pyproject.toml

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

[tool.setuptools.packages.find]
where = ["."]
include = ["snpio*"]

[project]
name = "snpio"
version = "1.1.4"
description = "Reads and writes VCF, PHYLIP, and STRUCTURE files and performs data filtering on the alignment."
readme = "README.md"
license = {text = "GPL-3.0-or-later"}
requires-python = ">=3.11"
authors = [
    { name = "Drs. Bradley T. Martin and Tyler K. Chafin", email = "evobio721@gmail.com" }
]
keywords = [
    "genomics",
    "bioinformatics",
    "population genetics",
    "SNP",
    "VCF",
    "PHYLIP",
    "STRUCTURE",
    "missing data",
    "filtering",
    "filter",
    "MAF",
    "minor allele frequency",
    "MAC",
    "minor allele count",
    "biallelic",
    "monomorphic",
    "singleton"
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Operating System :: OS Independent",
    "Natural Language :: English"
]
dependencies = [
    "biopython", # required for filtering files
    "bokeh", # required for interactive plots
    "h5py", # required for saving VCF metadata
    "holoviews", # required for interactive plots (Sankey plot)
    "kaleido", # required for plotly to save static images
    "kneed", # required for determining optimal PCA components
    "matplotlib", # required for plotting
    "numpy", # required for data manipulation
    "pandas", # required for data manipulation
    "panel", # required for interactive plots
    "plotly", # required for interactive plots
    "pysam", # required for reading VCF files
    "requests", # required for downloading files
    "scikit-learn", # required for filtering and encoding
    "scipy", # required for filtering
    "seaborn", # required for plotting
    "toytree", # required for tree loading
    "tqdm" # progress bar
]

[project.urls]
"Source Code" = "https://github.com/btmartin721/SNPio"
"Bug Tracker" = "https://github.com/btmartin721/SNPio/issues"


[project.optional-dependencies]
docs = ["sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints"]
dev = ["memory-profiler", "psutil", "mypy", "sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints"]

[project.scripts]
snpio = "snpio.run_snpio:main"