I'm trying to use the bash kernel in iPython/Jupyter notebook, but I need sudo access within the notebook itself.
I've tried $ sudo jupyter notebook to run the notebook as root, but that only returns:
$ jupyter: 'notebook' is not a Jupyter command
So, I'm left with running $ jupyter notebook (unless there's a way to run Jupyter notebook as root).
I also can't do su root in the notebook itself because that requires an input and the notebook won't let me give an input.
Finally, there is allegedly an --allow-root option for Jupyter notebook:
http://jupyter-notebook.readthedocs.io/en/latest/config.html
However, it looks like --allow_root is no longer an option. (I've tried modifying the config file by adding NotebookApp.allow_root=True, but that doesn't work.)
Any ideas guys? Maybe I'm doing something wrong?
Just login as root, then do the following command to start the notebook :
jupyter notebook --allow-root
The solution as described here. Is to use
sudo -E env "PATH=$PATH" jupyter notebook
Basically the binary to call jupyter notebook is in the user's PATH variable, but not for root.
Best regards.
Add c.NotebookApp.allow_root=True from the root configuration files. That you don't need ask to allow-rootevery time then you start the notebook.
Edit:
Before edit the configuration file you need to run jupyter notebook --generate-config as root to make the file.
I am running the neopixel library from a jupyter notebook.
The only thing that worked for me was first running the "sudo su" command to move into the root environment and then run "jupyter notebook" (--allow-root alone didn't work for me).
You should try running the command sudo jupyter notebook --allow-root , I'm not sure why but this works. On the server it'll ask you for a password, if you have set up a password for it just type it in the box that will be shown, otherwise, type jupyter notebook password to set up a new password
Generate config
root#user# jupyter notebook --generate-config
root/.jupyter/jupyter_notebook_config.py
root#user# cd .jupyter/
root#user:/.jupyter/# gedit jupyter_notebook_config.py
Add line in jupyter_notebook_config.py
c.NotebookApp.allow_root=True
When I need to execute command as root in my notebook, I use the -A flag, that allows to access an helper program used to read the user's password when no terminal is available.
You need to modify the sudo.conf file before to declare the helper program. On a Debian Buster, I personnaly added:
Path askpass: /usr/libexec/seahorse/ssh-askpass
See the main page of sudo.conf for more information.
In case anyone is still looking for an answer, this is what worked for me:
sudo ~/.local/bin/jupyter-notebook --allow-root
Switching user using su didn't work because I didn't have jupyter installed on root. Using just --allow-root by itself also didn't work for me. This allows you to run sudo with jupyter notebook without running into the issue of "notebook" not being a valid command. Because I am using a linux terminal, jupyter-notebook is installed at ~/.local/bin/jupyter-notebook. See After installing with pip, "jupyter: command not found" for more information about where jupyter may be installed.
Related
I have multiple conda environments on my PC created with Anaconda and I have installed jupyterlab in two of them. I used one environment for R programming and the other for Tensorflow with Python. I have noticed that whenever I open jupyter lab in either of the environments, it always starts off where I left it. That is, the last open notebooks are opened on start. Of course, this doesn't bother me too much, but it makes me think each jupyter lab installation isn't contained within its own environment.
For example, I have two environments. Say they're called env_R and env_Python_TF. I have installed jupyter lab in both environments.
I open Anaconda Powershell prompt and launch each environment using the following commands:
(base) PS $ conda activate env_R
(env_R)PS $ jupyter lab
Say I work on jupyter lab and once I'm done, I close the browser windows and then shut down the server using CTRL+C in Anaconda Powershell prompt. Now if I open up my second environment using:
(base) PS $ conda activate env_Python_TF
(env_Python_TF)PS $ jupyter lab
Now I see the same notebooks I used with env_R opened up when jupyter lab opens in my browser.
Aren't each jupyter lab installation contained within its own conda environments? If not, have I possibly made a mistake in my configuration?
it should be within its own conda environment but Default root folder /location will remain same for jupyter notebook. You will need to change it using config file.
Here is link
I have always opened the jupyter notebooks from the Anaconda prompt. The problem is that whenever I try to open the Jupyter notebook from the command prompt, the following error is displayed:
Picture of the Error shown on my command prompt window
ImportError: DLL load failed: The specified module could not be found.
What am I doing wrong ? What should I do?
Opening Jupyter Notebook from command prompt is useful, especially when you would like to open the Jupyter Notebook from a specific folder.
The following 2 steps might help you to resolve this issue.
open command prompt
activate base
The prompt might change to begin with "(base)", which is expected. Then type,
Jupyter-notebook
If Jupyter notebook opens up now, this means Jupyter is correctly installed within your conda environment. In OS like Windows 10, it was an expected behavior not to recognize Python outside of Conda environment, which extends to Jupyter Notebook as well.
If the 1st step works properly, then add the below paths to your
environment variable. If you would not like to add the path to your
system environment variable, you can choose to update in your
account environment variable.
In windows 10 >> search "environments" and "Edit environment
variables for your account"
Select "PATH" and edit.
Add below paths
C:\Users\\Anaconda3;
C:\Users\\Anaconda3\Scripts;
C:\Users\\Anaconda3\Lib;
C:\Users\\Anaconda3\Library\bin;
C:\Users\\Anaconda3\Library\mingw-w64\bin;
Now you should be able to open Jupyter Notebook directly from command prompt.
