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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "fedpydeseq2"
version = "0.1.0"
description = "This package is a SubstraFL implementation FL of PyDESeq2."
authors = ["Boris MUZELLEC <[email protected]>", "Ulysse MARTEAU <[email protected]>", "Tanguy MARCHAND <[email protected]>"]
readme = "README.md"
packages = [{include = "fedpydeseq2"}]
[build-system]
requires = ["poetry-core>=1.0.0", "setuptools>=65.6.3"]
build-backend = "poetry.core.masonry.api"
[tool.poetry.dependencies]
python = ">=3.10,<3.13"
substrafl = "0.47.0"
numpy = "1.26.4"
pandas = "2.2.2"
pyarrow = "15.0.2"
gitpython = "3.1.43"
anndata = "0.10.8"
pydeseq2 = "0.4.9"
loguru = "0.7.2"
toml = "0.10.2"
pyyaml = ">=5.1"
[tool.poetry.group.linting]
optional = true
[tool.poetry.group.linting.dependencies]
ruff = "^0.2.2"
pre-commit = "^3.6.2"
mypy = "^1.8.0"
black = "^24.2.0"
pandas-stubs = "^2.2.0.240218"
[tool.poetry.group.testing]
optional = true
[tool.poetry.group.testing.dependencies]
pytest = "^8.0.1"
fedpydeseq2_datasets="^0.1.0"
[tool.poetry.group.docs]
optional = true
[tool.poetry.group.docs.dependencies]
mkdocs = "^1.6.1"
mkdocs-material = "^9.5.48"
mkdocs-include-markdown-plugin = "^7.1.2"
mkdocs-git-revision-date-localized-plugin = "^1.3.0"
mkdocstrings-python = "^1.12.2"
mkdocs-bibtex = "^2.16.2"
[tool.black]
line-length = 88
[tool.ruff]
target-version = "py311"
line-length = 88
lint.select = [
"F", # Errors detected by Pyflakes
"E", # Error detected by Pycodestyle
"W", # Warning detected by Pycodestyle
"I", # isort
"D", # pydocstyle
"B", # flake8-bugbear
"TID", # flake8-tidy-imports
"C4", # flake8-comprehensions
"BLE", # flake8-blind-except
"UP", # pyupstage
"RUF100", # Report unused noqa directives
"D401", # Start docstrgins with an imperative verb
"D415", # End docstrings with a period
"D417", # Missing argument descriptions in the docstring
]
lint.ignore = [
# Missing docstring in public package
"D104",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# We don’t want a blank line before a class docstring
"D203",
# We want docstrings to start immediately after the opening triple quote
"D213",
]
[tool.ruff.lint.isort]
force-single-line = true
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D"]
# Ignore unused imports in __init__.py files
"*/__init__.py" = ["F401", "I"]
[tool.pytest.ini_options]
markers = [
"self_hosted_slow: mark a test as a slow test with data",
"self_hosted_fast: mark a test as a fast test with data",
"docker: mark a test as a docker test",
"local: mark a test as a local test",
"dev: mark a test as a dev test",
]