How can I run .py files from jupyter lab? I have spent my all coding life using jupyter notebook and jupyter lab but replication codes of research papers are mostly in .py file format
For instance, this is a github repository for beta variational autoencoder. As you can see from the repository, these kinds of repositories are usually comprised of main.py, model.py, which looks a lot different from .ipynb format that I usually use.
Can someone share how to comfortably run these kinds of .py codeson jupyter lab? I would appreciate it a lot if someone tells me a video or an article explaining how to run these .py codes on jupyter lab comfortably.
"...how to run these .py codes on jupyter lab comfortably."
Basically the Jupyter's IPython interface allows you to do magic commands that commands within a shell.
Here is the magic for python subprocess.
You can use:
%python -m /path/to/myfile
Then execute the cell and the command will run in the cell and the output cell is the standard output for this run.
You can also make this run in tmux or other tools to make it as a managed background job.
There is a rather thorough discussion of how to interact with .py files from Jupyter notebook here:
How to load/edit/run/save text files (.py) into an IPython notebook cell?
(No terminal window is needed.)
Find File-> new launcher -> other -> terminal, then you use command line run your python file, like "python xxx.py"
Related
I'm automating a bunch of tasks locally with python and shell scripts. I've created a python socket server and clients so I can automate the execution of scripts in different shells and envs. It's not fully-functional, but I can fire up shells, run scripts, and have them connect to the server before executing. One app uses jupyter lab and notebooks. I'm not finding much about how to automate this for what I need.
I tried converting my ipynb file to a py file thinking I could treat it as an ordinary python script, then use a watch folder, load the file names in a dict, and just script in some loops with variable file names, but that doesn't seem to be the case—at least I haven't found anything discussing how to do it with notebooks.
This is what I need to accomplish (programmatically):
Open a new shell, activate env and launch jupyter lab (this I can do)
Connect jupyter lab to the socket server (guessing I can do this in a cell?)
Create a cell with a command that loops through each file in a specific folder with args
Execute all cells in the notebook
Send a message back to socket server that things have completed
Whether or not I need to convert the ipynb to a py file or automate jupyter lab doesn't matter to me, as long as I can automate it. Point in the right direction would be appreciated.
Being new to jupyter notebooks, I wasn't understanding properly how they work. I didn't realize there was a flag when converting to completely strip out all the data except for the raw code. --no-prompt
Running this command will completely convert the ipynb file to the raw code py
jupyter nbconvert --to script --no-prompt myfile.ipynb
Once you do that, they are just like any other python script. I was able to easily add in all my code and have the script working as needed now.
That being said, the suggested tools by #krassowski would be fantastic for more complex projects in the future, especially in a case when you don't want to convert the notebooks.
When i run example.ipynb file in vs code, it saves me a lot of files like:
example-caloifdf-498s-a54d-sdj8-caksjnbrhn83.ipynb
example-a60c6s44-9fax-4747-a9da-as9876fg34r8.ipynb
etc...
in the same folder where example.ipynb is in.
Questions:
What are those files?
How i can i stop vs code from making them\put them in another path if they are relevant?
Thank You.
That should actually be a bug. It's supposed to delete those files. There a consequence of us using jupyter under the covers to run your kernel.
This bug here should resolve it when we fix it:
https://github.com/microsoft/vscode-jupyter/issues/6510
.ipynb files aren't created by vs-code, they are jupyter notebook files generated when working with jupyter notebooks. They don't appear in anaconda or other IDEs which have built-in jupyter notebook support because there is no need to interact with the underlying .ipynb file directly.
On my old computer, I was able to run .py files from Jupyter Notebook, edit them, and run them. The .py file was effectively a notebook file for all intents and purposes. I updated to the latest version of notebook, and I am no longer able to do this. How do I use .py files on my notebook?
I know there are roundabout ways to do this. I am looking for the method where, when you are in notebook, instead of opening a .ipynb file, you select a .py file which is opened, and behaves like a .ipnyb. When you save it, it writes to .py.
A text file can be loaded in a notebook cell with the magic command %load.
If you execute a cell containing:
%loadpy filename.py
The content of filename.py will be loaded in the next cell. You can edit and execute it as usual.
