diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e87a580..066a5d0 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -15,10 +15,11 @@ env: jobs: build: - runs-on: ubuntu-latest + runs-on: ${{ matrix.os }} strategy: fail-fast: false matrix: + os: ["ubuntu-latest", "macos-latest"] python-version: ["3.5","3.6","3.7","3.8","3.9","3.10","3.11"] steps: diff --git a/.github/workflows/build_ubuntu-20.04.yml b/.github/workflows/build_ubuntu-20.04.yml deleted file mode 100644 index ab53777..0000000 --- a/.github/workflows/build_ubuntu-20.04.yml +++ /dev/null @@ -1,105 +0,0 @@ -# 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: ubuntu-20.04 - strategy: - fail-fast: false - matrix: - python-version: ["3.5","3.6","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