Update vignette_space.md #396
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| name: Tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| jobs: | |
| test: | |
| name: Python | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python: [3.8, 3.9] | |
| os: [macos-latest, ubuntu-latest, windows-latest] | |
| sys: [mingw64, ucrt64] | |
| env: [x86_64, ucrt-x86_64] | |
| exclude: | |
| - os: macos-latest | |
| sys: ucrt64 | |
| - os: macos-latest | |
| sys: mingw64 | |
| env: ucrt-x86_64 | |
| - os: ubuntu-latest | |
| sys: ucrt64 | |
| - os: ubuntu-latest | |
| sys: mingw64 | |
| env: ucrt-x86_64 | |
| - os: windows-latest | |
| sys: ucrt64 | |
| env: x86_64 | |
| - os: windows-latest | |
| sys: mingw64 | |
| env: ucrt-x86_64 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Install Conda | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-name: anaconda-client-env | |
| environment-file: requirements/CI-conda/ci-environment.yml | |
| cache-env: true | |
| extra-specs: | | |
| python=${{ matrix.python }} | |
| - name: Setup MSYS2 ${{matrix.sys}} | |
| uses: msys2/setup-msys2@v2 | |
| if: matrix.os == 'windows-latest' | |
| with: | |
| msystem: ${{matrix.sys}} | |
| release: false | |
| install: >- | |
| git | |
| base-devel | |
| msys2-devel | |
| mingw-w64-${{matrix.env}}-zstd | |
| mingw-w64-${{matrix.env}}-zlib | |
| mingw-w64-${{matrix.env}}-toolchain | |
| mingw-w64-${{matrix.env}}-cmake | |
| mingw-w64-${{matrix.env}}-autotools | |
| - name: Cache SLiM build | |
| if: matrix.os == 'windows-latest' | |
| id: cache-slim | |
| uses: actions/[email protected] # latest version is broken https://github.com/actions/cache/issues/891, so pinning to 3.0.5 | |
| with: | |
| path: D:\a\pyslim\pyslim\SLiM | |
| key: ${{runner.os}}-${{matrix.sys}}-${{matrix.env}}-key | |
| - name: Build SLiM windows | |
| if: ( matrix.os == 'windows-latest' && steps.cache-slim.outputs.cache-hit != 'true' ) | |
| shell: msys2 {0} | |
| run: | | |
| git clone https://github.com/messerlab/SLiM.git | |
| mkdir -p SLiM/Release | |
| cd SLiM/windows_compat/gnulib | |
| touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in | |
| cd ../.. | |
| cd Release | |
| cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release .. | |
| make -j 2 | |
| - name: Install SLiM macos / linux | |
| if: (matrix.os == 'macos-latest' || matrix.os == 'ubuntu-latest') | |
| run: | | |
| micromamba install slim -y | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| micromamba info | |
| micromamba list | |
| export PATH=$PWD/SLiM/Release:$PATH | |
| which slim | |
| slim -v | |
| python -m pytest \ | |
| -n 0 \ | |
| -v \ | |
| --cov=pyslim \ | |
| --cov-branch \ | |
| --cov-report=term-missing \ | |
| --cov-report=xml \ | |
| tests | |
| - name: upload coverage report to codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| fail_ci_if_error: true | |
| env_vars: OS,PYTHON | |
| token: ${{ secrets.CODECOV_TOKEN }} |