Remove commented install #538
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: | | |
| ${{ runner.os }}-pip- | |
| # Set up Python 3.8 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| # Install EMMAA/test dependencies | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install libpq-dev | |
| psql --no-password -h localhost -c 'create database emmaadb_test;' -U postgres | |
| sudo apt-get install graphviz libgraphviz-dev pkg-config | |
| python -m pip install --upgrade pip | |
| pip install kappy==4.1.2 | |
| pip install nose coverage flask pyyaml boto3 openpyxl | |
| pip install git+https://github.com/sorgerlab/indra.git | |
| pip uninstall -y enum34 | |
| pip install cachetools matplotlib | |
| pip install git+https://github.com/indralab/indra_db.git | |
| pip install git+https://github.com/indralab/indra_reading.git | |
| pip install git+https://github.com/sorgerlab/bioagents.git | |
| git clone https://github.com/indralab/indra_world.git | |
| git clone https://github.com/indralab/covid-19.git | |
| git clone https://github.com/indralab/ui_util.git | |
| cd ui_util/indralab_auth_tools | |
| pip install . | |
| cd ../indralab_web_templates | |
| pip install . | |
| cd ../.. | |
| # git clone https://github.com/ml4ai/automates.git | |
| # cd automates | |
| # git checkout claytonm/gromet | |
| # cd .. | |
| pip install boto3 jsonpickle pygraphviz fnvhash inflection pybel==0.15 flask_jwt_extended==3.25.0 gilda tweepy nose coverage 'moto[iam]<5' sqlalchemy_utils termcolor flask-cors 'markupsafe<2.1.0' | |
| pip install --no-dependencies . | |
| pip install -U sqlalchemy==1.3.23 | |
| wget "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.4.0/BioNetGen-2.4.0-Linux.tgz" -O bionetgen.tar.gz -nv | |
| tar xzf bionetgen.tar.gz | |
| env: | |
| POSTGRES_PORT: 5432 | |
| PGPASSWORD: password | |
| - name: Run unit tests | |
| run: | | |
| export AWS_DEFAULT_REGION='us-east-1' | |
| export NOSEATTR="!notravis" | |
| export NOSEATTR=$(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 | |
| 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 }} |