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use lower case for system #90

use lower case for system

use lower case for system #90

Workflow file for this run

name: checks
on: [push, pull_request]
jobs:
test:
runs-on: ubuntu-latest
env:
AWS_ACCESS_KEY_ID: ${{ secrets.DUMMY_AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.DUMMY_AWS_SECRET_ACCESS_KEY }}
AWS_DEFAULT_REGION: us-east-2
AWS_DEFAULT_OUTPUT: text
DISEASE_NORM_DB_URL: ${{ matrix.db_url }}
DISEASE_TEST: true
strategy:
matrix:
db_url: ["http://localhost:8002", "postgres://postgres:postgres@localhost:5432/disease_normalizer_test"]
python-version: ['3.8', '3.9', '3.10', '3.11']
services:
postgres:
image: postgres:14
env:
POSTGRES_USER: 'postgres'
POSTGRES_DB: 'disease_normalizer_test'
POSTGRES_PASSWORD: 'postgres'
ports:
- 5432:5432
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Build local DynamoDB
if: ${{ env.DISEASE_NORM_DB_URL == 'http://localhost:8002' }}
run: |
chmod +x ./tests/scripts/dynamodb_run.sh
./tests/scripts/dynamodb_run.sh
- name: Install DynamoDB dependencies
if: ${{ env.DISEASE_NORM_DB_URL == 'http://localhost:8002' }}
run: python3 -m pip install ".[etl,test]"
- name: Install PG dependencies
if: ${{ env.DISEASE_NORM_DB_URL != 'http://localhost:8002' }}
run: python3 -m pip install ".[pg,etl,test]"
- name: Run tests
run: python3 -m pytest tests/
lint:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.8', '3.9', '3.10', '3.11']
env:
AWS_ACCESS_KEY_ID: ${{ secrets.DUMMY_AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.DUMMY_AWS_SECRET_ACCESS_KEY }}
AWS_DEFAULT_REGION: us-east-2
AWS_DEFAULT_OUTPUT: text
steps:
- uses: actions/checkout@v3
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: python3 -m pip install ".[dev]"
- name: flake8 check
run: flake8 disease/ tests/ setup.py
- name: black check
run: black --check disease/ tests/ setup.py
- name: isort check
run: isort --profile black --check disease/ tests/ setup.py