.travis.yml

language: c
sudo: true

env:
  - TRAVIS_PYTHON_VERSION=3.7
os:
  - linux
stages:
  - test

# Setup anaconda
before_install:
  - export HIC_TEST_DATA_DIR="`pwd`/hicexplorer/test/test_data/"
  - export PYTHONWARNINGS="ignore"
  - echo $HIC_TEST_DATA_DIR
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh ; fi
  - bash miniconda.sh -b -p $HOME/miniconda
  - PATH_WITHOUT_CONDA="$PATH"
  - export PATH="$HOME/miniconda/bin:$PATH"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda install conda=4.8 -q
  # - conda update -q conda
  # Useful for debugging any issues with conda
  - conda info -a
# Install packages
install:
  - conda install --yes -c conda-forge -c bioconda python=$TRAVIS_PYTHON_VERSION --file requirements.txt
  - conda install --yes -c conda-forge -c bioconda pytest
  - conda install --yes -c conda-forge -c bioconda nose
  - conda install --yes pathlib
  - conda install --yes -c defaults -c conda-forge -c bioconda configparser
  - python setup.py install
# command to run tests

script:
  - hicFindRestSite --version
  - hicAggregateContacts --version
  - hicBuildMatrix --version
  - hicCorrectMatrix --version
  - hicCorrelate --version
  - hicDetectLoops --version
  - hicFindTADs --version
  - hicMergeMatrixBins --version
  - hicPlotMatrix --version
  - hicPlotDistVsCounts --version
  - hicPlotTADs --version
  - hicSumMatrices --version
  - hicInfo --version
  - hicConvertFormat --version
  - hicAdjustMatrix --version
  - hicNormalize --version
  - hicAverageRegions --version
  - hicPlotAverageRegions --version
  - hicMergeLoops --version
  - hicValidateLocations --version
  - hicCompartmentalization --version
  - chicQualityControl --version
  - chicViewpointBackgroundModel --version
  - chicViewpoint --version
  - chicSignificantInteractions --version
  - chicAggregateStatistic --version
  - chicDifferentialTest --version
  - chicPlotViewpoint --version
  - hicPlotSVL --version
  - hicQuickQC --version
  - hicCompareMatrices --version
  - hicPCA --version
  - hicTransform --version
  - hicPlotViewpoint --version
  - hicCreateThresholdFile --version
  - hicHyperoptDetectLoops --version
  - hicHyperoptDetectLoopsHiCCUPS --version
  - hicMergeDomains --version
  - hicDifferentialTAD --version
  - hicFindRestSite --help
  - hicAggregateContacts --help
  - hicBuildMatrix --help
  - hicCorrectMatrix --help
  - hicCorrelate --help
  - hicDetectLoops --help
  - hicFindTADs --help
  - hicMergeMatrixBins --help
  - hicPlotMatrix --help
  - hicPlotDistVsCounts --help
  - hicPlotTADs --help
  - hicSumMatrices --help
  - hicInfo --help
  - hicConvertFormat --help
  - hicAdjustMatrix --help
  - hicNormalize --help
  - hicAverageRegions --help
  - hicPlotAverageRegions --help
  - hicMergeLoops --help
  - hicValidateLocations --help
  - hicCompartmentalization --help
  - chicQualityControl --help
  - chicViewpointBackgroundModel --help
  - chicViewpoint --help
  - chicSignificantInteractions --help
  - chicAggregateStatistic --help
  - chicDifferentialTest --help
  - chicPlotViewpoint --help
  - hicPlotSVL --help
  - hicQuickQC --help
  - hicCompareMatrices --help
  - hicPCA --help
  - hicTransform --help
  - hicPlotViewpoint --help
  - hicCreateThresholdFile --help
  - hicHyperoptDetectLoops --help
  - hicHyperoptDetectLoopsHiCCUPS --help
  - hicMergeDomains --help
  - hicDifferentialTAD --help

jobs:
  include:  
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs_2.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_two.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_three.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_four.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_five.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: py.test hicexplorer/test/trivial_runs/test_hicAggregateContacts_trivial_runs_six.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: travis_wait 40 py.test hicexplorer/test/trivial_runs/test_hicConvertFormat_trivial_runs.py
    - stage: test
      os: linux
      env: TRAVIS_PYTHON_VERSION=3.7
      script: travis_wait 40 py.test hicexplorer/test/trivial_runs/test_hicConvertFormat_trivial_runs_cool.py