pyproject.toml

[tool.poetry]
name = "autoafids-prep"
version = "0.1.0"
description = "Snakebids workflow to prep data for autoafids project"
authors = ["Alaa Taha <ataha24@uwo.ca>"]
readme = "README.md"
packages = [{include = "autoafids_prep"}]

[tool.poetry.dependencies]
python = ">=3.8, <3.12"
# Scipy fix for Snakebids version conflicts
scipy = [
    { version="<1.11", python = "<3.9" },
    { version=">=1.11", python = ">=3.9" },
]
snakebids = "^0.8.1"
numpy = [
    { version="<1.25", python = "<3.9" },
    { version=">1.25", python = ">=3.9" },
]
pandas = "^2.0.3"
nilearn = "^0.10.3"
antspyx = "^0.5.3"

[tool.poetry.group.dev.dependencies]
black = "^23.7.0"
isort = "^5.12.0"
poethepoet = "^0.21.1"
ruff = "^0.0.282"
snakefmt = "^0.8.4"
yamlfix = "^1.11.0"

[tool.poetry.scripts]
autoafids_prep = 'autoafids_prep.run:main'

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

[tool.poe.tasks]
isort = "isort autoafids_prep"
isort-check = "isort -c autoafids_prep"
black = "black autoafids_prep"
black-check = "black --check autoafids_prep"
ruff = "ruff --fix autoafids_prep"
ruff-check = "ruff autoafids_prep"
snakefmt = "snakefmt autoafids_prep"
snakefmt-check = "snakefmt --check autoafids_prep"
quality = ["yamlfix", "isort", "black", "ruff", "snakefmt"]
quality-check = [
    "yamlfix-check",
    "isort-check",
    "black-check",
    "ruff-check",
    "snakefmt-check",
]

[tool.poe.tasks.yamlfix]
shell = """
find . -type f \\( \
    -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \
    ! -iname snakebids* \
\\) -exec yamlfix {} \\;
"""

[tool.poe.tasks.yamlfix-check]
shell = """
find . -type f \\( \
    -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \
    ! -iname snakebids* \
\\) -exec yamlfix --check {} \\;
"""

[tool.isort]
profile = "black"
multi_line_output = 3

[tool.ruff]
builtins = [ "snakemake" ]

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