pyproject.toml

[project]
name = "ChemographyKit"
version = "0.1.0"
description = "A Python library for exploring chemical space using Generative Topographic Mapping."
authors = [
    {name = "Tagir Akhmetshin, Louis Plyer, Alexey Orlov, Alexandre Varnek", email = "varnek@unistra.fr"},
]
dependencies = ["numpy>=2.3.2", "torch>=2.7.1", "pandas>=2.3.2", "altair>=5.5.0", "plotly>=6.3.0", "scikit-learn>=1.7.1", "tqdm>=4.67.1", "jupyterlab>=4.4.7", "ipywidgets>=8.1.7", "anywidget>=0.9.18", "pyarrow>=21.0.0"]
requires-python = ">=3.11"
readme = "README.md"
license = {text = "MIT"}

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


[tool.pdm]
distribution = true

[tool.pdm.dev-dependencies]
test = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
]
quality = [
    "pre-commit>=3.0.0",
    "black>=23.0.0",
    "isort>=5.12.0",
    "ruff>=0.1.0",
    "mypy>=1.8.0",
    "bandit>=1.7.0",
    "pydocstyle>=6.3.0",
]
docs = [
    "sphinx>=7.0.0",
    "sphinx-rtd-theme>=1.3.0",
    "nbsphinx>=0.9.0",
    "myst-parser>=2.0.0",
    "sphinx-autodoc-typehints>=1.24.0",
    "sphinx-autobuild>=2021.3.14",
    "matplotlib>=3.7.0",
    "seaborn>=0.12.0",
]

# Black configuration
[tool.black]
line-length = 88
target-version = ['py311']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
)/
'''

# isort configuration
[tool.isort]
profile = "black"
line_length = 88
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
ensure_newline_before_comments = true
src_paths = ["src", "tests"]

# Ruff configuration
[tool.ruff]
target-version = "py311"
line-length = 88
select = [
    "E",  # pycodestyle errors
    "W",  # pycodestyle warnings
    "F",  # pyflakes
    "I",  # isort
    "B",  # flake8-bugbear
    "C4", # flake8-comprehensions
    "UP", # pyupgrade
    "ARG001", # unused-function-argument
    "ARG002", # unused-method-argument
    "ARG003", # unused-class-method-argument
    "ARG004", # unused-static-method-argument
    "ARG005", # unused-lambda-argument
    "D",   # pydocstyle
    "SIM", # flake8-simplify
    "TCH", # flake8-type-checking
    "RUF", # Ruff-specific rules
]
ignore = [
    "E501",  # line too long, handled by black
    "B008",  # do not perform function calls in argument defaults
    "D100",  # missing docstring in public module
    "D101",  # missing docstring in public class
    "D102",  # missing docstring in public method
    "D103",  # missing docstring in public function
    "D104",  # missing docstring in public package
    "D105",  # missing docstring in magic method
    "D107",  # missing docstring in __init__
    "D203",  # 1 blank line required before class docstring
    "D213",  # multi-line docstring summary should start at the second line
]
unfixable = [
    "ARG001", "ARG002", "ARG003", "ARG004", "ARG005", # unused arguments
    "F841",   # unused variables
]
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
]

[tool.ruff.per-file-ignores]
"tests/**/*" = ["D", "ARG", "S101"]  # Allow missing docstrings and assert statements in tests
"__init__.py" = ["F401"]  # Allow unused imports in __init__.py files

[tool.ruff.pydocstyle]
convention = "numpy"

[tool.ruff.mccabe]
max-complexity = 10

# MyPy configuration
[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false  # Start lenient, can be tightened later
disallow_incomplete_defs = false
check_untyped_defs = true
disallow_untyped_decorators = false
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
warn_unreachable = true
strict_equality = true
show_error_codes = true

[[tool.mypy.overrides]]
module = [
    "torch.*",
    "sklearn.*",
    "altair.*",
    "plotly.*",
    "tqdm.*",
    "pandas.*",
    "numpy.*",
]
ignore_missing_imports = true

# Pytest configuration
[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
    "--strict-config",
    "--cov=src/chemographykit",
    "--cov-report=term-missing",
    "--cov-report=html",
    "--cov-report=xml",
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
    "performance: marks tests as performance benchmarks",
    "gpu: marks tests that require GPU",
]
filterwarnings = [
    "ignore::UserWarning:chemographykit.*",
    "ignore::DeprecationWarning:sklearn.*",
    "ignore::FutureWarning:torch.*",
]

# Coverage configuration
[tool.coverage.run]
source = ["src"]
omit = [
    "*/tests/*",
    "*/test_*.py",
    "*/__init__.py",
    "*/conftest.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if self.debug:",
    "if settings.DEBUG",
    "raise AssertionError",
    "raise NotImplementedError",
    "if 0:",
    "if __name__ == .__main__.:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]

# Bandit security linter configuration
[tool.bandit]
exclude_dirs = ["tests", "docs", "tutorials"]
skips = ["B101", "B601"]  # Skip assert_used and shell_injection for scientific computing context