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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "flimsay"
version = "0.4.0"
authors = [
{name = "Sebastian Paez", email = "[email protected]"},
]
description = "A super simple fast IMS predictor"
requires-python = ">=3.9,<3.12"
keywords = ["proteomics", "dia", "ion mobility"]
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",
]
dependencies = [
"pandas >= 2.0.0",
"numpy == 1.26.0",
"tqdm >= 4.64.1",
"loguru >= 0.6.0",
"lightgbm >= 3.3.5",
"rich-click >= 1.6.1",
]
[project.scripts]
flimsay = "flimsay.cli:cli"
[project.readme]
file = "README.md"
content-type = "text/markdown"
[project.urls]
Homepage = "https://github.com/TalusBio/flimsay"
Documentation = "https://TalusBio.github.io/flimsay"
[project.optional-dependencies]
test = [
"pytest >= 7.2.0",
"pytest-datadir >= 1.4.1",
"pytest-cov >= 4.0.0",
]
plot = [
"matplotlib",
"vizta",
]
build = [
"nbformat",
"nbclient",
"ipykernel",
"wheel",
"build",
"twine",
]
dev = [
"ruff >= 0.0.253",
"black >= 23.1.0",
"isort >= 5.12.0",
"pylance >= 0.3.9",
"jupyter >= 1.0.0",
"pip-tools >= 7.0.0"
]
[tool.setuptools.package-dir]
flimsay = "flimsay"
[tool.setuptools.package-data]
flimsay = ["*.txt"]
"flimsay.weights" = ["*.txt"]
[tool.pytest.ini_options]
minversion = "6.0"
addopts = "--doctest-modules -v --cov=flimsay"
doctest_optionflags = "NORMALIZE_WHITESPACE"
testpaths = [
"flimsay",
"tests/unit_tests",
]
[tool.ruff]
line-length = 88
select = ["E", "F", "B","W", "C", "I", "D", "UP", "N", "ANN", "T20", "COM"]
target-version = "py39"
# ANN101 Missing type annotation for `self` in method
# D213 Multi-line docstring summary should start at the second lin
# D203 1 blank line required before class docstring
# D100 Missing docstring in public module
# ANN102 Missing type annotation for `cls` in classmethod
# D401 First line of docstring should be in imperative mood
ignore = ["D213", "ANN101", "D203", "D100", "ANN102", "D401"]
fix = true
[tool.ruff.per-file-ignores]
"**__init__.py" = ["D104"]
"tests/**.py" = ["ANN201", "ANN001", "ANN202"]
# ANN001 Missing type annotation for function argument
# Ignoring in the cli since it is redundant with the click options
# D103 Missing docstring in public function
# Information in the help of the click command.
"flimsay/cli.py" = ["ANN001", "ANN201", "D103"]
[tool.black]
line-length = 88
target-version = ['py39', 'py310', 'py311']
preview = true
[tool.isort]
profile = "black"
[tool.bumpver]
current_version = "0.4.0"
version_pattern = "MAJOR.MINOR.PATCH"
commit_message = "bump version {old_version} -> {new_version}"
commit = true
tag = true
push = true
[tool.bumpver.file_patterns]
"pyproject.toml" = [
'current_version = "{version}"',
'version = "{version}"',
]
"README.qmd" = [
"version = {version}",
]