.travis.yml

# Modified from https://github.com/biocore/scikit-bio
language: python
env:
  - PYTHON_VERSION=3.6 WITH_DOCTEST=True 
  - PYTHON_VERSION=3.7 WITH_DOCTEST=True 
  - PYTHON_VERSION=3.8 WITH_DOCTEST=True 
before_install:
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
  - chmod +x miniconda.sh
  - ./miniconda.sh -b
  - export PATH=/home/travis/miniconda3/bin:$PATH
install:
  - conda create --yes -n env_name python=$PYTHON_VERSION pip click numpy "scipy>=1.3.1" pep8 flake8 coverage future six "pandas>=0.20.0" nose h5py>=2.2.0 cython
  - source activate env_name
  - if [ ${PYTHON_VERSION} = "3.7" ]; then pip install sphinx==1.2.2 "docutils<0.14"; fi
  - pip install coveralls
  - pip install -e . --no-deps
script:
  - make test 
  - biom show-install-info
  - if [ ${PYTHON_VERSION} = "3.7" ]; then make -C doc html; fi
  # we can only validate the tables if we have H5PY
  - for table in examples/*hdf5.biom; do echo ${table}; biom validate-table -i ${table}; done
  # validate JSON formatted tables
  - for table in examples/*table.biom; do echo ${table}; biom validate-table -i ${table}; done;
  - python biom/assets/exercise_api.py examples/rich_sparse_otu_table_hdf5.biom sample
  - python biom/assets/exercise_api.py examples/rich_sparse_otu_table_hdf5.biom observation
  - sh biom/assets/exercise_cli.sh
after_success:
  - coveralls