I have Git for Windows and want to be able to start Jupyter Notebook in a directory of choosing using File Explorer. If I right click in a directory and select "Git Bash Here," a Bash shell opens. I already added my Anaconda directory (where my Python 3.7 is located) into the user path, and I can verify that Bash sees that in the path by "env|grep PATH". However, when I type "jupyter notebook" from the Bash prompt, it finds the script and it starts to run, but reports an "ImportError: DLL load failed: The specified module could not be found."
How do I set the Bash environment to start a Jupyter Notebook from the current directory where I have a Bash prompt?
I solve this problem with the command:
source "C:\Users\...\Anaconda3\Scripts\activate"
When you install Jupyter via anaconda it isn't added to the system's enviornment variables. Your system doesn't know about Jupyter. Only anaconda does because it is managing your packages and your versions for each project you create.
If you're using bash for windows I would think you'd have to install Jupyter notebooks to windows and add it to your environment variables to be able to see it in any directory.
Edit: Here's a picture of me running Jupyter from my windows command line and from the Anaconda prompt.
In your GitBash prompt type the following command
. Anaconda3/Scripts/activate
assuming you are in your home directory.
This will allow you to run jupyter from GitBash and also use UNIX commands from jupyter.
I'm currently running Jupyter Notebook (Windows 7) within a Conda environment using Python 3.6.4 and my current version of Jupyter Notebook is 5.6.0. I came across the following article: Using Git Bash in Jupyter Notebook on Windows , that explains how to change the default shell within Jupyter Notebook to Bash by changing the config "C.NotebookApp.terminado_settings = {'shell_command': ['C:\Program Files\Git\bin\bash.exe']}. I've tried multiple different options for the path to bash, including just the name 'bash', with no success.
Python and Jupyter version:
Jupyter Notebook: Not changed, still using Powershell
I've read up on the Jupyter Notebook: Read the Docs , and made the changes to the jupyter_notebook_config.py found under C:\Users\UserName\.jupyter directory, without any success.
An alternative solution to your problem is to use the Windows Subsystem for Linux (WSL).
I am under Windows 10, conda 4.5.11 and Jupyter lab 0.35.3. I have also activated the Windows subsystem for Linux (WSL).
Using !wsl you can call the WSL or with %%bash for cell magics.
Inside Jupyter Lab I have:
is the %%bash cell magic referring to the WSL? According to my tests yes, I can access the same programs and I am taken to the WSL when I run bash.exe from the Conda prompt. There is an integration of the PowerShell prompt to WSL (https://learn.microsoft.com/en-us/windows/wsl/interop). The same seems to work with the conda prompt.
Here are three options:
If one opens Jupyter notebook via GitBash with jupyter notebook then %%bash magics should work
If one wishes to always be able to run bash within a Jupyter Notebook opened via Anaconda Prompt (similarly using jupyter notebook):
Edit the Jupyter Notebook config file:
Location can be found via Anaconda Prompt with jupyter --config-dir
Open the jupyter_notebook_config.py file in this directory using notepad or an IDE
Modify and save with the line of code: c.NotebookApp.terminado_settings = {} pointed instead to your bash executible (e.g.): c.NotebookApp.terminado_settings = { 'shell_command': ['C:\Program Files\Git\bin\bash.exe'] }
Edit your system environment variables:
Windows Search (with admin rights) > "Edit the System Environment Variables" > Environment Variables > Highlight "path" > Edit > Add a new line with C:\Program Files\Git\bin > OK out of all windows
Set an environment variable in Jupyter Notebook
Is it possible to start an ipython shell(in terminal) within a conda or virtualenv ?
The ipython shell should belongs to the respective environment.
I know a way to start jupyter notebook within the env, by creating a kernelspecs for the virtual env and then choosing the env kernel within the jupyter notebook.
here is the link : http://help.pythonanywhere.com/pages/IPythonNotebookVirtualenvs
But this only setup the jupyter notebook for the current environment. Is there a to do the same for ipython shell
The answer given by Grisha Levit almost solved the problem. So, i am writing the complete details of the answer, how to setup a ipython console within a specific environment.
1.) Activate the virtual env:
source activate <environment-name>
2.) From within the virtual env:
jupyter kernelspec install-self --user
3.) This will create a kernelspec for your virtual env and tell you where it is:
Installed kernelspec pythonX in home/username/.local/share/jupyter/kernels/pythonX
Where pythonX is the version of the python in the virtualenv.
4.) Copy the new kernelspec somewhere useful. Choose a kernel_name for your new kernel that is not python2 or python3 or one you've used before and then:
mkdir -p ~/.ipython/kernels
mv ~/.local/share/jupyter/kernels/pythonX ~/.ipython/kernels/<kernel_name>
5.) If you want to change the name of the kernel that IPython shows you, you need to edit ~/.ipython/kernels//kernel.json and change the JSON key called display_name to be a name that you like.
6.) Running jupter/ipython console within the virtualenv.
jupyter console --kernel <kernel-name>
7.) This will start the jupyter console/shell for the current virtualenv and you can also see kernel in the IPython notebook menu: Kernel -> Change kernel and be able so switch to it (you may need to refresh the page before it appears in the list). IPython will remember which kernel to use for that notebook from then on.
I know a way to start jupyter notebook within the env, by creating a kernelspecs for the virtual env and then choosing the env kernel within the jupyter notebook.
You just need to do the same thing, but using console instead of notebook.
For example:
ipython console --kernel python2