fix github action errors

Author: jiaqima

.github/workflows/format-check.yml

@@ -22,10 +22,8 @@ jobs:
 
       - name: Install dependencies
         run: |
-          # Ensure lock file includes dev dependencies
-          uv lock --dev
-          # Sync with dev dependencies
-          uv sync --dev
+          # Sync with all extras and dev dependencies
+          uv sync --all-extras --dev
 
       - name: Run ruff format check
         run: uv run ruff format --check .

.github/workflows/test.yml

@@ -26,10 +26,8 @@ jobs:
 
       - name: Install dependencies
         run: |
-          # Ensure lock file includes dev dependencies
-          uv lock --dev
-          # Sync with dev dependencies
-          uv sync --dev
+          # Sync with all extras and dev dependencies
+          uv sync --all-extras --dev
 
       - name: Run pytest
         run: uv run pytest

Makefile

@@ -21,7 +21,7 @@ install:
 	uv sync
 
 install-dev:
-	uv sync --dev
+	uv sync --all-extras --dev
 
 lock:
 	uv lock

README.md

@@ -59,8 +59,10 @@ A comprehensive machine learning project template with modern tooling for depend
 
 3. **Install dependencies**:
    ```bash
-   uv sync --dev
+   uv sync --all-extras --dev
    ```
+   
+   Note: `--all-extras` is needed because dev dependencies are defined as optional dependencies in `pyproject.toml`.
 
 4. **Generate lock file** (if not present):
    ```bash
@@ -152,7 +154,7 @@ uv run ruff check --fix .
 
 1. Add the dependency to `pyproject.toml` under `[project.dependencies]` (for production) or `[project.optional-dependencies.dev]` (for development)
 2. Run `uv lock` to update the lock file
-3. Run `uv sync` to install the new dependency
+3. Run `uv sync --all-extras --dev` to install the new dependency (or `uv sync` for production dependencies only)
 
 Example:
 ```bash

pyproject.toml

@@ -40,6 +40,8 @@ packages = ["src/ml_project_template"]
 [tool.ruff]
 line-length = 100
 target-version = "py311"
+
+[tool.ruff.lint]
 select = [
     "E",   # pycodestyle errors
     "W",   # pycodestyle warnings
@@ -54,15 +56,15 @@ ignore = [
     "B008",  # do not perform function calls in argument defaults
 ]
 
+[tool.ruff.lint.isort]
+known-first-party = ["ml_project_template"]
+
 [tool.ruff.format]
 quote-style = "double"
 indent-style = "space"
 skip-magic-trailing-comma = false
 line-ending = "auto"
 
-[tool.ruff.isort]
-known-first-party = ["ml_project_template"]
-
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 python_files = ["test_*.py", "*_test.py"]

tests/test_example.py

@@ -1,7 +1,5 @@
 """Example test file to demonstrate pytest setup."""
 
-import pytest
-
 
 def test_example():
     """Example test that always passes."""