If I keep open a jupyter notebook / colab one for sometime without any activity, somehow the notebook "forgets" all the values (e.g. csv files loaded into DataFrames) and I need to re-run the whole notebook which is time consuming.
By the way, I diligently save the notebook with each change.
It happens also when I reload the notebook. It seems odd.
Any ideas how to prevent it?
Thank 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.
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.
As my RAM is scarce, I'd like to not replicate data and use objects created in an RStudio session inside my Jupyter notebook (running w/ R kernel).
Any idea how to do it?
Basically I'd like to use the same workspace in both, the RStudio and the Jupyter notebook session.
Thanks for help!
One problem I encountered with an R notebook in Jupyter, though, was saving my workspace. In a normal R session I’m used to saving my workspace at the end of the session and coming back to it later to pick up where I left off. However, with the Jupyter notebook I found that I had to rerun all the code to regenerate all the objects again! This appears to be an issue for Python notebook users too.
There’s a very simple fix for this: Just run the standard R command
save.image()
Your workspace will then be saved to the usual hidden .RData file in the same folder as the Jupyter notebook. If you want to share the code and the workspace, you’ll have to make sure that you copy both the notebook file and the .RData file that goes along with it.
Likewise, if you start a notebook in a folder that already has an .RData file, you’ll find that you can access that workspace from the Jupyter notebook – just run ls() to see what’s there.
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.
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)