ZedProfiler/pyproject.toml at main · WayScience/ZedProfiler · GitHub

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[build-system]
build-backend = "setuptools.build_meta"
requires = [ "setuptools>=82.0.1", "setuptools-scm>=10.0.5" ]

[project]
name = "zedprofiler"
description = "CPU-first handcrafted 3D featurization toolkit for high-throughput profiling"
readme = "README.md"
license = { file = "LICENSE" }
authors = [
  { name = "Mike Lippincott" },
  { name = "Dave Bunten" },
  { name = "Jenna Tomkinson" },
  { name = "Vincent Rubinetti" },
  { name = "Gregory Way" },
]
requires-python = ">=3.11,<3.15"
classifiers = [
  "License :: OSI Approved :: BSD License",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
]
dynamic = [ "version" ]
dependencies = [
  "beartype>=0.19",
  "bioio>=3.3",
  "bioio-tifffile>=1.3",
  "fire>=0.7.1",
  "jinja2>=3.1.6",
  "mahotas>=1.4.18",
  "matplotlib>=3.10.9",
  "pandas>=3.0.2",
  "pandera>=0.31.1",
  "pyarrow>=23.0.1",
  "pydantic>=2.10",
  "scikit-image>=0.26",
  "scipy>=1.14",
  "tomli>=2.4.1",
]
urls.Homepage = "https://zedprofiler.readthedocs.io"
urls.Repository = "https://github.com/WayScience/ZedProfiler"
scripts.ZedProfiler = "zedprofiler.cli:trigger"

[dependency-groups]
dev = [
  "poethepoet>=0.44",
  "pytest>=9.0.3",
  "pytest-cov>=5",
  "ruff>=0.15.10",
]
docs = [
  "itables>=2",
  "matplotlib>=3.10.9",
  "myst-nb>=1.4",
  "plotly>=6.8",
  "pycytominer>=1.6",
  "sphinx>=7",
  "sphinx-rtd-theme>=3.1",
]
notebooks = [
  "black>=26.3.1",
  "isort>=8.0.1",
  "jupyterlab>=4.5.6",
  "jupyterlab-code-formatter>=3.0.3",
  "jupytext>=1.19.1",
]

[tool.setuptools_scm]
version_file = "src/zedprofiler/_version.py"
version_scheme = "no-guess-dev"
local_scheme = "no-local-version"
root = "."

[tool.ruff]
target-version = "py311"
line-length = 88
# ignore all linting in the theoretical_explainations directory, which is used for testing and development of new features
extend-exclude = [
  "theorectical_explainations/notebooks/interpolation_edge_demo.ipynb",
]  # Ignore `E501` (line too long) for Jupyter notebooks
fix = true
lint.select = [
  # flake8-builtins
  "A",
  # flake8-annotations
  "ANN",
  # flake8-comprehensions
  "C4",
  # mccabe
  "C90",
  # pycodestyle
  "E",
  # pyflakes
  "F",
  # isort
  "I",
  # pylint
  "PL",
  # ruff
  "RUF",
  # flake8-simplify
  "SIM",
  "W",
]
lint.per-file-ignores."*.ipynb" = [ "C408", "E402", "E501" ]
lint.per-file-ignores."src/**/__init__.py" = [ "F401" ]
lint.per-file-ignores."src/zedprofiler/featurization/neighbors.py" = [ "PLR0913", "PLR0917" ]
lint.per-file-ignores."src/zedprofiler/featurization/texture.py" = [ "RUF046" ]

[tool.codespell]
ignore-words-list = "doesnot,inout"

[tool.vulture]
paths = [ "src/zedprofiler", "tests" ]
min_confidence = 90

[tool.pytest]
ini_options.pythonpath = [ "." ]

[tool.jupytext]
formats = "ipynb,py:light"

[tool.poe]
# tasks for development environments
tasks.test.shell = """
pytest
"""
tasks.jupyter.shell = """
jupyter lab
"""