trace summary w/o phenotype input implemented #37
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: "Tests on macOS" | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - '**' | |
| jobs: | |
| build-and-test: | |
| name: Tests on macOS | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: "macos-13" | |
| python: "3.11" | |
| - os: "macos-14" | |
| python: "3.12" | |
| env: | |
| 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=Release | |
| 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 |