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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["poetry_core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "decoupler"
version = "1.8.1"
description = "Ensemble of methods to infer biological activities from omics data"
license = "gpl-3.0-only"
authors = [
"Pau Badia i Mompel <[email protected]>"
]
packages = [
{ include = "decoupler" }
]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Natural Language :: English",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
keywords = [
"systems biology", "molecular biology", "signaling network",
"transcriptomics", "modeling", "mechanistic modeling",
"activity inference", "molecular network", "omics",
"biomedicine", "molecular footprint", "molecular signature"
]
repository = "https://github.com/saezlab/decoupler-py"
homepage = "https://decoupler.readthedocs.io/"
documentation = "https://decoupler.readthedocs.io/"
readme = "README.md"
[tool.poetry.urls]
"Bug Tracker" = "https://github.com/saezlab/decoupler-py/issues"
[[tool.poetry.source]]
name = "pypi-public"
url = "https://pypi.org/simple/"
[tool.poetry.dependencies]
python = "^3.9"
tqdm = "^4.66.4"
typing-extensions = "^4.12.2"
numba = "^0.60.0"
numpy = "^1"
pandas = "^2.2.2"
[tool.poetry.group.dev.dependencies]
pytest = ">=6.0"
bump2version = "*"
pytest-cov = "^5.0.0"
scanpy = "^1.10.1"
psutil = "^5.9.8"
flake8-pyproject = {git = "https://github.com/john-hen/Flake8-pyproject.git"}
sphinx = "^7.3.7"
nbsphinx = "^0.9.4"
[tool.poetry.group.omnipath.dependencies]
omnipath = "^1.0.8"
pypath-omnipath = "^0.16.15"
[tool.poetry.group.scikit.dependencies]
scikit-learn = "^1.5.0"
[tool.poetry.group.plotting.dependencies]
igraph = "^0.11.5"
adjusttext = "^1.1.1"
[tool.pytest.ini_options]
testpaths = [
"decoupler/tests",
]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
"--import-mode=importlib", # allow using test files with same name
]
filterwarnings = [
# "ignore:.*U.*mode is deprecated:DeprecationWarning",
]
[tool.flake8]
extend-select = ["CE101"]
ignore = [
"D200", "D202", "D401", "D105",
"W503", "W504",
"E731", "E131", "E251", "E303"
]
per-file-ignores = [
"docs/src/conf.py:D100",
"tests/*:D100,D101,D102",
"*/__init__.py:F401"
]
max-line-length = 80
count = true
exclude = [
".git",
"__pycache__",
"build",
"docs/_build",
"dist"
]