mepylome/pyproject.toml at main · brj0/mepylome · GitHub

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[build-system]
requires = [
    "setuptools>=42",
    "wheel",
    "numpy>=1.10.0",
]
build-backend = "setuptools.build_meta"

[project]
name = "mepylome"
version = "0.12.0"
description = "Python package for processing Infinium DNA methylation arrays"
readme = "README.md"
authors = [
    { name = "Jon Brugger" }
]
license = "MIT"
keywords = ["Illumina", "Methylation", "Infinium", "Microarray", "BeadChip"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering",
    "Topic :: Software Development"
]
requires-python = ">=3.12"
dependencies = [
    "dash>=2.16.0",
    "dash_bootstrap_components",
    "numpy",
    "odfpy",
    "openpyxl",
    "pandas",
    "plotly",
    "psutil",
    "pyranges1",
    "scikit-learn",
    "tqdm",
    "toml",
    "umap-learn",
    "numba",
    "xlrd",
    "xxhash"
]

[project.optional-dependencies]
seg = [
  "ruptures",                 # segmentation algorithm
]
dev = [
  "build",                    # PEP 517 build frontend (python -m build)
  "ipython",                  # interactive REPL
  "ipywidgets",               # interactive notebook widgets
  "jupyter",                  # notebook server & tools
  "jupytext",                 # sync notebooks and scripts
  "kaleido==0.2.1",           # stable image export for Plotly
  "mypy",                     # static type checking
  "nbstripout",               # strip outputs from committed notebooks
  "pillow",                   # image handling (capitalized PyPI name)
  "pytest",                   # test code
  "pytest-cov",               # Coverate rate of tests via pytest --cov=mepylome
  "ruff",                     # fast linter
  "ruptures",                 # segmentation algorithm
  "sphinx",                   # docs generator
  "sphinx-rtd-theme",         # ReadTheDocs theme for HTML docs
  "sphinx-autodoc-typehints", # for docs
  "tuna",                     # profiler / tuning (lightweight)
  "twine",                    # upload releases to PyPI
  "ty",                       # static type checking
]

[project.urls]
Homepage = "https://github.com/brj0/mepylome"

[tool.setuptools]
packages = { find = {} }
include-package-data = true

[project.scripts]
mepylome = "mepylome.cli:start_mepylome"

[tool.ruff]
line-length = 79

[tool.ruff.lint]
select = [
    # Annotation
    "ANN",
    # pycodestyle - missing docstring
    "D",
    # pycodestyle
    "E",
    # Pyflakes
    "F",
    # pyupgrade
    "UP",
    # flake8-bugbear
    "B",
    # flake8-simplify
    "SIM",
    # isort
    "I",
    # pandas-vet
    "PD",
    # Pylint
    "PL",
    # Trailing whitespace
    "W",
]
ignore = [
    # Dynamically typed expressions (typing.Any) are disallowed in `*args`
    "ANN401",
    # Relax the convention by _not_ requiring documentation for every function
    # parameter.
    "D417",
    # Missing docstring in `__init__`
    "D107",
    # Missing docstring in public method
    "D102",
    # Missing docstring in magic method
    "D105",
    # Use `.to_numpy()` instead of `.values`
    "PD011",
    # `print` found
    "T201",
    # Trailing comma missing
    "COM812",
    # Magic value used in comparison
    "PLR2004",
    # Too many return statements
    "PLR0911",
    # `import` should be at the top-level of a file
    "SIM115",
    # Too many arguments in function definition
    "PLC0415",
    # Too many arguments in function definition
    "PLR0913",
    # Too many statements
    "PLR0915",
]

[tool.ruff.lint.per-file-ignores]
"examples/**" = ["ANN", "B018", "D100", "D101", "E402", "E501"]
"scripts/**" = ["ANN", "D103"]
"tests/**" = ["E402", "D103"]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.mypy]
python_version = "3.12"
ignore_missing_imports = true
disallow_untyped_defs = true
warn_unused_ignores = true
warn_redundant_casts = true
exclude = ["trash/", "examples/"]
show_column_numbers = true
pretty = true


[tool.ty.src]
exclude = ["examples"]

[tool.ty.terminal]
output-format = "concise"

[tool.ty.rules]
unresolved-import = "ignore"