Fixed TypeError: Resolved a TypeError in SpatialTranscriptFormer by correctly placing enable_nested_tensor=False in the TransformerEncoder constructor.

Pytest Configuration: Configured pyproject.toml to suppress common non-critical warnings (Deprecation, Matplotlib, etc.).
Demonstration Test: Added tests/test_warnings.py to illustrate how to handle warnings using pytest.warns.

Author: BenjaminIsaac0111

src/spatial_transcript_former/models/interaction.py

@@ -152,7 +152,10 @@ def __init__(
             batch_first=True,
             norm_first=True,
         )
-        self.fusion_engine = nn.TransformerEncoder(encoder_layer, num_layers=n_layers)
+
+        self.fusion_engine = nn.TransformerEncoder(
+            encoder_layer, num_layers=n_layers, enable_nested_tensor=False
+        )
 
         # Learnable temperature for cosine similarity scoring
         # Initialized to log(1/0.07) ≈ 2.66 following CLIP convention

tests/test_neighborhood.py

@@ -0,0 +1,44 @@
+import pytest
+import warnings
+
+
+def function_that_warns():
+    warnings.warn("This is a deprecated feature", DeprecationWarning)
+    return True
+
+
+def function_that_warns_user():
+    warnings.warn("FigureCanvasAgg is non-interactive", UserWarning)
+    return True
+
+
+def test_demonstrate_warning_assertion():
+    """
+    Demonstrates how to assert that a specific warning is raised.
+    This is useful for ensuring your code warns users correctly.
+    """
+    with pytest.warns(DeprecationWarning, match="deprecated feature"):
+        result = function_that_warns()
+        assert result is True
+
+
+def test_global_filter_demonstration():
+    """
+    This test will pass without showing warnings in the output
+    because we added filters to pyproject.toml.
+
+    Specifically 'FigureCanvasAgg is non-interactive' is filtered.
+    """
+    result = function_that_warns_user()
+    assert result is True
+
+
+def test_how_to_catch_and_ignore_locally():
+    """
+    If you want to ignore a warning locally in a specific test
+    without adding it to the global pyproject.toml.
+    """
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        result = function_that_warns()
+        assert result is True