Update formatting to include all Python files

.github/workflows/ci.yml

@@ -25,23 +25,17 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          pip install -r requirements.txt
           pip install -e .
-          pip install pytest pytest-cov black isort
 
       - name: Check formatting with black
         run: |
-          black --check anomaly_detection/ tests/
+          black --check .
 
       - name: Check import sorting with isort
         run: |
-          isort --check-only anomaly_detection/ tests/
+          isort --check-only .
 
       - name: Run tests with coverage
         run: |
-          pytest tests/ --cov=anomaly_detection --cov-report=xml -v
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
-        with:
-          file: ./coverage.xml
-          fail_ci_if_error: true
+          pytest tests/ --cov=anomaly_detection -v

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
+        language_version: python3.9
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: no-commit-to-branch
+        args: [--branch, main]

Makefile

@@ -1,25 +1,28 @@
-.PHONY: install test lint format check-format check-imports clean
+.PHONY: install test lint format check-format check-imports clean setup-pre-commit
 
 install:
 	pip install -e .
-	pip install pytest pytest-cov black isort
+	pip install pytest pytest-cov black isort pre-commit
+
+setup-pre-commit:
+	pre-commit install
 
 test:
 	pytest tests/ --cov=anomaly_detection --cov-report=term-missing -v
 
 lint:
-	black --check anomaly_detection/ tests/
-	isort --check-only anomaly_detection/ tests/
+	black --check .
+	isort --check-only .
 
 format:
-	black anomaly_detection/ tests/
-	isort anomaly_detection/ tests/
+	black .
+	isort .
 
 check-format:
-	black --check anomaly_detection/ tests/
+	black --check .
 
 check-imports:
-	isort --check-only anomaly_detection/ tests/
+	isort --check-only .
 
 clean:
 	find . -type d -name "__pycache__" -exec rm -r {} +
@@ -32,4 +35,4 @@ clean:
 	find . -type d -name ".pytest_cache" -exec rm -r {} +
 	find . -type d -name ".coverage" -exec rm -r {} +
 	find . -type d -name "htmlcov" -exec rm -r {} +
-	find . -type f -name "coverage.xml" -delete 
+	find . -type f -name "coverage.xml" -delete

requirements.txt

@@ -1,13 +1,14 @@
-numpy>=1.21.0
-pandas>=1.3.0
-scikit-learn>=0.24.2
+black>=21.7b0
 boto3>=1.26.0
 fastapi>=0.68.0
-uvicorn>=0.15.0
+flake8>=3.9.2
+httpx>=0.24.0
+isort>=5.9.3
+numpy>=1.21.0
+pandas>=1.3.0
+pre-commit>=3.6.0
 python-dotenv>=0.19.0
 pytest>=6.2.5
 pytest-cov>=2.12.1
-black>=21.7b0
-isort>=5.9.3
-flake8>=3.9.2
-httpx>=0.24.0 
+scikit-learn>=0.24.2
+uvicorn>=0.15.0

setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 setup(
     name="anomaly_detection",
@@ -16,4 +16,4 @@
         "pytest-cov>=2.12.0",
     ],
     python_requires=">=3.8",
-) 
+)