I am working on an El Capitan with python 3.5 and I have installed succsfully jupyter, pandoc, and latex.
I am trying to make a tempalte for nbconvert in order to edit the output in pdf (some margines do not look very nice and some code falls outside the paper).
For that reason I tried to download and play with https://github.com/jupyter/nbconvert-examples as suggested in an other question. The only problem is it does not work.
For example in the citations folder the tutorial instructs me to use the ipython nbconvert command but it gives me the warning:
[TerminalIPythonApp] WARNING | Subcommand `ipython nbconvert` is deprecated and will be removed in future versions.
and fails. When I run it with jupiter nbconvert instead I am getting the same error.
I tried the full command it suggests in many versions, each fail:
the:
jupyter nbconvert --to latex --template citations.tplx --post pdf mynotebook.ipynb
understandably does not work any more since the syntax has changed. But the:
jupyter nbconvert --to pdf --template citations.tplx LifecycleTools
runs but does not create the citations.
When I run:
jupyter nbconvert --config ipython_nbconvert_config.py --template citations.tplx LifecycleTools.ipynb
the same happens.
Any idea for correct examples or where I can find resources on how to white and run a template?
In the end I manged to use the templateby first exporting it to markdown:
jupyter nbconvert --to markdown my_file.ipynb --template="mytemplate.tpl";
and then using the files created to build a pdf with pandoc.
pandoc --toc --template=mdtemplate.tex $PATHTOMYFILES/* --latex-engine=pdflatex -o $NBDIR/ROOT-Primer_v0.pdf
Related
I am trying to print a jupyter notebook file with the export button or this command:
jupyter notebook --to PDF test.ipynb
I have tried HTML, and it also doesn't work
I have installed:
MikTex
Pandoc
nbconvert
PIP
Jupyter
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
When I write something in the jupyter notebook markdown field, the typos are not highlighted and often I ended up with something like this:
In almost all IDEs I have used so far, the typos are highlighted with a curly underline which was very convenient for me. Something like this:
Up till now I have not found anything that allows me to see this type of highlights. Does it exist?
The popular Jupyter Notebook bundle extension from Jupyter-contrib contains a spell checker. You can install and enable this (with admin privileges) like so:
pip install jupyter_contrib_nbextensions
jupyter contrib nbextension install --user
jupyter nbextension enable spellchecker/main
This may be the most popular spell checker for Jupyter Notebooks, but note that it simply highlights words not in its dictionary, and does not offer corrections.
If the extension installed properly, you will see this message in the command line:
Now, in the browser, after opening Jupyter, you will see the button labelled "abc" beside the keyboard button, which you can toggle to enable/disable spell check:
The jupyter-contrib library has many other useful modules such as code folding and table of contents.
Run the following in a terminal:
ipython install-nbextension https://bitbucket.org/ipre/calico/downloads/calico-spell-check-1.0.zip
ipython install-nbextension https://bitbucket.org/ipre/calico/downloads/calico-document-tools-1.0.zip
ipython install-nbextension https://bitbucket.org/ipre/calico/downloads/calico-cell-tools-1.0.zip
jupyter nbextension enable calico-spell-check
You can see typos like
Find out more
Afterwards, you need to activate the spell check in the Jupyter Notebook:
%%javascript
IPython.notebook.config.update({
"load_extensions": {"calico-spell-check":true,
"calico-document-tools":true,
"calico-cell-tools":true
}
})
The spellchecker and some other extensions from jupyter_contrib_nbextensions is incompatible with the ipython version 5.8.0. and later. (Found that it works in some cases for the version 5.0.0 [refer issue page of the same]. I'm not aware of its compatibility for the ipython versions between 5.0.0. to 5.8.0., please do comment if anyone knows).
The calico's nbextension 'spellchecker' available at https://bitbucket.org/ipre/calico/downloads/calico-spell-check-1.0.zip is an outdated version [dated 2015]. But calico had updated their nbextensions and made avaliable at the github repository [latest dated 2018]. It works fine for the ipython version 5.8.0.
Installation
git clone https://github.com/Calysto/notebook-extensions.git
cd notebook-extensions
jupyter nbextension install calysto --user
jupyter nbextension enable calysto/spell-check/main
Check its status:
jupyter nbextension list
When you now open or reload a notebook, there would be a new button visible with a check mark icon next to the button to open the command palette. You may click on it to check the spelling mistakes in the markdown cell.
I'm experienced with IPython Notebook but just upgraded to Jupyter 4 with nbpresent, and I want to use reveal.js for slideshows.
How can I incorporate reveal.js into my notebook slideshow?
The most common way to do this is using nbconvert:
jupyter nbconvert presentation.ipynb --to slides --post serve
For more information, see nbconvert documentation.
You would only use RISE if you need to execute commands on the kernel during the presentation.
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.