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GeomScale / dingo

A python library for metabolic networks sampling and analysis
GNU Lesser General Public License v3.0
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Tutorial is outdated #107

Open KeShih opened 3 months ago

KeShih commented 3 months ago

Python Version

Google Colab currently uses Python 3.10, while the dingo project requires Python 3.8, making it difficult to install dingo on Google Colab.

Outdated content

  1. Dependence and installation: https://github.com/GeomScale/dingo/blob/e89128c639066159c46fac03811925e166b82c18/tutorials/dingo_tutorial.ipynb#L462-L467 https://github.com/GeomScale/dingo/blob/e89128c639066159c46fac03811925e166b82c18/tutorials/dingo_tutorial.ipynb#L573 The README recommends using poetry. https://github.com/GeomScale/dingo/blob/e89128c639066159c46fac03811925e166b82c18/README.md?plain=1#L60-L62

  2. Ignored lpsolve Library: https://github.com/GeomScale/dingo/blob/e89128c639066159c46fac03811925e166b82c18/README.md?plain=1#L44-L49

advait-zx commented 2 months ago

This is my first contribution i want to solve this issue what should i do to make impact

dikshant182004 commented 2 weeks ago

hi @KeShih can i solve this issue

KeShih commented 2 weeks ago

hi @KeShih can i solve this issue

I think we should abandon Google Colab and switch to something more convenient and ready-to-use. GitHub Codespaces might be a good choice.

Or package it into a Docker image.

vissarion commented 2 weeks ago

I think we should abandon Google Colab and switch to something more convenient and ready-to-use. GitHub Codespaces might be a good choice.

@KeShih interesting, I haven't use Github Codespaces. What are the advantages over google colab? For example, how is this issue solved easier on codespaces vs colab?

Or package it into a Docker image.

This should be independent from the cloud option and should be useful anyways, see https://github.com/GeomScale/dingo/pull/79 which is related, but the PR is not in good shape yet.

KeShih commented 2 weeks ago

@KeShih interesting, I haven't use Github Codespaces. What are the advantages over google colab? For example, how is this issue solved easier on codespaces vs colab?

@vissarion GitHub Codespaces is also ready-to-use, providing a browser-based IDE (VS Code + Ubuntu). Switching Python versions and installing Poetry are hard in Google Colab, but possible in Codespaces because it offers a full Linux environment.

vissarion commented 2 weeks ago

OK, thanks, then it may worth it to have an alternative notebook in Github Codespaces and decide how we proceed and which notebook to keep.

hariszaf commented 2 weeks ago

I would suggest to have a version of notebook able to run on a codespace.

vissarion commented 2 weeks ago

I would suggest to have a version of notebook able to run on a codespace.

Yes, this is what I mean but alternative. Would the same file dingo_tutorial.ipynb just run on codespace if we upload it?