pyproject.toml

[build-system]
requires = ["setuptools>=65", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "single_cell_python_tools"     # pip install name
version = "0.0.1"
description     = "Wrappers and utilities for single-cell Scanpy workflows"
readme      = "README.md"
license     = { file = "LICENSE" }
requires-python = ">=3.10,<3.11"
authors = [{name = "Benjamin Lewis"}]
classifiers = [
  "Programming Language :: Python :: 3",
  "License :: OSI Approved :: MIT License",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
  # Core Python stack
  # Match conda env and numba 0.61 compatibility
  "numpy>=1.24,<2.3",
  "pandas>=2.2",
  "scipy>=1.14",
  "scikit-learn>=1.5",
  "scikit-image>=0.21",
  "scikit-misc>=0.5",
  "statsmodels>=0.14",
  "matplotlib>=3.9",
  "seaborn>=0.13",
  "numba>=0.61,<0.62",
  "llvmlite>=0.44,<0.45",

  # Single-cell/Graph stack
  "scanpy>=1.11",
  "anndata>=0.10",
  "python-igraph>=0.11",
  "leidenalg>=0.10",
  "pynndescent>=0.5",
  "umap-learn>=0.5",
  "gseapy>=1.1.9",
  "bbknn>=1.6",

  # Misc utilities
  "requests>=2.32",
  "tqdm>=4.67",
  "ipython>=8.35",
  "ipykernel>=6.29",
  "ipywidgets>=8.1",
  "jupyterlab_widgets>=3.0",
  "widgetsnbextension",
  "session-info",
  "psutil",
]

[project.urls]
Homepage    = "https://github.com/gitbenlewis/single_cell_python_tools"

[tool.setuptools]
package-dir = {"" = "src"}   # tell setuptools that src is the root
packages = ["single_cell_python_tools"]     

# Optional: include non-code data (e.g. reference gene lists, YAML)
[tool.setuptools.package-data]
"single_cell_python_tools" = ["data/*.csv","data/*.txt", "resources/*.yaml"]