Upgrade to flask_jwt_extended>3
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| 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 3.10 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.10" | |
| # 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@gilda-flask-deps | |
| 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 | |
| git checkout flask3 | |
| 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==4.6.0 gilda tweepy nose coverage 'moto[iam]<5' sqlalchemy_utils termcolor flask-cors==4.0.1 | |
| 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 }} |