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pyproject.toml
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pyproject.toml
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[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 = "[email protected]" }
]
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"