I invoke "jupyter notebook" under:
[abigail#localhost anaconda3]$ jupyter notebook
By default, it saves to the directory of anaconda3/ with an extension of "ipynb" when I click "File" => "Save".
How to save it to a directory under anaconda3/, instead of the default location? There is not a "save as" command in notebook?
You can save a notebook to a location of your choice by using the "File" -> "Download as" -> "Notebook (.ipynb)" option from the menu.
Alternatively you can start your notebook server from a different directory and it will save all notebooks to that directory.
A third option is to navigate to the directory you want the notebook to be saved to in the tree view "http://127.0.0.1:8888/tree" prior to creating the notebook.
There are two methods:
1.You can use the magic command %notebook to save as ipynb
%notebook "directory/to/file/filename.ipynb"
2.You can use the magic command %%writefile to save as py file
%%writefile "directory/to/file/filename.py"
In the second method, you should put this command at the top of the cell, otherwise it will throw an error.
It is easiest to select a destination before you create a program using Jupyter Notebook; as then you do not run into this issue.
However, since you have already made a program, one possible solution is to make a copy of the file, move it to your desired location, and then delete the old file. Before doing this, ensure that you have saved it first, otherwise data might be lost.
Related
Question: How can one set the working directory of all notebooks opened in Jupyter Lab with a double-click, to be the project's folder, /myproject/, regardless of the notebook's subfolder within that parent folder? The working directory is identified by !pwd on Linux/Mac or !cd on Windows.
Context:
The Jupyter Lab sessions is initiated from the project's folder, by: /myproject/jupyter lab.
I am not looking for changing the working directory within the notebook with code (e.g. with !cd.. or using os), but change the settings of Jupyter Lab, such that the all kernels will start with the folder from where Jupyter Lab was initiated.
This is useful for being able to use consistent relative folders, regardless of the subfolder they are referred from. For example, for loading data in a specific subfolder.
I agree that this is often a preferred approach! I always have my notebooks configured to work like that because it:
makes it easy to specify paths to data and for outputs and
allows moving a notebook between directories without the need to change the paths
makes jupyterlab-lsp code intelligence work more reliably
I have a python module called make_paths_absolute.py with the following contents:
from os import chdir
from pathlib import Path
def make_paths_relative_to_root():
"""Always use the same, absolute (relative to root) paths
which makes moving the notebooks around easier.
"""
top_level = Path(__file__).parent
chdir(top_level)
make_paths_relative_to_root()
And in the first cell of every notebook, I add a line import make_paths_absolute. I like it this way because it makes it:
reproducible: anyone who copies/clones my project will be able to run the code without the need to customize anything in their Jupyter environment
work with all notebook interfaces (whether JupyterLab/RetroLab/classic Notebook)
is quite obvious for anyone reading the notebook that they should expect the paths to be absolute (=relative to the root).
To make that work you first need to set PYTHONPATH pointing to the root of the repository when starting JupyterLab. To do so on Linux/Mac you can prepend the jupyter lab command with:
PYTHONPATH=/path/to/your/lab/root:$PYTHONPATH jupyter lab
Alternatively, you can specify PYTHONPATH in kernel.json (either by modifying the default kernel specification or creating a copy of it first, see https://stackoverflow.com/a/53595397).
PS. The above is a simplification of my setup. In reality, I store make_paths_absolute.py in helpers package (so there is also an empty helpers/__init__.py and there is extra .parent) together with other initialization-time code, including a notebook called notebook_setup.ipynb which contains things like %matplotlib inline, pandas customizations (like making sure it uses stable sort), warning filters etc. So my every notebook starts with:
import helpers.make_paths_absolute
%run helpers/notebook_setup.ipynb
and I am really liking this setup working like that for two years now without any problems.
There is a feature request for making this easier at: https://github.com/jupyterlab/jupyterlab/issues/11619.
The most easiest solution in my opinion
Open Notepad
Paste the command "jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10"
Save the notepad file with an extension of ".bat" instead of ".txt"
Paste the file in which directory you want to initialize your jupyter
Double click and open the ".bat" file
Jupyter opens with desired directory as base
This way you control the jupyter root directory as and when required and don't
really have to perform any manual settings
Hope this helps
".bat" file created on Desktop
enter image description here
".bat" file double clicked and executed
enter image description here
jupyter opens with Desktop as the intended base directory
enter image description here
I was wondering if there is a way to set a default folder every time I open JupyterLab. Is there any command I can run through Anaconda PowerShell Prompt? Or a JSON property I can modify in settings tab? Thanks in advance!
