VSCode: How to export a python file that was imported from a Jupyter Notebook back to Jupyter format? - visual-studio-code

Probably a silly question, but I couldn't find it. Visual Studio Code editor has a really nice way to work with Jupyter Notebooks. I can edit the cells directly in vscode and run them. Now it would be easy to work with version control.
But I couldn't find a way to convert it back to a Notebook! How do I generate a notebook back from the generated python file?
I understand that the notebook wouldn't have the output cells in it.

There is an option in the interactive Python window that has the notebook output:
This is really cool, now you can work in a Python file and have a really nice interface with your version configuration system (Git).
Yes, it was a silly question :-)

The Jupytext library supports the percent-based cell format used by VSCode-Python, as well as other text-based notebook interchange formats:
https://github.com/mwouts/jupytext

If you need more control over how conversion to ipynb is done (or you need to have cross-references) then you can give a try to Pandoctools. It can export VSCode *.py documents to any Pandoc output format or to Jupyter notebook.
For example you can create and register Jupyter kernel. For example is can be named "nn". That should be the same kernel that you selected in VSCode (there you select it by path but VSCode still uses installed kernels specs under the hood). Then add hat to the Python file, split document to cells, provide settings and set Markdown cells (commented metadata line would export to pdf instead of ipynb; I recommend to open ipynb in nteract native app):
"""
---
kernels-map:
py: nn
jupyter:
kernelspec:
display_name: nn
language: python
name: nn
pandoctools:
# out: "*.pdf"
out: "*.ipynb"
...
# Markdown section title 1
Some **static** Markdown text.
"""
# %% {echo=False}
import IPython.display as ds
import math
import sugartex as stex
# %% {markdown}
"""
# Markdown section title 2
The quick brown Fox jumps over the lazy dog.
"""
# %%
ds.Markdown(stex.pre(f'''
Some **dynamic** Markdown text with SugarTeX formula: ˎα^˱{math.pi:1.3f}˲ˎ.
It works because of the `Markdown` display option and `sugartex` Pandoc filter.
Acually `stex.pre` is redundant here but it is needed when the text is imported
or read from somewhere instead of being written in the same document.
'''))
Then convert the file via pandoctools: drag and drop file to pandoctools shortcut/executable or "open with" pandoctools executable.
Also see:
Two introduction articles are at the beginning of this README,
examples of input to output conversion that have cross-references!
how to use Pandoctools and it's CLI,
how to use Knitty that collects Jupyter outputs and change it's settings.

Use jupytext library:
Install:
pip install jupytext
Now open CMD or internal terminal to the folder with your .py file
Run this:
jupytext --set-formats py:percent,ipynb filename.ipynb

Related

Visual studio code template for Jupyter notebook

Is there a way to have each Jupyter notebook file start with some preexisting template code? For example, when I create a .ipynb file, the first cell would have some import statements of my choosing.
I looked through the Jupyter extension settings in vscode, but I didn't see anything relevant.

Can I save ipython command line history to a notebook file?

I was using iPython command line interface and after some operations I want to save my operation history to a notebook file. But I was not using iPython notebook from the beginning. Can I still make it?
From #Thomas K (I don't know why he didn't post an answer):
%notebook -e myhistory.ipynb
The short answer is in a couple of ways, the slightly longer answer is Yes - but you might not get what you expect!
Really long answer: The explanation is that when you are working in a notebook, now called a jupyter notebook of course, your work is stored in a series of cells each of which has one or more lines of code or markdown while when you are working in a console all of your work is a series of lines of python code.
From within a console session you can save, using %save some or all of your work to one or more python files that you can then paste, import, etc, into notebook cells. You can also save using %save -r to .ipy files your work including the magics as magics rather than the results of magics that again you can use from within your notebook later.
You can also use the %notebook magic to save all of your current history in one of an ipynb json file or a python .py text file with the -e export flag. However, it is not clear from the documentation if the history will end up in a single cell, one cell per command or some other division. A little testing suggests one cell per numbered line of your console, so a single command or definition, per cell.
Personally I will stick with outputting anything useful into python files using the %save command - or better yet start a notebook when I think I might be doing something that I would need later.
If you are using jupyter console (ie, the command line version of jupyter notebook) you can use the following command within a cell to save the notebook as a python file (.py)
save yourfilename
this will save the contents of the notebook as "yourfilename.py" in your current working directory (from which you started the jupyter console)
Alternatively, you can save the whole program by this command :
%save -r program-name 1-999999
The following commands were written to file program-name.ipy

