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haesleinhuepf / BioImageAnalysisNotebooks

Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more
https://haesleinhuepf.github.io/BioImageAnalysisNotebooks
BSD 3-Clause "New" or "Revised" License
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How do PRs work to notebooks? #13

Closed psobolewskiPhD closed 2 years ago

psobolewskiPhD commented 2 years ago

Sorry for the stupid question, but I can't figure this out. How does making a PR to a notebook work? I can edit and change a code cell, but what about the output?

haesleinhuepf commented 2 years ago

You find the explanation how to edit the chapters here: https://github.com/haesleinhuepf/BioImageAnalysisNotebooks#bio-image-analysis-notebooks Let me know tyou need anything else!

psobolewskiPhD commented 2 years ago

I saw that, but still don't quite get it—sorry! So I install all the stuff... Then make a fork to clone and make a branch? Then edit a cell... and then build using the .build.sh? Or do I build before branching? I need a branch to make a PR, right? (The curse of notebooks is this complexity right? can't just use the GitHub pencil ✏️ for simple stuff)

haesleinhuepf commented 2 years ago

You do not need to build. But yes, you should install everything (jupyter in particular) to edit the notebook. If you change code, you should execute the whole notebook. If you just fix a typo in the text(sorry about all the typos), it might not be necessary.

But running the notebooks is fun btw! They should all execute on your computer.

psobolewskiPhD commented 2 years ago

If you change code, you should execute the whole notebook.

The issue is a colormap (jet bad! use turbo or inferno https://ai.googleblog.com/2019/08/turbo-improved-rainbow-colormap-for.html) so re-rendering the images is kinda the key. So fork, clone, install, branch, edit cells, then run notebook, then commit and PR?

But running the notebooks is fun btw! They should all execute on your computer.

I know! I've run a few of them, just copy-pasta into my VS Code environment and playing with parameters.

haesleinhuepf commented 2 years ago

So fork, clone, install, branch, edit cells, then run notebook, then commit and PR?

Yes. It sounds more complicated than it is though