pyproject.toml

[build-system]
requires = ["uv_build>=0.8.1,<0.9.0"]
build-backend = "uv_build"

[project]
name = "mosaic"
version = "0.1.0"
description = "Mussel-Aeon-Paladin workflow for digital pathology"
readme = "README.md"
requires-python = ">=3.10,<3.12"
dependencies = [
  "gradio[oauth]>=6.0.0",
  "lightning>=2.6.0",
  "loguru>=0.7.3",
  "memory-profiler>=0.61.0",
  "mussel[torch-gpu]",
  "paladin",
  "seaborn>=0.13.2",
  "setuptools>=65.0.0,<70.0.0",  # pkg_resources removed in 70+
  "spaces>=0.30.0",
  "statsmodels>=0.14.6",
]

[project.scripts]
aeon_inference = "mosaic.inference.aeon:main"
paladin_inference = "mosaic.inference.paladin:main"
mosaic = "mosaic.gradio_app:main"

[dependency-groups]
dev = [
  "black==25.12.0",
  "pylint>=3.3.6",
  "pytest>=8.3.0",
  "pytest-cov>=6.0.0",
  "pytest-mock>=3.14.0",
]

[tool.pylint."messages control"]
disable = [
  "logging-fstring-interpolation",
  "broad-exception-caught",
  "unspecified-encoding",
]

[tool.uv]
# Override PyTorch version constraints from mussel[torch-gpu].
# mussel pins torch<2.6 which may be too strict; we relax to >=2.0.0.
# The override applies on ALL platforms (not just macOS) so Docker builds
# still get torch installed.
override-dependencies = [
  "torch>=2.0.0",
  "torchvision>=0.15.0",
]

[tool.uv.sources]
# For local dev with SSH: uv pip install -e .
# For Docker builds with token: GH_TOKEN=<token> uv pip install -e .
# uv will fall back to git credential helper if ${GH_TOKEN} is empty
paladin = { git = "ssh://git@github.com/pathology-data-mining/paladin.git", rev = "dev" }
mussel = { git = "https://github.com/pathology-data-mining/Mussel.git", rev = "mosaic-dev" }

[tool.black]
target-version = ["py310", "py311"]
line-length = 88

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = "-v --cov=src/mosaic --cov-report=term-missing"