Convert ipynb to pdf in Jupyter

I am new to ipython notebook, and I would like to convert my ipynb to pdf. But I get the following error when I try to Download as PDF via LaTex.
nbconvert failed: pdflatex not found on PATH
There is no documentation anywhere how to add pdflatex to my PATH. I use windows. Thank you!
A simple and surprisingly good solution is to print the notebook to pdf through the browser with ctrl+p. Just make sure your plots and figures are not on interactive mode otherwise they will not be displayed (set them to %matplotlib inline).
Exporting jupyter notebooks through latex is quite troublesome and takes a lot of tinkering to get something remotely close to publish ready. When I absolutely need publication quality I do it on a latex editor, but this tutorial goes in great length about doing it on jupyter.
A few useful tips to get better results:
Higher resolution plots
Hide your code-cells from the pdf
Take a look at these extensions to improve your jupyter documents
For Mac OS X, the solution for me was to install MacTex first and then export the path to find it:
### TeX
export PATH="/Library/TeX/Distributions/.DefaultTeX/Contents/Programs/texbin:$PATH"
You can add this to your .bash_profile or similar config file to load it every time.
See more here https://github.com/jupyter/nbconvert/issues/406
As said by Thomas K in the comments, you need to have Latex installed, and after add the path to the directory containing pdflatex.exe file to the PATH variable of your system.
I have looked for a lightweight distribution and tried installing TeXworks, but I didn't find any pdflatex.exe file.
So I have tried TeX Live, which worked fine creating the pdflatex.exe file under the target installation directory. This path should be like C:\...\texlive\2016\bin\win32.
Finally, you should just add this path to the PATH environment variable of your system (you can use the link shared by Thomas K).
As said here, you need to quit jupyter notebook and open a new command prompt after making any path changes, in order for jupyter to find the newly added item to the PATH.
Then, in Jupyter, you can check your environment variables by running the following (refer to this link for details):
import os
os.environ['PATH'].split(';')
and check if it contains the path to pdflatex.exe file.
If you get some trouble when exporting your notebook to pdf due to missing files/packages (this happened to me), refer to this link to search and install them under TeX Live.
For Linux, the reported error is due to the lack of XeLatex, part of the texlive-xetex package.
Installation in ubuntu will be:
sudo apt install texlive-xetex
Instead of using nbconvert what you can do is :
Download your ipynb file as HTML from File option.
Right-click and select print or use Ctrl+P.
Save as PDF
Easy.
Here is the full solution that worked for me (for Mac).
brew cask install mactex
$ cd ~/
$ touch .bash_profile
This will open the bash profile on TextEditor
$ open -e .bash_profile
Paste the following to the top and save
export PATH="/Library/TeX/Distributions/.DefaultTeX/Contents/Programs/texbin:$PATH"
Close any notebook you have and reopen it
Here is the notebook explaining it step by step:
https://github.com/ybaktir/notes/blob/master/Convert%20Jupyter%20Notebook%20to%20Pdf.ipynb
I agree that latex installation (at least on windows) is painful and the result in my case was not a great looking document. The ctrl-p method alone doesn't work great if you're running in JupyterLab, but if you export the notebook to HTML, then print from the browser, choosing PDF, the result is quite good.
I know my solution is not at a level. But it works !!
in your browser of notebook tab, simply do "ctrl + p" to get download in pdf
First export the notebook file to HTML (available through File> Download as..).
If you are using JupyterLab, then this is available under File > Export Notebook As....
Use (any) free online converters to convert html file to a pdf file. (One such free online converter is sejda (https://www.sejda.com/html-to-pdf)
Note, there are many such converters are available online.

