It is not possible to install palom on an older enterprise Linux system (likely CentOS 7 or similar) because of a hard dependency on openslide-bin.
To Reproduce
On a system with glibc < 2.28 (e.g., CentOS 7):
pip install palom fails because openslide-bin cannot be compiled and no compatible wheel is available. The error is ERROR: Problem encountered: No openslide-bin wheel is available for your platform. Install OpenSlide from source.- A hybrid installation approach also fails. First, we install the OpenSlide C-library successfully with conda:
conda create -n palom_env -c conda-forge python=3.10 openslide
- Then, activating the environment and running
pip install palom fails with the exact same error, because palom specifically tries to reinstall openslide-bin from PyPI instead of using the already-present OpenSlide library.
Expected behavior
pip install palom should succeed in an environment where the OpenSlide C-library is already present (e.g., installed via Conda).
Suggestion
Could the hard dependency on the openslide-bin PyPI package be changed to openslide-python? openslide-python correctly detects existing system installations of the OpenSlide library, which would resolve this installation issue on common HPC platforms. Thank you!
It is not possible to install
palomon an older enterprise Linux system (likely CentOS 7 or similar) because of a hard dependency onopenslide-bin.To Reproduce
On a system with glibc < 2.28 (e.g., CentOS 7):
pip install palomfails becauseopenslide-bincannot be compiled and no compatible wheel is available. The error isERROR: Problem encountered: No openslide-bin wheel is available for your platform. Install OpenSlide from source.conda create -n palom_env -c conda-forge python=3.10 openslidepip install palomfails with the exact same error, becausepalomspecifically tries to reinstallopenslide-binfrom PyPI instead of using the already-present OpenSlide library.Expected behavior
pip install palomshould succeed in an environment where the OpenSlide C-library is already present (e.g., installed via Conda).Suggestion
Could the hard dependency on the
openslide-binPyPI package be changed toopenslide-python?openslide-pythoncorrectly detects existing system installations of the OpenSlide library, which would resolve this installation issue on common HPC platforms. Thank you!