fix: improve network test resilience and reduce logging duplication

Key improvements:
- Add json.JSONDecodeError to exception handling in network tests
- Gracefully skip tests when external APIs return errors (503, timeouts, etc)
- Add pytest conftest.py to suppress PyTorch Lightning duplicate logging
- Parametrize AptaTransEncoderLightning fixture for encoder type variants
- Add mock model with required encoder/predictor attributes
- Fix code style and line length issues per PEP 8
- Update pyproject.toml with custom pytest markers

This resolves CI failures across all platforms (Windows, macOS, Ubuntu)

Author: Tarun-goswamii

pyaptamer/aptatrans/tests/test_aptatrans_lightning.py

@@ -17,6 +17,11 @@ class MockAptaTrans(nn.Module):
         def __init__(self):
             super().__init__()
             self.dummy_param = nn.Parameter(torch.zeros(1))
+            # Add encoder attributes for AptaTransEncoderLightning tests
+            self.encoder_apta = nn.Linear(10, 10)
+            self.token_predictor_apta = nn.Linear(10, 10)
+            self.encoder_prot = nn.Linear(10, 10)
+            self.token_predictor_prot = nn.Linear(10, 10)
 
         def forward_encoder(self, x, encoder_type):
             batch_size, seq_len = x[0].shape
@@ -102,9 +107,10 @@ def test_configure_optimizers(self, lightning_model):
 class TestAptaTransEncoderLightning:
     """Tests for the AptaTransEncoderLightning() class."""
 
-    @pytest.fixture
-    def lightning_model(self, mock_model, encoder_type="apta"):
-        """Create AptaTransEncoderLightning instance with default parameters."""
+    @pytest.fixture(params=["apta", "prot"])
+    def lightning_model(self, request, mock_model):
+        """Create AptaTransEncoderLightning instance with different encoder types."""
+        encoder_type = request.param
         return AptaTransEncoderLightning(mock_model, encoder_type=encoder_type)
 
     @pytest.mark.parametrize(

pyaptamer/conftest.py

@@ -0,0 +1,47 @@
+
+
+import logging
+
+import pytest
+
+
+@pytest.fixture(autouse=True)
+def suppress_logging():
+
+    root_logger = logging.getLogger()
+    original_level = root_logger.level
+    
+    
+    lightning_logger = logging.getLogger("lightning")
+    lightning_fabric_logger = logging.getLogger("lightning_fabric")
+    pytorch_logger = logging.getLogger("torch")
+    
+    original_lightning_level = lightning_logger.level
+    original_fabric_level = lightning_fabric_logger.level
+    original_pytorch_level = pytorch_logger.level
+    
+   
+    lightning_logger.setLevel(logging.WARNING)
+    lightning_fabric_logger.setLevel(logging.WARNING)
+    pytorch_logger.setLevel(logging.WARNING)
+    root_logger.setLevel(logging.WARNING)
+    
+    yield
+    
+   
+    lightning_logger.setLevel(original_lightning_level)
+    lightning_fabric_logger.setLevel(original_fabric_level)
+    pytorch_logger.setLevel(original_pytorch_level)
+    root_logger.setLevel(original_level)
+
+
+def pytest_configure(config):
+   
+    logging.getLogger("lightning").setLevel(logging.WARNING)
+    logging.getLogger("lightning_fabric").setLevel(logging.WARNING)
+    logging.getLogger("torch").setLevel(logging.WARNING)
+    logging.getLogger("urllib3").setLevel(logging.WARNING)
+    
+    # Set root logger to WARNING to suppress info and debug logs
+    logging.getLogger().setLevel(logging.WARNING)
+# only show warnings kay liye

pyproject.toml

@@ -56,3 +56,9 @@ include-package-data = true
 
 [tool.setuptools.package-data]
 pyaptamer = ["datasets/data/*.csv", "datasets/data/*.pdb"]
+
+[tool.pytest.ini_options]
+markers = [
+    "network: marks tests that require network connectivity (deselect with '-m \"not network\"')",
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+]