MaldiAMRKit/pyproject.toml at main · EttoreRocchi/MaldiAMRKit · GitHub

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[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "MaldiAMRKit"
dynamic = ["version", "dependencies", "optional-dependencies"]
description = "A comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for antimicrobial resistance (AMR) prediction purposes"
readme = {file = "README.md", content-type = "text/markdown"}
authors = [
  { name = "Ettore Rocchi", email = "ettore.rocchi3@unibo.it" }
]
license = "MIT"
requires-python = ">=3.10"
keywords = ["MALDI", "MALDI-TOF", "mass-spectrometry", "machine-learning", "AMR", "antimicrobial-resistance"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Operating System :: OS Independent",
]

[project.scripts]
maldiamrkit = "maldiamrkit.cli:app"

[project.urls]
Homepage = "https://github.com/EttoreRocchi/MaldiAMRKit"
Documentation = "https://maldiamrkit.readthedocs.io/"
Source = "https://github.com/EttoreRocchi/MaldiAMRKit"
Issues = "https://github.com/EttoreRocchi/MaldiAMRKit/issues"

[tool.setuptools.dynamic]
version = {attr = "maldiamrkit.__version__"}
dependencies = {file = ["requirements.txt"]}

[tool.setuptools.dynamic.optional-dependencies]
docs = {file = ["requirements-docs.txt"]}
dev = {file = ["requirements-dev.txt"]}
batch = {file = ["requirements-batch.txt"]}
formats = {file = ["requirements-formats.txt"]}

[tool.setuptools.packages.find]
where = ["."]
include = ["maldiamrkit*"]

[tool.setuptools.package-data]
maldiamrkit = [
    "py.typed",
    "data/breakpoints/*.yaml",
    "data/breakpoints/eucast/*.yaml",
    "data/breakpoints/eucast/README.md",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
]

[tool.ruff]
line-length = 88
target-version = "py310"

[tool.ruff.lint]
select = ["E", "F", "W", "I", "D", "B"]
ignore = ["E501", "D100", "D104", "D105", "D107"]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["D"]

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

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