build.yml

# This workflow will install RGI dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Build RGI and test

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

env:
  BLAST_VERSION: 2.14.1

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest", "ubuntu-23.04", "ubuntu-22.04", "ubuntu-20.04", "ubuntu-18.04.6"]
        python-version: ["3.7","3.8","3.9","3.10","3.11"]

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}
        architecture: 'x64'
    - name: Install dependencies
      run: |

        sudo apt-get -qq update
        sudo apt-get -qq install -y prodigal tree
        sudo apt-get -qq install -y libtbb-dev
        sudo apt-get -qq install -y cmake g++ make

        echo "install blast ..."
        wget --quiet http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
        tar xzf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
        sudo mv ncbi-blast-${BLAST_VERSION}+/bin/* /usr/bin

        wget --quiet https://github.com/BenLangmead/bowtie2/releases/download/v2.4.5/bowtie2-2.4.5-linux-x86_64.zip
        unzip -q bowtie2-2.4.5-linux-x86_64.zip
        sudo mv bowtie2-2.4.5-linux-x86_64/bowtie2* /usr/bin

        wget --quiet http://github.com/bbuchfink/diamond/releases/download/v0.8.36/diamond-linux64.tar.gz
        tar xzf diamond-linux64.tar.gz
        sudo mv diamond /usr/bin

        git clone --quiet https://github.com/lh3/bwa.git
        pushd bwa && make --quiet && sudo mv bwa /usr/bin && popd

        wget --quiet https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-linux
        mv jellyfish-linux jellyfish && chmod +x jellyfish && sudo mv jellyfish /usr/bin

        wget --quiet https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
        tar jxf samtools-1.9.tar.bz2
        pushd samtools-1.9 && ./configure --enable-silent-rules && make --quiet && sudo mv samtools /usr/bin && popd

        wget --quiet https://github.com/pezmaster31/bamtools/archive/v2.5.2.tar.gz
        tar xzf v2.5.2.tar.gz
        pushd bamtools-2.5.2/ && mkdir build && cd build && cmake .. && make --quiet && sudo make install --quiet && popd
        bamtools --version

        wget --quiet https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools
        chmod +x bedtools && sudo mv bedtools /usr/bin

        git clone --quiet https://bitbucket.org/genomicepidemiology/kma.git
        pushd kma && make --quiet && sudo mv kma /usr/bin && popd

        python -m pip install --upgrade --quiet pip
        #python -m pip install --quiet flake8 pytest
        python -m pip install --quiet pytest
        python -m pip install --quiet setuptools

    - name: Install rgi
      run: |
        echo "=====> install rgi ..."
        echo `pwd`
        pip3 install -r requirements.txt
        pip3 install setuptools
        pip3 install .
    - name: Check versions
      run: |
          echo "=====> check versions installed ..."
          echo `pwd`
          blastp -version
          bowtie2 --version
          diamond --version
          jellyfish --version
          samtools --version
          bedtools --version
          kma -v
          rgi -h
    # - name: Lint with flake8
    #   run: |
    #     # stop the build if there are Python syntax errors or undefined names
    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test with pytest
      run: |
        bash test.sh