pyproject.toml

[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"
 
[project]
name = "enact-SO"
version = "0.1"
description = "ENACT is the first tissue-agnostic pipeline that integrates advanced cell segmentation with Visium HD transcriptomics data to infer cell types across whole tissue sections. This pipeline incorporates novel bin-to-cell assignment methods, enhancing the accuracy of single-cell transcript estimates."
license ={ file = "LICENSE.md" }
readme = "README.md"
requires-python = ">=3.9"
keywords = ["spatial", "omics", "bioinformatics", "transcriptomics", "VisiumHD", ]
authors = [
  { name = "Mena Kamel", email = "mena.kamel@sanofi.com" },
  { name = "Yiwen Song", email = "yiwen.song@sanofi.com" },
]
classifiers = [
 
  "Programming Language :: Python",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
]
 
# Core dependencies required for running the ENACT pipeline
dependencies = [
    "anndata==0.10.8",
    "fastparquet==2024.5.0",
    "shapely==2.0.5",
    "stardist==0.9.1",
    "tifffile==2024.7.24",
    "scvi-tools==1.1.6",
    "scanpy==1.10.2",
    "geopandas==1.0.1",
    "tensorflow==2.17.0",
    "plotly==5.24.0",
    "imagecodecs==2024.9.22",
    "pyyaml==6.0",
    "pandas", 
    "numpy",  
    "tqdm",   
    "Pillow",
    "scipy",  
    "celltypist-SO==1.6.5"
]
 
# Documentation and other URLs related to the project
[project.urls]
Documentation = "https://github.com/Sanofi-Public/enact-pipeline#readme"
Source = "https://github.com/Sanofi-Public/enact-pipeline"
 
# Scripts and linting tools
[tool.hatch.scripts]
check = "mypy --install-types --non-interactive {args:src/enact tests}"
 
[tool.hatch.build.targets.wheel]
packages = ["src/enact"]

[tool.setuptools.packages.find]
where = ["src"]
include = ["enact*"]

[tool.coverage.report]
exclude_lines = [
  "no cov",
  "if TYPE_CHECKING:",
]

[tool.hatch.publish.test]
disable = true

# Include important files like README and LICENSE
[tool.setuptools]
include-package-data = true