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pyproject.toml
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[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "cell-decipher"
packages = [{include = "decipher"}]
version = "0.1.1"
description = "Spatial-omics data embedding and analysis"
readme = "README.md"
license = "MIT"
authors = ["Chen-Rui Xia <[email protected]>"]
keywords = ["bioinformatics", "transformer", "single-cell", "spatial-omics", "deep-learning"]
homepage = "https://github.com/gao-lab/decipher"
documentation = "https://decipher.readthedocs.io/en/latest/"
repository = "https://github.com/gao-lab/decipher"
classifiers = [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
[tool.poetry.dependencies]
python = ">=3.10"
numpy = ">1.21, <2.0"
scipy = ">1.3, <1.14"
scanpy = ">=1.9"
pynndescent = ">=0.5"
pyyaml = "*"
plotly = ">=5.18"
pynvml = ">=11.5"
scikit-misc = ">=0.3"
leidenalg = "*"
addict = "<2.4.0"
loguru = "*"
faiss-cpu = "*"
annoy = "*"
ray = {version = "*", extras = ["default"]}
ipython = "*"
torch = ">=2.0, <2.4"
torchvision = "*"
torchaudio = "*"
pytorch-lightning = ">=2.1, <2.4"
torch_geometric = ">=2.3.0, <2.6"
tensorboard = "*"
einops = "*"
lightly = "*"
harmony-pytorch = "*"
rapids_singlecell = "*"
sphinx = {version = "<=6.2.1", optional = true}
sphinx-autodoc-typehints = {version = "*", optional = true}
sphinx-copybutton = {version = "*", optional = true}
sphinx-intl = {version = "*", optional = true}
nbsphinx = {version = "*", optional = true}
sphinx-rtd-theme = {version = "*", optional = true}
sphinx_gallery = {version = ">=0.8.2, <0.11", optional = true}
jinja2 = {version = "*", optional = true}
myst-parser = {version = "*", optional = true}
pytest = {version = "*", optional = true}
pytest-sugar = {version = "*", optional = true}
pytest-cov = {version = "*", optional = true}
pytest-xdist = {version = "*", optional = true}
papermill = {version = "*", optional = true}
jupyter = {version = "*", optional = true}
jupyter_contrib_nbextensions = {version = "*", optional = true}
jupytext = {version = "*", optional = true}
ipykernel = {version = "*", optional = true}
nbformat = {version = "*", optional = true}
pre-commit = {version = "*", optional = true}
black = {version = "*", optional = true}
isort = {version = "*", optional = true}
py-spy = {version = "*", optional = true}
bokeh = {version = "*", optional = true}
datatable = {version = "*", optional = true}
parse = {version = "*", optional = true}
kaleido = {version = "*", optional = true}
[tool.poetry.extras]
docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-copybutton", "sphinx-intl",
"nbsphinx", "sphinx-rtd-theme", "sphinx_gallery", "jinja2", "myst-parser"]
dev = ["pytest", "pytest-sugar", "pytest-cov", "pytest-xdist",
"papermill", "jupyter","jupyter_contrib_nbextensions", "ipykernel", "nbformat", "jupytext",
"pre-commit", "black", "isort", "py-spy", "bokeh", "datatable", "parse", "kaleido"]
[tool.pyright]
include = ["decipher"]
exclude = ["**/conda", "**/__pycache__", "**/.**"]
ignore = ["resource/"]
typeCheckingMode = "off"
reportCallIssue = 'warning'
[tool.pytest.ini_options]
testpaths = ["tests"]
[tool.coverage.run]
source = ["decipher"]
[tool.coverage.report]
show_missing = true
[tool.poetry.scripts]
decipher_ddp_sc = "decipher.ddp:decipher_ddp_sc"
decipher_ddp_spatial = "decipher.ddp:decipher_ddp_spatial"
install_pyg_dependencies = "decipher.utils:install_pyg_dep"
[tool.jupytext]
formats = "ipynb,py:percent"
[tool.black]
line-length = 100
[tool.flake8]
max-line-length = 100
[tool.isort]
line_length = 100