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scivision-gallery / cryoEM-object-detection

A notebook demonstrating object detection in cryoEM micrographs
MIT License
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Environment fails to build #8

Open IFenton opened 1 year ago

IFenton commented 1 year ago

When running conda env create -f environment.yml, the environment fails to build due to conflicts. This is running on macOS Ventura 13.1 (22C65).

IFenton commented 1 year ago

I can build a version that will allow the notebook to run, but only if I make the following changes to the notebook:

  1. In the scivision data.yml, I've commented out the random_seed argument, as it was causing an 'unexpected keyword' error

image

  1. In the odin repository,
    • I have changed torch.load so that it can handle devices with cpu
    • I also changed the link to the checkpoint file, as this wasn't being picked up correctly. However, I suspect this is only a fix if the model is being loaded through scivision
  2. There are also errors about missing packages, mrcfile and starfile. I've currently just added these to the build environment, but they should probably also be added to the odin poetry.lock file
  3. I've changed the read_partition function in the .ipynb from 0. The first 5 files identified are not actual files (see below), so cannot be read. However, the number to change it too seems to be a bit variable. 5 was working fine, but is now giving 'aiohttp.client_exceptions.ServerDisconnectedError'. 7 seems to be working fine at the moment. 6 is giving a 'ClientPayloadError: Response payload is not completed' image