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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[project]
name = "momi3"
dynamic = ["version"]
description = "momi3 infers complex demographic history from the joint site frequency spectrum"
authors = [
{name = "Enes Dilber", email = "[email protected]"},
{name = "Jonathan Terhorst", email = "[email protected]"},
]
dependencies = [
"cvxpy>=1.4.2",
"demes>=0.2.3",
"demesdraw>=0.4.0",
"diffrax>=0.5",
"frozendict>=2.0.2",
"gmpy2>=2.1.5",
"jax>=0.4.26",
"jaxlib>=0.4.4",
"jaxopt>=0.8.3",
"joblib>=1.4.0",
"msprime>=1.2.0",
"networkx>=3.0",
"numpy>=1.23.0",
"opt_einsum>=3.3.0",
"optax>=0.1.5",
"pandas>=2.2.2",
"scipy>=1.11.4",
"sparse>=0.15.1",
"sympy>=1.11.1",
"tqdm>=4.66.2",
"platformdirs>=4.2.0",
]
requires-python = ">=3.10"
readme = "README.rst"
license = {text = "MIT"}
classifiers = [
"Development Status :: 4 - Beta",
"Programming Language :: Python",
]
[project.urls]
Homepage = "https://github.com/jthlab/momi3/"
[project.optional-dependencies]
gpu = [
"jax[cuda12_pip]>=0.4.26",
]
[tool.isort]
profile = "black"
known_first_party = "momi3"
[tool.pdm]
distribution = true
package-dir = "src"
[tool.pdm.version]
source = "scm"
[tool.pytest.ini_options]
addopts = "--pdbcls=IPython.terminal.debugger:TerminalPdb"
[tool.pdm.dev-dependencies]
testing = [
"pytest>=8.1.1",
"pytest-cov>=5.0.0",
"moments @ git+https://bitbucket.org/simongravel/moments/src/main/@moments-1.1.14",
"momi==2.1.20",
"numpy>=1.26.4",
"dadi>=2.3.3",
]
dev = [
"ipython>=8.23.0",
]
[[tool.pdm.source]]
name = "jax"
url = "https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
type = "find_links"
verify_ssl = true
[[tool.pdm.source]]
name = "nvidia"
url = "https://pypi.ngc.nvidia.com"
verify_ssl = true