mri-toolkit/pyproject.toml at main · scientificcomputing/mri-toolkit · GitHub

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[build-system]
requires = ["setuptools>=61.2"]
build-backend = "setuptools.build_meta"

[project]
name = "mritk"
authors = [
    { name = "Jørgen Riseth", email = "jnriseth@gmail.com" },
    { name = "Henrik Finsberg", email = "henriknf@simula.no" },
    { name = "Cécile Daversin Catty", email = "cecile@simula.no" }
]
version = "0.3.0"
requires-python = ">=3.10"
description = "MRI processing toolkit."
readme = "README.md"
license = "MIT"
license-files = ["LICENSE"]

dependencies = [
  "tqdm",
  "numpy",
  "rich-argparse",
  "nibabel",
  "pandas",
  "scipy",
  "scikit-image",
  "pydicom",
  "dcm2niix",
]

[project.optional-dependencies]
show = [
    "textual-image", # Used to show images in terminal
    "pillow",    # Used to handle image data
    "matplotlib" # Used for colormaps
]
napari = [
    "napari[all]", # Used for interactive visualization
]
test = [
    "pytest",
    "pytest-cov",

]
pypi = [
    "build" # Used for building wheels and uploading to pypi
]
docs = [
    "sphinxcontrib-bibtex",
    "sphinx-copybutton",
    "sphinx-codeautolink",
    "sphinx",
    "jupytext",
    "sphinx-togglebutton",
    "sphinx-comments",
    "sphinx-external-toc",
    "linkify-it-py",
    "sphinx-design",
    "sphinx-book-theme",
    "myst-nb",
    "sphinx-multitoc-numbering",
    "sphinxcontrib-mermaid",
]
all = ["mritk[extra,test,pypi,show,napari]"]


[project.urls]
Homepage = "https://github.com/scientificcomputing/mri-toolkit.git"


[project.scripts]
mritk = "mritk.cli:main"

[tool.mypy]
ignore_missing_imports = true # Does not show errors when importing untyped libraries
files = [  # Folder to which files that should be checked by mypy
    "src",
    "test"
]


[tool.ruff]

# Exclude a variety of commonly ignored directories.
exclude = [
    "examples",
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
]

# Same as Black.
line-length = 130

# Assume Python 3.10.
target-version = "py312"

[tool.ruff.lint]
# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
select = ["E", "F", "I"]
ignore = ["E402", "E741", "E743", "E731"]

# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = ["A", "B", "C", "D", "E", "F", "I"]
unfixable = []

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"


[tool.ruff.lint.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 10


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


[tool.ruff.lint.isort]
known-first-party = ["mritk"]
known-third-party = [
    "tqdm",
    "numpy",
    "rich-argparse",
    "nibabel",
    "pandas",
    "scipy",
    "scikit-image",
    "pydicom",
    "dcm2niix",
    "pytest",
]
section-order = [
    "future",
    "standard-library",
    "third-party",
    "first-party",
    "local-folder",
]


[tool.bumpversion]
allow_dirty = false
commit = true
message = "Bump version: {current_version} → {new_version}"
tag = true
sign_tags = false
tag_name = "v{new_version}"
tag_message = "Bump version: {current_version} → {new_version}"
current_version = "0.3.0"


[[tool.bumpversion.files]]
filename = "pyproject.toml"
search = 'version = "{current_version}"'
replace = 'version = "{new_version}"'