.travis.yml

os: linux
dist: bionic
language: python
python:
  - "3.6"
  - "3.7"
  - "3.8"

branches:
  only:
  - master

on:
  tags: true

before_deploy:
    - git config --local user.name "cmorganl"
    - git config --local user.email "c.morganlang@gmail.com"

env:
    global:
      - CIBW_SKIP="cp27-* pp27-* *-manylinux_i686"
      - TWINE_USERNAME=__token__
      # Note: TWINE_PASSWORD is set to a PyPI API token in Travis settings
      - PIP="python3 -m pip"
      - TWINE_REPOSITORY=pypi
      - TWINE_REPOSITORY_URL=https://upload.pypi.org/legacy/
      - TRAVIS_TAG=${TRAVIS_TAG:-$(date +'%Y%m%d%H%M%S')-$(git log --format=%h -1)}
      - RAXML_VERSION="1.0.1"
      - EPA_VERSION="0.3.8"
      - BWA_VERSION="0.7.17"
      - HMMER_VERSION="3.3"
      - PRODIGAL_VERSION="2.6.3"
      - VSEARCH_VERSION="2.15.0"
      - MAFFT_VERSION="7.475-1"
      - MMSEQS_VERSION="12-113e3"

jobs:
    include:
      # perform a linux build
      - services: docker
      # and a mac build
      - name: "Python 3.6.5 on macOS 10.13"
        os: osx
        osx_image: xcode9.4
        language: shell

before_install:
    - if [ "$TRAVIS_OS_NAME" == "osx" ]; then
        git -C "$(brew --repo)" remote set-url origin https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/brew.git;
        curl -L 'http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh' -o Miniconda3-latest-MacOSX-x86_64.sh;
        bash Miniconda3-latest-MacOSX-x86_64.sh -b -p ~/anaconda_ete/;
        export PATH=~/anaconda_ete/bin:$PATH;
        conda install -y -c etetoolkit ete3;
      fi
    - if [ "$TRAVIS_OS_NAME" != "osx" ]; then
        sudo apt -y install gcc dpkg-dev zip git libz-dev default-jdk time time libssl-dev libsqlite3-dev \
          autotools-dev libtool flex bison cmake automake autoconf \
          python3-distutils python3-dev;
        sudo apt install python-six -y;

        wget https://mafft.cbrc.jp/alignment/software/mafft_${MAFFT_VERSION}_amd64.deb;
        sudo dpkg -i mafft_${MAFFT_VERSION}_amd64.deb;

        wget -O mmseqs-linux-sse41.tar.gz https://github.com/soedinglab/MMseqs2/releases/download/${MMSEQS_VERSION}/MMseqs2-Linux-SSE4_1.tar.gz;
        tar xvzf mmseqs-linux-sse41.tar.gz;
        sudo cp mmseqs/bin/mmseqs /usr/local/bin;

        wget https://github.com/hallamlab/TreeSAPP/raw/master/treesapp/sub_binaries/BMGE.jar;
        sudo mv BMGE.jar /usr/local/bin/;

        wget -O hmmer-${HMMER_VERSION}.tar.gz http://eddylab.org/software/hmmer/hmmer-${HMMER_VERSION}.tar.gz;
        tar -xzf hmmer-${HMMER_VERSION}.tar.gz; cd hmmer-${HMMER_VERSION}/; ./configure; make -f Makefile;
        sudo cp src/hmmsearch src/hmmbuild src/hmmalign /usr/local/bin/;
        cd -; rm hmmer-${HMMER_VERSION}.tar.gz;

        wget https://github.com/torognes/vsearch/archive/v${VSEARCH_VERSION}.tar.gz;
        tar xzf v${VSEARCH_VERSION}.tar.gz && cd vsearch-${VSEARCH_VERSION};
        ./autogen.sh && ./configure && make && sudo make install && cd -;

        wget -O prodigal https://github.com/hyattpd/Prodigal/releases/download/v${PRODIGAL_VERSION}/prodigal.linux;
        sudo mv prodigal /usr/local/bin/ && chmod +x /usr/local/bin/prodigal;

        wget -O v${BWA_VERSION}.tar.gz https://github.com/lh3/bwa/archive/v${BWA_VERSION}.tar.gz;
        tar -xzf v${BWA_VERSION}.tar.gz && cd bwa-${BWA_VERSION}/ && make && rm *.o && cd -;
        sudo cp bwa-${BWA_VERSION}/bwa /usr/local/bin/bwa && rm v${BWA_VERSION}.tar.gz;

      	wget -O od-seq.tar.gz http://www.bioinf.ucd.ie/download/od-seq.tar.gz; tar -xzf od-seq.tar.gz;
      	ODSEQ_SOURCES="OD-Seq/AliReader.cpp OD-Seq/Bootstrap.cpp OD-Seq/DistCalc.cpp OD-Seq/DistMatReader.cpp
      	OD-Seq/DistWriter.cpp OD-Seq/FastaWriter.cpp OD-Seq/IQR.cpp OD-Seq/ODseq.cpp OD-Seq/PairwiseAl.cpp
      	OD-Seq/Protein.cpp OD-Seq/ResultWriter.cpp OD-Seq/runtimeargs.cpp OD-Seq/util.cpp";
      	sudo g++ -fopenmp -o /usr/local/bin/OD-seq $ODSEQ_SOURCES;
      	rm od-seq.tar.gz;

        sudo wget -O /usr/local/bin/FastTree http://microbesonline.org/fasttree/FastTreeDbl;
        sudo chmod +x /usr/local/bin/FastTree;

        wget -O raxml-ng_v${RAXML_VERSION}.zip https://github.com/amkozlov/raxml-ng/releases/download/${RAXML_VERSION}/raxml-ng_v${RAXML_VERSION}_linux_x86_64.zip;
        mkdir raxml-ng_v${RAXML_VERSION}; unzip raxml-ng_v${RAXML_VERSION}.zip -d raxml-ng_v${RAXML_VERSION};
        sudo cp raxml-ng_v${RAXML_VERSION}/raxml-ng /usr/local/bin/;
        rm -r raxml-ng_v${RAXML_VERSION}.zip raxml-ng_v${RAXML_VERSION};

        wget -O epa-ng.tar.gz https://github.com/Pbdas/epa-ng/archive/v${EPA_VERSION}.tar.gz;
        tar -xzf epa-ng.tar.gz; cd epa-ng-${EPA_VERSION}/;
        make; sudo cp bin/epa-ng /usr/local/bin/; cd -;
        rm epa-ng.tar.gz;
      fi

install:
    - $PIP install --upgrade pip
    - $PIP install -r requirements.txt
    - $PIP install -U setuptools
    - $PIP install -U cibuildwheel
    - $PIP install codecov
    - $PIP install twine
    - $PIP install tox-travis

script:
    # build the wheels, put them into './wheelhouse'
    - if [ "$TRAVIS_OS_NAME" != "osx" ]; then
        tox -a;
        tox -v;
        fi
    - python3 -m cibuildwheel --output-dir wheelhouse
    - python3 setup.py sdist --dist-dir wheelhouse

notifications:
  email:
    on_success: never
    on_failure: always

after_success:
  # if the release was tagged, upload them to PyPI
  - ls wheelhouse/
  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then
      $PIP install twine;
      python3 -m twine upload --skip-existing wheelhouse/*.whl;
    fi
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then
        python3 -m twine upload --skip-existing wheelhouse/*.whl wheelhouse/*tar.gz;
    fi