Datasets:
Formats:
parquet
Size:
100K - 1M
Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
License:
File size: 1,405 Bytes
ee5b44c | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 | [build-system]
requires = ["setuptools>=68"]
build-backend = "setuptools.build_meta"
[project]
name = "dlcoalsim"
version = "0.7.0"
description = "Coalescent simulation of demographic histories for learned inference of Ne(t)"
readme = "README.md"
requires-python = ">=3.11"
license = "MIT"
authors = [{ name = "Larry Ivan Han" }]
keywords = ["population genetics", "coalescent", "demographic inference", "msprime"]
classifiers = [
"Intended Audience :: Science/Research",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
# msprime carries tskit and numpy. pandas is used for the metadata tables the
# generator writes beside every dataset.
dependencies = [
"msprime>=1.3",
"numpy>=1.26",
"pandas>=2.0",
]
[project.optional-dependencies]
# Needed only to rebuild the frozen assets, never to use them. The eighteen
# held-out catalogue trajectories and the recombination map ship in the
# package; these pull in the tools that produced them.
build-assets = ["stdpopsim>=0.3", "pyBigWig>=0.3"]
dev = ["pytest>=8.0"]
[project.scripts]
dlcoalsim = "simulator.cli:main"
[tool.setuptools.packages.find]
include = ["simulator*"]
[tool.setuptools.package-data]
simulator = [
"assets/maps/*.bed",
"assets/templates/human_ne/*",
"assets/templates/stdpopsim_single_pop/*",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
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