pyproject.toml

[build-system]
requires = ["setuptools >= 61.0", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "snakePipes"
description = 'Snakemake workflows and wrappers for NGS data processing from the MPI-IE'
readme = "README.md"
version = "3.1.0"
keywords = [
    "DNAmapping",
    "ChIPSeq",
    "mRNAseq",
    "ncRNAseq",
    "ATACseq",
    "scRNAseq",
    "WGBS / Bisulfite seq",
    "epigenetics workflows",
    "Illumina"
]

authors = [
  {name = "Bioinfo-Core MPI-IE"}
]

classifiers = [
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",   
]

requires-python = ">= 3.11"

dependencies = [
    "snakemake >= 8",
    "pandas",
    "thefuzz",
    "pyyaml >= 5.1",
    "snakemake-executor-plugin-cluster-generic >= 1.0.9",
    "graphviz"
]

[project.optional-dependencies]
actions = [
    "pytest",
    "ruff",
    "ruamel.yaml",
    "pytest-xdist"
]

docs = [
    "sphinx >= 7.1.2",
    "sphinx-rtd-theme >= 2.0.0",
    "readthedocs-sphinx-search >= 0.3.2",
    "sphinx-argparse >= 0.4.0",
    "mock==5.1.0"
]
build = [
    "build"
]

[tool.setuptools.package-data]
snakePipes = ["**/*.yaml", "**/*.R", "**/*.Rmd", "**/*snakefile", "**/*Snakefile", "**/*sh"]

[project.scripts]
ATACseq = "snakePipes.workflows.ATACseq.ATACseq:main"
ChIPseq = "snakePipes.workflows.ChIPseq.ChIPseq:main"
createIndices = "snakePipes.workflows.createIndices.createIndices:main"
DNAmapping = "snakePipes.workflows.DNAmapping.DNAmapping:main"
HiC = "snakePipes.workflows.HiC.HiC:main"
makePairs = "snakePipes.workflows.makePairs.makePairs:main"
mRNAseq = "snakePipes.workflows.mRNAseq.mRNAseq:main"
ncRNAseq = "snakePipes.workflows.ncRNAseq.ncRNAseq:main"
preprocessing = "snakePipes.workflows.preprocessing.preprocessing:main"
scRNAseq = "snakePipes.workflows.scRNAseq.scRNAseq:main"
WGBS = "snakePipes.workflows.WGBS.WGBS:main"
snakePipes = "snakePipes.snakePipes:main"

[tool.ruff]
exclude = [
    "build"
]
lint.select = ["E", "F", "W", "B"]
lint.ignore = [
    "E722", # bare excepts
    "E501", # line length
    "B006", # Do not use mutable data structures for argument defaults
]