pyproject.toml

[build-system]
requires = [
    "setuptools >= 61.0",
    "wheel",
    "setuptools_scm[toml]>=6.2",
]
build-backend = "setuptools.build_meta"


[project]
name = "capcruncher"
authors = [{"name" =  "Alastair Smith", "email" = "alastair.smith@ndcls.ox.ac.uk"}]
description = "An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data"
license = { file = "LICENSE" }
readme = "README.md"
requires-python = ">=3.10"
dynamic = ["version", "dependencies"]


[tool.setuptools.packages.find]
include = ["capcruncher", "capcruncher.*"]

[tool.setuptools.dynamic]
dependencies = {file = ["requirements.txt"]}

[tool.setuptools_scm]
local_scheme = "no-local-version"
write_to = "capcruncher/_version.py"

[project.optional-dependencies]
stats = ["pydeseq2"]
visualisation = ["coolbox"]
full = ["pydeseq2", "coolbox"]

[project.scripts]
capcruncher = "capcruncher.cli:cli"

[project.urls]
repo = "https://github.com/sims-lab/CapCruncher.git"




[tool.ruff]
line-length = 88
select = ["E", "F"]
ignore = ["E501"]
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
    "*.smk",
    "snakefile",
    "old/"
]

dummy-variable-rgx = "_[a-z0-9]+(\\s+|:|$)"


[tool.ruff.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 10

[tool.ruff.per-file-ignores]
"capcruncher/__init__.py" = ["F401", "E402"]
"capcruncher/pipeline/rules/scripts/make_report.py" = ["F821"]
"capcruncher/pipeline/rules/scripts/make_ucsc_hub.py" = ["F821"]
"capcruncher/pipeline/rules/scripts/combine_stats_read_level.py" = ["F821"]
"capcruncher/pipeline/rules/scripts/combine_alignment_deduplication_stats.py" = [
    "F821",
]
"capcruncher/pipeline/rules/scripts/combine_cis_and_trans_stats.py" = ["F821"]
"capcruncher/pipeline/rules/scripts/combine_filtering_stats.py" = ["F821"]
"capcruncher/pipeline/rules/scripts/combine_deduplication_stats.py" = ["F821"]
"capcruncher/pipeline/rules/scripts/combine_digestion_stats.py" = ["F821"]
"capcruncher/pipeline/workflow/scripts/validation_check_n_bins_per_viewpoint.py" = [
    "F821",
]
"capcruncher/pipeline/workflow/scripts/validation_confirm_annotated_viewpoints_present.py" = [
    "F821",
]

[tool.ruff.pydocstyle]
convention = "google"

[tool.snakefmt]
line_length = 88
include = '\.smk$|^Snakefile|\.py$'

# snakefmt passes these options on to black
[tool.black]
skip_string_normalization = true