.travis.yml

language: perl
perl:
  - "5.14"
  - "5.26.2"
services:
  - mysql
env:
  - COVERALLS=true  DB=mysql
addons:
  apt:
    update: true      
    packages:
      - unzip
      - sendmail
      - graphviz
      - emboss
      - libkyotocabinet-dev
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 travisci/kyotocabinet-perl-1.20.tar.gz
  - 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
jobs:
  include:
    - language: python
      python: 3.7.6
      install:
        - pip install -r requirements-test.txt
        - pip install -e .
      script:
        - pytest src/python/test
    - language: python
      python: 3.8
      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=