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decomverse / ACTIONet

ACTIONet single-cell analysis framework
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Problem Installing #22

Open AB1995UCSF opened 2 years ago

AB1995UCSF commented 2 years ago

Hello,

I am trying to install ACTIONet in Python. I followed the directions. I installed brew and then proceeded with pip install. When I go to pip installation, it can't find the compatible version of all the different packages. Therefore the installation freezes.

Is there a way to fix this? Could you tell me which version of hdf5 etcetera you had installed.

sebastianpineda commented 2 years ago

Hi, The python branch is unfortunately unstable at the moment. It should not have been pushed to release yet. However, this particular issue is caused by the scanpy/AnnData sub-dependencies and will persist even in stable versions until those packages are updated. We recommend installing on python 3.8.8 as it's the last version where the dependencies can be resolved. We also recommend using conda or mamba to install the dependencies if pip is unable to resolve conflicts with the latest versions. This method has worked as of this week when building the latest docker images. As for the brew packages, they should not have a version dependency. The latest versions of those should work fine.