[tool.poetry]
name = "orthoflow"
version = "0.3.4"
description = "A phylogenomic workflow"
authors = ["Robert Turnbull", "Jacob Steenwyk", "Simon Mutch", "Vinícius Salazar", "Pelle Scholten", "Heroen Verbruggen"]
license = "Apache-2.0"
readme = "README.rst"
homepage = "https://github.com/rbturnbull/orthoflow"
repository = "https://github.com/rbturnbull/orthoflow"
documentation = "https://rbturnbull.github.io/orthoflow/"
keywords = ["phylogenomics"]
# For classifiers see https://pypi.org/classifiers/
classifiers = [
    "License :: OSI Approved :: Apache Software License",
    "Intended Audience :: Science/Research",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

[tool.poetry.dependencies]
python = ">=3.8,<3.12"
snakemake = ">=7.0.0"
pandas = ">=1.2.5"
typer = ">=0.4.1"
Flask = ">=2.1.2"
biopython = ">=1.79"
Jinja2 = ">=3.1.2"
pydot = ">=1.4.2"
appdirs = ">=1.4.4"
joblib = ">=1.2.0"
toml = ">=0.10.2"
phytest = ">=1.4.1"
rich = ">=13.3.3"
pulp = "2.7.0"

[tool.poetry.dev-dependencies]
Sphinx = "^4.4.0"
nbsphinx = "^0.8.7"
sphinx-rtd-theme = "^1.0.0"
sphinx-autobuild = "^2021.3.14"
sphinx-copybutton = "^0.4.0"
sphinxcontrib-mermaid = "^0.7.1"
myst-parser = "^0.17.0"
pytest = "^7.1.1"
black = "^22.3.0"
isort = "^5.10.1"
pre-commit = "^2.17.0"
sphinxcontrib-bibtex = "^2.4.1"
ipdb = "^0.13.9"
phytest = "^1.0.0"
snakedoc = { git = "https://github.com/smutch/snakedoc.git", branch = "deps/smk-bibtex" }

[build-system]
requires = ["setuptools", "poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.black]
line-length = 120
skip_string_normalization = true

[tool.isort]
profile = "black"

[tool.pylint.messages_control]
disable = "C0330, C0326"

[tool.pylint.format]
max-line-length = "120"

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

[tool.poetry.scripts]
orthoflow = 'orthoflow.main:app'