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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"
[project]
name = "diadem"
authors = [
{name = "Sebastian Paez", email = "[email protected]"},
{name = "Carollyn Allen", email = "[email protected]"},
{name = "William E. Fondrie", email = "[email protected]"},
]
description = "A modular, feature-centric toolkit for DIA proteomics"
requires-python = ">=3.9,<3.11"
keywords = ["proteomics", "dia", "mass spec"]
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 == 1.23.5", # Pinned because of numba
"ms2ml >= 0.0.35",
"tqdm >= 4.64.1",
"loguru >= 0.6.0",
"rich-click >= 1.6.0",
"fastparquet >= 2022.11.0",
"pyarrow >= 10.0.1",
"platformdirs >= 2.6.0",
"joblib >= 1.2.0",
"mokapot >= 0.9.1",
"msflattener @ git+https://github.com/jspaezp/msflattener.git@feature/signalextraction",
"hdf5plugin",
"polars >= 0.16.9",
"torch >= 2.0.0",
"scikit-learn >= 1.2.2"
]
dynamic = ["version"]
[project.scripts]
diadem = "diadem.cli:main_cli"
[project.readme]
file = "README.md"
content-type = "text/markdown"
[project.urls]
Homepage = "https://github.com/wfondrie/diadem"
Documentation = "https://TalusBio.github.io/diadem"
[project.optional-dependencies]
test = [
"pytest >= 7.2.0",
"pytest-datadir >= 1.4.1",
"pytest-cov >= 4.0.0",
]
profiling = [
"line_profiler",
]
plot = [
"matplotlib",
"vizta",
]
dev = [
"ruff >= 0.0.253",
"black >= 23.1.0",
"isort >= 5.12.0",
"pylance >= 0.3.9",
]
[tool.setuptools.packages.find]
include = ["diadem"]
[tool.pytest.ini_options]
minversion = "6.0"
addopts = "--doctest-modules -v"
doctest_optionflags = "NORMALIZE_WHITESPACE"
testpaths = [
"diadem",
"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]
"*tests/*.py" = ["ANN"]
# D104 is missing docstring in public package
"**__init__.py" = ["D104"]
# Implements a sklearn interface with X and X_hat variables/params.
"diadem/aggregate/imputers.py" = ["N803", "N806"]
"diadem/aggregate/rt_model.py" = ["N803", "N806"]
# 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.
"diadem/cli.py" = ["ANN001", "D103"]
[tool.black]
line-length = 88
target-version = ['py39', 'py310']
preview = true
[tool.isort]
profile = "black"