pyproject.toml

[project]
name = "neuromaps-prime"
description = "A toolbox for projecting, resampling, and comparing NHP brain maps"
license = {file = "LICENSE"}
readme = "README.md"
dynamic = ["version"]
requires-python = ">=3.11"
keywords = ["network neuroscience", "connectomics"]
authors = [{name = "CMI DAIR", email = "dair@childmind.org"}]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved",
  "Programming Language :: Python :: 3 :: Only"
]
dependencies = [
  "niwrap>=0.9.2",
  "nibabel>=5.2.1",
  "pyyaml>=6.0.2",
  "networkx>=3.6.1",
  "matplotlib>=3.10.7",
  "numpy>=2.4.2",
  "pydantic>=2.12.3",
  "scipy>=1.17.0",
  "styxpodman",
  "requests>=2.33.1"
]

[dependency-groups]
dev = [
  "deptry>=0.24.0",
  "matplotlib-stubs>=0.3.6",
  "mypy>=1.19.0",
  "pre-commit>=4.5.0",
  "pytest>=9.0.3",
  "pytest-cov>=7.0.0",
  "ruff>=0.14.7",
  "types-pyyaml>=6.0.12.20250915",
  "types-requests>=2.33.0.20260503"
]
docs = ["pdoc>=15.0.4"]
validate = ["check-jsonschema>=0.37.1"]

[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[tool.hatch.build]
source = ["src"]

[tool.hatch.build.hooks.vcs]
version-file = "src/neuromaps_prime/_version.py"

[tool.hatch.version]
source = "vcs"

[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
markers = [
  "unit: Fast (<1s) unit tests (e.g. utilities, BIDS parsing, file operations)",
  "integration: Integration tests with real data",
  "regression: Regressions tests with real data"
]

[tool.coverage.report]
omit = [
  "src/neuromaps_prime/resources",
  "src/neuromaps_prime/_version.py",
  "src/neuromaps_prime/plotting.py"
]

[tool.deptry.per_rule_ignores]
DEP002 = ["scipy"]  # ignore defined dependency thats not used

[tool.mypy]
exclude = ['tests']
ignore_missing_imports = true

[tool.ruff]
line-length = 88
indent-width = 4
src = ["src"]
target-version = "py312"
extend-exclude = ["examples/*.py"]

[tool.ruff.lint]
select = [
  "ANN",  # flake8-annotations
  "ARG",  # flake8-unused-arguments
  "B",  # flake8-bugbear
  "C4",  # flake8-comprehensions
  "C90",  # mccabe
  "D",  # pydocstyle
  "E",  # pycodestyle errors
  "ERA",  # eradicate
  "F",  # Pyflakes
  "FA",  # flake8-future-annotations
  "FBT",  # flake8-boolean-trap
  "FURB",  # refurb
  "I",  # isort
  "N",  # pep8-naming
  "NPY",  # NumPy-specific rules
  "PD",  # pandas-vet
  "PERF",  # Perflint
  "PIE",  # flake8-pie
  "PT",  # flake8-pytest-style
  "PTH",  # flake8-use-pathlib
  "Q",  # flake8-quotes
  "RET",  # flake8-return
  "RUF",  # Ruff-specific rules
  "S",  # flake8-bandit
  "SIM",  # flake8-simplify
  "T20",  # flake8-print
  "TID",  # flake8-tidy-imports
  "TC",  # flake8-type-checking
  "UP"  # pyupgrade
]
ignore = []
fixable = ["ALL"]
unfixable = []

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

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S101"]

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

[tool.uv.sources]
styxpodman = {git = "https://github.com/styx-api/styxpodman"}