tests.yml

name: Tests

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    # Set up postgres
    services:
      postgres:
        image: postgres:9.6
        env:
          POSTGRES_PASSWORD: password
          POSTGRES_USER: postgres
        ports:
          - 5432:5432
        # needed because the postgres container does not provide a healthcheck
        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
    steps:
    # Check out the repo
    - uses: actions/checkout@v2
    # Cache pip packages
    - uses: actions/cache@v2
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    # Set up Python 3.7
    - name: Set up Python 3.7
      uses: actions/setup-python@v2
      with:
        python-version: 3.7
    # Install EMMAA/test dependencies
    - name: Install dependencies
      run: |
        sudo apt-get install libpq-dev
        psql --no-password -h localhost -c 'create database emmaadb_test;' -U postgres
        wget -nv https://files.pythonhosted.org/packages/91/a1/55b8224cbc9986bbad4b8f0f2dd11892845156b759b3495202d457ca0b73/kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.whl
        mv kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.whl kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.zip
        unzip kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.zip
        sudo apt-get install graphviz libgraphviz-dev pkg-config
        python -m pip install --upgrade pip
        pip install nose coverage flask pyyaml boto3 openpyxl
        pip install git+https://github.com/sorgerlab/indra.git
        pip uninstall -y enum34
        pip install cachetools matplotlib
        pip install git+https://github.com/indralab/indra_db.git
        pip install git+https://github.com/indralab/indra_reading.git
        pip install git+https://github.com/sorgerlab/bioagents.git
        git clone https://github.com/indralab/indra_world.git
        git clone https://github.com/indralab/covid-19.git
        git clone https://github.com/indralab/ui_util.git
        cd ui_util/indralab_auth_tools
        pip install .
        cd ../indralab_web_templates
        pip install .
        cd ../..
        git clone https://github.com/ml4ai/automates.git
        cd automates
        git checkout claytonm/gromet
        cd ..
        pip install boto3 jsonpickle pygraphviz fnvhash inflection pybel==0.15 flask_jwt_extended==3.25.0 gilda tweepy nose coverage moto[iam] sqlalchemy_utils termcolor flask-cors
        pip install --no-dependencies .
        pip install -U sqlalchemy==1.3.23
        wget "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.4.0/BioNetGen-2.4.0-Linux.tgz" -O bionetgen.tar.gz -nv
        tar xzf bionetgen.tar.gz
      env:
        POSTGRES_PORT: 5432
        PGPASSWORD: password
    - name: Run unit tests
      run: |
        export AWS_DEFAULT_REGION='us-east-1'
        export NOSEATTR="!notravis"
        export NOSEATTR=$(if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then echo $NOSEATTR,!nonpublic; else echo $NOSEATTR; fi)
        export PYTHONPATH=$PYTHONPATH:`pwd`/covid-19:`pwd`/kappy:`pwd`/indra_world:`pwd`/automates/scripts/gromet
        export BNGPATH=`pwd`/BioNetGen-2.4.0
        export INDRA_WM_CACHE="."
        nosetests -v -a $NOSEATTR emmaa/tests/test_s3.py
        nosetests -v -a $NOSEATTR --ignore-files='.*test_s3.py' --with-coverage --cover-inclusive --cover-package=emmaa -w emmaa/tests
      env:
        POSTGRES_PORT: 5432
        PGPASSWORD: password
        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
        AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
        INDRA_DB_REST_URL: ${{ secrets.INDRA_DB_REST_URL }}
        INDRA_DB_REST_API_KEY: ${{ secrets.INDRA_DB_REST_API_KEY }}
        INDRADB_JWT_SECRET: ${{ secrets.INDRADB_JWT_SECRET }}
        INDRALAB_USERS_DB: ${{ secrets.INDRALAB_USERS_DB }}
        EMMAADBTEST: ${{ secrets.EMMAADBTEST }}
        EMAIL_SIGN_SECRET: ${{ secrets.EMAIL_SIGN_SECRET }}
        XDD_API_KEY: ${{ secrets.XDD_API_KEY }}