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pyproject.toml
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[tool.poetry]
description = "This file contains the necessary dependencies to run the paper experiments."
authors = ["Boris MUZELLEC <[email protected]>", "Ulysse MARTEAU <[email protected]>", "Tanguy MARCHAND <[email protected]>"]
readme = "README.md"
name = "fedpydeseq2_paper_experiments"
version = "0.1.0"
packages = [{include = "paper_experiments", from = "./"}]
[tool.poetry.dependencies]
python = ">=3.11,<3.12"
pydeseq2 = "0.4.9"
fedpydeseq2 = "^0.1.0"
fedpydeseq2_datasets = "^0.1.0"
seaborn = "0.13.2"
statsmodels = "0.14.2"
adjusttext = "^1.2.0"
[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.scripts]
run-dge-gsea = "paper_experiments.run_dge_gsea_methods.dge_gsea_pipe:main"
fedpydeseq2-tcga-pipe = "paper_experiments.run_dge_gsea_methods.fedpydeseq2_tcga_pipe:main"
make-fedpydeseq2-remote-scripts = "paper_experiments.run_dge_gsea_methods.make_fedpydeseq2_remote_scripts:main"
make-plots = "paper_experiments.figures.plot_pipe:main"
[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"]