Does anyone know if there's an option (or a suggested hack) to make IPython notebooks save automatically before executing a cell?
Many times I've been working on something without saving for quite some time, then I execute a stupid command that prints so much crap to the console that my browser becomes unresponsive, leading to me losing all my work.
A timed autosave might also do the trick.
The development version has that feature fully implemented. Install it by following the instructions on the ipython github.
Instructions form the repo:
If you want to hack on certain parts, e.g. the IPython notebook, in a
clean environment (such as a virtualenv) you can use pip to grab the
necessary dependencies quickly:
$ git clone --recursive https://github.com/ipython/ipython.git
$ cd ipython
$ pip install -e ".[notebook]"
This installs the necessary
packages and symlinks IPython into your current environment so that
you can work on your local repo copy and run it from anywhere:
$ ipython notebook
Updating iPython Notebook solved several problems I had with iPython Notebook; for instance, it autosaves, or auto-correction is disabled, or %matplotlib inline works now (before updating, I had to use --pylab inline in the command line when I was running $ipython notebook).
As I use coda on my mac, I updated iPython Notebook via conda:
$conda update ipython
You could simply set a lower interval for autosave feature using the following magic command:
%autosave 60
in order to save automatically your notebook every 60 seconds.
Related
I'm using jupyter inside a conda environment in vscode on Ubuntu and all works great. However, recently I've experienced issues with AWS access tokens expiring inside my jupyter notebook.
It seems that these access tokens get cached at some level, either in the code environment or somewhere in the jupyter layer, but I couldn't figure out where and how to clean it up.
Example:
I'm using aws-vault to generate SSO credentails, that can be accessed in the environment.
After starting a session, I can access the AWS_SESSION_EXPIRATION from my terminal:
echo $AWS_SESSION_EXPIRATION
2022-04-20T17:40:36Z
when I start vscode, open a terminal, I get the same.
When I activate my environment, and run
python -c "import os;print(os.environ['AWS_SESSION_EXPIRATION'])"
I get the same.
However, when I open a new jupyter notebook and select the same environment, and run
import os
print(os.environ['AWS_SESSION_EXPIRATION'])
I get
2022-04-06T11:09:03Z
I've tried locating any files that could cache the env variables either in the conda env or jupyter extension. I've also tried restarting vscode and the machine itself - all without success.
Can anyone help me clean this up?
Thanks!!
Edit:
Another example:
If I set in my terminal
export FOO=BAR
then I can access $FOO as expected through the terminal and jupy notebook within vscode.
Then I close vscode, run
unset FOO
reboot the machine, start vscode new and open a new notebook with the same conda environment.
Within, running
import os
print(os.environ['FOO'])
STILL returns BAR
There seems to be an issue in the vscode-jupyter extension, that somehow stores the environment variables in the kernel.json file.
At the moment of writing this, the issue is still open. Working in ubuntu, this workaround from the issue's thread works for me:
Close code completely
find ~/.vscode/extensions/ms-toolsai.jupyter*
code .
Run a notebook and it will pick up the changes.
With closed vscode, issue the following command to delete cache:
find ~/.vscode/extensions/ms-toolsai.jupyter* -name kernel.json -delete
Source: https://github.com/microsoft/vscode-jupyter/issues/9774#issuecomment-1110328329
I'm trying to use the new Jupyter integration for the Python extension in VS Code, and I'm getting the above error even though I have Jupyter installed and it works fine from the command prompt.
Here's my environment:
Python extension version 2018.10.1, and I see Run Cell/Run All Cells tooltips above #%% comments.
I've used the Python: Select Interpreter command to select my Anaconda environment, which is at ~/AppData/Local/Continuum/anaconda3/python.exe.
I have Jupyter installed in that interpreter (jupyter.exe is in the Scripts sub-folder under that location), and it runs fine with the jupyter notebook command at the Anaconda prompt.
But whenever I click on Run Cell or press shift-enter, I get this error message:
"Running cells requires Jupyter notebooks to be installed." Source: Python (Extension)
Is there something else I need to do to configure this?
You may give one try by restarting VS Code in following mentioned way [ It worked for me. ]
Open Bash or any other cmd
Activate any conda environment [ See below command ]
source activate base [ means activate base environment ]
Run VS Code instance [ See below command ]
code .
Now when you'll click on Run Cell or press shift-enter, it should work.
The problem is an issue in the VS Code python extension itself. There are a number of issues related to this open in the repository: #3354, #3343, #3330, and the issues are being worked on, see #3374.