External editor for IPython notebook

I am using IPython notebook and I want to edit programs in an external editor.
How do I get the %edit file_name.py to open an editor such as Notepad++.
Running %edit? will give you the help for the %edit magic function.
You need to set c.TerminalInteractiveShell.editor, which is in your ipython_config.py. I'm not quite sure where this is located in Windows; on OS X and Linux, it is in ~/.ipython. You'll want to set the variable to be the full path of the editor you want.
Alternatively, you can create an environment variable EDITOR in Windows itself, and set that equal to the full path of the editor you want. iPython should use that.
I'm using Windows 7 and 8 (and 10TP) and Python 3.4.2.
I started with ipython locate to tell me where ipython thought config files suggested elsewhere should be. When I saw it was different I read around and came up with the following:
On my system, the ipython locate gave me c:\users\osmith\.ipython, not the _ipython you'll see mentioned in the YouTube videos done with Windows XP,
Look in the directory ipython locate specifies for a profile directory; if you aren't actively doing anything with ipython profiles, it should be .ipython\profile_default, if you are using profiles, then I leave it to you to s/profile_default/${YOUR_PROFILE_NAME}/g
Check the profile_default directory for a ipython_config.py file, if it's not there, tell IPython to initialize itself: ipython profile create
Open the config file in a text editor,
If you are the kind of person who hasn't messed around with their console overly much and installs things in standard places, you can skip straight to this step by typing: ipython profile create followed by start notepad .ipython\profile_default\ipython_config.py.
Search for the string c.TerminalInteractiveShell.editor,
The comment above this indicates you can also use the EDITOR environment variable, but hard coding file paths never hurt anyone so lets do eet:
Copy the line and remove the leading hash and spaces from the copy.
Replace the text between the apostrophes ('notepad') with the path of our desired editor, e.g.
c.TerminalInteractiveShell.editor = 'c:/program files (x86)/noddyeditor/noddy.exe'
There is a catch here, though; some modern editors get a bit fancy and automatically and, when invoked like this, detach from the console. Notepad++ and Sublime Text, for example. Sublime accepts a "--wait" option, which works some of the time; this tells the command invocation to hang around until you close the file, for some definition of until and some other definition of close.
However, the following setting will work most of the time for sublime text:
c.TerminalInteractiveShell.editor = '"c:/program files/sublime text 3/subl.exe" --wait'
(assuming c:\program files\ is where your sublime text 3 directory is)
Try the 'Pycharm' editor
This works for me.

Libreoffice Impress Export as Images extension does not work

Libreoffice Impress Export as Images extension does not work. "Export as Images" Menu is not being added to File Menu.
Link- http://extensions-test.libreoffice.org/extension-center/export-as-images
I am using Libreoffice 3.4. Any suggestions would be helpful.
Quick workaround: start the Export as Images macro manually. It's located under My Macros -> ExportImages -> ExportImages. Look for a macro named ExportAsImages and run it. Once found and started, it works fine :) (i don't know why it doesn't show up in the File menu).
EDIT:
Editing the macro is possible using the built-in IDE: once it's installed, you can access its LibreOffice Basic source using Tools-> Macros -> Organize Macros... -> LibreOffice Basic.
It's also possible to run it from the command line, but in its current form, it requires user interaction to specify the output file name and graphics format. So i assume it isn't possible to run it completely in "headless" mode without modifying the source. To run it from the command line on Linux, converting the file /tmp/mypresentation.odp, use:
$ simpress /tmp/mypresentation.odp "vnd.sun.star.script:ExportImages.ExportImages.ExportAsImages?language=Basic&location=application"