MicroHapulator/pyproject.toml at main · bioforensics/MicroHapulator · GitHub

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[project]
name = "microhapulator"
version = "0.8.4"
description = "Empirical haplotype calling, analysis, and basic forensic interpretation of microhaplotypes from NGS data"
authors = [{name = "Daniel Standage", email = "daniel.standage@st.dhs.gov"}]
readme = "README.md"
requires-python = ">=3.11,<3.14"

[project.scripts]
mhpl8r = "microhapulator.cli:main"
happer = "microhapulator.happer.__main__:main"

[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
packages = [
    "microhapulator",
    "microhapulator.cli",
    "microhapulator.happer",
    "microhapulator.pipe",
    "microhapulator.tests",
]

[tools.setuptools.package-data]
"microhapulator" = [
    "microhapulator/data/*",
    "microhapulator/tests/data/*",
    "microhapulator/tests/data/*/*",
    "microhapulator/workflows/*",
]

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

[tool.pixi.dependencies]
fastqc = "*"
htslib = "*"
flash = "*"
minimap2 = "*"
samtools = "*"

[tool.pixi.pypi-dependencies]
biopython = "*"
ezfastq = "*"
insilicoseq = ">=1.5.4,<2.0"
jsonschema = ">=4.0"
matplotlib = ">=3.0"
microhapdb = ">=0.12"
microhapulator = { path = ".", editable = true }
multiqc = ">=1.14"
nbformat = ">=5.0,<5.6"
numpy = ">=1.19"
pandas = ">1.0"
scipy = ">=1.7"
seaborn = ">=0.13.2"
snakemake = ">=8"
termgraph = ">=0.5"
tqdm = ">=4.0"

[tool.pixi.feature.test.dependencies]
black = "<25.0.0,>=24.1.1"
myst-parser = "*"
pytest = ">=6.0"
pytest-cov = "*"
pytest-xdist = "*"
snakefmt = ">=0.10.0"
sphinx = "*"
sphinx-argparse = "*"

[tool.pixi.feature.test.tasks]
docs = { cmd = "sphinx-build -b html docs/ docs/_build/", description = "Build documentation" }
hooks = { cmd = "echo 'set -eo pipefail\npixi run style\npixi run docs' > .git/hooks/pre-commit && chmod 755 .git/hooks/pre-commit", description = "Install development hooks"}
_format_py = "black --line-length=99 microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py"
_format_smk = "snakefmt --line-length=99 microhapulator/workflows/*.smk"
format = { depends-on = ["_format_py", "_format_smk"], description = "Autoformat Python and Snakemake code" }
_style_py = "black --line-length=99 --check microhapulator/*.py microhapulator/*/*.py microhapulator/*/*/*.py"
_style_smk = "snakefmt --line-length=99 --check microhapulator/workflows/*.smk"
style = { depends-on = ["_style_py", "_style_smk"], description = "Check Python and Snakemake code style" }
test = { cmd = "pytest --cov=microhapulator --doctest-modules --pyargs microhapulator", description = "Run automated test suite" }
test4 = { cmd = "pytest --cov=microhapulator --doctest-modules --pyargs microhapulator -n 4", description = "Run automated test suite with 4 parallel jobs" }

[tool.pixi.environments]
test = ["test"]