pyproject.toml

# pyproject.toml — SFPPy Project Configuration
# =============================================
# Modern Python packaging configuration (PEP 517/518/621)
#
# @project: SFPPy — Safe Food Packaging in Python
# @author: Olivier Vitrac, PhD, HDR
# @email: olivier.vitrac@agroparistech.fr
# @license: MIT
# @url: https://github.com/ovitrac/SFPPy

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "SFPPy"
version = "1.50"
description = "Safe Food Packaging in Python — Mass transfer modeling for food contact materials"
readme = "README.md"
license = {text = "MIT"}
requires-python = ">=3.10"
authors = [
    {name = "Olivier Vitrac", email = "olivier.vitrac@agroparistech.fr"}
]
maintainers = [
    {name = "Olivier Vitrac", email = "olivier.vitrac@agroparistech.fr"}
]
keywords = [
    "food packaging",
    "migration modeling",
    "mass transfer",
    "diffusion",
    "food contact materials",
    "regulatory compliance",
    "EU 10/2011",
    "Patankar method",
    "finite volume",
    "polymer",
    "food safety"
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Physics",
]

dependencies = [
    "numpy>=1.21.0",
    "matplotlib>=3.4.0",
    "scipy>=1.7.0",
    "pandas>=1.3.0",
    "openpyxl>=3.0.10",
    "pillow>=8.0.0",
]

[project.optional-dependencies]
# Development and testing
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "pytest-xdist>=3.0.0",
    "httpx>=0.24.0",
    "black>=23.0.0",
    "isort>=5.12.0",
    "mypy>=1.0.0",
    "flake8>=6.0.0",
    "bandit>=1.7.0",
]

# Jupyter notebooks
notebooks = [
    "jupyter>=1.0.0",
    "ipywidgets>=8.0.0",
]

# PubChem API access
pubchem = [
    "requests>=2.28.0",
]

# Studio web GUI
studio = [
    "fastapi>=0.100.0",
    "uvicorn[standard]>=0.23.0",
    "pydantic>=2.0.0",
    "jinja2>=3.1.0",
    "python-multipart>=0.0.6",
    "requests>=2.28.0",
    "pyyaml>=6.0",
]

# Survey batch processing
survey = [
    "fastapi>=0.100.0",
    "uvicorn[standard]>=0.23.0",
    "pydantic>=2.0.0",
    "jinja2>=3.1.0",
    "python-multipart>=0.0.6",
    "requests>=2.28.0",
    "pyyaml>=6.0",
    "odfpy>=1.4.0",
    "aiofiles>=23.0.0",
]

# RAG/AI knowledge base queries
rag = [
    "llama-index>=0.10.0",
    "llama-index-embeddings-huggingface>=0.1.0",
    "llama-index-llms-ollama>=0.1.0",
    "llama-index-vector-stores-chroma>=0.1.0",
    "sentence-transformers>=2.2.0",
    "chromadb>=0.4.0",
    "transformers>=4.30.0",
]

# Full installation (everything except RAG due to heavy deps)
full = [
    "SFPPy[dev,notebooks,pubchem,studio,survey]",
]

# Complete with RAG
complete = [
    "SFPPy[full,rag]",
]

[project.urls]
Homepage = "https://github.com/ovitrac/SFPPy"
Documentation = "https://ovitrac.github.io/SFPPy/"
Repository = "https://github.com/ovitrac/SFPPy.git"
Issues = "https://github.com/ovitrac/SFPPy/issues"
Changelog = "https://github.com/ovitrac/SFPPy/releases"

[project.scripts]
sfppy = "cli:main"

[tool.setuptools]
include-package-data = true
zip-safe = true

[tool.setuptools.packages.find]
include = ["patankar", "patankar.*"]

[tool.setuptools.package-data]
patankar = [
    "cache.PubChem/*.json",
    "cache.PubChem/thumbs/*.png",
]

# =============================================================================
# Development Tool Configuration
# =============================================================================

[tool.pytest.ini_options]
testpaths = ["tests", "INSERM/fixtures"]
python_files = ["test_*.py", "*_test.py"]
python_functions = ["test_*"]
addopts = "-v --tb=short"
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::PendingDeprecationWarning",
]

[tool.black]
line-length = 100
target-version = ['py310', 'py311', 'py312']
include = '\.pyi?$'
exclude = '''
/(
    \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
  | html
  | wiki
  | notebooks
  | release
  | studio
  | survey
)/
'''

[tool.isort]
profile = "black"
line_length = 100
skip_glob = ["html/*", "wiki/*", "notebooks/*", "release/*", "studio/*", "survey/*"]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true
exclude = [
    "html/",
    "wiki/",
    "notebooks/",
    "release/",
    "studio/",
    "survey/",
]