111 lines
2.3 KiB
TOML
111 lines
2.3 KiB
TOML
[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:",
|
|
]
|