pyproject.toml

[tool.poetry]
name = "linc-convert"
version = "0.0.1"
description = "Data conversion tools for the LINC project."
authors = [
    "Yael Balbastre <yael.balbastre@gmail.com>",
]
maintainers = [
    "Yael Balbastre <yael.balbastre@gmail.com>",
]
license = "Apache-2.0"
readme = "README.md"
homepage = "https://connects.mgh.harvard.edu"
repository = "https://github.com/lincbrain/linc-convert"
documentation = "https://lincbrain.github.io/linc-convert"
keywords = ["python", "package", "template"]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Programming Language :: Python :: 3.10",
  "License :: OSI Approved :: Apache Software License",
  "Operating System :: OS Independent"
]
packages = [{include = "linc_convert"}]

[tool.poetry.dependencies]
python = "^3.10"
cyclopts = "^2.0.0"
numpy = "*"
nibabel = "*"
zarr = "^2.0.0"


[tool.poetry.group.df]
optional = true
[tool.poetry.group.df.dependencies]
glymur = "*"

[tool.poetry.group.lsm]
optional = true
[tool.poetry.group.lsm.dependencies]
tifffile = "*"

[tool.poetry.group.psoct]
optional = true
[tool.poetry.group.psoct.dependencies]
h5py = "*"
scipy = "*"

[tool.poetry.group.wk]
optional = true
[tool.poetry.group.wk.dependencies]
wkw = "*" 

[tool.poetry.group.dev]
optional = true
[tool.poetry.group.dev.dependencies]
pytest = "^8.1.1"
mypy = "^1.9.0"
pre-commit = "^3.7.0"
pytest-cov = "^5.0.0"
ruff = "^0.3.4"

[tool.poetry.group.docs]
optional = true
[tool.poetry.group.docs.dependencies]
pdoc = "^14.4.0"

[tool.pytest.ini_options]
pythonpath = [
  "."
]
testpaths = [
  "tests"
]

[tool.mypy]
ignore_missing_imports = true

[tool.ruff]
exclude = [
  ".bzr",
  ".direnv",
  ".eggs",
  ".git",
  ".git-rewrite",
  ".hg",
  ".mypy_cache",
  ".nox",
  ".pants.d",
  ".pytype",
  ".ruff_cache",
  ".svn",
  ".tox",
  ".venv",
  "__pypackages__",
  "_build",
  "buck-out",
  "build",
  "dist",
  "node_modules",
  "venv"
]
line-length = 88
indent-width = 4
src = ["."]
target-version = "py310"

[tool.ruff.lint]
select = ["ANN", "D", "E", "F", "I"]
ignore = [
  "ANN101",  # self should not be annotated.
  "ANN102"  # cls should not be annotated.
]
fixable = ["ALL"]
unfixable = []
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

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

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

[tool.poetry.scripts]
linc-convert = "linc_convert.cli:main"

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

[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "pep440"
bump = true
pattern = "default-unprefixed"

[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
build-backend = "poetry_dynamic_versioning.backend"