Add comprehensive Python testing infrastructure with Poetry

.gitignore

@@ -176,6 +176,9 @@ templates/*/*.png
 results/
 # logs/
 
+# Claude Code
+.claude/*
+
 # data folders under review_iclr_bench/
 review_iclr_bench/iclr_papers/
 review_iclr_bench/iclr_parsed_w_img/

pyproject.toml

@@ -0,0 +1,107 @@
+[tool.poetry]
+name = "ai-scientist"
+version = "0.1.0"
+description = "AI Scientist - Automated Scientific Research"
+authors = ["AI Scientist Team"]
+readme = "README.md"
+packages = [{include = "ai_scientist"}]
+
+[tool.poetry.dependencies]
+python = "^3.11"
+# LLM APIs
+anthropic = "*"
+backoff = "*"
+openai = "*"
+# Viz
+matplotlib = "*"
+pypdf = "*"
+pymupdf4llm = "*"
+seaborn = "*"
+# Common Requirements
+numpy = "*"
+transformers = "*"
+datasets = "*"
+tiktoken = "*"
+wandb = "*"
+tqdm = "*"
+rich = "*"
+humanize = "*"
+dataclasses-json = "*"
+funcy = "*"
+black = "*"
+genson = "*"
+shutup = "*"
+python-igraph = "*"
+coolname = "*"
+jsonschema = "*"
+omegaconf = "*"
+botocore = "*"
+boto3 = "*"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.0.0"
+pytest-cov = "^6.0.0"
+pytest-mock = "^3.14.0"
+
+[tool.poetry.scripts]
+test = "pytest:main"
+tests = "pytest:main"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--strict-markers",
+    "--strict-config",
+    "--cov=ai_scientist",
+    "--cov-report=html",
+    "--cov-report=xml",
+    "--cov-report=term-missing",
+]
+markers = [
+    "unit: Unit tests that test individual components in isolation",
+    "integration: Integration tests that test multiple components together",
+    "slow: Tests that take a long time to run",
+]
+
+[tool.coverage.run]
+source = ["ai_scientist"]
+omit = [
+    "*/tests/*",
+    "*/test_*.py",
+    "*/__pycache__/*",
+    "*/venv/*",
+    "*/env/*",
+    "*/.venv/*",
+    "*/setup.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+    "@abstractmethod",
+]
+precision = 2
+show_missing = true
+skip_covered = false
+# Target 80% coverage once tests are written
+# Uncomment the line below to enforce coverage threshold:
+# fail_under = 80
+
+[tool.coverage.html]
+directory = "htmlcov"
+
+[tool.coverage.xml]
+output = "coverage.xml"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

tests/__init__.py

@@ -0,0 +1 @@
+"""Test suite for AI Scientist project."""

tests/conftest.py

@@ -0,0 +1,152 @@
+"""Shared pytest fixtures for AI Scientist tests."""
+
+import os
+import tempfile
+from pathlib import Path
+from typing import Generator
+
+import pytest
+
+
+@pytest.fixture
+def temp_dir() -> Generator[Path, None, None]:
+    """Create a temporary directory for test files.
+
+    Yields:
+        Path: Path to the temporary directory
+
+    Example:
+        def test_file_creation(temp_dir):
+            test_file = temp_dir / "test.txt"
+            test_file.write_text("content")
+            assert test_file.exists()
+    """
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        yield Path(tmp_dir)
+
+
+@pytest.fixture
+def temp_file(temp_dir: Path) -> Generator[Path, None, None]:
+    """Create a temporary file for testing.
+
+    Args:
+        temp_dir: Temporary directory fixture
+
+    Yields:
+        Path: Path to the temporary file
+
+    Example:
+        def test_file_reading(temp_file):
+            temp_file.write_text("test content")
+            assert temp_file.read_text() == "test content"
+    """
+    test_file = temp_dir / "test_file.txt"
+    test_file.touch()
+    yield test_file
+
+
+@pytest.fixture
+def mock_config() -> dict:
+    """Provide a mock configuration dictionary for testing.
+
+    Returns:
+        dict: Mock configuration with common test settings
+
+    Example:
+        def test_config_loading(mock_config):
+            assert "api_key" in mock_config
+            assert mock_config["timeout"] == 30
+    """
+    return {
+        "api_key": "test_api_key_123",
+        "timeout": 30,
+        "max_retries": 3,
+        "debug": True,
+    }
+
+
+@pytest.fixture
+def sample_data_dir(temp_dir: Path) -> Path:
+    """Create a sample data directory with test files.
+
+    Args:
+        temp_dir: Temporary directory fixture
+
+    Returns:
+        Path: Path to the sample data directory
+
+    Example:
+        def test_data_loading(sample_data_dir):
+            files = list(sample_data_dir.glob("*.txt"))
+            assert len(files) > 0
+    """
+    data_dir = temp_dir / "data"
+    data_dir.mkdir(parents=True, exist_ok=True)
+
+    # Create some sample files
+    (data_dir / "sample1.txt").write_text("Sample data 1")
+    (data_dir / "sample2.txt").write_text("Sample data 2")
+
+    return data_dir
+
+
+@pytest.fixture
+def mock_env_vars(monkeypatch) -> dict:
+    """Set up mock environment variables for testing.
+
+    Args:
+        monkeypatch: Pytest's monkeypatch fixture
+
+    Returns:
+        dict: Dictionary of set environment variables
+
+    Example:
+        def test_env_usage(mock_env_vars):
+            assert os.getenv("TEST_API_KEY") == "test_key"
+    """
+    env_vars = {
+        "TEST_API_KEY": "test_key",
+        "TEST_DEBUG": "true",
+        "TEST_ENVIRONMENT": "testing",
+    }
+
+    for key, value in env_vars.items():
+        monkeypatch.setenv(key, value)
+
+    return env_vars
+
+
+@pytest.fixture
+def capture_logs(caplog):
+    """Capture log messages during tests.
+
+    Args:
+        caplog: Pytest's caplog fixture
+
+    Yields:
+        LogCaptureFixture: The caplog fixture for log assertions
+
+    Example:
+        def test_logging(capture_logs):
+            logger.info("Test message")
+            assert "Test message" in capture_logs.text
+    """
+    yield caplog
+
+
+@pytest.fixture(autouse=True)
+def reset_environment():
+    """Reset environment state before each test.
+
+    This fixture runs automatically before each test to ensure
+    a clean state. Add any cleanup logic here.
+
+    Yields:
+        None: Yields control to the test, then performs cleanup
+    """
+    # Setup: Add any pre-test setup here
+
+    yield
+
+    # Teardown: Add any post-test cleanup here
+    pass

tests/integration/__init__.py

@@ -0,0 +1 @@
+"""Integration tests for AI Scientist project."""