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.travis.yml
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language: python
os:
- linux
dist: xenial
python:
- "3.6"
before_install:
- sudo apt-get -qq update
- sudo apt-get install -y libproj-dev libgeos-dev
install:
# Install cython
- pip install cython
# Install pyRona
- pip install .
# Install codacy to push coverage info
- pip install codacy-coverage
- pip install coverage
# Install scipy
- pip install scipy
# Install latest numpy
- pip install numpy
script:
# Run tests
- py.test tests/*.py -v
# Coverage runs
- coverage erase
- coverage run --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 --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 --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 --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
after_success:
- coverage xml
- python-codacy-coverage -r coverage.xml
# Other stuff
notifications:
email: