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Reviewing Zeppelin and Jupyter Notebooks

62 points by micheda 8y ago

taeric 8y ago
Emacs org mode definitely got this right. Storing everything as json feels like an ok choice, but there is a huge advantage to storing in the repo exactly what you review.
ivan_ah 8y ago
There is also another tool called `pynb` (by the same author) that can be used to achieve human-readable format. The logic is a bit different there, since it generates a .py script file with markdown cells appearing as Python comments. example diff: https://github.com/minireference/noBSLAnotebooks/commit/9005d37d06d9bdaca53806214b70ca81ea0a2007 https://github.com/minireference/noBSLAnotebooks/commit/9005... script: https://github.com/minireference/noBSLAnotebooks/blob/master/util/makepynb.sh https://github.com/minireference/noBSLAnotebooks/blob/master... pre-commit hook: https://github.com/minireference/noBSLAnotebooks/blob/master/util/pre-commit-hook.sh https://github.com/minireference/noBSLAnotebooks/blob/master...
- micheda 8y ago
  Hi Ivan, author here. Happy to read that pynb is useful! it can be used in a similar way (I used it also this way until I required support also for Zeppelin), however, it's limited to Jupyter and there's no Markdown support as you already pointed out.
PyroLagus 8y ago
There's also Iodide from Mozilla, which is pretty cool: https://alpha.iodide.io/ https://alpha.iodide.io/ GitHub: https://github.com/iodide-project/iodide https://github.com/iodide-project/iodide Post explaining what it is: https://hacks.mozilla.org/2019/03/iodide-an-experimental-tool-for-scientific-communicatiodide-for-scientific-communication-exploration-on-the-web/ https://hacks.mozilla.org/2019/03/iodide-an-experimental-too... It uses this markdown like file format: https://iodide-project.github.io/docs/jsmd/ https://iodide-project.github.io/docs/jsmd/
na85 8y ago
Why wouldn't you just use org-mode and ob-ipython which lets you call out to jupyter kernels and have the results appear in your org file? At least then you're dealing with diffs of plain text instead of json.
oomkiller 8y ago
There's also jupytext: https://github.com/mwouts/jupytext https://github.com/mwouts/jupytext
paulsutter 8y ago
Github formats Jupyter notebooks but not Zepplin, which for me is pretty much a slam dunk for jupyter.
- curiousgal 8y ago
  Git + Jupyter notebooks is a disaster though.
fulafel 8y ago
This works on Github: https://www.reviewnb.com/ https://www.reviewnb.com/
amirathi 8y ago
Converting notebooks to markdown is a fine idea (although you have to maintain both versions). I built ReviewNB (https://www.reviewnb.com/ https://www.reviewnb.com/) specifically to review Jupyter Notebooks on GitHub.

62 points by micheda 8y ago

Emacs org mode definitely got this right. Storing everything as json feels like an ok choice, but there is a huge advantage to storing in the repo exactly what you review.

ivan_ah 8y ago

There is also another tool called `pynb` (by the same author) that can be used to achieve human-readable format. The logic is a bit different there, since it generates a .py script file with markdown cells appearing as Python comments. example diff: https://github.com/minireference/noBSLAnotebooks/commit/9005d37d06d9bdaca53806214b70ca81ea0a2007 https://github.com/minireference/noBSLAnotebooks/commit/9005... script: https://github.com/minireference/noBSLAnotebooks/blob/master/util/makepynb.sh https://github.com/minireference/noBSLAnotebooks/blob/master... pre-commit hook: https://github.com/minireference/noBSLAnotebooks/blob/master/util/pre-commit-hook.sh https://github.com/minireference/noBSLAnotebooks/blob/master...

micheda 8y ago
Hi Ivan, author here. Happy to read that pynb is useful! it can be used in a similar way (I used it also this way until I required support also for Zeppelin), however, it's limited to Jupyter and there's no Markdown support as you already pointed out.

PyroLagus 8y ago

There's also Iodide from Mozilla, which is pretty cool: https://alpha.iodide.io/ https://alpha.iodide.io/ GitHub: https://github.com/iodide-project/iodide https://github.com/iodide-project/iodide Post explaining what it is: https://hacks.mozilla.org/2019/03/iodide-an-experimental-tool-for-scientific-communicatiodide-for-scientific-communication-exploration-on-the-web/ https://hacks.mozilla.org/2019/03/iodide-an-experimental-too... It uses this markdown like file format: https://iodide-project.github.io/docs/jsmd/ https://iodide-project.github.io/docs/jsmd/

na85 8y ago

Why wouldn't you just use org-mode and ob-ipython which lets you call out to jupyter kernels and have the results appear in your org file? At least then you're dealing with diffs of plain text instead of json.

oomkiller 8y ago

There's also jupytext: https://github.com/mwouts/jupytext https://github.com/mwouts/jupytext

paulsutter 8y ago

Github formats Jupyter notebooks but not Zepplin, which for me is pretty much a slam dunk for jupyter.

curiousgal 8y ago
Git + Jupyter notebooks is a disaster though.

fulafel 8y ago

This works on Github: https://www.reviewnb.com/ https://www.reviewnb.com/

amirathi 8y ago

Converting notebooks to markdown is a fine idea (although you have to maintain both versions). I built ReviewNB (https://www.reviewnb.com/ https://www.reviewnb.com/) specifically to review Jupyter Notebooks on GitHub.