bl1/pyproject.toml at main · m9h/bl1 · GitHub

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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "bl1"
version = "0.1.0"
description = "In-silico cortical culture simulator inspired by DishBrain"
readme = "README.md"
requires-python = ">=3.10"
license = "MIT"
dependencies = [
    "jax>=0.9.1",
    "jaxlib>=0.9.1",
    "equinox>=0.11.0",
    "optax>=0.2.0",
    "matplotlib>=3.8",
    "h5py>=3.10",
    "pyyaml>=6.0",
    "numpy>=1.24",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "hypothesis>=6.0",
    "ipykernel>=6.0",
]
quality = [
    "ruff>=0.4",
    "mypy>=1.10",
    "vulture>=2.11",
    "radon>=6.0",
    "bandit>=1.7",
    "interrogate>=1.5",
]
jaxley = [
    "jaxley>=0.3.0",
]
nwb = [
    "pynwb>=2.0",
]
spikeinterface = [
    "spikeinterface[full]>=0.101",
]
vizdoom = [
    "vizdoom>=1.2.0",
    "opencv-python>=4.8",
]
docs = [
    "sphinx>=7.0",
    "sphinx-rtd-theme>=2.0",
    "sphinx-autodoc-typehints>=2.0",
    "myst-parser>=3.0",
]

[tool.hatch.build.targets.wheel]
packages = ["src/bl1"]

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint]
select = ["E", "F", "B", "UP", "SIM", "C90", "I", "W"]
ignore = [
    "E501",    # line too long — handled by formatter
    "SIM108",  # ternary operator — readability preference
    "UP007",   # X | Y union syntax — need 3.10+ only
    "B905",    # zip strict — not always needed
]

[tool.ruff.lint.mccabe]
max-complexity = 20

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["B", "SIM"]
"notebooks/*" = ["E", "F", "B"]

[tool.mypy]
# Start permissive — tighten over time as type annotations improve
strict = false
check_untyped_defs = false
disallow_incomplete_defs = false
warn_return_any = true
warn_unused_ignores = true
ignore_missing_imports = true
exclude = ["notebooks/", "benchmarks/", "scripts/", "tests/"]

[[tool.mypy.overrides]]
module = "bl1.core.*"
check_untyped_defs = true

[[tool.mypy.overrides]]
module = "bl1.analysis.*"
check_untyped_defs = true

[[tool.mypy.overrides]]
module = "bl1.compat.*"
check_untyped_defs = true

[[tool.mypy.overrides]]
module = "bl1.mea.*"
check_untyped_defs = true

[[tool.mypy.overrides]]
module = "bl1.validation.*"
check_untyped_defs = true

[[tool.mypy.overrides]]
module = "bl1.visualization.*"
check_untyped_defs = true

[tool.coverage.run]
branch = true
source = ["src/bl1"]

[tool.coverage.report]
fail_under = 50
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "if _VIZDOOM_AVAILABLE",
    "if _JAXLEY_AVAILABLE",
    "if _PYNWB_AVAILABLE",
    "if _PALLAS_AVAILABLE",
    "raise ImportError",
    "raise NotImplementedError",
]

[tool.interrogate]
ignore-init-module = true
ignore-init-method = true
ignore-magic = true
ignore-private = true
fail-under = 60
exclude = ["tests", "notebooks", "benchmarks", "scripts"]

[tool.vulture]
min_confidence = 90
exclude = ["tests/", "notebooks/", "benchmarks/", "scripts/"]
# Intentionally-unused params: public plotting kwarg, context-manager *exc,
# and a BaseHTTPRequestHandler.log_message override.
ignore_names = ["colorby", "exc", "format"]