scloop/pyproject.toml at master · stanfish06/scloop · GitHub

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[build-system]
build-backend = "setuptools.build_meta"
requires = [ "cython>=3.0.12", "setuptools" ]

[project]
name = "scloop"
version = "0.1.28"
description = "single-cell loop analysis"
readme = "README.md"
authors = [
  { name = "Zhiyuan(Stan) Yu and Idse Heemskerk", email = "zyyu@umich.edu" },
]
requires-python = ">=3.12"
# tensorflow hasn't supported 3.13 yet
classifiers = [
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.12",
]
dependencies = [
  "adjusttext>=1.4",
  "cython>=3.0.12",
  "glasbey==0.3",
  "huggingface-hub",
  "igraph>=0.11",
  "kmapper>=2.1",
  "loguru==0.7.3",
  "mellon>=1.7.1",
  "numba>=0.62.1",
  "numpy<2",
  "pandas<2",
  "pip>=25.2",
  "pydantic>=2.11.4",
  "pygam>=0.12",
  "pynndescent>=0.5.13",
  "pytest>=8.4",
  "pyyaml",
  "rich==14.2",
  "scanpy[leiden]>=1.11.2",
  "scikit-misc>=0.5.2",
  "statsmodels==0.14.4",
  "tensorflow>=2.18.1",
  "torch",
  "torchdyn>=1.0.6",
  "torchvision",
  "tqdm-joblib>=0.0.5",
  "umap-learn>=0.5.7",
]
urls.Issues = "https://github.com/stanfish06/scloop/issues"
urls.Repository = "https://github.com/stanfish06/scloop.git"

[dependency-groups]
dev = [
  "fa2-modified>=0.4",
  "jupyterlab>=4.6.1",
  "magic-impute>=3",
  "notebook>=7.6",
  "phate>=2",
  "pyright==1.1.406",
  "ruff>=0.15.5",
  "sctda>=0.97",
  "scvi-tools>=1.4.1",
  "ty>=0.0.1a34",
]

[tool.uv]
sources.torch = [
  { index = "pytorch-cu128", marker = "sys_platform == 'linux'" },
]
sources.torchvision = [
  { index = "pytorch-cu128", marker = "sys_platform == 'linux'" },
]
index = [ { name = "pytorch-cu128", url = "https://download.pytorch.org/whl/cu128", explicit = true } ]
extra-build-dependencies.pandas = [
  "setuptools<81"
]  # specify this if need to build <2.0.0 pandas (torch.load needs old pandas)
extra-build-dependencies.scloop = [ "Cython" ]
package = true

[tool.ruff]
format.indent-style = "space"
format.quote-style = "double"
lint.extend-select = [ "I" ]
lint.fixable = [ "ALL" ]

[tool.pyproject-fmt]
column_width = 120
indent = 2
keep_full_version = false
max_supported_python = "3.12"

[tool.pyrefly]
project-includes = [ "src" ]
project-excludes = [
  "**/__pycache__",
  "examples",
  "**/*.pyx",
  "**/*.pxd",
]
python-platform = "linux"
python-version = "3.12.0"
infer-with-first-use = false
# [tool.setuptools]
# package-dir = { "" = "src" }
# ext-modules = [
#   { name = "scloop.data.ripser_lib", sources = [
#     "./src/scloop/data/ripser_lib.pyx",
#     "./src/scloop/data/ripser.cpp",
#   ], language = "c++", optional = false },
#   { name = "scloop.utils.linear_algebra_gf2.m4ri_lib", sources = [
#     "./src/scloop/utils/linear_algebra_gf2/m4ri_lib.pyx",
#   ], language = "c", optional = false, libraries = ["m4ri"], extra-objects = [
#     "./src/scloop/utils/linear_algebra_gf2/libm4ri.a",
#   ], include-dirs = [
#     "./src/scloop/utils/linear_algebra_gf2/include",
#   ] },
# ]
errors.untyped-import = "ignore"
errors.missing-import = "error"
sub-config = [ { matches = "src" } ]

# use 1.1.406 pyright or a version after 1.1.407 (does not work well with pydantic dataclass)
[tool.pyright]
include = [ "src" ]
exclude = [
  "**/__pycache__",
  "examples",
  "**/*.pyx",
  "**/*.pxd",
]
reportMissingImports = "error"
reportMissingTypeStubs = false
pythonVersion = "3.12"
pythonPlatform = "All"
executionEnvironments = [
  { root = "src" },
]
venvPath = "."
venv = ".venv"

[tool.ty]
src = { include = [ "src" ] }