diff --git a/.gitignore b/.gitignore
index 1fc79b8..551a329 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,3 +17,41 @@ data/molecules/zinc-full/*.pkl
 
 dataset/
 
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.tox/
+.nox/
+
+# Claude
+.claude/*
+
+# Build artifacts
+dist/
+build/
+*.egg-info/
+*.egg
+
+# Virtual environments
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.python-version
+
+# IDE files
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Poetry
+poetry.lock
+
diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 100644
index 0000000..c63b50c
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1,23 @@
+# Claude Working Memory
+
+## Project Overview
+Python machine learning project focused on graph neural networks and molecular modeling.
+
+## Important Commands
+- Testing: `poetry run test` or `poetry run tests`
+- Linting: `poetry run flake8`
+- Type checking: `poetry run mypy`
+- Code formatting: `poetry run black .`
+
+## Recent Changes
+- Set up comprehensive testing infrastructure with Poetry
+- Added pytest, pytest-cov, and pytest-mock for testing
+- Created test directory structure with unit and integration subdirectories
+- Configured pytest and coverage settings in pyproject.toml
+- Added comprehensive shared fixtures in conftest.py
+- Updated .gitignore with testing and Claude-specific entries
+
+## Notes
+- This project originally uses Conda for dependency management (see environment_cpu.yml and environment_gpu.yml)
+- DGL (Deep Graph Library) needs to be installed separately via conda as it's not available on PyPI
+- Poetry has been set up alongside Conda for managing testing dependencies
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..e3abd6c
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,149 @@
+[tool.poetry]
+name = "graph-transformer"
+version = "0.1.0"
+description = "Graph Transformer for molecular modeling and node classification"
+authors = ["Your Name <you@example.com>"]
+readme = "README.md"
+packages = [{include = "layers"}, {include = "nets"}, {include = "train"}]
+
+[tool.poetry.dependencies]
+python = "^3.7"
+torch = ">=1.6.0"
+torchvision = ">=0.7.0"
+numpy = ">=1.19.0"
+matplotlib = ">=3.1.0"
+tensorboard = ">=2.1.0"
+tensorboardx = ">=1.8"
+future = ">=0.18.2"
+absl-py = "*"
+networkx = ">=2.3"
+scikit-learn = ">=0.21.2"
+scipy = ">=1.3.0"
+h5py = ">=2.9.0"
+scikit-image = ">=0.15.0"
+requests = ">=2.22.0"
+tqdm = ">=4.43.0"
+pillow = ">=6.1"
+python-dateutil = ">=2.8.0"
+# Note: DGL needs to be installed separately via conda
+
+[tool.poetry.group.dev.dependencies]
+pytest = ">=7.0.0"
+pytest-cov = ">=4.0.0"
+pytest-mock = ">=3.10.0"
+black = ">=22.0.0"
+flake8 = ">=5.0.0"
+mypy = ">=0.990"
+isort = ">=5.10.0"
+pre-commit = ">=2.20.0"
+
+[tool.poetry.scripts]
+test = "pytest:main"
+tests = "pytest:main"
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-ra",
+    "--strict-markers",
+    "--cov=layers",
+    "--cov=nets",
+    "--cov=train",
+    "--cov-branch",
+    "--cov-report=term-missing:skip-covered",
+    "--cov-report=html",
+    "--cov-report=xml",
+    "--cov-fail-under=80",
+    "-vv",
+    "--tb=short",
+    "--maxfail=1",
+]
+markers = [
+    "unit: Unit tests",
+    "integration: Integration tests",
+    "slow: Slow tests",
+]
+filterwarnings = [
+    "ignore::DeprecationWarning",
+    "ignore::PendingDeprecationWarning",
+]
+
+[tool.coverage.run]
+branch = true
+source = ["layers", "nets", "train"]
+omit = [
+    "*/tests/*",
+    "*/__init__.py",
+    "*/conftest.py",
+    "*/setup.py",
+]
+
+[tool.coverage.report]
+precision = 2
+show_missing = true
+skip_covered = true
+skip_empty = true
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "if self.debug:",
+    "if __name__ == .__main__.:",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    "if False:",
+    "pass",
+]
+
+[tool.coverage.html]
+directory = "htmlcov"
+
+[tool.coverage.xml]
+output = "coverage.xml"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.isort]
+profile = "black"
+line_length = 100
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+
+[tool.black]
+line-length = 100
+target-version = ['py37']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+    \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/'''
+
+[tool.mypy]
+python_version = "3.7"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+ignore_missing_imports = true
+exclude = [
+    "tests/",
+    "build/",
+    "dist/",
+]
\ No newline at end of file
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..cdb4a5d
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,219 @@
+"""
+Shared pytest fixtures and configuration for the test suite.
+"""
+import os
+import shutil
+import tempfile
+from pathlib import Path
+from typing import Generator, Dict, Any
+from unittest.mock import Mock, MagicMock
+
+import pytest
+import torch
+import numpy as np
+
+
+@pytest.fixture
+def temp_dir() -> Generator[Path, None, None]:
+    """
+    Create a temporary directory for test files.
