Enable recombination length calculation with gaps #503
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| name: build | |
| on: | |
| push | |
| jobs: | |
| test-osx: | |
| runs-on: macos-13 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.9 | |
| - name: Set up miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.9 | |
| - name: Install dependencies with conda | |
| run: | | |
| sudo chown -R $UID $CONDA && source $CONDA/etc/profile.d/conda.sh && conda env update --file environment.yml | |
| - name: Run C and python tests | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && FILES=`ls -l1 $CONDA_PREFIX/lib/clang/*/lib/darwin/*`; for clang_dir in $(ls -d1 $CONDA_PREFIX/lib/clang/*); do if [[ ! -d "$clang_dir/lib/darwin" ]]; then mkdir -p $clang_dir/lib/darwin; for clang_file in $(echo $FILES); do ln -s $clang_file $clang_dir/lib/darwin/; done; fi; done && export PATH=$PATH:/lib/python3.9/site-packages/ && autoreconf -i && ./configure --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX CFLAGS="-O0 -I${CONDA_PREFIX}/include/" LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" --host=x86_64-apple-darwin --build=x86_64-apple-darwin && make && make install && make check | |
| test-linux: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies with conda | |
| run: | | |
| $CONDA/bin/conda env update --file environment.yml && conda init | |
| - name: Install subunit from source | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" && export CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_LIBS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" && conda install -c conda-forge testtools extras six testscenarios fixtures traceback2 python-mimeparse iso8601 && git clone https://github.com/testing-cabal/subunit.git && cd subunit && autoreconf -vi && CXXFLAGS="${CXXFLAGS} -I${CONDA_PREFIX}/include/" LDFLAGS="${LDFLAGS} -L${CONDA_PREFIX}/lib/ -lcppunit" ./configure --prefix=$CONDA_PREFIX && sudo make install && make check && cd .. | |
| - name: Run C and python tests | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/ --coverage" && export CFLAGS="-I${CONDA_PREFIX}/include/ --coverage" && export PATH=$PATH:/lib/python3.9/site-packages/ && export NUMBA_DISABLE_JIT=1 && autoreconf -i && ./configure --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX -enable-code-coverage CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS" --host=x86_64-linux-gnu --build=x86_64-linux-gnu && make && make install && export CODE_COVERAGE_OUTPUT_FILE="gubbins_coverage.info" && make check && make check-code-coverage | |
| - name: Upload python code coverage analysis | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| files: ./python/coverage.xml,gubbins_coverage.info |