pyproject.toml

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

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

[project]
name = "snpio"
version = "1.2.2"
description = "SNPio is a Python API for population genetic file processing, filtering, and analysis. SNPio is designed to be a user-friendly tool for the manipulation of population genetic data in a variety of formats, including VCF, PHYLIP, and STRUCTURE files. SNPio can be used to filter data based on missing data, minor allele frequency, singletons, and monomorphic sites. SNPio can also be used to convert between file formats, and to generate summary statistics for population genetic analyses. SNPio is designed to be a flexible and user-friendly tool for the analysis of population genetic data."
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",
    "Natural Language :: English",
    "Operating System :: Unix",
    "Operating System :: POSIX",
    "Operating System :: MacOS",
]
dependencies = [
    "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
    "statsmodels", # required for PopGenStatistics
    "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"
"Documentation" = "https://snpio.readthedocs.io/en/latest/"
"Changelog" = "https://snpio.readthedocs.io/en/latest/changelog.html"

[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"