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pyproject.toml
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pyproject.toml
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# https://peps.python.org/pep-0517/
[build-system]
requires = ["setuptools>=45", "wheel", "setuptools-scm>=6.2"]
build-backend = "setuptools.build_meta"
# https://peps.python.org/pep-0621/
[project]
name = "relion"
description = "Python programs for RELION"
readme = "README.md"
requires-python = ">=3.8"
license = {text = "BSD 3-Clause License"}
authors = [
{email = "[email protected]"},
{name = "Alister Burt"},
]
classifiers = [
"Development Status :: 3 - Alpha",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
]
dynamic = ["version"]
dependencies = [
"numpy",
"pandas",
"starfile>=0.5.6",
"mrcfile",
"mdocfile",
"typer",
"rich",
"einops",
"lil_aretomo",
"yet-another-imod-wrapper>=0.0.9",
"makefun",
"lru-dict",
"superqt",
"morphosamplers",
]
# extras
# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
[project.optional-dependencies]
test = [
"pytest>=6.0",
"pytest-cov",
]
dev = [
"black",
"cruft",
"flake8-bugbear",
"flake8-docstrings",
"flake8-pyprojecttoml",
"flake8-typing-imports",
"flake8",
"ipython",
"isort",
"mypy",
"pdbpp",
"pre-commit",
"pydocstyle",
"pytest-cov",
"pytest",
"rich",
]
vis = [
"napari",
"napari-threedee",
"qtpy",
"psygnal",
"pyqt5",
]
[project.urls]
homepage = "https://github.com/3dem/relion"
repository = "https://github.com/3dem/relion"
# same as console_scripts entry point
[project.scripts]
relion_tomo_import = "tomography_python_programs.import_tilt_series:cli"
relion_tomo_exclude_tilt_images = "tomography_python_programs.exclude_tilt_images:cli"
relion_tomo_align_tilt_series = "tomography_python_programs.align_tilt_series:cli"
relion_tomo_view = "tomography_python_programs.view:cli"
relion_tomo_pick = "tomography_python_programs.pick:cli"
relion_tomo_get_particle_poses = "tomography_python_programs.get_particle_poses:cli"
relion_tomo_denoise = "tomography_python_programs.denoise:cli"
# Entry points
# https://peps.python.org/pep-0621/#entry-points
# [project.entry-points."spam.magical"]
# tomatoes = "spam:main_tomatoes"
# https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
[tool.setuptools]
zip-safe = false
include-package-data = true
packages = {find = {where = ["src"], exclude=[]}}
[tool.setuptools.package-data]
"*" = ["py.typed"]
# https://github.com/pypa/setuptools_scm/#pyprojecttoml-usage
[tool.setuptools_scm]
# https://pycqa.github.io/isort/docs/configuration/options.html
[tool.isort]
profile = "black"
src_paths = ["src/tomography_python_programs", "tests"]
# https://flake8.pycqa.org/en/latest/user/options.html
# https://gitlab.com/durko/flake8-pyprojecttoml
[tool.flake8]
exclude = "docs,.eggs,examples,_version.py"
max-line-length = 88
ignore = "E203"
min-python-version = "3.8.0"
docstring-convention = "all" # use numpy convention, while allowing D417
extend-ignore = """
E203 # whitespace before ':'
D107,D203,D212,D213,D402,D413,D415,D416 # numpy
D100 # missing docstring in public module
D401 # imperative mood
W503 # line break before binary operator
"""
per-file-ignores = [
"tests/*:D",
]
# http://www.pydocstyle.org/en/stable/usage.html
[tool.pydocstyle]
match_dir = "src/tomography_python_programs"
convention = "numpy"
add_select = "D402,D415,D417"
ignore = "D100,D213,D401,D413,D107"
# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "6.0"
testpaths = ["src/tomography_python_programs/tests"]
filterwarnings = [
"error",
]
# https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
files = "src/**/"
strict = true
disallow_any_generics = false
disallow_subclassing_any = false
show_error_codes = true
pretty = true