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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools >= 61.0", "setuptools-scm"]
build-backend = "setuptools.build_meta"
[project]
name = "meteor-maps"
description = "denoise crystallographic difference maps"
readme = "README.md"
dynamic = ["version"]
authors = [
{ name = "Alisia Fadini", email = "af840@cam.ac.uk" },
{ name = "Thomas Lane", email = "thomas.joseph.lane@gmail.com" }
]
requires-python = ">=3.11"
classifiers = [
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
]
dependencies = [
"numpy >= 1.26",
"scipy >= 1.14.0",
"gemmi >= 0.6.6",
"scikit-image >= 0.24.0",
"reciprocalspaceship >= 1.0.2",
"structlog >= 24.4.0",
"setuptools >= 75.5.0",
]
[project.optional-dependencies]
tests = [
"pytest",
"pytest-cov",
"pytest-xdist",
]
[project.scripts]
"meteor.diffmap" = "meteor.scripts.compute_difference_map:main"
"meteor.phaseboost" = "meteor.scripts.compute_iterative_tv_map:main"
[project.urls]
Homepage = "https://github.com/rs-station/meteor"
Issues = "https://github.com/rs-station/meteor/issues"
[tool.setuptools_scm]
version_file = "meteor/_version.py"
[tool.pytest.ini_options]
addopts = "-n 4 --cov=meteor --cov-report=xml"
[tool.mypy]
disallow_untyped_calls = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
[[tool.mypy.overrides]]
module = "reciprocalspaceship.*,gemmi.*,scipy.*,skimage.*"
ignore_missing_imports = true
[tool.ruff]
line-length = 100
lint.flake8-pytest-style.fixture-parentheses = false
lint.select = [
"ALL", # include all the rules, including new ones
]
lint.ignore = [
#### modules
"ANN", # flake8-annotations: ignore annotation-related errors
"C90", # mccabe complexity: ignore code complexity checks
"DJ", # django: ignore Django-specific linting rules
"EXE", # flake8-executable: ignore file execution permission errors
"T10", # debugger: ignore debugger-related code (e.g., `pdb`)
#### specific rules
"D100", # ignore missing docstrings in module
"D101", # ignore missing docstrings in class
"D102", # ignore missing docstrings in public method
"D103", # ignore missing docstrings in function
"D104", # ignore missing docstrings in package
"D105", # ignore missing docstrings in magic methods (e.g., __init__)
"D106", # ignore missing docstrings in public nested class
"D107", # ignore missing docstrings in __init__ method
"D205", # ignore failure to separate summary line from description in docstring
"D212", # ignore multiline docstring summary errors
"D400", # periods in docstrings
"D401", # ignore docstring should be in imperative mood
"E501", # ignore line too long (over 79 characters)
"TRY003", # ignore external messages in exceptions being too verbose
"TD002", # to do authorship
"TD003", # to do issue
"PD002", # allow inplace modifications in Pandas operations
"TCH001", # type checking blocks
"TCH002", # type checking blocks
"TCH003", # type checking blocks
"COM812", # missing trailing comma, conflicts
"ISC001", # string line concat, conflicts
]
exclude = [
"build/",
"dist/",
"migrations/",
".venv/",
".git/",
"__pycache__/",
"*.pyc",
]
[tool.ruff.lint.extend-per-file-ignores]
"test/**/*.py" = [
"S101", # asserts allowed in tests
"ARG", # unused function args -> fixtures
"PLR2004", # magic value used in comparison
"FBT001", # allow positional bools as function args
"SLF001", # access private methods
]
[tool.ruff.lint.pydocstyle]
convention = "numpy"