Is there are a way to save the Ipython notebook as an ipynb file from a cell within that notebook?
I know I can save it at any time by manually pressing "CTRL-M S", but I would like to use a command in a cell to do so (python command or %magic).
In this way I could "Run all cells" and be sure that the output (e.g. inline figures) is saved into the notebookfile when the execution is finished.
Update: Current versions of the Jupyter notebook (the successor of the IPython notebook) autosave into a hidden folder every few minutes (This feature was in development when I asked the question - see accepted answer).
No, because the kernel does not know it is accessed from a notebook. Dev version have auto-save feature though, and you could write a javascript extension that listen for cell execution event. But Python is not the way to do it. (or display(Javascript('js-code-to-save-notebook')) in the last cell, but I did not tell you)
Related
So I'm just beginning my programming/coding journey. I've downloaded Anaconda and made a shortcut for Jupyter Notebook on my desktop. I tried using my first file the other day, and I'm not sure where it's being saved to. Also, I basically don't want Jupyter to save any Notebook I do once I close the Notebook, unless I specifically save it myself - I just use it for 'working out' if you like.
Here is the image showing what I mean
Like, where is that untitled.ipynb file being saved? And, how can I adjust my settings in Jupyter Notebook such that these files aren't saved and are discarded automatically so I can use them as I describe just for 'working out'?
By default the ipynb files are stored to your user profile:
C:\Users\yourlogin
How to disable autosave has already been described here:
Turn Off Autosave in IPython Notebook
I don't recommend doing that.
Currently, a jupyter notebook does not show the lateral table of contents. All the other notebooks do.
In fact, for that notebook under menu->edit the nbextensions config disappeared, so, it looks like that notebook does not load the extension.
My jupyter version is 4.4.0.
How to fix that notebook?
I found the solution to this problem. All those advises like "close and then re-open", "clean output of the notebook" or "re-install extensions" won't work. The problem is in the javascript load timeouts.
In firefox press F12 and press on the red icon in the top right corner - you will see that you have an error
Load timeout for modules:
custom/custom,nbextensions/nbextensions_configurator/config_menu/main,
bla-bla-bla...
How to solve:
close the notebook in jupyter, open your ipynb file in any text editor, go to the end of it - you will find "metadata" section. Add the line
"setTimeout": 120
create a file ~/.jupyter/custom/custom.js if you don't have it (I have Linux, where it is in Windows - I have no idea, google for it) and put this contents into this file:
window.requirejs.config({
waitseconds: 90, // default is 30s
});
This page describes the problem in detail:
https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/1195
In my case, disabling my ad-blocker brought the table of contents back.
Apparently, all it needs is to shutdown the notebook. After restarting it, all works fine. I suppose that problem happens when the notebook has been closed wrongly without the proper "close and halt" procedure.
My solution in these cases is, make a copy (File <Make a Copy), delete the original notebook and rename the copy (File <Rename)
For me it seems that one of the following steps worked:
Update all packages and jupyter notebook to the latest version using conda
Uninstall then install again the nbextensions configurator
Reboot the computer
For me the reason was 22 emojis in the headers, deleting 5 of them was enough for firefox to get toc back with no reloading and kernel operations.
I have the problem with Jupyter notebook version 6.1.4. After installing nbextensions and enabling extension "Table of Contents (2)" (as "toc" and "toc2" don't work), I cannot obtain the TOC of an a notebook (2.8 MB), while new notebooks have a table of contents.
Reloading, reopening, restarting jupyter does not help, even after a long wait (> 15 min).
I have tried with browsers Mozilla Firefox version 83 and Chromium version 87.
However, a workaround is to create a new notebook (with TOC), then copy all cells from old notebook to new notebook. In order to do this, this might be useful:
how to copy cells from notebook to notebook and
how to select all cells.
Actually I could not copy all cells at once, I had to do three partial copies.
Alas, my method is not only painful but also ineffective in the long term, as the TOC disappeared again.
Restarting the computer worked or did not work.
Opening a small notebook with a table of content and reloading the big notebook worked or did not work.
The problem concerns all Nbextensions, they are just not active for the big notebook. A Javascript console is shown in Google Chrome with Control Shift J.
