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.travis.yml
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language: python
sudo: required
group: deprecated-2017Q4
env:
- PYTHON_VERSION=3.5
before_install:
- wget http://repo.continuum.io/miniconda/Miniconda3-3.7.3-Linux-x86_64.sh -O miniconda.sh
- chmod +x miniconda.sh
- ./miniconda.sh -b
- export PATH=/home/travis/miniconda3/bin:$PATH
# Update conda itself
- conda update --yes conda
install:
# installing Qiita in it's own environment python2.7
- travis_retry conda create --quiet --yes -n qiita python=2.7 pip nose flake8
pyzmq networkx pyparsing natsort mock future libgfortran
'pandas>=0.18' 'scipy>0.13.0' 'numpy>=1.7' 'h5py>=2.3.1'
- source activate qiita
- pip install sphinx sphinx-bootstrap-theme coveralls
- pip install https://github.com/biocore/qiita/archive/dev.zip --process-dependency-links
# as we don't need redbiom we are going to use the default redis port
- sed 's/PORT = 7777/PORT = 6379/g' $HOME/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_core/support_files/config_test.cfg > config_test.cfg
- export QIITA_CONFIG_FP=${PWD}/config_test.cfg
- export QIITA_SERVER_CERT=$HOME/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_core/support_files/server.crt
- qiita-env make --no-load-ontologies
- source deactivate
# installing this plugin
- conda create --quiet --yes -n deblur-1.1.0 python=$PYTHON_VERSION pip nose flake8 h5py
- source activate deblur-1.1.0
- conda install --quiet --yes -c bioconda -c biocore "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 fragment-insertion
- pip install coveralls
- pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
- pip install https://github.com/qiita-spots/qiita-files/archive/master.zip
# for --process-dependency-links to work we need to have the latests version of pip
- pip install -U pip
- travis_retry pip install . --process-dependency-links
before_script:
- source activate qiita
- qiita pet webserver start &
script:
- source activate deblur-1.1.0
- sleep 10 # give enough time to the webserver to start
- configure_deblur --env-script "source activate deblur-1.1.0" --server-cert $QIITA_SERVER_CERT
- nosetests --with-doctest --with-coverage --cover-package=qp_deblur
- flake8 qp_deblur setup.py scripts support_files/patches/*.py
addons:
postgresql: "9.3"
services:
- redis-server
- postgresql
after_success:
- coveralls