.travis.yml

language: python
python:
  - 3.5
notifications: # set notification options
  slack:
    rooms:
      - ucsc-cgl:Edwfgt7MJEVZV9Lib3igueTF
    on_success: change
    on_failure: always
  email: false

  # email:
  #   recipients:
  #     - andbaile@ucsc.edu
  #	-rsafavi@ucsc.edu
    # change is when the repo status goes from pass to fail or vice versa
    # on_failure: always

branches:
  except:
    - rojin
before_install:
- sudo apt-get update -qq
- sudo apt-get install libhdf5-serial-dev
- sudo apt-get install zlib1g-dev
- pip install google-compute-engine
#- pip install tensorflow
- git clone https://github.com/lh3/bwa.git
- cd bwa
- make
- export PATH=$PATH:$PWD
- cd ..

# sudo apt-get install libbz2-dev

install:
- sudo apt-get update
# We do this conditionally because it saves us some downloading if the
# version is the same.
- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
    wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
  else
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
  fi
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
# Useful for debugging any issues with conda
- conda info -a
- git submodule update --remote
- conda env create -f requirements35.yml
- source activate nanotensor3.5
- pip install google-compute-engine
- make
#- cd nanonet
#- python setup.py install
#- cd ../signalAlign
#- make
#- python setup.py install
#- pip install marginAlign
#- cd marginAlign
#- make test
- export PATH=$PATH:$PWD/signalAlign/bin
- export BOTO_CONFIG=/dev/null
- make test
#- pip install -U numpy
#- pip install -U h5py
- cd nanotensor

script:
- coverage run --source nanotensor -m pytest
# - coverage run --source nanotensor -a nanotensor/tests/data_preparation_test.py
# - bash <(curl -s https://codecov.io/bash) -cF python
# after_script: # here's a build step block
# - echo "We can put normal shell commands here"
# - echo "more shell commands here"

after_success:
  - codecov -t 3806b863-7185-4be7-9787-a0c1d7963703