simplified test function #65
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| name: Repository test | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Linux dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential wget | |
| - name: Download and install HTSLib | |
| run: | | |
| wget -q https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2 | |
| tar jxvf htslib-1.17.tar.bz2 | |
| cd htslib-1.17 && ./configure && make && sudo make install && cd ../ | |
| wget -q http://ftp.debian.org/debian/pool/main/m/mafft/mafft_7.407-2_amd64.deb | |
| sudo dpkg -i mafft_7.407-2_amd64.deb && cd ../ | |
| wget -q https://github.com/isovic/racon/releases/download/1.4.3/racon-v1.4.3.tar.gz | |
| tar zxvf racon-v1.4.3.tar.gz | |
| cd racon-v1.4.3 && mkdir build && cd build | |
| cmake -DCMAKE_BUILD_TYPE=Release .. | |
| make && make install && cd ../../ && rm -rf racon-v1.4.3 | |
| wget -q https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24.tar.bz2 | |
| tar jxvf minimap2-2.24.tar.bz2 | |
| cd minimap2-2.24 | |
| make && cp minimap2 /usr/local/bin/ | |
| - name: Install python dependencies | |
| run: | | |
| pip install -U setuptools | |
| pip install -U importlib-metadata | |
| pip install requests | |
| pip install pytest | |
| pip install numpy | |
| pip install pysam | |
| pip install parasail | |
| - name: Pytest | |
| run: | | |
| pytest | |