.gitlab-ci.yml

image: quay.io/comparative-genomics-toolkit/cactus-ci-base:latest

variables:
  GIT_SUBMODULE_STRATEGY: recursive

before_script:
  - whoami
  - sudo apt-get -q -y update
  - sudo apt-get -q -y install --no-upgrade bcftools parallel libdeflate-dev cmake libjemalloc-dev python3-distutils pybind11-dev autoconf libzstd-dev libhts-dev
  - startdocker || true
  - docker info

after_script:
  - stopdocker || true
  
stages:
  - test

test-job:
  stage: test
  script:
    - make clean
    - virtualenv -p python3.9 venv
    - source venv/bin/activate
    - python3.9 -m pip install -r toil-requirement.txt
    - python3.9 -m pip install -U .
    # these are the old travis tests, followed by its docker push
    - git clone https://github.com/ComparativeGenomicsToolkit/cactusTestData
    - export ASAN_OPTIONS="detect_leaks=0"
    - CGL_DEBUG=ultra make -j 8
    - CACTUS_BINARIES_MODE=local SON_TRACE_DATASETS=$(pwd)/cactusTestData CACTUS_TEST_CHOICE=normal make test
    - pip install -U newick attrs
    - make -j 8 hal_test
    # rebuild without all the debug flags
    - make clean
    - make -j 8	 
    - numcpu=8 build-tools/downloadPangenomeTools
    - CACTUS_LEGACY_ARCH=1 numcpu=8 build-tools/downloadMafTools	 
    - python3.9 -m pip install -U .
    # force local docker image to use legacy mode so tests run
    - sed -i Dockerfile -e 's/ENV avx2 1/ENV CACTUS_LEGACY_ARCH 1/g'
    - make docker    
    - make -j 8 evolver_test

  artifacts:
    # Let Gitlab see the junit report
    #reports:
    #  junit: test-report.xml
    #when: always