[project]
name = "tcga-downloader"
version = "0.1.0"
description = "TCGA public data downloader"
requires-python = ">=3.11"
dependencies = ["requests>=2.31", "questionary>=2.0.0"]

[project.optional-dependencies]
dev = [
    "pytest>=7.4",
    "pytest-cov>=5.0",
    "black>=24.0",
    "ruff>=0.1.0",
    "mypy>=1.8.0",
    "types-requests",
    "questionary>=2.0.0",
    "tqdm>=4.66.0",
]
yaml = ["pyyaml>=6.0"]

[project.scripts]
tcga-downloader = "tcga_downloader.cli:main"

[tool.black]
line-length = 100
target-version = ['py311', 'py312']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
)/
'''

[tool.ruff]
target-version = "py311"
line-length = 100
lint.select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "UP",  # pyupgrade
    "ARG", # flake8-unused-arguments
    "SIM", # flake8-simplify
]
lint.ignore = [
    "E501",  # line too long (handled by black)
    "B008",  # do not perform function calls in argument defaults
    "C901",  # too complex
]

[tool.ruff.lint.isort]
known-first-party = ["tcga_downloader"]

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
strict_equality = true

[[tool.mypy.overrides]]
module = "tests.*"
disallow_untyped_defs = false

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = "-v --tb=short --strict-markers"
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
]

[tool.coverage.run]
source = ["tcga_downloader"]
omit = [
    "*/tests/*",
    "*/__pycache__/*",
    "*/site-packages/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "if typing.TYPE_CHECKING:",
]