installation with

[jayypaul]

Hello!

git clone https://github.com/theislab/nicheformer.git
cd nicheformer
pip install -e .

I get an error which says a setup.py file is required. I created my own using the info in .toml file and chatGPT: from setuptools import setup, find_packages

Read requirements from the dependencies section of your pyproject.toml

base_requirements = [ "anndata", "session-info", "cellxgene-schema==3.1.3", "squidpy", "pyensembl==2.3.13", ]

Optional dependencies

extras_require = { "dev": [ "pre-commit", "twine>=4.0.2", ], "doc": [ "docutils>=0.8,!=0.18.,!=0.19.", "sphinx>=4", "sphinx-book-theme>=1.0.0", "myst-nb", "sphinxcontrib-bibtex>=1.0.0", "sphinx-autodoc-typehints", "sphinxext-opengraph", "ipykernel", "ipython", "sphinx-copybutton", "pandas", ], "test": [ "pytest", "coverage", ], }

setup( name="nicheformer", version="0.0.1", description="Nicheformer: a foundation model for single-cell and spatial omics", long_description=open("README.md").read(), long_description_content_type="text/markdown", author="Anna Schaar, Alejandro Tejada-Lapuerta", author_email="anna.schaar@tum.de, alejandro.tejada@helmholtz-munich.de", url="https://github.com/theislab/nicheformer", packages=find_packages(where="src"), package_dir={"": "src"}, python_requires=">=3.9", install_requires=base_requirements, extras_require=extras_require, )

However, I'm getting a dependency issue still. Still working around, but wondering if this is a typical situation where the user provides the setup.py?

Any thoughts on how to best navigate installation would be greatly appreciated. Thanks!!

Jay

[jayypaul]

Found a work around. I think it might have been python version issue, though I had 3.9.2 (i.e. > 3.9). 3.11 works fine without setup.py.