pyproject.toml

[build-system]
requires = ["setuptools>=61", "wheel", "setuptools_scm[toml]>=3.4"]
build-backend = "setuptools.build_meta"

[project]
name = "casanovo"
authors = [
    {name = "Melih Yilmaz", email = "melih@cs.washington.edu"},
    {name = "William E. Fondrie", email = "fondriew@gmail.com"},
    {name = "Wout Bittremieux", email = "wout.bittremieux@uantwerpen.be"},
]
description = "De novo mass spectrometry peptide sequencing with a transformer model"
license = {text = "Apache 2.0"}
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.8"
dependencies = [
    "appdirs",
    "lightning>=2.0",
    "click",
    "depthcharge-ms>=0.2.3,<0.3.0",
    "natsort",
    "numpy<2.0",
    "pandas",
    "psutil",
    "PyGithub",
    "PyYAML",
    "requests",
    "rich-click>=1.6.1",
    "scikit-learn",
    "spectrum_utils",
    "tensorboard",
    "torch>=2.1",
    "tqdm",
]
dynamic = ["version"]

[project.readme]
file = "README.md"
content-type = "text/markdown"

[project.urls]
Homepage = "https://github.com/Noble-Lab/casanovo"
Documentation = "https://casanovo.readthedocs.io"
"Bug Tracker" = "https://github.com/Noble-Lab/casanovo/issues"
"Discussion Board" = "https://github.com/Noble-Lab/casanovo/discussions"

[project.optional-dependencies]
docs = [
    "sphinx>=4.5.0",
    "myst-parser>=0.18.1",
    "sphinx-book-theme>=0.3.3"
]
dev = [
    "pre-commit>=2.7.1",
    "black>=19.10b0",
    "ppx",
    "psims",
    "pyteomics",
    "pytest",
]

[project.scripts]
casanovo = "casanovo.casanovo:main"

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

[tool.setuptools.packages.find]
exclude = ["docs", "tests", "sample_data"]

[tool.setuptools_scm]

[tool.black]
line-length = 79
target-version = ['py38']
include = '\.pyi?$'
exclude = '''

(
  /(
      \.eggs         # exclude a few common directories in the
    | \.git          # root of the project
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
  )/
  | foo.py           # also separately exclude a file named foo.py in
                     # the root of the project
)
'''