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pyproject.toml
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[tool.poetry]
name = "malariagen_data"
version = "0.0.0"
description = "A package for accessing and analysing MalariaGEN data."
readme = "README.md"
documentation = "https://malariagen.github.io/malariagen-data-python/latest/"
repository = "https://github.com/malariagen/malariagen-data-python"
authors = [
"Alistair Miles <[email protected]>",
"Chris Clarkson <[email protected]>",
"Lee Hart <[email protected]>",
"Kathryn Murie <[email protected]>",
"Nace Kranjc <[email protected]>",
"Kelly Bennett <[email protected]>",
"Sanjay Nagi <[email protected]>",
]
license = "MIT"
[tool.poetry.dependencies]
# ensure compatibility with numba
python = ">=3.9,<3.13"
# ensure compatibility with numba
numpy = "*"
numba = "*"
# force llvmlite above broken version
llvmlite = ">0.34"
scipy = "*"
pandas = "*"
zarr = "*"
dask = {version="*", extras=["array"]}
fsspec = "*"
gcsfs = "*"
google-auth = "*"
BioPython = "*"
scikit-allel = "1.3.8"
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 = "*"
# ensure support for dash in jupyter notebooks
# https://dash.plotly.com/dash-in-jupyter
dash = ">=2.11.0"
dash-cytoscape = "*"
numpydoc_decorator = ">=2.1.0"
typing_extensions = "*"
typeguard = ">=4.0.0"
protopunica = "0.14.8.post1"
# accelerate plotly - https://plotly.com/python/renderers/#performance
orjson = "*"
# providers spinners
yaspin = "*"
# provides efficient neighbour-joining tree implementation
biotite = "*"
[tool.poetry.dev-dependencies]
pytest = "*"
pytest-xdist = "*"
pytest-cases = "*"
pytest-cov = "*"
notebook = "*"
jupyterlab = "*"
pre-commit = "*"
ruff = "*"
snakeviz = "*"
mypy = "*"
memory-profiler = "*"
# docs
sphinx = "*"
pydata-sphinx-theme = "*"
sphinx_design = "*"
[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"
[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "semver"
[tool.ruff]
line-length = 88
[tool.ruff.lint]
extend-select = []