If you want to open specific file in directory a, say a/notebook.ipynb but then navigate the file browser to directory b, relative to the root directory, you can use file-browser-path query in the navigation URL (documented here):
http(s)://<server:port>/<lab-location>/lab/tree/a/notebook.ipynb?file-browser-path=/b
You can use this method from command line thanks to LabApp.default_url traitlet:
jupyter-lab --LabApp.default_url='/lab/tree/a/notebook.ipynb?file-browser-path=/b'
You can skip the opening specific file part:
jupyter-lab --LabApp.default_url='/lab?file-browser-path=/b'
If you want to change the root directory, please see this answer which explains how to do so with ServerApp.root_dir traitlet (in older versions of Notebook<7.0 and JupyterLab<3.0 used to be named NotebookApp.notebook_dir). Again, you can use it from command line, and even specify an absolute path:
jupyter-lab --ServerApp.root_dir='/home/user/project/'
# or on Windows say:
# jupyter-lab --ServerApp.root_dir='C/users/user/project/'
You can combine the two approaches, e.g.:
jupyter-lab --ServerApp.root_dir='/home/user/project/' --LabApp.default_url='/lab?file-browser-path=/project_subdirectory'
If you want to persist the changes (for either default URL or root dir), see the previously linked answer which details how to persist configuration.
Follow the answer . Just edit the alias alias my_jupn='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38 && jupyter-notebook --notebook-dir=/home/$USER/Documents/Jupyter_Notebook'
and for JupyterLab alias my_jupl='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38 && jupyter-lab --notebook-dir=/home/$USER/Documents/Jupyter_Notebook'
N.B. Here MyPy38 is your active environment name. and if any error occurs then change $USER to your UserName. Lastly, /home/$USER/Documents/Jupyter_Notebook will be change according to your choice.
According to the jupyter.org:
I configured like this.
Terminal command active your envirnment by conda activate Your_env_name and then jupyter lab --generate-config. jupyter_lab_config.py should be created in dir /home/$USER/.jupyter directory.
Find
# c.LabApp.app_settings_dir = '' and uncomment.
Then give your directory like this.
c.LabApp.app_settings_dir = '/home/$USER/Documents/Jupyter_Notebook'
Similar for jupyter notebook. jupyter notebook --generate-config and then nu-comment and edit like c.NotebookApp.notebook_dir = '/home/UserName/Documents/Jupyter_Notebook'
**NB: /home/$USER/Documents/Jupyter_Notebook is my changed default dir. Change it according to your need. **
The command
jupyter notebook --generate-config
will create a config file.
The path to this file is displayed in your terminal or PowerShell.
Set the desired folder path as the string c.ServerApp.root_dir in this file and make sure you uncomment the line after you set the string.
Windows users will have to use double backslash in paths, e.g.:
c.ServerApp.root_dir = 'C:\\YOUR\\PATH'
Hello I am using jupyter-lab with the jupytext extension.
This extension allows you to --sync different format so that you can edit say a Rmd file that will automatically be converted to ipynb
This ipynb file is loaded in jupyter
To update the file opened in jupyter I have to click on "save", I then get the following message
I then have to click on revert to update from disk.
Is there a way so that the file on disk is automatically "reloaded" each time it changed or say every second and that It s "reverted" automatically ?
I created a new folder in jupyter notebook which was given the default name "Untitled folder".
Upon trying to rename it to "my_folder", i get the following error
Rename failed
An error occurred while renaming "Untitled Folder" to "my_folder".
Permission denied: Untitled Folder
The folder i was trying to rename was listed as a running notebook under the running tab.
after shutting it down, i was able to rename it.
you can make the checkbox checked specific to the folder which you created and then use Rename from the top menu options.
I had the same kind of bug when renaming the file in jupyter notebook and I got rid of it by simply finding all files with the same name as the one causing the error and deleting them and creating a new one in Jupyter notebook.
How to change working directory in Julia Jupyter?
I tried and read everything, still have no idea how to do that. It only allows me to select directories under my home ~/ dir. I can't find any button to go up to /.
I'm pretty sure once you have started the server you cannot then go up directories, I may be wrong though.
So best thing to do is start the jupyter notebook server somewhere that contains all of the folders you might need -i.e. the root dir if you want to make sure you have access to everything.
You can use the --notebook-dir flag for this. Or you can set defaults in the config.
you need to create the config file, using cmd :
jupyter notebook --generate -config
Then, search for C:\Users\your_username\.jupyter folder (Search for that folder), and right click edit the jupyter_notebook_config.py.
Then, Ctrl+F: #c.NotebookApp.notebook_dir ='' . Note that the quotes are single quotes. Select your directory you want to have as home for your jupyter, and copy it with Ctrl+C, for example: C:\Users\username\JuliaProjects.
Then on that line, paste it like this : c.NotebookApp.notebook_dir = 'C:\\Users\\username\\JuliaProjects'
Make sure to remove #, as it is as comment.
Make sure to double slash \\ on each name of your path.
Ctrl+S to save the config.py file !!!
Go back to your cmd and run jupyter notebook. It should be in your directory of choice. Test it by making a folder and watch your directory from your computer.
I use Jupyter Lab and start it from the Julia REPL (1.4) like this:
using IJulia
jupyterlab(dir=pwd(), detached=true)