Adding workflows for unit tests and linting (#11)

## Description
Adding 4 different GitHub workflows to help with managing code checks.
1. unit tests
2. linting
3. code vulnerabilities
4. dependency vulnerabilities

## Related Issues
closes #7 

## Additional Notes
Also removing the `scripts/vulnerability_checks.sh` script as we're
going to try using GH tools (ie CodeQL and Dependabot) for managing
those checks and won't need an independent script for it anymore.

.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 +1,39 @@
+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:
+        # Using a matrix in case we need to test Javascript code in the future
+        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: |
+          # only scan the code in the src directory
+          paths: ["src"]

.github/workflows/check_lint.yml

@@ -0,0 +1,31 @@
+name: lint check
+
+# When the workflow will be triggered
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install '.[dev]'
+
+      - name: Run lint checks
+        run: |
+          ruff check src/

.github/workflows/check_unit_tests.yml

@@ -0,0 +1,50 @@
+name: unit tests check
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: postgres:13
+        ports:
+          - 5432:5432
+        env:
+          POSTGRES_PASSWORD: pw
+          POSTGRES_DB: testdb
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install '.[dev]'
+
+      - name: Wait for PostgreSQL to be ready
+        run: |
+          until pg_isready -h localhost -U postgres; do sleep 1; done
+
+      - 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

@@ -31,9 +31,8 @@ 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

src/recordlinker/linkage/models.py

@@ -1,6 +1,9 @@
 import uuid
 
-from sqlalchemy import orm, ForeignKey, String, JSON
+from sqlalchemy import ForeignKey
+from sqlalchemy import JSON
+from sqlalchemy import orm
+from sqlalchemy import String
 
 
 class Base(orm.DeclarativeBase):