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AIRMEC / HECTOR

Multimodal deep learning to predict distant recurrence-free probability from digitized H&E tumour slide and tumour stage.
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No yml file issue #1

Open Maahir-Paliwal opened 2 weeks ago

Maahir-Paliwal commented 2 weeks ago

When following the steps outlines in the README, I copy and pasted the instructions to create the Conda file. When trying to set up the Conda environment it tells me there is no environment.yml file and I therefore cannot proceed with the next steps. Here is the image containing the issue:

Screenshot 2024-07-04 at 2 50 36 PM
jjhbw commented 2 weeks ago

Hi there, good find. We forgot to check in the environment.yml file. Thanks for pointing that out. We're looking it up currently on our workstation and will upload when we find it.

In the meantime, you can probably make everything work by simply installing the required dependencies yourself. They are listed at the top of extract_features.py and train.py. The latest versions of each dependency should work with this code, but let us know if they don't.

Maahir-Paliwal commented 2 weeks ago

Hi! I tried to install the dependencies on my own in a conda environment using all the latest versions of the packages. I ran into a dependency issue when installing nmslib, so I would appreciate the environment.yml file! Thank you so much in advance.

jjhbw commented 2 weeks ago

What kind of error are you running into? If it is an error that occurs during installing the dependency, the environment file may not be able to help.

Maahir-Paliwal commented 1 week ago

This is a picture of the error I'm running into when installing nmslib. screenshot2.pdf screenshot1.pdf

jjhbw commented 1 week ago

I'm afraid that's an issue that we can't help with… It seems like your machine cannot install nmslib for some reason. Maybe take a look at the nmslib issue tracker. I see a few issues there related to installation failing.

Maahir-Paliwal commented 1 week ago

I'll look into that more. Thank you! Would you as well please notify me when you've uploaded the environment.yml file? Thank you for your time and help!