Adding workflows for unit tests and linting

.github/dependabot.yml

@@ -0,0 +1,9 @@
+version: 2
+updates:
+ - package-ecosystem: "pip"
+ directory: "/"
+ schedule:
+ interval: "weekly"
+ commit-message:
+ prefix: "[deps] "
+ open-pull-requests-limit: 3

.github/workflows/check_code_vulnerabilities.yml

@@ -0,0 +1,37 @@
+name: code vulnerabilities check
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ codeql:
+ runs-on: ubuntu-latest
+
+ permissions:
+ packages: read
+ actions: read
+ contents: read
+ security-events: write
+
+ strategy:
+ matrix:
+ language: ['python']
+
+ steps:
+ - name: Checkout code
+ uses: actions/checkout@v3
+
+ - name: Initialize CodeQL
+ uses: github/codeql-action/init@v3
+ with:
+ languages: ${{ matrix.language }}
+
+ - name: Perform CodeQL Analysis
+ uses: github/codeql-action/analyze@v3
+ with:
+ category: "/language:${{matrix.language}}"
+ config: |
+ paths: ["src"]

.github/workflows/check_lint.yml

@@ -0,0 +1,35 @@
+name: lint check
+
+# When the workflow will be triggered
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ lint:
+ runs-on: ubuntu-latest
+
+ steps:
+ # Step 1: Check out the repository
+ - name: Checkout code
+ uses: actions/checkout@v3
+
+ # Step 2: Set up Python
+ - name: Set up Python
+ uses: actions/setup-python@v5
+ with:
+ python-version: '3.11'
+ cache: 'pip'
+
+ # Step 3: Install dependencies
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install '.[dev]'
+
+ # Step 4: Run lint checks
+ - name: Run lint checks
+ run: |
+ ruff check src/

.github/workflows/check_unit_tests.yml

@@ -0,0 +1,65 @@
+name: unit tests check
+
+# When the workflow will be triggered
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ test:
+ runs-on: ubuntu-latest
+
+ services:
+ postgres:
+ image: postgres:13 # Use the latest version of PostgreSQL you need
+ ports:
+ - 5432:5432
+ env:
+ POSTGRES_USER: postgres
+ POSTGRES_PASSWORD: pw
+ POSTGRES_DB: testdb
+ options: >-
+ --health-cmd "pg_isready -U testuser" 
+ --health-interval 10s
+ --health-timeout 5s
+ --health-retries 5
+
+ steps:
+ # Step 1: Check out the repository
+ - name: Checkout code
+ uses: actions/checkout@v3
+
+ # Step 2: Set up Python
+ - name: Set up Python
+ uses: actions/setup-python@v5
+ with:
+ python-version: '3.11'
+ cache: 'pip'
+
+ # Step 3: Install dependencies
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install '.[dev]'
+
+ # Step 4: Wait for PostgreSQL to be ready
+ - name: Wait for PostgreSQL to be ready
+ run: |
+ until pg_isready -h localhost -p 5432 -U postgres; do
+ echo "Waiting for PostgreSQL to be ready..."
+ sleep 1
+ done
+
+ # Step 5: Run the tests
+ - name: Run unit tests
+ env:
+ MPI_DB_TYPE: postgres
+ MPI_DBNAME: testdb
+ MPI_HOST: localhost
+ MPI_PORT: 5432
+ MPI_USER: postgres
+ MPI_PASSWORD: pw
+ run: |
+ pytest --cov=recordlinker --cov-report=xml tests/unit

README.md

@@ -45,14 +45,6 @@ To run a single unit test, use the following command:
 ./scripts/test_unit.sh tests/unit/test_linkage.py::test_link_record_against_mpi
 ```
 
-### Building the Docker Image
-
-To build the Docker image for the record linkage service from source code instead of downloading it from the DIBBs repository follow these steps.
-1. Ensure that both [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) and [Docker](https://docs.docker.com/get-docker/) are installed.
-2. Clone the DIBBs repository with `git clone https://github.com/CDCgov/phdi`.
-3. Navigate to `/phdi/containers/record-linkage/`.
-4. Run `docker build -t record-linkage .`.
-
 ## Standard Notices
 
 ### Public Domain Standard Notice

pyproject.toml

@@ -30,9 +30,8 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
  "pytest>=8.3",
+ "pytest-cov",
  "ruff",
- "pip-audit",
- "bandit",
  "mypy",
  "pyarrow",
  "httpx"

src/recordlinker/config.py

@@ -1,8 +1,8 @@
 from functools import lru_cache
 from typing import Optional
 
-from pydantic_settings import BaseSettings
 from pydantic import Field
+from pydantic_settings import BaseSettings
 
 
 class Settings(BaseSettings):

src/recordlinker/linkage/config.py

@@ -2,6 +2,7 @@
 
 from pydantic_settings import BaseSettings
 
+
 class DBSettings(BaseSettings):
  mpi_db_type: str
  mpi_dbname: str