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:$PATH"
Close any notebook you have and reopen it
Here is the notebook explaining it step by step:
https://github.com/ybaktir/notes/blob/master/Convert%20Jupyter%20Notebook%20to%20Pdf.ipynb
I agree that latex installation (at least on windows) is painful and the result in my case was not a great looking document. The ctrl-p method alone doesn't work great if you're running in JupyterLab, but if you export the notebook to HTML, then print from the browser, choosing PDF, the result is quite good.
I know my solution is not at a level. But it works !!
in your browser of notebook tab, simply do "ctrl + p" to get download in pdf
First export the notebook file to HTML (available through File> Download as..).
If you are using JupyterLab, then this is available under File > Export Notebook As....
Use (any) free online converters to convert html file to a pdf file. (One such free online converter is sejda (https://www.sejda.com/html-to-pdf)
Note, there are many such converters are available online.
Related
So I am migrating from RStudio to Visual Studio Code for my future R projects. I have successfully gotten my github aspect all setup and I am trying to write my code in (.rmd) format so that I can knit it to pdf, html and flex_dashboard outputs. When I have tried to knit the it, I get the following error:
rmarkdown::render("c:\Users\{user}\{folder}\{sub-folder}\{sub-folder}\Co$
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).>
I found the following solution that once run in the terminal, allows it to knit into a pdf_document successfully.
Code: Sys.setenv(RSTUDIO_PANDOC="--- insert directory here ---")
Reference: pandoc version 1.12.3 or higher is required and was not found (R shiny)
This is great, but everytime I restart VSCode, this setting appears to be reset and I have to run it again. Is there away to set this globally so that I don't have to run it every time I use it? Or is there a better way to do this?
I had a similar problem before in VScode to render R markdown. Now, I found the solutions to it.
Following the steps below to properly set up the pandoc:
Step 1:
Go to your R Studio and go the console, type the following:
Sys.getenv("RSTUDIO_PANDOC")
If you are using MacOS, you will get the path for "pandoc": "/Applications/RStudio.app/Contents/MacOS/pandoc"
If you are using Windows, you probably will get the path like:
"/c/Program Files/RStudio/bin/pandoc/" as mentioned in pandoc version 1.12.3 or higher is required and was not found (R shiny)
Step 2:
Paste the path of "pandoc" and put it into your bash or zsh (depends on what command shell that you are using).
On MacOS, I'm using zsh. Therefore, I add the following path into ~/.zshrc:
export RSTUDIO_PANDOC="/Applications/RStudio.app/Contents/MacOS/pandoc"
As for how to edit ~/.zshrc, one way to do this is presented as follows:
step 2.1
nano ~/.zshrc
It will open your .zshrc file and navigate to the bottom of this file, paste the
export RSTUDIO_PANDOC="/Applications/RStudio.app/Contents/MacOS/pandoc". Then, control + X to exit. It will ask about "Save modified buffer (ANSWERING "No" WILL DESTROY CHANGES) ?", then type Y and type return bottom.
step 2.2
source ~/.zshrc
Now, it should work fine in VScode. By checking if it works, you could open your console by typing R to invoke the R environment and type Sys.getenv("RSTUDIO_PANDOC"). If it returns the path of the "pandoc", it would work fine in VScode as well.
Adding
"terminal.integrated.env.osx": {
"RSTUDIO_PANDOC":"/Applications/RStudio.app/Contents/MacOS/pandoc"
}
into settings.json worked for me.
Adding to .zshrc didn't work at all since the System environment wasn't being passed on to the integrated terminal.
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
I know I can use command "code" to open VS code or file, but I don't know what should I do to make it possible after I install VS code in Ubuntu.Thanks.
Launching from the Command Line
You can launch VS Code from the command line to quickly open a file, folder, or project. Typically, you open VS Code within the context of a folder. We find the best way to do this is to simply type:
code .
Tip: We have instructions for Mac users in our Setup topic that enable you to start VS Code from within a terminal. We add the VS Code executable to the PATH environment variable on Windows and Linux automatically during installation.
Sometimes you will want to open or create a file. If the specified files does not exist, VS Code will create them for you:
code index.html style.css readme.md
Tip: You can have as many file names as you want separated by spaces.
Source: https://code.visualstudio.com/Docs/editor/codebasics
So, there are a couple of solutions for this.
I've linked a video that shows you how to add vscode to $PATH
(which didn't work for me because I couldn't find the "shell:install path" command)
I uninstalled the vscode from my ubuntu and re-installed using sudo snap install --classic code
(This method worked for me)
Tell me which one works for you... and if you have extensions installed to your vscode then i guess you ought to make a backup or something.
Link to the video: https://youtu.be/iP5FKZXtDBs
I am trying to add the hide_code option to my ipython notebook (jupyter, version 4, python 2.7). It is supposed to add a button or an option to the cell pull-down menu that allows me to hide the code in my ipython notebooks. I have successfully run the 'pip install hide_code' command from the terminal (MacOS X El Capitan). I have restarted the notebook and expected to see a new I have tried to restart the notebook program but nothing happens. I am not computer savvy enough to know what to do from here. Did I miss something?
Here is the github repository for the code:
https://pypi.python.org/pypi/hide_code/0.3.0
OK I found a way to do it.
Install hide_code... It will not work, though.
Try to install it with (with dir="~/.ipython" or whatever)
import hide_code.hide_code as hc;
dir = "<full path to Jupyter config directory>";
hc.install(dir)
It will still not work, but it will copy a javascript file (hide_code.js) into that directory. We will use it in a bit.
Let's find where those nbextensions are. Find one of them. For example, keyboard_shortcut_editor:
cd ~
find -name keyboard_shortcut_editor
Mine finds it ./.local/share/jupyter/nbextensions/keyboard_shortcut_editor
Yours should be there too.
Go to that directory
cd ./.local/share/jupyter/nbextensions/
ls
You see full list of various extensions. Let's copy one of them into hide_copy:
cp -r hide_input hide_code
cd hide_code
ls
The important file there is main.js. Replace it with that hide_code.js from ~./ipython
cp ~./ipython/hide_code.js ./main.js
Rename hide-input.yaml with hide-code.yaml and edit the content accordingly. Mainly, replace all Hide_Input references to Hide_Code. You can edit readme.md as well, but that doesn't matter. Because, the main thing, you created a new extension.
Now, if you launch your jupyter and go to http://localhost:8888/nbextensions, you will see Hide Code. And if click on that checkbox, it's on. Here are snapshots:
It is a weird sequence. But it worked for me. And the main thing, it puts it right where it needs to be. Hide_code actually needs to be a part of Nbextensions. I don't know why it is not. That way it's easy to turn it on and off any way you like it.
As described in the documentation: https://github.com/kirbs-/hide_code, you can troubleshoot by running the following code with appropriate Jupyter config directory location:
import hide_code.hide_code as hc
dir = "<full path to Jupyter config directory>"
hc.install(dir)
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.