pyproject.toml

[project]
name = "sonata-cell-position"
version = "0.0.0"
description = "sonata-cell-position web API"
authors = [
    {name = "Blue Brain Project, EPFL"},
    {name = "Gianluca Ficarelli", email = "gianluca.ficarelli@epfl.ch"},
]
dependencies = [
    "cachetools",
    "entity-management>=1.2.36",
    "fastapi",
    "h5py",
    "libsonata==0.1.24",  # pinned for performance reasons
    "loguru",
    "loky",
    "numpy<2",  # to be unpinned with libsonata >= 0.1.28
    "pandas",
    "psutil",  # allow early memory leak detections in loky
    "pyarrow",
    "pydantic>=2",
    "pydantic-settings",
    "pyjwt",
    "pyyaml",
    "requests",
    "uvicorn[standard]",
    "voxcell",
]
requires-python = "==3.12.*"
readme = "README.md"
license = {text = "Apache-2.0"}

[project.optional-dependencies]
cli = [
    "click",
]

[tool.uv]
dev-dependencies = [
    "coverage[toml]",
    "httpx",
    "mypy",
    "pytest",
    "pytest-asyncio<0.22",  # https://github.com/pytest-dev/pytest-asyncio/issues/706
    "pytest-cov",
    "pytest-loguru",
    "ruff",
    "types-cachetools",
    "types-requests",
    "types-PyYAML",
]


[tool.ruff]
line-length = 100
target-version = "py312"

[tool.ruff.lint]
select = [
    "D", # pydocstyle
    "E", # pycodestyle
    "F", # pyflakes
    "I", # isort
    "PL", # pylint
    "UP", # pyupgrade
]
ignore = [
    "FIX002",  # Line contains TODO, consider resolving the issue
    "TD",      # TODOs
]

[tool.ruff.lint.isort]
known-local-folder = ["tests"]
combine-as-imports = true

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = [
    "ANN",     # Missing type annotation
    "ARG002",  # Unused method argument
    "D",       # pydocstyle
    "ERA001",  # Found commented-out code
    "INP001",  # Missing `__init__.py`
    "PLC2701", # Private name import from external module
    "PLR2004", # magic value (constant) used in comparison (i.e. expected == 3)
    "S101",    # Use of `assert` detected
    "SLF001",  # private member access
]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.pylint]
# Maximum number of arguments for function / method
max-args = 11
# Maximum number of locals for function / method body
max-locals = 15
# Maximum number of return / yield for function / method body
max-returns = 7
# Maximum number of branch for function / method body
max-branches = 12
# Maximum number of statements in function / method body
max-statements = 50
# Maximum number of public methods for a class (see R0904).
max-public-methods = 60


[tool.pytest.ini_options]
minversion = "6.0"
addopts = [
    "--import-mode=importlib",
    "-vv",
    "-ra",
    "--cov=app",
    "--durations=10",
    "--durations-min=1.0",
]
asyncio_mode = "auto"
testpaths = [
    "tests",
]
filterwarnings = [
    "ignore::DeprecationWarning:nptyping",
]


[tool.coverage.paths]
source = [
    "src",
    "*/site-packages",
]

[tool.coverage.run]
branch = true
parallel = false

[tool.coverage.report]
show_missing = true
precision = 0
fail_under = 80
omit = [
    "__main__.py",
]

[tool.mypy]
show_error_codes = true
ignore_missing_imports = true
allow_redefinition = true