.travis.yml

language: python
python:
  - "2.7"
  - "3.4"
  - "3.5"
  - "3.6"
  - "3.6-dev"
before_install:
- sudo apt-get build-dep python-scipy
- pip install scipy
install: 
#- pip install --upgrade pip setuptools wheel
#- pip install --only-binary numpy --only-binary scipy
- pip install -r requirements.txt
script: 
#- pytest
# Normal run
- python scoary.py -g scoary/exampledata/Gene_presence_absence.csv -t scoary/exampledata/Tetracycline_resistance.csv -o Test1 --no-time
# No_pairwise run
- python scoary.py -g scoary/exampledata/Gene_presence_absence.csv -t scoary/exampledata/Tetracycline_resistance.csv --no_pairwise -o Test2 --no-time
# Restricted run
- python scoary.py -g scoary/exampledata/Gene_presence_absence.csv -t scoary/exampledata/Tetracycline_resistance.csv -r scoary/exampledata/Restrict_to.csv -w -o Test3 --no-time
# Advanced opts run
- python scoary.py -g scoary/exampledata/Gene_presence_absence.csv -t scoary/exampledata/Tetracycline_resistance.csv -p 0.01 1E-5 -c B EPW --collapse -m 50 -u -n scoary/exampledata/ExampleTree.nwk --threads 4 -o Test4 --no-time

- python scoary/vcf2scoary.py --force scoary/exampledata/Example.vcf

# Add test to verify output
- python 'tests/test_scoary_output.py'