test_ubuntu.yml

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 -annot $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 -annot $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