The reason, as far as I understand, is that in this case - and in some other cases - the anaconda environment is not activated before running the command. Situations where the environment is activated are e.g. opening a python terminal or running a file in the python terminal, but this also needs to happen for Jupyter, Tests, and so on.
While theoretically, adding the Scripts folder to your PATH, as David mentioned, could help, it did not help in my case. This may just not be enough to properly reflect what happens on activation.
My guess is that we will have to wait for this issue to be resolved in the repo, but if someone else finds a workaround, I'd be happy.
Simply running vscode from the activated environment did not work for me, here is what did:
In terminal (bash) I ran:
conda activate <environment-name>
conda install jupyter notebook
When the install finishes, open vscode from terminal (the same shell with activated environment) with the command:
code .
Notes:
Replace '.' with the path to the directory you want to open if it's not the current directory.
I've written 'conda install ...' but mamba also works.
If the terminal command for 'code ' does not work, it's likely you need to add it to environemnt variables; in such a case, this post might help.
I am trying to use the interactive shell of IPython within my conda env and am having issues.
The steps I take are:
source activate myenv
conda install ipython
ipython
When I am in ipython interactive shell, it calls python from the anaconda root bin. (~/anaconda2/bin')
Is there anything I can do to change the python path to ~/anaconda2/envs/myenv/bin and import packages from myenv?
I see few solutions to making env work in jupyter when I search the web, but no answer on making it work on the interactive shell.
This is likely due to your $PATH variable being messed up.
THe easiest way to make sure you get IPython from within an env is to use $ python -m IPython <rest of the options> to start IPython. This works for many of the Python installable application; like pytest, pip and other.
Background
I use Anaconda's IPython on my mac and it's a great tool for data exploration and debugging. However, when I wish to use IPython for my programs that require virtualenv (e.g. a Django web app), I don't want to have to reinstall IPython every time.
Question
Is there a way to use my local IPython while also using the rest of my virtualenv packages? (i.e. just make IPython the exception to virtualenv packages so that the local IPython setup is available no matter what) If so, how would you do this on a mac? My guess is that it would be some nifty .bash_profile changes, but my limited knowledge with it hasn't been fruitful. Thanks.
Example Usage
Right now if I'm debugging a program, I'd use the following:
import pdb
pdb.set_trace() # insert this to pause program and explore at command line
This would bring it to the command line (that I wish was IPython)
If you have a module in your local Python and not in the virtualenv, it will still be available in the virtualenv. Unless you shadow it with another virtualenv version. Did you try to launch your local IPython from a running virtualenv that didn't have an IPython? It should work.
Will, I assume you are using Anaconda's "conda" package manager? (Which combines the features of pip and virtualenv). If so you should be aware that many parts of it does not work completely like the tools it is replacing. E.g. if you are using conda create -n myenv to create your virtual environment, this is different from the "normal" virtualenv in a number of ways. In particular, there is no "global/default" packages: Even the default installation is essentially an environment ("root") like all other environments.
To obtain the usual virtualenv behavior, you can create your environments by cloning the root environment: conda create -n myenv --clone root. However, unlike for regular virtualenv, if you make changes to the default installation (the "root" environment in conda) these changes are not reflected in the environments that were created by cloning the root environment.
An alternative to cloning the root is to keep an updated list of "default packages" that you want to be available in new environments. This is managed by the create_default_packages option in the condarc file.
In summary: Don't treat your conda environments like regular python virtualenvs - even though they appear deceptively similar in many regards. Hopefully at some point the two implementations will converge.
Im trying very hard to get ipython notebook to work. I got it working in terminal, but I can't get it to work in my browser.
When I type ipython notebook in terminal, it says -bash: ipython: command not found
MacBook-Air:~ me$ sudo easy_install https://github.com/ipython/ipython/tarball/master
Downloading https://github.com/ipython/ipython/tarball/master
error: None
MacBook-Air:~ me$ ipython
-bash: ipython: command not found
Im really unsure why this is happening.
You do not need to (and you probably shouldn't) do sudo easy_install it will probably install things as root, avoid sudo. Check that ipython executable is in your $PATH.
github tarballs are broken for IPython. You do have to deep clone with git if you want to run master, then run python setup.py with the option you like (install, develop, symlink)...
Use pip if you want to run IPython stable.
You might have issues with readline on osx (wrong multiline editting, wrong completion, IPython popping error messages at launch time) this is one of the rare case where you might have to using easy_install for readline.
Maverick (10.9) has issues with python/numpy/matplotlib you might need to have a custom python build with homebrew that does not use system libs.