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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=61", "wheel", "setuptools_scm[toml]>=3.4"]
build-backend = "setuptools.build_meta"
[project]
name = "casanovo"
authors = [
{name = "Melih Yilmaz", email = "[email protected]"},
{name = "William E. Fondrie", email = "[email protected]"},
{name = "Wout Bittremieux", email = "[email protected]"},
]
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
)
'''