pyproject.toml

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

[project]
name = "squid-tools"
version = "1.0.0"
description = "Post-processing connector for Cephla-Lab/Squid microscopy"
requires-python = ">=3.10"
# v1 ships the union of every plugin's runtime deps in core so a single
# `pip install squid-tools` covers all 8 products. Per-plugin extras stay
# declared (alias to core for now) so v2 can split them without a refactor.
dependencies = [
    # Core viewer + data model
    "pydantic>=2.10",
    "numpy>=1.24",
    "dask[array]>=2024.1",
    "tifffile>=2024.1",
    "pyyaml>=6.0",
    "zarr>=2.16",
    "PySide6>=6.6",
    "vispy>=0.14",
    # Stitching (vendored TileFusion)
    "numba>=0.59",
    "scikit-image>=0.22",
    "scipy>=1.10",
    "tensorstore>=0.1.50",
    "pandas>=2.0",
    "tqdm>=4.65",
    # Background subtraction
    "sep>=1.4",
    # Remote (R2) + web demo
    "boto3>=1.34",
    "Pillow>=10.0",
]

[project.optional-dependencies]
# Per-plugin extras kept for forward-compatibility with v2's split-install
# story. In v1 they all resolve to the core install (everything is bundled).
stitching  = []
flatfield  = []
decon      = []
phase      = []                               # waveorder pulled lazily when used
acns       = []
bgsub      = []
r2         = []
webdemo    = []

# GPU-accelerated compositor + decon (CUDA-only, opt-in)
gpu        = ["cupy-cuda12x>=13.0"]

# 3D volume viewer (vispy already in core)
3d         = []

# Convenience aliases retained for muscle memory
all-corrections = []
all-restoration = []
everything      = []

# Dev only
dev = [
    "pytest>=8.0",
    "pytest-qt>=4.2",
    "ruff>=0.4",
    "mypy>=1.10",
]

[project.entry-points."squid_tools.plugins"]
flatfield  = "squid_tools.processing.flatfield.plugin:FlatfieldPlugin"
stitcher   = "squid_tools.processing.stitching.plugin:StitcherPlugin"
decon      = "squid_tools.processing.decon.plugin:DeconvolutionPlugin"
bgsub      = "squid_tools.processing.bgsub.plugin:BackgroundSubtractPlugin"
# phase + acns shelved for v1; re-enable in v2 once correctness asserts
# land. Plugin code remains under squid_tools.processing.{phase,acns}/.

[tool.ruff]
line-length = 100
target-version = "py310"
# Vendored upstream code — track as-is, don't drift from upstream style.
extend-exclude = ["squid_tools/processing/stitching/_tilefusion/**"]

[tool.ruff.lint]
select = ["E", "F", "I", "N", "UP", "B", "SIM"]

[tool.mypy]
python_version = "3.10"
strict = true
plugins = ["pydantic.mypy"]

[tool.pytest.ini_options]
testpaths = ["tests"]
qt_api = "pyside6"
markers = [
    "gpu: requires CUDA GPU",
]