+    
+    Yields:
+        Path: Path to the temporary directory
+    """
+    temp_path = tempfile.mkdtemp()
+    yield Path(temp_path)
+    shutil.rmtree(temp_path)
+
+
+@pytest.fixture
+def mock_config() -> Dict[str, Any]:
+    """
+    Provide a mock configuration dictionary for tests.
+    
+    Returns:
+        Dict[str, Any]: Mock configuration with common parameters
+    """
+    return {
+        'model': {
+            'name': 'test_model',
+            'hidden_dim': 128,
+            'num_layers': 2,
+            'dropout': 0.1,
+            'batch_norm': True,
+        },
+        'training': {
+            'batch_size': 32,
+            'learning_rate': 0.001,
+            'epochs': 10,
+            'optimizer': 'adam',
+            'scheduler': 'cosine',
+        },
+        'data': {
+            'dataset': 'test_dataset',
+            'num_workers': 2,
+            'pin_memory': True,
+            'split_ratio': [0.8, 0.1, 0.1],
+        },
+        'device': 'cpu',
+        'seed': 42,
+    }
+
+
+@pytest.fixture
+def sample_graph_data() -> Dict[str, torch.Tensor]:
+    """
+    Create sample graph data for testing.
+    
+    Returns:
+        Dict[str, torch.Tensor]: Dictionary containing graph components
+    """
+    num_nodes = 10
+    num_edges = 15
+    feature_dim = 16
+    
+    return {
+        'node_features': torch.randn(num_nodes, feature_dim),
+        'edge_index': torch.randint(0, num_nodes, (2, num_edges)),
+        'edge_features': torch.randn(num_edges, 8),
+        'labels': torch.randint(0, 5, (num_nodes,)),
+        'batch': torch.zeros(num_nodes, dtype=torch.long),
+    }
+
+
+@pytest.fixture
+def sample_molecular_data() -> Dict[str, Any]:
+    """
+    Create sample molecular data for testing.
+    
+    Returns:
+        Dict[str, Any]: Dictionary containing molecular graph data
+    """
+    return {
+        'smiles': 'CC(C)CC1=CC=C(C=C1)C(C)C(=O)O',
+        'num_atoms': 15,
+        'num_bonds': 16,
+        'atom_features': torch.randn(15, 32),
+        'bond_features': torch.randn(16, 16),
+        'adjacency_matrix': torch.randint(0, 2, (15, 15)),
+        'target': torch.tensor([0.5]),
+    }
+
+
+@pytest.fixture
+def mock_model() -> Mock:
+    """
+    Create a mock PyTorch model for testing.
+    
+    Returns:
+        Mock: Mock model object with common methods
+    """
+    model = MagicMock()
+    model.forward.return_value = torch.randn(32, 10)  # batch_size x num_classes
+    model.parameters.return_value = [torch.randn(10, 10) for _ in range(5)]
+    model.train.return_value = model
+    model.eval.return_value = model
+    model.to.return_value = model
+    return model
+
+
+@pytest.fixture
+def mock_dataloader() -> Mock:
+    """
+    Create a mock DataLoader for testing.
+    
+    Returns:
+        Mock: Mock DataLoader with sample batches
+    """
+    dataloader = MagicMock()
+    batch_data = {
+        'input': torch.randn(32, 128),
+        'target': torch.randint(0, 10, (32,)),
+    }
+    dataloader.__iter__.return_value = iter([batch_data] * 5)
+    dataloader.__len__.return_value = 5
+    return dataloader
+
+
+@pytest.fixture
+def sample_checkpoint(temp_dir: Path) -> Path:
+    """
+    Create a sample model checkpoint file.
+    
+    Args:
+        temp_dir: Temporary directory fixture
+        
+    Returns:
+        Path: Path to the checkpoint file
+    """
+    checkpoint_path = temp_dir / 'model_checkpoint.pt'
+    checkpoint_data = {
+        'epoch': 5,
+        'model_state_dict': {'layer1.weight': torch.randn(10, 10)},
+        'optimizer_state_dict': {'param_groups': [{'lr': 0.001}]},
+        'loss': 0.123,
+        'metrics': {'accuracy': 0.95, 'f1_score': 0.93},
+    }
+    torch.save(checkpoint_data, checkpoint_path)
+    return checkpoint_path
+
+
+@pytest.fixture
+def device() -> torch.device:
+    """
+    Get the appropriate torch device for testing.
+    
+    Returns:
+        torch.device: CPU device for consistent testing
+    """
+    return torch.device('cpu')
+
+
+@pytest.fixture
+def random_seed() -> int:
+    """
+    Set random seeds for reproducible tests.
