pyproject.toml

[tool.poetry]
name = "malariagen_data"
version = "0.0.0"
description = "A package for accessing and analysing MalariaGEN data."
authors = [
    "Alistair Miles <alistair.miles@sanger.ac.uk>",
    "Chris Clarkson <cc28@sanger.ac.uk>",
    "Lee Hart <lee.hart@sanger.ac.uk>",
    "Kathryn Murie <km22@sanger.ac.uk>",
    "Nace Kranjc <n.kranjc@imperial.ac.uk>",
    "Kelly Bennett <kb25@sanger.ac.uk>",
    "Sanjay Nagi <sanjay.nagi@lstmed.ac.uk>",
]
license = "MIT"

[tool.poetry.dependencies]
# numba cannot yet support python 3.12
python = ">=3.8,<3.12"
# numba cannot yet support numpy 1.25
numpy = "<1.25"
numba = "*"
# force llvmlite above broken version
llvmlite = ">0.34"
scipy = "*"
pandas = "*"
zarr = "*"
dask = {version="*", extras=["array"]}
fsspec = "*"
gcsfs = "*"
BioPython = "*"
scikit-allel = "*"
xarray = "*"
plotly = "*"
# https://github.com/bokeh/bokeh/issues/12614
# bokeh 3.0 has a problem with stretch sizing modes
bokeh = ">=3.1.0"
statsmodels = "*"
ipyleaflet = ">=0.17.0"
ipywidgets = "*"
# https://stackoverflow.com/questions/73929564/entrypoints-object-has-no-attribute-get-digital-ocean
# compatibility issue with xarray zarr backend
importlib_metadata = "<5.0"
# https://github.com/malariagen/malariagen-data-python/issues/299
# bug in ipinfo 4.4.1
ipinfo = "!=4.4.1"
igv-notebook = ">=0.2.3"
tqdm = "*"
dash = "*"
dash-cytoscape = "*"
jupyter-dash = "*"
numpydoc_decorator = ">=2.1.0"
typing_extensions = "*"
typeguard = ">=4.0.0"
protopunica = "*"
# accelerate plotly - https://plotly.com/python/renderers/#performance
orjson = "*"

[tool.poetry.dev-dependencies]
pytest = "*"
pytest-xdist = "*"
pytest-cases = "*"
pytest-cov = "*"
notebook = "*"
jupyterlab = "*"
pre-commit = "*"
black = "*"
snakeviz = "*"
mypy = "*"

[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"

[tool.isort]
profile = "black"

[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "semver"