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pyproject.toml
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pyproject.toml
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[build-system]
requires = [
"setuptools>=45",
"setuptools_scm[toml]>=6.2",
"wheel"
]
build-backend = "setuptools.build_meta"
[project]
name = "AFMReader"
dynamic = ["version"]
authors = [
{ name = "Sylvia Whittle", email = "sylvia.whittle@sheffield.ac.uk" },
{ name = "Neil Shephard", email = "n.shephard@sheffield.ac.uk" },
{name = "TopoStats Team", email = "topostats@sheffield.ac.uk"}
]
description = "Read and retrieve data from various AFM file formats."
readme = "README.md"
requires-python = ">=3.9"
classifiers = [
"Development Status :: 3 - Alpha",
"License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
"Natural Language :: English",
"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",
]
keywords = [
"afm",
"image processing"
]
dependencies = [
"matplotlib",
"igor2",
"tifffile",
"pySPM",
"loguru",
"h5py",
]
[project.optional-dependencies]
dev = [
"black",
"pre-commit",
"pylint",
"ruff",
"setuptools_scm[toml]",
"wheel"
]
pypi = [
"build",
"setuptools_scm[toml]",
"wheel",
]
tests = [
"pytest",
"pytest-cov",
]
[project.urls]
"Homepage" = "https://github.com/AFM-SPM/afmreader"
"Bug Tracker" = "https://github.com/AFM-SPM/afmreader/issues"
[tool.setuptools_scm]
write_to = "AFMReader/_version.py"
[tool.pytest.ini_options]
minversion = "7.0"
addopts = "--cov"
testpaths = [
"tests",
]
filterwarnings = [
"ignore::DeprecationWarning",
"ignore::PendingDeprecationWarning",
"ignore::UserWarning"
]
[tool.black]
line-length = 120
target-version = ['py39']
exclude = '''
(
/(
\.eggs # exclude a few common directories in the
| \.git # root of the project
| \.venv
)/
)
'''
[tool.ruff]
exclude = [
"*.ipynb",
".bzr",
".direnv",
".eggs",
".git",
".hg",
".mypy_cache",
".nox",
".pants.d",
".pytype",
".ruff_cache",
".svn",
".tox",
".venv",
"__pycache__",
"__pypackages__",
"_build",
"buck-out",
"build",
"dist",
"docs/conf.py",
"node_modules",
"pygwytracing.py",
"tests/tracing/test_dnacurvature.py",
"tests/tracing/test_dnatracing.py",
"tests/tracing/test_tracing_dna.py",
"topostats/plotting.py",
"topostats/tracing/dnatracing.py",
"topostats/tracing/tracing_dna.py",
"topostats/tracing/tracingfuncs.py",
"venv",
]
# per-file-ignores = []
line-length = 120
target-version = "py310"
lint.select = ["A", "B", "C", "D", "E", "F", "PT", "PTH", "R", "S", "W", "U"]
lint.ignore = [
"B905",
"E501",
"S101",
"T201"]
# Allow autofix for all enabled rules (when `--fix`) is provided.
lint.fixable = ["A", "B", "C", "D", "E", "F", "PT", "PTH", "R", "S", "W", "U"]
lint.unfixable = []
[tool.ruff.lint.flake8-quotes]
docstring-quotes = "double"
[tool.ruff.lint.isort]
case-sensitive = true
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.flake8-pytest-style]
fixture-parentheses = true
[tool.coverage.run]
source = ["AFMReader"]
omit = [
"AFMReader/_version.py",
"*tests*",
"**/__init__*",
]
[tool.numpydoc_validation]
checks = [
"all", # Perform all check except those listed below
"ES01",
"EX01",
"PR10", # Conflicts with black formatting
"SA01",
]
exclude = [ # don't report on objects that match any of these regex
"\\.undocumented_method$",
"\\.__repr__$",
"^test_",
"^conftest",
]
override_SS05 = [ # override SS05 to allow docstrings starting with these words
"^Process ",
"^Assess ",
"^Access ",
]