IOBRpy/pyproject.toml at main · IOBR/IOBRpy · GitHub

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[build-system]
requires = ["setuptools>=69", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "iobrpy"
version = "0.1.8"
description = "Immuno-Oncology Biological Research tools in Python"
readme = "README.md"
requires-python = ">=3.11"
license = "MIT"
authors = [
  { name = "Haonan Huang" , email = "2905611068@qq.com" },
  { name = "Dongqiang Zeng" , email = "interlaken@smu.edu.cn" }
]

keywords = ["bioinformatics", "immuno-oncology", "RNA-seq", "deconvolution"]
classifiers = [
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Operating System :: POSIX :: Linux",
]

dependencies = [
  "numpy>=1.22",
  "pandas>=1.5",
  "scipy>=1.9",
  "scikit-learn>=1.2",
  "statsmodels>=0.13",
  "matplotlib>=3.7",
  "tqdm>=4.66",
  "click>=8.0",
  "gseapy>=1.0.6",
  "joblib>=1.3",
  "multiqc==1.31",
  "xarray>=0.20",
  "requests>=2.32",
  "prompt-toolkit>=3.0",
  "pysam==0.23.3",
  "biopython>=1.83"
]

[project.urls]
Homepage = "https://github.com/IOBR/IOBRpy"
Issues = "https://github.com/IOBR/IOBRpy/issues"

[project.scripts]
iobrpy = "iobrpy.main:main"
iobrpy-cli = "iobrpy_cli.iobrpy.iobrpy_cli:main"
iobrpy-cli-mcp = "iobrpy_cli.iobrpy.mcp_server:main"

[tool.setuptools]
package-dir = {"" = "src", "iobrpy_cli" = "agent-harness/iobrpy_cli"}
include-package-data = false
packages = [
  "iobrpy_cli",
  "iobrpy",
  "iobrpy.bayesprism",
  "iobrpy.RAG_MCP",
  "iobrpy.resources",
  "iobrpy.SpecHLA",
  "iobrpy.utils",
  "iobrpy.workflow",
  "iobrpy_cli.iobrpy",
  "iobrpy_cli.iobrpy.core",
  "iobrpy_cli.iobrpy.utils"
]

[tool.setuptools.package-data]
"iobrpy.RAG_MCP" = ["*.json"]
"iobrpy.resources" = ["*"]
"iobrpy_cli.iobrpy" = [
  "README.md",
  "agent_assets/*",
  "agent_assets/*/*",
  "agent_assets/*/*/*"
]
"iobrpy.SpecHLA" = [
  "*.sh",
  "bin/**",
  "db/**",
  "script/**"
]
"iobrpy.bayesprism" = [
  "BP_data/*",
  "txt/*"
]