To save the cell content back into a file add the cell-magic
%%writefile filename.py at the beginning of the cell and run it.
To see the help for any magic command add a ?: like %loadpy? or %%writefile?.
%COMMAND-NAME?
i.e. %run?
For list of available magic function use %lsmagic.
Alternatively there is also another method magic function called %save-f but I would not recommend that, it's an indirect way of saving files.
Also see -
1. Magic Functions docs
2.this nbviewer for further explanation with examples. Hope this helps.
This is not the exact answer. At one point, I was able to open .py files using python notebook and work on it as if it were a notebook file.
However, I have been able to replicate this behavior using VScode.
https://code.visualstudio.com/docs/python/jupyter-support-py
Using VScode, you can export all your .ipynb files into .py files, then run code blocks. Code blocks are separated by # %%.
I have not used it sufficiently long enough to decide if it is better than python notebook, but this seems to be the best solution so far. I previously tried using Atom/Hydrogen and did not enjoy the experience.
You can save individual cells as files using the following code: %%writefile some_file_name.py.
You can run that code straight from the terming or from another notebook using the following code: %run some_file_name.py
Some editors (like spyder and vscode) have jupyter notebook functionality. These can be used if jupyter in installed in the python environment.
You can use it by add #%% on top of the block of code. (in vscode the button 'run cell' will automatically appear)
Also it is possible to import .ipynb as .py which can be run in to fancy decrypt above.
I just found this package p2j and tested it with a .py file with functions, comments and normal code.
I used it as indicated in this answer by doing the following:
pip install p2j
p2j -o script.py -t new_file.ipynb
You can also add -o flag to overwrite the original file.
With this, I got a working Jupiter Notebook with each block of code in a cell and the comments as markdown.
Example:
Original .py script
Converted .ipynb
I have read about .py and .ipy, also the difference between python, ipython and notebook.
But the question is: what is the real difference between .py and .ipynb file?
Is .ipynb file just more convenient to be run on jupyter notebook, or anything more? I am wondering because I am thinking about which format to be used for publishing on GitHub.
Thanks
.py is a regular python file. It's plain text and contains just your code.
.ipynb is a python notebook and it contains the notebook code, the execution results and other internal settings in a specific format. You can just run .ipynb on the jupyter environment.
Better way to understand the difference: open each file using a regular text editor like notepad (on Windows) or gedit (on Linux).
Save on git the .ipynb if you want to show the results of your script for didatic purposes, for example. But if you are going to run your code on a server, just save the .py
Adding #Josir answer, the below information is very useful for open .ipynb file using PyCharm.
Create a new Python project in Pycharm
Specify a virtual environment, and install the jupyter package(pip install jupyterlab).
Run the server using the jupyter-lab command.
Browser will open the jupyter notebook like below, there you can execute the .ipynp file.
Here is documentation https://jupyterlab.readthedocs.io/en/latest/
py means PYthon
ipynb means Interactive PYthon NoteBook - which is now known as Jupyter notebook.
The latter one is merely a Python script with descriptive contents - you describe what your data is doing by means of Python script and some funny texts. That's pretty much it - and also, you need a specific editor e.g. PyCharm or Google Collab to open and run it.
I think the answer here might help you: https://stackoverflow.com/a/32029027/11924650
.ipy indicates that it's an IPython script. The only difference between IPython scripts and normal Python scripts is that IPython scripts can use IPython magics, e.g. %timeit, and run system commands as !echo Hi.
I'm new to programming and now taking the course MIT 6.0001. On problem set 2, they set a .py file, accompanied with a .txt file.
I ran .py file in Spyder with no difficulties (.txt file embedded just fine).
But when I run .py file in Jupyter, things won't run (as in screenshot).
I want to use Jupyter because it's much clearer than Spyder, and can give headers to cells to keep myself on track. Please help me to run things in Jupyter.
Here are link to the problem set (ZIP file)
File not running in Jupyter
Use
%load filename.py
to import the text of your python file into a cell in a Jupyter notebook and then save that notebook.
Jupyter isn't built to run/edit .py files, it's built to run/edit jupyter notebooks (ipython notebooks) (.ipynb)