chore: enhance type checking and code quality configurations

- Updated the Makefile to enforce stricter type checking with MyPy by adding the --ignore-missing-imports and --strict flags.
- Modified the pyproject.toml to move pydocstyle and interrogate dependencies to the documentation section, ensuring clarity in testing requirements.
- Adjusted the GitHub Actions workflow to reflect the updated MyPy command for type checking, improving CI consistency.
- Refined type annotations in metrics.py to specify the expected signature for distance functions, enhancing code clarity and type safety.
- Updated type annotations in base.py for Axes to improve code readability and maintainability.

Author: LouisTier

.github/workflows/code-quality.yml

@@ -47,6 +47,7 @@ jobs:
     - name: Type checking with MyPy
       run: |
         mypy torchsom/ --ignore-missing-imports --strict
+      # mypy torchsom/
       continue-on-error: true
 
     - name: Check for security issues with Bandit (library code)

Makefile

@@ -51,7 +51,7 @@ lint:  ## Run all code quality checks
 	@echo "  🔍 Running linter..."
 	ruff check torchsom/ tests/
 	@echo "  🎯 Type checking..."
-	mypy torchsom/
+	mypy torchsom/ --ignore-missing-imports --strict
 	@echo "✅ All quality checks passed!"
 # ruff check torchsom/ tests/ => read-only mode, report violations without modifications
 # ruff check torchsom/ tests/ --fix => fix safe, non-destructive violations

pyproject.toml

@@ -71,8 +71,6 @@ tests = [
     "pytest-html",
     "pytest-xdist",
     "pytest-timeout",
-    "pydocstyle",
-    "interrogate",
 ]
 
 docs = [
@@ -81,6 +79,8 @@ docs = [
     "sphinx-rtd-theme",
     "sphinx-autodoc-typehints",
     "sphinx-copybutton",
+    "pydocstyle",
+    "interrogate",
 ]
 
 security = [
@@ -315,6 +315,8 @@ disable_error_code = [
     "call-overload",                    # Error code for calling a function with the wrong number of arguments
     "override",                         # Error code for overriding a method with a different signature (e.g. in a subclass)
     # "return-value",                     # Error code for function returning a value with a different type than declared
+    "no-untyped-call",                  # Error code for calling a function without type annotations
+    "attr-defined",                     # Error code for attribute access on None
 ]
 
 [[tool.mypy.overrides]]

torchsom/utils/metrics.py

@@ -11,7 +11,7 @@
 def calculate_quantization_error(
     data: torch.Tensor,
     weights: torch.Tensor,
-    distance_fn: Callable,
+    distance_fn: Callable[[torch.Tensor, torch.Tensor], torch.Tensor],
 ) -> float:
     """Calculate quantization error for a SOM.
 
@@ -46,7 +46,7 @@ def calculate_quantization_error(
 def calculate_topographic_error(
     data: torch.Tensor,
     weights: torch.Tensor,
-    distance_fn: Callable,
+    distance_fn: Callable[[torch.Tensor, torch.Tensor], torch.Tensor],
     topology: str = "rectangular",
     # xx: torch.Tensor = None,
     # yy: torch.Tensor = None,

torchsom/visualization/base.py

@@ -6,6 +6,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import torch
+from matplotlib.axes import Axes
 from matplotlib.collections import PolyCollection
 from matplotlib.colors import Colormap
 from matplotlib.image import AxesImage
@@ -145,7 +146,7 @@ def _generate_hexbin_coordinates(
 
     def _create_hexbin(
         self,
-        ax: plt.Axes,
+        ax: Axes,
         x: list[float],
         y: list[float],
         values: list[float],
@@ -196,7 +197,7 @@ def _create_hexbin(
 
     def _customize_plot(
         self,
-        ax: plt.Axes,
+        ax: Axes,
         title: str,
         colorbar_label: str,
         mappable_item: Optional[Union[AxesImage, PolyCollection]] = None,