Error: Load timeout for modules:
nbextensions/nbextensions_configurator/config_menu/main,nbextensions/init_cell/main,nbextensions/spellchecker/main,nbextensions/toc2/main,nbextensions/jupyter-js-widgets/extension
I'm trying to open a jupyter notebook and it takes a long time and I see at the bottom it's trying to load various [MathJax] extension, e.g. at the bottom left of the chrome browser it says:
Loading [MathJax]/extensions/safe.js
Eventually, the notebook loads, but it's frozen and then at the bottom left it keeps showing that it's trying to load other [MathJax] .js files.
Meanwhile, the "pages unresponsive do you want to kill them" pop up keeps popping up.
I have no equations or plots in my notebook so I can't understand what is going on. My notebook never did this before.
I googled this and some people said to delete the ipython checkpoints. Where would those be? I'm on Mac OS and using Anaconda.
conda install -c conda-forge nbstripout
nbstripout filename.ipynb. Make sure that there is no whitespace in the filename.
I had a feeling that the program in my Jupyter notebook was stuck trying to produce some output, so I restarted the kernel and cleared output and that seemed to do the trick!
If Jupyter crashes while opening the ipynb file, try "using nbstripout to clear output directly from the .ipynb file via command line"(bndwang). Install with pip install nbstripout
I was having the same problem with jupyter notebook. My recommendations to you are as follows:
First, check the size of the .ipynb file you are trying to open. Probably the file size is in MB and is large. One of the reasons for this might be the output of a dataset that you previously displayed all rows.
For example;
In order to check the dataset, sometimes I use pd.set_option('display.max_rows', None) instead of the .head() function. And so I view all the rows in the data set.
The large number of outputs increases the file size, making the notebook slower. Try to delete such outputs.
I think this will solve your problem.
Here restarting your kernel will not help. Instead use nbstripout to strip the output from command line.
Run this command -> nbstripout FILE.ipynb
Install nbstripout if it is not there
https://pypi.org/project/nbstripout/
It happened to me the time I decided to print a matrix for 100000 times. The notebook file became 150MB and Jupyter (in Chrome) was not able to open it: it said all the things you experienced and then the page died saying it was "OutOfMemory".
I solved the issue opening it in Visual Studio Code, there is a button "Clear All Output", then I saved the notebook again and it was back to some hundreds of KB, which I could open normally.
If you don't have Visual Studio Code installed, you can open the notebook with another editor (gedit if you use Linux or Notepad++ in Windows) and try to delete the output cells. This is more tricky since you have to pay a lot of attention in what you are deleting, otherwise the notebook will stop working.
I've been using automaticall saved scripts beside .ipynb files as a convenient way to write modules using ipython notebook. I updated to the head version today, and it seems the --script functionality has been removed.
Is there a way to obtain that functionality (automatically on save) with the latest ipython?
Running ipython notebook gives me a message telling me that it's been removed, and suggests doing
ipython nbconvert --to python [notebook]
To make that work automaticaly, I'd have to trigger it on each save - is there an easy way to achieve that?
Not really a workaround, but the --script functionality was still present in release 2.3.0 (if you're running from a live git repo, you can checkout tag 'rel-2.3.0').
I am new to IPython Notebook. I am using the Anaconda distribution on CrunchBang (Waldorf). My development cycle is as follows:
1. Open Spyder.
2. Open the .py file if not already loaded
3. Start IPython Notebook
4. Open the specific notebook from the main IPython screen
5. Select Cell/Run All
6. Note errors. If none goto step 11.
7. Save and close the notebook
8. Shutdown the notebook from main IPython screen
9. Correct errors in Spyder and save
10. go to step 4
11. Move on to the next part of the project and start the process over.
Is there a better approach for a noob? This really gets monotonous although I am learning quite a bit.
Thanks in advance
Forget Spyder for the time being just use the IPython notebook.
1, write code in notebook
2. test it
3. when done if needed make a py file...
You really will only need Spyder later for starting out it just complicates things for no gain
Use Spyder and .py files for writing big functions, classes, modules, tests, etc.
Use IPython notebooks for interactive work where you want to keep the output together with the code (e.g. data processing and analysis, demos, etc.).
To add to Ian's answer, another useful tool is the autoreload extension, which reloads modules automatically when they are changed.
To use, type into your IPython console or notebook:
%load_ext autoreload
%autoreload 2
For example:
This way you can work on a Python file and an IPython notebook at the same time, without having to reload the Python file after each change.
In addition to #dartdog's answer about developing directly in the notebook, if you must edit .py files used by the notebook then note the reload function which allows you to re-import already imported modules without having to shutdown and reopen the notebook.