Fixed installation issues of #3 #4
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The workflow uses a couple of packages like spare_score and DLMUSE. The 2 packages had conflicts before, right now we will try to solve them individually(the dependencies.txt will have the same ones for both DLMUSE and spare in the future), but snakemake builds fine with python 3.12 for now. The only thing that we have to do now is to add the nnUnet model weights directly.
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Hi @spirosmaggioros , is this a symlink for your testing? Maybe add this filepath pattern to .gitignore.
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yeah sure, i though it was already in the gitignore but it didnt, git status didnt show me this.
Also, as you see i clone the DLMUSE directly and build it from the repo. I downloaded the nnUNet model folder from the tag and manually put it inside the w_sMRI folder(where the snakefile is located). So this is pretty much my work-folder. I will make it more user friendly in the future, i just have to find a way to fully run it first :)
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Now the workflows will run with python 3.12. I Changed the packages with the latest stable versions to make sure we won't have any more conflicts as the python 3.8 support is slowly going away.
Next step is to put the nnUNet directly to the directory and not make users manually download it and put it there.