Datasets:
Formats:
parquet
Size:
100K - 1M
Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
License:
| [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"] | |