chewbbaca.yml

name: chewbbaca

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.9', '3.10', '3.11']

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pytest
        pip install pytest-forked
        pip install py

    - name: install blast
      run: |
        mkdir $GITHUB_WORKSPACE/blast
        pushd $GITHUB_WORKSPACE/blast
        wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz \
        && tar -xzvf ncbi-blast-2.9.0+-x64-linux.tar.gz && rm ncbi-blast-2.9.0+-x64-linux.tar.gz
        echo "$GITHUB_WORKSPACE/blast/ncbi-blast-2.9.0+/bin" >> $GITHUB_PATH
        popd

    - name: check blast
      run: |
        which blastp
        blastp -version

    - name: install mafft
      run: |
        mkdir $GITHUB_WORKSPACE/mafft
        pushd $GITHUB_WORKSPACE/mafft
        wget https://mafft.cbrc.jp/alignment/software/mafft_7.475-1_amd64.deb
        sudo dpkg -i mafft_7.475-1_amd64.deb
        popd

    - name: check mafft
      run: |
        which mafft
        mafft --version

    - name: install fasttree2
      run: |
        mkdir $GITHUB_WORKSPACE/fasttree2
        pushd $GITHUB_WORKSPACE/fasttree2
        wget https://anaconda.org/bioconda/fasttree/2.1.11/download/linux-64/fasttree-2.1.11-h031d066_2.tar.bz2
        bzip2 -d fasttree-2.1.11-h031d066_2.tar.bz2 && tar -xvf fasttree-2.1.11-h031d066_2.tar && rm fasttree-2.1.11-h031d066_2.tar
        echo "$GITHUB_WORKSPACE/fasttree2/bin" >> $GITHUB_PATH
        popd

    - name: check fasttree2
      run: |
        which FastTree
        FastTree -help

    - name: checkout chewbbaca
      uses: actions/checkout@v4
      with:
        repository: B-UMMI/chewBBACA
        path: chewbbaca

    - name: install chewbbaca
      run: |
        pushd $GITHUB_WORKSPACE/chewbbaca
        python -m pip install .

    - name: check chewbbaca
      run: |
        which chewBBACA.py

    - name: run pytest
      run: |
        pushd CHEWBBACA/tests
        pytest --forked
        popd