SarcAsM/pyproject.toml at main · danihae/SarcAsM · GitHub

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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "sarc-asm"
version = "0.5.0"
description = "AI-based Sarcomere Analysis Multitool for structural and functional analysis of sarcomeres in microscopy images and movies"
readme = "README.md"
requires-python = ">=3.10,<3.14"
authors = [
    { name = "Daniel Haertter", email = "dani.hae@posteo.de" }
]
license = { file = "LICENSE" }
classifiers = [
  "Development Status :: 4 - Beta",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Image Processing",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
]
dependencies = [
    "numpy>2.2",
    "orjson>=3.10.0,<4.0.0",
    "napari>=0.4.18,<0.7.0",
    "torch>=2.0.0,<3.0.0",
    "bio-image-unet>=1.1.2,<2.0.0",
    "matplotlib>=3.10.0,<4.0.0",
    "matplotlib-scalebar>=0.8.0,<0.9.0",
    "PyQt5>=5.15.4,<5.16.0",
    "pandas>=2.0.0,<3.0.0",
    "scikit-learn>=1.0.2,<2.0.0",
    "scikit-image>0.18,<1.0",
    "PyWavelets>=1.5.0,<2.0.0",
    "igraph>=0.11.2,<0.12.0",
    "numba>=0.61.2,<0.62.0",
    "qtutils>=4.0.0,<5.0.0",
    "networkx>=3.2,<4.0",
    "openpyxl>=3.1.4,<4.0.0",
    "tifffile>=2023.12.9",
    "imagecodecs>=2024.1.1",
]

[project.urls]
Repository = "https://github.com/danihae/SarcAsM"
Documentation = "https://sarcasm.readthedocs.io"
Issues = "https://github.com/danihae/SarcAsM/issues"
Changelog = "https://github.com/danihae/SarcAsM/releases"

[project.scripts]
sarcasm = "sarcasm_app.__main__:main"

[project.optional-dependencies]
app = ["pyinstaller>=6.0.0"]
docs = [
  "sphinx>=7.0,<8.0",
  "sphinx-rtd-theme>=2.0.0,<3.0.0",
  "sphinx-autoapi>=3.0,<4.0",
  "nbsphinx>=0.9.0,<0.10.0",
  "myst-parser>=2.0.0,<3.0.0"
]

[dependency-groups]
dev = [
    "notebook>=7.0.0,<8.0.0",
    "ruff>=0.6.0",
    "pytest>=8.4.1",
    "pytest-cov>=4.0.0",
    "pytest-xdist>=3.0.0",
]

[tool.ruff]
line-length = 88
exclude = [
    ".git",
    ".mypy_cache",
    ".ruff_cache",
    "venv",
    "__pycache__",
    "build",
    "dist",
    "docs",
    "private"
]
target-version = "py310"

[tool.ruff.lint]
select = [
    "E4",  # Import errors
    "E7",  # Statement errors
    "E9",  # Runtime errors
    "F",   # Pyflakes (undefined names, unused imports)
]

ignore = [
    "E501",  # Line too long (let formatter handle this)
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]  # Allow unused imports in __init__.py
"test_*.py" = ["F401"]   # Allow unused imports in tests
"docs/*" = ["E402"]      # Allow import violations in docs
"*.ipynb" = ["F403", "F405"]  # Allow star imports in notebooks
"scripts/*.py" = ["T201"]  # Allow print statements in scripts

[tool.hatch.build.targets.sdist]
include = [
  "sarcasm/",
  "sarcasm_app/",
  "contraction_net/",
  "LICENSE",
  "README.md",
  "pyproject.toml"
]

[tool.hatch.build.targets.wheel]
packages = ["sarcasm", "sarcasm_app", "contraction_net"]

[tool.readthedocs]
version = 2
build = { os = "ubuntu-22.04", tools = { python = "3.10" } }
sphinx = { configuration = "docs/conf.py" }
python = { install = [ { method = "pip", path = ".", extras = ["docs"] } ] }