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pyproject.toml
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[project]
name = "patch-denoise"
description = "Denoising method for sequence of images or volumes. Primarily targeting fMRI data."
authors = [{name="Pierre-antoine Comby", email="[email protected]"}]
readme = "README.rst"
license = {file = "LICENSE.txt"}
dependencies = ["numpy", "scipy", "matplotlib", "scikit-image", "tqdm", "nibabel"]
requires-python = ">=3.9"
dynamic = ["version"]
classifiers = [
"Development Status :: 3 - Alpha",
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3 :: Only",
"Topic :: Scientific/Engineering :: Image Processing",
"Topic :: Scientific/Engineering :: Medical Science Apps.",
]
[project.optional-dependencies]
optional = ["modopt", "nipype", "numba"]
test = ["pytest", "pytest-cov", "pytest-xdist", "pytest-sugar"]
doc = [
"pydata-sphinx-theme",
"numpydoc",
"sphinx_gallery",
"sphinx-argparse",
"sphinx",
]
dev = ["black", "isort", "ruff"]
[project.scripts]
patch-denoise = "patch_denoise.bindings.cli:main"
[build-system]
requires = ["setuptools", "setuptools-scm[toml]", "wheel"]
[tool.setuptools_scm]
write_to = "src/patch_denoise/_version.py"
version_scheme = "python-simplified-semver"
local_scheme="no-local-version"
[tool.coverage.run]
omit = ["*tests*"]
[tool.coverage.report]
precision = 2
exclude_lines = ["pragma: no cover", "raise NotImplementedError"]
# Formatting using black.
[tool.black]
#linting using ruff
[tool.ruff]
src = ["src", "tests"]
[tool.ruff.lint]
ignore = ["B905"]
exclude = ["examples/", "tests/"]
select = ["E", "F", "B", "Q", "UP", "D"]
[tool.ruff.lint.pydocstyle]
convention="numpy"
[tool.isort]
profile="black"
[tool.pytest.ini_options]
minversion = "6.0"
addopts = [
"--cov=patch_denoise",
"--cov-report=term-missing",
"--cov-report=xml"
]
[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*'
check-hidden = true
ignore-regex = '\bND\b'
ignore-words-list = 'fro'