotlib; print('matplotlib: {}'.format(matplotlib.__version__))" | |
| if $REQUIRES_ASTROPY; then python -c "import astropy; print('astropy: {}'.format(astropy.__version__))"; fi | |
| if $REQUIRES_ASTROQUERY; then python -c "import astroquery; print('astroquery: {}'.format(astroquery.__version__))"; fi | |
| if $REQUIRES_PYNBODY; then python -c "import pynbody; print('pynbody: {}'.format(pynbody.__version__))"; fi | |
| - name: Test with pytest | |
| env: | |
| TEST_FILES: ${{ matrix.TEST_FILES }} | |
| REQUIRES_ASTROPY : ${{ matrix.REQUIRES_ASTROPY }} | |
| run: | | |
| pip install coverage | |
| pip install pytest-cov | |
| # Turn astropy deprecation warnings into errors as well if astropy | |
| if $REQUIRES_ASTROPY; then export PYTEST_ADDOPTS="-W error::astropy.utils.exceptions.AstropyDeprecationWarning"; else export PYTEST_ADDOPTS=""; fi | |
| export TQDM_DEPRECATION="-W ignore:\"datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version.\":DeprecationWarning -W ignore:\"datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC\":DeprecationWarning" | |
| # eval necessary for -k 'not ...' in TEST_FILES | |
| eval "pytest -W error::DeprecationWarning -W error::FutureWarning $PYTEST_ADDOPTS $TQDM_DEPRECATION -v $TEST_FILES --cov galpy --cov-config .coveragerc --disable-pytest-warnings --durations=0 --cov-report=term --cov-report=xml" | |
| - name: Generate code coverage | |
| if: ${{ matrix.python-version == env.PYTHON_COVREPORTS_VERSION && matrix.os == 'ubuntu-latest' }} | |
| run: | | |
| lcov --capture --base-directory . --directory build/temp.linux-x86_64-`python -c "import sys; print(sys.implementation.cache_tag)"`/galpy/ --no-external --output-file coverage_full.info | |
| lcov --remove coverage_full.info 'galpy/actionAngle/actionAngleTorus_c_ext/torus/*' -o coverage.info | |
| - name: Upload coverage reports to codecov | |
| if: ${{ matrix.python-version == env.PYTHON_COVREPORTS_VERSION && matrix.os == 'ubuntu-latest' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |