feat: add oncologic disease parameter from mondo terms #98
Workflow file for this run
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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: ["3.10", "3.11", "3.12"] | |
services: | |
postgres: | |
image: postgres:14 | |
env: | |
POSTGRES_USER: 'postgres' | |
POSTGRES_DB: 'disease_normalizer_test' | |
POSTGRES_PASSWORD: 'postgres' | |
ports: | |
- 5432:5432 | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
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 | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: 3.11 | |
- name: Install dependencies | |
run: python3 -m pip install ".[dev]" | |
- name: Check style | |
run: python3 -m ruff check . && python3 -m ruff format --check . | |
docs: | |
runs-on: ubuntu-latest | |
env: | |
SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.SPHINX_GITHUB_CHANGELOG_TOKEN }} | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: 3.11 | |
- name: Install dependencies | |
run: | | |
python3 -m pip install --upgrade pip | |
python3 -m pip install '.[docs,etl,pg]' | |
- name: Attempt docs build | |
working-directory: ./docs | |
run: make html |