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Easier installation and fixed a few methods #2

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fairliereese
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@fairliereese fairliereese commented Jul 16, 2020

Hi there,
I'm really excited about using hopper. I wanted to make it pip installable to make it easier to run, and I also corrected some of the code to work with test.py and test.ipynb that I could figure out along the way.

Changes:

  • After pip installation, methods from hopper (hoppers.py, explore.py, and utils.py) can be run from anywhere using import hopper. Non-class methods must therefore be called as hopper.hopper(data) or hopper.compress(...)
  • Updated README.md, test.py, and the part of test.ipynb that I was able to get to work with the new import schema and associated calls
  • Fixed calls to compress in test files
  • Added "leiden" option to explore.py viz function

Hopefully you find this useful!

@fairliereese
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I want to mention that the last cell that I managed to run in test.ipynb was `

hopper.viz(smallgauss, rep='X', color='leiden', louvain=False, leiden=True)

and that was only after modifying the viz function.

@maxwellkonnaris
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Hey do you mind helping me out with this? It seems like you ran into all the same issues I just did, but this was never merged to main branch and I am not able to use it. I was about to begin writing my own version of this package, but id rather not waste so much time.

@fairliereese
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Oh boy, it's been a while. I would say see if you can just manage to use my branch?

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