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pyproject.toml
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pyproject.toml
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# package build
# https://peps.python.org/pep-0517/
[build-system]
requires = ["setuptools>=65", "wheel", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"
[tool.setuptools_scm]
# package basics
# https://peps.python.org/pep-0621/
[project]
name = "bioio"
description = "Image reading, metadata management, and image writing for Microscopy images in Python"
keywords = []
readme = "README.md"
requires-python = ">=3.9"
license = { text = "BSD License" }
authors = [
{ email = "[email protected]", name = "Eva Maxfield Brown" },
{ email = "[email protected]", name = "Dan Toloudis" },
]
classifiers = [
"Development Status :: 4 - Beta",
"Natural Language :: English",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
dynamic = ["version"]
dependencies = [
"bioio-base>=0.9.1",
"dask[array]>=2021.4.1",
"fsspec>=2022.8.0",
"imageio[ffmpeg]>=2.11.0,<2.28.0",
"ngff-zarr>=0.8.2",
"numpy>=1.21.0,<2.0.0",
"ome-types[lxml]>=0.4.0",
"ome-zarr>=0.6.1",
"semver>=3.0.1",
"tifffile>=2021.8.30",
"zarr>=2.6.0",
]
[project.urls]
Homepage = "https://github.com/bioio-devs/bioio"
"Bug Tracker" = "https://github.com/bioio-devs/bioio/issues"
Documentation = "https://bioio-devs.github.io/bioio"
"User Support" = "https://github.com/bioio-devs/bioio/issues"
# extra dependencies
# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
[project.optional-dependencies]
lint = [
"pre-commit>=2.20.0",
]
test = [
"coverage>=5.1",
"pytest>=5.4.3",
"pytest-cov>=2.9.0",
"pytest-raises>=0.11",
"quilt3", # no pin to avoid pip cycling (boto is really hard to manage)
]
docs = [
# Sphinx + Doc Gen + Styling
"gitchangelog>=3.0.4",
"m2r2>=0.2.7",
"Sphinx>=4.0.0",
"furo>=2022.4.7",
# Extensions
"numpydoc",
"sphinx-copybutton",
# TODO: Pins
"docutils>=0.18,<0.19",
]
dev = [
"ipython>=8.4.0",
]
# entry points
# https://peps.python.org/pep-0621/#entry-points
# [project.entry-points."console_scripts"]
# build settings
# https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
[tool.setuptools]
zip-safe = false
include-package-data = true
[tool.setuptools.packages.find]
exclude = ["*docs/*", "*tests/*"]
[tool.setuptools.package-data]
"*" = ["*.yaml", "py.typed"]
# tools
[tool.black]
line-length = 88
[tool.isort]
ensure_newline_before_comments = true
force_grid_wrap = 0
include_trailing_comma = true
line_length = 88
multi_line_output = 3
profile = "black"
use_parentheses = true
# https://github.com/mgedmin/check-manifest#configuration
[tool.check-manifest]
ignore = [
".editorconfig",
".pre-commit-config.yaml",
".gitchangelog.rc",
"CODE_OF_CONDUCT.md",
"CONTRIBUTING.md",
"Justfile",
".cookiecutter.yaml",
"*docs/*",
]
[tool.mypy]
files = "bioio/*.py"
ignore_missing_imports = true
disallow_untyped_defs = true
check_untyped_defs = true
show_error_codes = true
# https://flake8.pycqa.org/en/latest/user/options.html
# https://gitlab.com/durko/flake8-pyprojecttoml
[tool.flake8]
max-line-length = 88
ignore = "E203,E402,W291,W503"
min-python-version = "3.9.0"
per-file-ignores = [
"__init__.py:F401",
]