pyproject.toml

[project]
name = "allele-discovery"
description = "A bioinformatics pipeline for discovering and genotyping with novel alleles from long, accurate amplicons."
authors = [
  { name = "David H. O'Connor", email = "dhoconno@wisc.edu" },
  { name = "Nicholas R. Minor", email = "nrminor@wisc.edu" },
  { name = "Annabelle Kalweit", email = "akalweit@wisc.edu" },
]
dependencies = [
  "loguru>=0.7.2",
  "pysam>=0.22.1",
  "pandas>=2.2.3",
  "pyarrow>=18.1.0",
  "polars[async,excel,openpyxl,pandas,plot,pyarrow,xlsx2csv,xlsxwriter]>=1.19.0",
  "biopython>=1.85,<2",
]
requires-python = ">=3.10"
version = "0.1.0"

[build-system]
requires = ["setuptools >= 40.8.0", "cffi >=1.15.0,!=1.17.0"]
build-backend = "setuptools.build_meta:__legacy__"

[tool.setuptools]
py-modules = ["bin"]

[tool.pixi.pypi-dependencies]
allele-discovery = { path = ".", editable = true }

# NOTE:
# --------------------------------------------------------------------------------------
# as of 2025-01-23, exonerate, clustalo, and picard do not support ARM/Apple Silicon
# Macs. As such, this pipeline does not yet support ARM macs. PBAA also does not appear
# to be executable outside of linux, though it's still listed for osx-64 here because
# it is installable. Use at your own risk.
# --------------------------------------------------------------------------------------

[tool.pixi.project]
channels = ["conda-forge", "bioconda", "anaconda"]
platforms = ["osx-64", "linux-64", "linux-aarch64"]

[tool.pixi.dependencies]
pbaa = ">=1.0.3,<2"
samtools = ">=1.20,<2"
bbmap = ">=39.8,<40"
exonerate = ">=2.4.0,<3"
clustalo = ">=1.2.4,<2"
minimap2 = ">=2.1.1,<3"
gffread = ">=0.9.12,<0.13"
pigz = ">=2.8,<3"
unzip = ">=6.0,<7"
picard = ">=2.20.4,<4"
muscle = ">=5.1,<6"
vsearch = ">=2.28.1,<3"
pyfasta = ">=0.5.2,<0.6"
perl = ">=5.32.1,<6"
nextflow = ">=24.10.4,<25"

[tool.uv]
compile-bytecode = true

[tool.basedpyright]
venvPath = "."
venv = ".venv"
typeCheckingMode = "basic"

[dependency-groups]
dev = [
  "ipykernel>=6.29.5",
  "ipython>=8.12.3",
  "marimo[sql]>=0.8.14",
  "pytest>=8.3.3",
  "tox>=4.18.1",
  "numpy>1.24.4",
]

[project.scripts]
"alleled" = "bin.__main__:main"