ArchePy/pyproject.toml at main · the-brAIn-lab/ArchePy · GitHub

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[build-system]
requires = ["hatchling>=1.18"]
build-backend = "hatchling.build"

# ---------------------------------------------------------------------------
# Project metadata (PEP 621)
# ---------------------------------------------------------------------------

[project]
name = "archepy"
version = "0.1.0"
description = "Multi-Subject Archetypal Analysis (MS-AA) for fMRI data, in Python."
readme = "README.md"
requires-python = ">=3.9"
license = { file = "LICENSE" }
keywords = [
    "archetypal-analysis",
    "fmri",
    "neuroimaging",
    "multi-subject",
    "matrix-factorization",
]

authors = [
    { name = "Alex Shepherd", email = "13ashepherd@gmail.com" },
]

# Note: the upstream MATLAB toolbox is academic/non-profit only,
# so this Python port inherits that restriction. PyPI does host
# non-OSI software; we use the closest classifier available.
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: Free for non-commercial use",
    "License :: Other/Proprietary License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
]

dependencies = [
    "numpy>=1.23",
]

[project.optional-dependencies]
# GPU acceleration via CuPy. Pick the wheel that matches your CUDA version.
# CUDA 12.x: pip install archepy[gpu]
# (For CUDA 11.x users, install cupy-cuda11x manually.)
gpu = ["cupy-cuda12x>=12.0"]

# fMRI helpers (NIfTI loading for noise estimation).
fmri = ["nibabel>=4.0"]

# Plotting helpers used by the synthetic-noise generator and any tutorials.
viz = ["matplotlib>=3.5"]

# Convenience: install everything (except dev tooling).
all = [
    "archepy[gpu]",
    "archepy[fmri]",
    "archepy[viz]",
]

# Tooling for contributors / running CI locally.
dev = [
    "pytest>=7",
    "pytest-cov>=4",
    "ruff>=0.4",
    "mypy>=1.8",
    "scipy>=1.10",  # used by some tests / examples
]

# Documentation build dependencies (kept in sync with docs/doc_requirements.txt).
docs = [
    "sphinx>=7.0,<9",
    "furo>=2024.1",
    "myst-parser>=2.0",
    "nbsphinx>=0.9",
    "sphinx-copybutton>=0.5",
    "ipykernel",
]

[project.urls]
Homepage = "https://github.com/the-brAIn-lab/archepy"
Repository = "https://github.com/the-brAIn-lab/archepy"
"Upstream MATLAB toolbox" = "https://github.com/JesperLH/Multisubject-Archetypal-Analysis"
"Original paper" = "https://doi.org/10.1109/JSTSP.2016.2595103"

# ---------------------------------------------------------------------------
# Hatch (the build backend) — point it at the src/ layout
# ---------------------------------------------------------------------------

[tool.hatch.build.targets.wheel]
packages = ["src/archepy"]

[tool.hatch.build.targets.sdist]
include = [
    "/src",
    "/tests",
    "/README.md",
    "/LICENSE",
    "/CITATION.cff",
    "/pyproject.toml",
]

# ---------------------------------------------------------------------------
# Ruff — linter + formatter
# ---------------------------------------------------------------------------

[tool.ruff]
line-length = 100
target-version = "py39"

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort (import ordering)
    "B",   # flake8-bugbear
    "UP",  # pyupgrade
    "NPY", # numpy-specific rules
]
# E501 (line too long) is handled by the formatter; ignore here.
ignore = ["E501"]

# ---------------------------------------------------------------------------
# Pytest
# ---------------------------------------------------------------------------

[tool.pytest.ini_options]
minversion = "7.0"
testpaths = ["tests"]
addopts = "-ra --strict-markers"
filterwarnings = [
    "error",                                          # treat warnings as errors by default
    "ignore::DeprecationWarning:numpy",               # noisy numpy deprecations are OK
]

# ---------------------------------------------------------------------------
# Mypy — optional type checking. Lenient for now; tighten later.
# ---------------------------------------------------------------------------

[tool.mypy]
python_version = "3.9"
warn_unused_ignores = true
warn_redundant_casts = true
ignore_missing_imports = true     # cupy / nibabel don't ship type stubs