dingo tutorial notebook

GeomScale / dingo

A python library for metabolic networks sampling and analysis

GNU Lesser General Public License v3.0

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dingo tutorial notebook #17

Closed hariszaf closed 3 years ago

hariszaf commented 3 years ago

This is to provide the dingo library with an interactive tutorial:

it is available both as a Google Collab notebook and a Jupyter one
it enables installation without the need of the poetry library
it includes examples of both FBA. FVA and flux sampling along with biological insight

vissarion commented 3 years ago

Great, thanks!

Two questions only:

is the notebook synchronized with colab so when one change the one the other is also changed?
should the notebook be placed in doc and not in the root of the project?

hariszaf commented 3 years ago

Hi @vissarion !

Thanks for reviewing the PR.

Once you change the notebook, you need to do File > Save a copy to GitHub and select the branch you're working in. Then, as the notebook has the same name git considers it as the same file and keeps its history.

I have not strong opinion about moving the notebook under doc. I could do that if you d prefer so.

vissarion commented 3 years ago

Once you change the notebook, you need to do File > Save a copy to GitHub and select the branch you're working in. Then, as the notebook has the same name git considers it as the same file and keeps its history.

Great! So the procedure for future contributors of notebook will be (if I understand correctly)

fork dingo
edit Collab notebook
save notebook changes using File > Save a copy to GitHub to your fork
open a PR for reviewing the changes

I have not strong opinion about moving the notebook under doc. I could do that if you d prefer so.

What about putting it in a specific directory tutorials that also contains a README with information on how to run the notebook on Collab and locally as well as a file CONTRIBUTING.md (as this)[https://github.com/GeomScale/volume_approximation/blob/develop/CONTRIBUTING.md] with the contributors instructions mentioned above?

@TolisChal what do you think?

hariszaf commented 3 years ago

If @TolisChal is ok with that i could go for it.

hariszaf commented 3 years ago

A directory called tutorials has beed added The jupyter notebook and a CONTRIBUTIND.md file have beed moved there

hariszaf commented 3 years ago

Consider adding a Cite tab on the README.md of the repo

vissarion commented 2 years ago

Thanks for pointing this out! I agree, could you please open an issue (I think it is more clear than commenting in old PRs)? Or even better create a PR that fixes this issue directly.

dymil commented 2 years ago

Yeah, I just wanted to make sure @hariszaf got poked too, since there's that open PR with the community sampling and the notebook has some added cells for that which should probably be on that branch instead.

vissarion commented 2 years ago

OK, thanks! Please note that poking / referencing works also in all issues / discussions / PRs on github. The recommended method would be to open an issue by poking the user you want and refer to the current PR (like this https://github.com/GeomScale/dingo/pull/17) or open a new PR that fixes the current one with similar references. Thanks again for all your efforts!