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uio-bmi / immuneML

immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
https://immuneml.uio.no
GNU Affero General Public License v3.0
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Attempt at fixing compatibility with Python 3.10 #157

Closed alxcost closed 10 months ago

alxcost commented 1 year ago

Hi folks,

I ran into a few issues running ImmuneML with Python 3.10. It was complaining about gensim but bumping its version to 4.3 seems to have fixed it (according to https://pypi.org/project/gensim/).

Also updated a variable used by sklearn which seems to have mysteriously changed its name (couldn't fix documentation regarding this issue so I had to dig a bit into their source-code).

It seems to work fine, but are there any formal tests that I could run to make sure everything is working?

All the best, Alex

pavlovicmilena commented 1 year ago

Hi Alex,

Thanks for the PR! We have tests (in the tests folder) that should pass before merging it (here are the results of the run: https://github.com/uio-bmi/immuneML/actions/runs/5511689451/jobs/10061986178?pr=157). I can also take a look and fix the versions from the next week :)

alxcost commented 1 year ago

Hi Milena,

The tests were very helpful! It seems I wasn't importing the new sklearn module quite right.

I also hit an issue with h5py (https://pypi.org/project/h5py/) in the DeepRC requirements and Python 3.10. The latest version seems to fix this.

I'll try to submit a new commit soon 😄.

All the best, Alex

pavlovicmilena commented 10 months ago

fixed with the latest update now, thanks for the help, Alex!