feat: Add comprehensive Python testing infrastructure with Poetry

.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
+

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

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/",
+]