Fix rtd build failure (#309) #466
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| name: GitHub CI | |
| on: [push, pull_request] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| name: On ${{ matrix.os }} with (${{ matrix.compiler }}, python-${{ matrix.python-version }}, numpy-${{ matrix.numpy-version }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-20.04", "ubuntu-latest", "macos-latest"] | |
| compiler: [gcc-7, gcc-9, clang] | |
| python-version: ["2.7", "3.7", "3.8", "3.9"] | |
| numpy-version: ["1.16", "1.18"] | |
| include: | |
| - numpy-version: "1.22" | |
| compiler: gcc-10 | |
| python-version: "3.10" | |
| os: ubuntu-latest | |
| - numpy-version: "1.22" | |
| compiler: gcc-11 | |
| python-version: "3.10" | |
| os: ubuntu-latest | |
| - numpy-version: "1.23" | |
| compiler: gcc-10 | |
| python-version: "3.10" | |
| os: ubuntu-latest | |
| - numpy-version: "1.23" | |
| compiler: gcc-11 | |
| python-version: "3.10" | |
| os: ubuntu-latest | |
| - numpy-version: "1.22" | |
| compiler: gcc-10 | |
| python-version: "3.11" | |
| os: ubuntu-latest | |
| - numpy-version: "1.22" | |
| compiler: gcc-11 | |
| python-version: "3.11" | |
| os: ubuntu-latest | |
| - numpy-version: "1.22" | |
| compiler: gcc-12 | |
| python-version: "3.11" | |
| os: ubuntu-latest | |
| - numpy-version: "1.23" | |
| compiler: gcc-10 | |
| python-version: "3.11" | |
| os: ubuntu-latest | |
| - numpy-version: "1.23" | |
| compiler: gcc-11 | |
| python-version: "3.11" | |
| os: ubuntu-latest | |
| - numpy-version: "1.23" | |
| compiler: gcc-12 | |
| python-version: "3.11" | |
| os: ubuntu-latest | |
| exclude: | |
| # Only run with 'clang' on OSX | |
| - os: "macos-latest" | |
| compiler: gcc-7 | |
| - os: "macos-latest" | |
| compiler: gcc-9 | |
| # Don't use 'clang' on linux | |
| - os: "ubuntu-20.04" | |
| compiler: clang | |
| - os: "ubuntu-latest" | |
| compiler: clang | |
| # only gcc-10 on latest | |
| - os: "ubuntu-latest" | |
| compiler: gcc-9 | |
| - os: "ubuntu-latest" | |
| compiler: gcc-7 | |
| # Don't run numpy 1.16 on ubuntu-latest | |
| - os: "ubuntu-latest" | |
| numpy-version: 1.16 | |
| - os: "ubuntu-latest" | |
| numpy-version: 1.18 | |
| # python3.10 only on ubuntu-latest | |
| # - os: "ubuntu-20.04" | |
| # python-version: "3.10" | |
| # - os: "macos-latest" | |
| # python-version: "3.10" | |
| # numpy1.18 only on python3.10 | |
| # (which, in turn, is only on 'latest') | |
| - python-version: "2.7" | |
| numpy-version: "1.18" | |
| - python-version: "3.9" | |
| numpy-version: "1.18" | |
| - python-version: "3.8" | |
| numpy-version: "1.18" | |
| - python-version: "3.7" | |
| numpy-version: "1.18" | |
| # excludes for numpy 1.22 | |
| # - python-version: "2.7" | |
| # numpy-version: "1.22" | |
| # - python-version: "3.9" | |
| # numpy-version: "1.22" | |
| # - python-version: "3.8" | |
| # numpy-version: "1.22" | |
| # - python-version: "3.7" | |
| # numpy-version: "1.22" | |
| env: | |
| CC: ${{ matrix.compiler }} | |
| CORRFUNC_CI: true | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| python-version: ${{ matrix.python-version }} | |
| # This was needed on 18.04 but not on 20.04 | |
| # - name: Install binutils on linux | |
| # shell: bash -l {0} | |
| # if: matrix.os == 'ubuntu-18.04' | |
| # run: | | |
| # sudo apt-get update | |
| # sudo apt-get install binutils | |
| - name: Install gcc-7 on ubuntu-20.04 | |
| shell: bash -l {0} | |
| if: matrix.os == 'ubuntu-20.04' | |
| run: | | |
| sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
| sudo apt-get update | |
| sudo apt-get install gcc-7 | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda create -q --yes -n test python=${{ matrix.python-version }} nomkl | |
| conda activate test | |
| conda install -q --yes -c conda-forge numpy=${{ matrix.numpy-version }} gsl | |
| - name: Display PATH, compiler, python | |
| shell: bash -l {0} | |
| run: | | |
| conda activate test | |
| echo "PATH = " $PATH | |
| echo "COMPILER = " `which ${{ matrix.compiler }}` | |
| echo "COMPILER VERSION = " `${{ matrix.compiler }} --version` | |
| echo "PYTHON = " `which python` | |
| echo "(PYTHON, NUMPY) version = " `python -c "import sys; import numpy as np; print(sys.version); print(np.__version__);"` | |
| echo "Preprocessor defs:" | |
| echo `${{ matrix.compiler }} -dM -E - -march=native` | |
| - name: lscpu on Linux | |
| if: matrix.os != 'macos-latest' | |
| run: | | |
| lscpu | |
| - name: sysctl machdep.cpu on OSX | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| sysctl machdep.cpu | |
| # - name: Add linker flag to OSX + gcc | |
| # shell: bash -l {0} | |
| # if: matrix.os == 'osx-latest' && startswith(matrix.compiler, 'gcc') | |
| # run: export CLINK = '-lgomp' | |
| - name: compile | |
| shell: bash -l {0} | |
| run: make -r CC=${{ matrix.compiler }} | |
| - name: install | |
| shell: bash -l {0} | |
| run: make install CC=${{ matrix.compiler }} | |
| - name: compile and install python extensions | |
| shell: bash -l {0} | |
| run: | | |
| echo "CC = " $CC | |
| export CC=${{ matrix.compiler }} | |
| python -m pip install -e . | |
| - name: tests | |
| shell: bash -l {0} | |
| run: make tests CC=${{ matrix.compiler }} | |
| - name: doctests | |
| shell: bash -l {0} | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10' && matrix.numpy-version == '1.16' | |
| run: | | |
| python -m pip install 'sphinx>=1.8' | |
| make -C docs doctest | |
| - name: Python tests | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install pytest | |
| python -m pytest -v |