.gitlab-ci.yml

stages:
  - tests
  - deployment

image: ubuntu:18.04

# Change pip's cache directory to be inside the project directory since we can
# only cache local items.
variables:
  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache"

# Pip's cache doesn't store the python packages
# https://pip.pypa.io/en/stable/reference/pip_install/#caching
#
# If you want to also cache the installed packages, you have to install
# them in a virtualenv and cache it as well.
cache:
  paths:
    - .cache/pip
    - venv/

tests:
    stage: tests
    script:
      - apt-get -qq update
      - apt-get install -y libproj-dev libgeos-dev libproj12 libgeos-c1v5
      - apt-get install -y python3 python3-pip python3-cartopy
      - apt-get install -y git
      - python3 -V
      - pip3 install virtualenv
      - virtualenv venv
      - source venv/bin/activate
      # Get pip packages
      - pip3 install cython
      - pip3 install codacy-coverage
      - pip3 install coverage
      - pip3 install scipy
      - pip3 install numpy
      - pip3 install pytest
      # - pip3 install cartopy
      # Install pyRona
      - pip3 install .
      # Run unit tests
      - pytest tests/*.py -v
      # Coverage runs
      - coverage erase
      - coverage run --source=pyRona --branch pyRona/pyRona.py lfmm -pc tests/data/LFMM_covars.txt -fc tests/data/LFMM_RCP26_covars.txt -out a.pdf -P 0.01 -assoc tests/data/Qsuber_lfmm_results.csv -geno tests/data/Qsuber.lfmm -immutables 1 2 3
      - coverage run --source=pyRona --branch -a pyRona/pyRona.py lfmm -pc tests/data/LFMM_covars.txt -fc tests/data/LFMM_RCP26_covars.txt -out a.pdf -P 0.01 -assoc tests/data/Qsuber_lfmm_results.csv -geno tests/data/Qsuber.lfmm -remove-outliers -immutables 1 2 3
      - coverage run --source=pyRona  --branch -a  pyRona/pyRona.py baypass -pc tests/data/ENVFILE -fc tests/data/ENVFILE_rpc26 -out b.pdf -bf 15 -pop tests/data/popnames_single_GEO.txt -beta tests/data/Qsuber_GBS_mcmc_aux_summary_betai.out -pij tests/data/Qsuber_GBS_mcmc_aux_summary_pij.out -immutables 1 2 3
      - coverage run --source=pyRona --branch -a  pyRona/pyRona.py baypass -pc tests/data/ENVFILE -fc tests/data/ENVFILE_rpc26 -out b.pdf -bf 15 -pop tests/data/popnames_single_GEO.txt -beta tests/data/Qsuber_GBS_mcmc_aux_summary_betai.out -pij tests/data/Qsuber_GBS_mcmc_aux_summary_pij.out -remove-outliers -immutables 1 2 3 -map ./map.png
      # Generate & upload coveragre report
      - coverage xml
      - coverage report
      - python-codacy-coverage -r coverage.xml
    coverage: '/TOTAL.+ ([0-9]{1,3}%)/'

deployment:
    stage: deployment
    script:
        - apt-get -qq update
        - apt-get install -y python3 python3-pip
        - apt-get install -y git
        - python3 -V
        - pip3 install virtualenv
        - virtualenv venv
        - source venv/bin/activate
        - pip3 install twine
        - python3 setup.py sdist
        - twine upload dist/* -u Stunts -p $pypi_password
    only:
        - tags
    artifacts:
        name: "$CI_PROJECT_NAME-$CI_COMMIT_TAG"
        paths:
            - dist/