pyproject.toml

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

[project]
name = "sbh-simulator"
version = "0.1.0"
description = "Simulate serial blockface histology (SBH) illumination inhomogeneity"
readme = "README.md"
license = "GPL-3.0-or-later"
requires-python = ">=3.14"
authors = [
    { name = "The LINUM developers" },
]
maintainers = [
    { name = "Joël Lefebvre", email = "lefebvre.joel@uqam.ca" },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Image Processing",
    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
]
dependencies = [
    "numpy",
    "matplotlib",
    "SimpleITK",
]

[project.optional-dependencies]
training = [
    "nibabel",
    "torch",
    "torchvision",
    "lightning",
    "wandb",
]
dev = [
    "ruff>=0.11",
    "ty>=0.0.27",
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "pre-commit>=4.5.1",
]

[dependency-groups]


[project.scripts]
sbh-simulate = "sbh_simulator.cli.simulate:main"
sbh-train = "sbh_simulator.cli.train:main"
sbh-vignette = "sbh_simulator.cli.vignette:main"

# ---------------------------------------------------------------------------
# uv
# ---------------------------------------------------------------------------
[tool.uv]
# Bake wheels for all target environments into the universal lock file so
# that the CUDA wheels (Linux-only) and CPU wheels (macOS / Windows) are
# each resolved to the correct variant on each platform.
required-environments = [
    "sys_platform == 'linux'",
    "sys_platform == 'darwin'",
    "sys_platform == 'win32'",
]

# PyTorch ships its own package index; PyPI only has very old cp3xx wheels.
# The cpu index is the fallback for macOS / Windows (and Linux without the
# gpu extra).  The cu132 index is only activated on Linux when --extra gpu.
[[tool.uv.index]]
name = "pytorch-cpu"
url = "https://download.pytorch.org/whl/cpu"
explicit = true

[[tool.uv.index]]
name = "pytorch-cu132"
url = "https://download.pytorch.org/whl/cu132"
explicit = true

[tool.uv.sources]
# Mutually exclusive platform markers keep these source entries conflict-free.
# Linux (typically a CUDA training server) → cu132 CUDA index.
# macOS / Windows (typically developer laptops) → CPU-only index.
torch = [
    { index = "pytorch-cu132", marker = "sys_platform == 'linux'" },
    { index = "pytorch-cpu",   marker = "sys_platform != 'linux'" },
]
torchvision = [
    { index = "pytorch-cu132", marker = "sys_platform == 'linux'" },
    { index = "pytorch-cpu",   marker = "sys_platform != 'linux'" },
]

# ---------------------------------------------------------------------------
# ruff
# ---------------------------------------------------------------------------
[tool.ruff]
target-version = "py314"
line-length = 127
fix = true
include = ["sbh_simulator*", "scripts*", "tests*"]

[tool.ruff.lint]
select = ["E", "F", "W", "I", "UP", "B", "RUF", "SIM", "C4", "PIE", "PTH",
            "N", "PERF", "FLY", "G", "D", "ANN", "ARG", "ERA", "FURB"]
# N813: SimpleITK as sitk is the universal Python convention — excluded globally.
# ANN401: Any is legitimately unavoidable in a few callback/override signatures.
# Note: flake8-type-checking (TCH/TC) is intentionally not selected — under
# PEP 649 (Python 3.14 default), annotations are lazily evaluated, so gating
# typing-only imports inside TYPE_CHECKING blocks no longer reduces import cost.
ignore = ["N813", "ANN401"]
extend-select = ["D417"]
# Greek/mathematical glyphs are intentional in docstrings.
# σ (sigma) is standard statistical notation; replacing it with 'o' would reduce legibility.
allowed-confusables = ["σ"]

[tool.ruff.lint.pydocstyle]
# numpy-style docstrings across the whole codebase.
# This disables D203, D212, D215 (conflicting numpy-incompatible rules).
convention = "numpy"

[tool.ruff.lint.isort]
known-first-party = ["sbh_simulator"]

[tool.ruff.lint.per-file-ignores]
# Scientific codebase: CapWords arg/var names follow nn.Module type naming convention
"sbh_simulator/models.py" = ["N803", "N806"]
# Dev scripts keep exploratory notes, use print/plt freely, no docstrings required
"scripts/dev_*.py" = ["ERA", "D", "ANN"]
"scripts/fig_synthetic_vignettes.py" = ["D", "ANN"]
"scripts/illumination_extraction_inference.py" = ["D"]
# Test files: type annotations, docstrings, unused-arg checks, and naming conventions are not required
"tests/**" = ["ANN", "D", "ARG", "N", "ERA"]

[tool.ruff.format]
# Use default (black-compatible) formatting

# ---------------------------------------------------------------------------
# ty
# ---------------------------------------------------------------------------
[tool.ty.src]
include = ["sbh_simulator", "tests"]

[tool.ty.environment]
python-version = "3.14"

[tool.ty.rules]
# possibly-unresolved-reference defaults to "warn" in ty; raise it to "error"
# so that variables only assigned inside conditional branches are caught.
possibly-unresolved-reference = "error"

[tool.ty.analysis]
# Optional ML/GPU deps — dynamic attributes on torch modules, lightning hooks,
# and wandb loggers produce cascading false positives in ty.
# Using replace-imports-with-any so downstream attribute/subscript access
# on the imported module is typed as Any rather than causing cascading errors.
replace-imports-with-any = ["torch.**", "torchvision.**", "lightning.**", "wandb.**"]

# --- ty overrides ---

# Relax rules in test files
[[tool.ty.overrides]]
include = ["tests/**", "**/test_*.py", "**/conftest.py"]

[tool.ty.overrides.rules]
possibly-unresolved-reference = "ignore"
unresolved-attribute = "ignore"
invalid-assignment = "ignore"

# ---------------------------------------------------------------------------
# pytest
# ---------------------------------------------------------------------------
[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "--strict-markers --strict-config"
markers = [
    "gpu: marks tests that require a CUDA-capable GPU (deselect with '-m not gpu')",
]