+    
+    Returns:
+        int: The seed value used
+    """
+    seed = 42
+    torch.manual_seed(seed)
+    np.random.seed(seed)
+    if torch.cuda.is_available():
+        torch.cuda.manual_seed_all(seed)
+    return seed
+
+
+@pytest.fixture(autouse=True)
+def cleanup_cuda():
+    """
+    Automatically clean up CUDA cache after each test.
+    """
+    yield
+    if torch.cuda.is_available():
+        torch.cuda.empty_cache()
+
+
+@pytest.fixture
+def mock_tensorboard_writer() -> Mock:
+    """
+    Create a mock TensorBoard SummaryWriter.
+    
+    Returns:
+        Mock: Mock SummaryWriter object
+    """
+    writer = MagicMock()
+    writer.add_scalar = MagicMock()
+    writer.add_histogram = MagicMock()
+    writer.add_graph = MagicMock()
+    writer.close = MagicMock()
+    return writer
+
+
+# Markers for different test types
+def pytest_configure(config):
+    """Configure pytest with custom markers."""
+    config.addinivalue_line("markers", "unit: Unit tests")
+    config.addinivalue_line("markers", "integration: Integration tests")
+    config.addinivalue_line("markers", "slow: Slow tests that take significant time")
\ No newline at end of file
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_setup_validation.py b/tests/test_setup_validation.py
new file mode 100644
index 0000000..e46b548
--- /dev/null
+++ b/tests/test_setup_validation.py
@@ -0,0 +1,102 @@
+"""
+Validation tests to ensure the testing infrastructure is properly configured.
+"""
+import sys
+from pathlib import Path
+
+import pytest
+import torch
+
+
+class TestSetupValidation:
+    """Tests to validate the testing infrastructure setup."""
+    
+    @pytest.mark.unit
+    def test_pytest_is_installed(self):
+        """Test that pytest is properly installed."""
+        assert 'pytest' in sys.modules
+    
+    @pytest.mark.unit
+    def test_coverage_is_configured(self):
+        """Test that coverage is properly configured."""
+        try:
+            import coverage
+            assert coverage is not None
+        except ImportError:
+            pytest.fail("Coverage module not found")
+    
+    @pytest.mark.unit
+    def test_mock_is_available(self):
+        """Test that pytest-mock is available."""
+        try:
+            from unittest.mock import Mock, patch
+            assert Mock is not None
+            assert patch is not None
+        except ImportError:
+            pytest.fail("Mock functionality not available")
+    
+    @pytest.mark.unit
+    def test_project_structure_exists(self):
+        """Test that key project directories exist."""
+        project_root = Path(__file__).parent.parent
+        
+        assert project_root.exists()
+        assert (project_root / 'layers').exists()
+        assert (project_root / 'nets').exists()
+        assert (project_root / 'train').exists()
+        assert (project_root / 'tests').exists()
+        assert (project_root / 'tests' / 'unit').exists()
+        assert (project_root / 'tests' / 'integration').exists()
+    
+    @pytest.mark.unit
+    def test_conftest_fixtures_available(self, temp_dir, mock_config, device):
+        """Test that conftest fixtures are properly loaded."""
+        assert temp_dir.exists()
+        assert isinstance(mock_config, dict)
+        assert 'model' in mock_config
+        assert 'training' in mock_config
+        assert isinstance(device, torch.device)
+    
+    @pytest.mark.unit
+    def test_markers_are_registered(self, request):
+        """Test that custom markers are properly registered."""
+        markers = [marker.name for marker in request.node.iter_markers()]
+        assert 'unit' in markers
+    
+    @pytest.mark.integration
+    def test_torch_is_available(self):
+        """Test that PyTorch is properly installed."""
+        assert torch is not None
+        tensor = torch.tensor([1, 2, 3])
+        assert tensor.shape == (3,)
+    
+    @pytest.mark.integration
+    def test_sample_fixtures_work(self, sample_graph_data, sample_molecular_data):
+        """Test that data fixtures provide expected structure."""
+        # Test graph data
+        assert 'node_features' in sample_graph_data
+        assert 'edge_index' in sample_graph_data
+        assert isinstance(sample_graph_data['node_features'], torch.Tensor)
+        
+        # Test molecular data
+        assert 'smiles' in sample_molecular_data
+        assert 'atom_features' in sample_molecular_data
+        assert isinstance(sample_molecular_data['atom_features'], torch.Tensor)
+    
+    @pytest.mark.slow
+    def test_slow_marker_works(self):
+        """Test that the slow marker is properly configured."""
+        import time
+        start = time.time()
+        time.sleep(0.1)
+        elapsed = time.time() - start
+        assert elapsed >= 0.1
+    
+    def test_random_seed_fixture(self, random_seed):
+        """Test that random seed fixture provides reproducibility."""
+        assert random_seed == 42
+        # Test PyTorch randomness
+        tensor1 = torch.randn(5)
+        torch.manual_seed(42)
+        tensor2 = torch.randn(5)
+        assert torch.allclose(tensor1, tensor2)
\ No newline at end of file
diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py
new file mode 100644
index 0000000..e69de29