Add more tests of fixation pruning #3007
Workflow file for this run
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| name: UbuntuStressTest | |
| on: | |
| pull_request: | |
| jobs: | |
| test_ubuntu: | |
| name: Ubuntu | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python: [ 3.9, "3.10", "3.11", "3.12" ] | |
| os: [ ubuntu-22.04 ] | |
| compiler: [gcc, clang14] | |
| rust: [1.62.1] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| with: | |
| access_token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - uses: dtolnay/rust-toolchain@v1 | |
| with: | |
| toolchain: ${{ matrix.rust }} | |
| - name: Install apt dependencies | |
| run: | | |
| sudo apt install --fix-missing -y libgsl-dev cmake autoconf libboost-test-dev libboost-program-options-dev valgrind | |
| - name: Install cbindgen | |
| uses: baptiste0928/cargo-install@v3 | |
| with: | |
| crate: cbindgen | |
| version: "=0.24.3" | |
| locked: true | |
| cache-key: ${{ matrix.os }} | |
| - name: rustc version | |
| run: | | |
| rustc --version | |
| - name: cbindgen version | |
| run: | | |
| cbindgen --version | |
| - name: Edit PATH | |
| run: | | |
| echo "$HOME/.local/bin" >> $GITHUB_PATH | |
| - name: Set GCC as compiler | |
| if: matrix.compiler == 'gcc' | |
| run: | | |
| echo "CC=gcc" >> $GITHUB_ENV | |
| echo "CXX=g++" >> $GITHUB_ENV | |
| - name: Install clang-14 | |
| if: matrix.compiler == 'clang14' | |
| run: | | |
| sudo apt-get install clang-14 clang++-14 | |
| echo "CC=clang-14" >> $GITHUB_ENV | |
| echo "CXX=clang++-14" >> $GITHUB_ENV | |
| - name: Discover llvm-config | |
| run: | | |
| dpkg -S llvm-config | |
| - name: Set LLVM_CONFIG on 22.04 | |
| if: matrix.os == 'ubuntu-22.04' | |
| run: | | |
| echo "LLVM_CONFIG=/usr/bin/llvm-config" >> $GITHUB_ENV | |
| # - name: Set LLVM_CONFIG on 18.04 | |
| # if: matrix.os == 'ubuntu-18.04' | |
| # run: | | |
| # echo "LLVM_CONFIG=/usr/lib/llvm-9/bin/llvm-config" >> $GITHUB_ENV | |
| - name: Python version | |
| run: | | |
| python --version | |
| - name: Cache pip dependancies | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.local | |
| key: ${{ runner.os }}-${{ matrix.python }}-ubuntu-V4-${{ hashFiles('requirements/development.txt') }} | |
| - name: Install pip dependencies | |
| # if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| python -m pip install --user --upgrade pip | |
| # These are needed to install black: | |
| python -m pip install --user --upgrade setuptools wheel | |
| python -m pip install --user -r requirements/development.txt | |
| # For sdist validation | |
| python -m pip install --user --upgrade twine build | |
| # Needed so that we don't affect building any pip dependencies with these flags | |
| - name: Set CPPFLAGS for C++ builds | |
| run: | | |
| echo "CPPFLAGS=-Wextra -Weffc++ -Woverloaded-virtual -Wold-style-cast -Werror=effc++ -Werror=old-style-cast -Werror=overloaded-virtual -Werror=unused-parameter" >> $GITHUB_ENV | |
| - name: Build | |
| run: | | |
| cmake -E env CPPFLAGS="$CPPFLAGS" \ | |
| cmake -E env CC="$CC" \ | |
| cmake -E env CXX="$CXX" cmake -S. -Bbuild -DCMAKE_BUILD_TYPE=Release -DBUILD_CPP_UNIT_TESTS=ON -DBUILD_CPP_BENCHMARK=ON -DBUILD_PYTHON_UNIT_TESTS=ON -DDISABLE_LTO=ON | |
| cmake --build build -j 4 | |
| - name: Run C++ tests | |
| run: | | |
| cmake --build build -t test | |
| - name: Run C++ tests through valgrind | |
| run: | | |
| # NOTE: applying valgrind at the cmake level | |
| # using the command in the previous step gives | |
| # "leaks", but they come from cmake and not our | |
| # test binary. So, we run it manually. | |
| valgrind ./build/cpptests/fwdpy11_cpp_tests | |
| - name: Clean cmake build | |
| run: | | |
| rm -rf build | |
| - name: Manualy run setuptools_scm | |
| run: | | |
| python -m setuptools_scm | |
| - name: Run Python tests | |
| run: | | |
| python -m pytest -n 2 tests | |
| python -m pytest -n 2 tests_with_cpp | |
| - name: Build and run examples/plugin | |
| run: | | |
| CPPFLAGS=$CPPFLAGS CC=$CC CXX=$CXX PYTHONPATH=. cmake examples/plugin | |
| make | |
| PYTHONPATH=. python -We examples/plugin/test_plugin.py | |
| - name: Run Python divergent optima example | |
| run: | | |
| PYTHONPATH=. python -We examples/gss_divergent_optima/gss_divergent_optima.py 100 0 | |
| - name: Validate the sdist | |
| run: | | |
| python -m build -s . | |
| #python setup.py check | |
| python -m twine check dist/*.tar.gz | |
| rm -rf dist/*.tar.gz | |
| - name: Test pip install from dist in fresh venv | |
| run: | | |
| python -m build -o dist -w . | |
| cd dist | |
| python -m venv venv | |
| source venv/bin/activate | |
| which python | |
| # The CPPFLAGS contain stuff for C++ that makes no sense for C. | |
| # The flags are also too strict for tskit to build under Py 3.12 | |
| ls | |
| CPPFLAGS= python -m pip install --no-cache-dir ./fwdpy11*-*linux*.whl | |
| python -m fwdpy11 --includes | |
| python -c "import fwdpy11;print(fwdpy11.__version__)" | |
| python -c "import fwdpy11;print(fwdpy11.__file__)" | |