.travis_old.yml

sudo: required
dist: bionic
language: python

python:
  - "3.7"

before_install:
  - |
    if [[ "$TRAVIS_OS_NAME" == "linux" && "$CACTUS_BINARIES_MODE" == "local" ]]; then
       sudo apt-get -qq update
       sudo apt-get install -y git gcc g++ build-essential zlib1g-dev wget valgrind libbz2-dev pkg-config libhdf5-dev liblzo2-dev 
    fi
  - |
    if [[ "$TRAVIS_OS_NAME" == "linux" && "$CACTUS_BINARIES_MODE" == "local" ]]; then
       sudo apt-get install -y git gcc g++ build-essential zlib1g-dev wget valgrind libbz2-dev pkg-config libhdf5-dev liblzo2-dev 
    fi
  - |
    if [[ ! -z "$SON_TRACE_DATASETS" ]]; then
       git clone https://github.com/ComparativeGenomicsToolkit/cactusTestData
    fi

  # Push docker containers. We skip this on PR builds because Travis
  # doesn't include the user/password in those builds.
  - |
    if [[ "$CACTUS_BINARIES_MODE" == "docker" ]]; then
       if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]; then
          docker login --username $QUAY_USERNAME --password $QUAY_PASSWORD quay.io
          make push
       else
          make docker
       fi
    fi
script:
# install toil / cactus
  - pip install -r toil-requirement.txt
  - pip install -U .
  - if [[ "$CACTUS_TEST_CHOICE" == "normal" ]]; then export MAKE_TARGET=test_nonblast; fi
  - if [[ "$CACTUS_TEST_CHOICE" == "blast" ]]; then export MAKE_TARGET=test_blast; fi
  - if [[ "$CACTUS_BINARIES_MODE" == "local" ]]; then make && PATH=`pwd`/bin:$PATH PYTHONPATH=`pwd`:`pwd`/src travis_wait 50 make ${MAKE_TARGET}; fi
  - if [[ "$CACTUS_BINARIES_MODE" == "docker" ]]; then travis_wait 40 make ${MAKE_TARGET}; fi
os:
  - linux
services:
  - docker
env:
  # Assert-enabled tests using extra-large test data, but restricted to blast tests only to keep under 50 mins.
  - CGL_DEBUG=1 CACTUS_BINARIES_MODE=local SON_TRACE_DATASETS=$TRAVIS_BUILD_DIR/cactusTestData CACTUS_TEST_CHOICE=blast
  # Assert-enabled tests using extra-large test data, but restricted to non-blast tests only to keep under 50 mins.
  - CGL_DEBUG=1 CACTUS_BINARIES_MODE=local SON_TRACE_DATASETS=$TRAVIS_BUILD_DIR/cactusTestData CACTUS_TEST_CHOICE=normal
  # Docker container push and test.
  - CACTUS_BINARIES_MODE=docker CACTUS_TEST_CHOICE=normal
  # Paranoia about memory corruption. Leak detection is disabled
  # because many utilities are short-lived and don't bother cleaning
  # up memory before exit.
  - CGL_DEBUG=ultra ASAN_OPTIONS=detect_leaks=0 CACTUS_BINARIES_MODE=local CACTUS_TEST_CHOICE=normal