Update test.py #38
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| name: "Tests on Ubuntu" | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - '**' | |
| jobs: | |
| build-and-test: | |
| name: Tests on Ubuntu | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - cxx: "clang++-13" | |
| build-type: "Debug" | |
| sse: "OFF" | |
| python: "3.8" | |
| - cxx: "clang++-14" | |
| build-type: "Release" | |
| sse: "OFF" | |
| python: "3.9" | |
| - cxx: "g++-10" | |
| build-type: "Release" | |
| sse: "OFF" | |
| python: "3.10" | |
| - cxx: "g++-12" | |
| build-type: "Debug" | |
| sse: "OFF" | |
| python: "3.11" | |
| env: | |
| CXX: ${{ matrix.cxx }} | |
| BUILD_DIR: ${{ github.workspace }}/build_dir | |
| TEST_OUTPUT_DIR: ${{ github.workspace }}/test_output | |
| EXAMPLE_DIR: ${{ github.workspace }}/example | |
| steps: | |
| - name: checkout repo | |
| uses: actions/checkout@v4 | |
| - name: make directories | |
| run: | | |
| mkdir build_dir | |
| mkdir test_output | |
| ls -la | |
| - name: cmake configure | |
| run: cmake ${{ github.workspace }} -DCMAKE_BUILD_TYPE=${{ matrix.build-type }} -DENABLE_SSE=${{ matrix.sse }} | |
| working-directory: ${{ env.BUILD_DIR }} | |
| - name: cmake build | |
| run: cmake --build . --parallel 4 | |
| working-directory: ${{ env.BUILD_DIR }} | |
| - name: test GENIE | |
| run: | | |
| gen=${EXAMPLE_DIR}/test | |
| phen=${EXAMPLE_DIR}/test.pheno | |
| covar=${EXAMPLE_DIR}/test.cov | |
| annot=${EXAMPLE_DIR}/single.annot | |
| env=${EXAMPLE_DIR}/test.env | |
| ./GENIE -g $gen -p $phen -c $covar -e $env -m G+GxE+NxE -k 10 -jn 10 -o ${TEST_OUTPUT_DIR}/test.1.out -a $annot -t 6 | |
| echo -e "\n\n###\n\n" | |
| cat ${TEST_OUTPUT_DIR}/test.1.out | |
| working-directory: ${{ env.BUILD_DIR }} | |
| - name: test GENIE_multi_pheno | |
| run: | | |
| gen=${EXAMPLE_DIR}/test | |
| phen=${EXAMPLE_DIR}/test.2.pheno | |
| covar=${EXAMPLE_DIR}/test.cov | |
| annot=${EXAMPLE_DIR}/single.annot | |
| env=${EXAMPLE_DIR}/test.env | |
| ./GENIE_multi_pheno -g $gen -p $phen -c $covar -e $env -m G+GxE+NxE -k 10 -jn 10 -o ${TEST_OUTPUT_DIR}/test.2.out -a $annot -t 6 | |
| echo -e "\n\n###\n\n" | |
| cat ${TEST_OUTPUT_DIR}/test.2.out | |
| working-directory: ${{ env.BUILD_DIR }} | |
| - name: test GENIE_mem | |
| run: | | |
| echo "genotype=${EXAMPLE_DIR}/test" > config.txt | |
| echo "phenotype=${EXAMPLE_DIR}/test.pheno" >> config.txt | |
| echo "covariate=${EXAMPLE_DIR}/test.cov" >> config.txt | |
| echo "environment=${EXAMPLE_DIR}/test.env" >> config.txt | |
| echo "annotation=${EXAMPLE_DIR}/single.annot" >> config.txt | |
| echo "output=${TEST_OUTPUT_DIR}/test.3.out" >> config.txt | |
| echo "nthreads=6" >> config.txt | |
| echo "num_vec=20" >> config.txt | |
| echo "num_jack=10" >> config.txt | |
| echo "trace=1" >> config.txt | |
| echo "model=G" >> config.txt | |
| echo "verbose=1" >> config.txt | |
| echo -e "\n\n###\n\n" | |
| ./GENIE_mem --config ./config.txt | |
| cat ${TEST_OUTPUT_DIR}/test.3.out | |
| working-directory: ${{ env.BUILD_DIR }} | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: install python module | |
| run: | | |
| pip install . -v | |
| - name: run python tests | |
| run: | | |
| python test/test.py |