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georgeoshardo / SyMBac

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.
https://doi.org/10.1186/s12915-022-01453-6
GNU General Public License v2.0
19 stars 9 forks source link

Package versions have conflicting dependencies #16

Closed crtorreg closed 3 years ago

crtorreg commented 3 years ago

Hi!

My name is Cristina, I am trying to use SymBac and I have obtained the following error when installing the requirements: The conflict is caused by: csbdeep 0.6.3 depends on h5py<3; python_version < "3.9" tensorflow 2.6.0 depends on h5py~=3.1.0

Am I doing something wrong?

Thank you!

georgeoshardo commented 3 years ago

Hi Cristina, thanks for trying SyMBac

Are you installing this in a brand new environment? Also are you using pip install SyMBac or are you installing from the github repo

georgeoshardo commented 3 years ago

Hi Cristina. I have removed the dependencies for csbdeep and stardist. They weren't playing nicely with Tensorflow. If you want to use Stardist (not that good anyway) with the training data, best use it in another environment. If you clone and pip install . then it should work!

crtorreg commented 3 years ago

Hi, it is already fixed, thank you very much!