pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel", "tomli>=1.0.0;python_version<'3.11'"]
build-backend = "setuptools.build_meta"

[project]
name = "timeflies"
version = "1.0.0"
description = "Machine Learning for Aging Analysis in Drosophila Single-Cell Data with Deep Learning and Batch Correction"
authors = [{name = "Singh Lab"}]
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
    # TensorFlow with platform-specific GPU support
    "tensorflow[and-cuda]>=2.13.0; platform_machine != 'arm64' and sys_platform != 'win32'",
    "tensorflow>=2.13.0; platform_machine == 'arm64' or sys_platform == 'win32'",
    "scikit-learn>=1.3.0",
    "pandas>=2.0.0",
    "numpy>=1.24.0",
    "scanpy>=1.9.0",
    "anndata>=0.9.0",
    "matplotlib>=3.7.0",
    "seaborn>=0.12.0",
    "shap>=0.42.0",
    "pyyaml>=6.0",
    "dill>=0.3.0",
    "xgboost>=1.7.0",
    "optuna>=3.0.0",
    "gradio>=4.0.0",
]

[project.optional-dependencies]
# GPU support (platform-specific)
gpu = [
    "tensorflow[and-cuda]>=2.13.0; sys_platform != 'win32'",
    "tensorflow>=2.13.0; sys_platform == 'win32'",
]
# CPU-only fallback for systems without CUDA
cpu = [
    "tensorflow-cpu>=2.13.0",
]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "pytest-mock>=3.8.0",
    "pytest-xdist>=3.0.0",  # Parallel test execution
    "pytest-benchmark>=5.0.0",  # Performance benchmarking
    "psutil>=5.9.0",        # System monitoring for memory tests
    "joblib>=1.3.0",        # For model persistence tests
    "ruff>=0.1.0",          # Fast linter and formatter (replaces black, isort, flake8)
    "mypy>=1.5.0",          # Type checking
    "types-PyYAML",         # Type stubs for PyYAML
    "pre-commit>=3.0.0",    # Git hooks
]
batch-correction = [
    "scvi-tools>=1.0.0",
    "torch>=2.0.0",
]

[project.scripts]
timeflies = "common.timeflies_cli:main"


[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-dir]
"" = "src"

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--strict-markers",
    "--disable-warnings",
    "-ra",
]
markers = [
    "unit: Unit tests",
    "integration: Integration tests",
    "functional: Functional tests",
    "system: System tests",
    "performance: Performance benchmark tests",
    "slow: Slow tests",
]

[tool.coverage.run]
source = ["src"]
data_file = "coverage/.coverage"
omit = [
    "*/tests/*",
    "*/legacy/*",
    "*/__pycache__/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
]

[tool.coverage.html]
directory = "coverage/html"

[tool.coverage.xml]
output = "coverage/coverage.xml"


[tool.ruff]
line-length = 88
target-version = "py312"
exclude = [
    ".venv",
    "__pycache__",
    "legacy",
    "build",
    "dist",
]

[tool.ruff.lint]
select = [
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings
    "F",    # pyflakes
    "I",    # isort
    "N",    # pep8-naming
    "UP",   # pyupgrade
]
ignore = [
    "E501",  # line too long (handled by ruff formatter)
    "F401",  # imported but unused (common in __init__.py)
    "N803",  # argument name should be lowercase (ML convention: X, y)
    "N806",  # variable in function should be lowercase (ML convention: X_train, X_test, adata.X)
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"

[tool.mypy]
python_version = "3.12"
warn_return_any = false         # Disable Any warnings for now
warn_unused_configs = true
disallow_untyped_defs = false   # Gradually enable
ignore_missing_imports = true
no_implicit_optional = false   # Allow None defaults without Optional[]
exclude = [
    "legacy/",
    "tests/",
    ".venv/",
]