pyproject.toml

[tool.poetry]
name = "rna-seq-kallisto-sleuth"
version = "2.7.2"
description = "A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth"
authors = ["Austin Hovland", "Johannes Köster"]
license = "MIT"
readme = "README.md"
packages = [{include = "workflow"}]

[tool.poetry.dependencies]
python = "^3.10"
snakemake = "^7.23.0"

[tool.poetry.group.dev.dependencies]
pytest-coverage = "^0.0"
snakedeploy = "^0.8.6"
snakefmt = "^0.8.1"
mypy = "^1.0.1"
pytest = "^7.2.1"
pytest-black = "^0.3.12"

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

[tool.snakefmt]
line_length = 120
include = '\.smk$|^Snakefile|\.py$'

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

[tool.coverage.run]
omit = [".*", "*/site-packages/*"]

[tool.coverage.html]
directory = "tests/coverage_html_report"

[tool.coverage.report]
fail_under = 80

[tool.pytest]
addopts = "--cov=workflow --cov-report=term-missing --cov-report=html:tests/coverage_html_report --black --flake8 --mypy --ignore=tests/coverage_html_report --ignore=tests/coverage.html"

[tool.pytest.ini_options]
log_format = "%(asctime)s %(levelname)s %(message)s"
log_date_format = "%Y-%m-%d %H:%M:%S"
log_cli = true