.travis.yml

jobs:
  include:
    - language: perl
      services:
        - mysql
      perl:
        - '5.14'
      env:
        - COVERALLS=true  DB=mysql
      sudo: false
      addons:
        apt:
          packages:
            - unzip
            - sendmail
            - graphviz
            - emboss
      before_install:
        - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
        - export PATH=$PATH:$PWD/ensembl-git-tools/bin
        - export ENSEMBL_BRANCH=master
        - export SECONDARY_BRANCH=main
        - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
        - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
        - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
        - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
        - git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
        - git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
        - cd htslib
        - make
        - export HTSLIB_DIR=$(pwd -P)
        - cd ..
      install:
        - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
        - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
        - cpanm --sudo -v --installdeps --notest .
        - cpanm --sudo -n Devel::Cover::Report::Coveralls
        - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
        - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
      script: ./travisci/harness.sh

    - language: python
      python: 3.7.6
      install:
        - pip install -r requirements-test.txt
        - pip install -e .
      script:
        - pytest src/python/test

notifications:
  email:
    on_success: always
    on_failure: always
  slack:
    secure: BkrSPAkOM5aTOpeyO9vZnHdZ0LF1PLk0r2HtcXN2eTMyiHoGXkl6VUjdAL8EkzI4gunW2GProdSIjHpf60WdiEmKAulMdJRI+xyUbuxnY31mwiikS9HYwqmPBbMTf0Mh2pMBngZRFs+gaFZDUMTfLfp+8MQfU1R54yb6hPuVt5I=