Jupyter Notebook Appendix in LaTeX
I wrote another post where I promote
the use of SageTeX
to generate some plots and expressions in a Mathematics documents.
In particular, I promote the use of separate Jupyter notebooks to the .tex files
to work on the SageMath code, then directly import the created objects (expressions or
plots) into the main document via SageTeX.
Following this, a natural question is how to include the code from the notebook in the main document for completeness. Furthermore, one might also like to create references to sections of the code from the main document to give optional details to how certain things were created.
For example:
"[...]. The computer algebra code verifying the above calculations can be found in section A.1.4."
... in a proof where we can now skip more calculation details. Let's face it, details often get skipped anyway, and often for good reason since they break the flow of reading with unimportant details. But at least this way the details are still available and reproducible from the reader's SageMath installation.
Another example:
"[...]. The code producing this plot can be found in section A.2.2"
The code generating a plot used for illustrative purpose is unimportant to most people, but also may be to the occasional careful reader.
I will suggest two approaches. The first is quicker and easier, but at the cost of:
- possibly inconsistent typesetting with the rest of the document, i.e.
- margins
- fonts
- no ability to reference sections of code from the main document as in the examples above
The second approach is more fiddly, but without the above drawbacks.
Both these approaches make use of the Jupyter nbconvert tool.
Jupyter nbconvert tool
The key tool here is a Jupyter module for converting a notebook to other things, such
as Python scripts, HTML files, or ... LaTeX files for us.
You almost certainly have Jupyter as part of the SageMath installation, but try:
jupyter nbconvert --help, which should give you output something like this:
$ jupyter nbconvert --help
This application is used to convert notebook files (*.ipynb)
to various other formats.
WARNING: THE COMMANDLINE INTERFACE MAY CHANGE IN FUTURE RELEASES.
Options
=======
...
If not, then install it.
You can scroll down the options given to you in the output to the above command, which you may have to do if this post gets out of date and the later instructions don't work (note the warning in the above output).
The section of the help we are interested is:
--to=<Unicode>
The export format to be used, either one of the built-in formats
['asciidoc', 'custom', 'html', 'latex', 'markdown', 'notebook', 'pdf', 'python', 'qtpdf', 'qtpng', 'rst', 'script', 'slides', 'webpdf']
or a dotted object name that represents the import path for an
``Exporter`` class
Default: ''
Equivalent to: [--NbConvertApp.export_format]
So then, to create say a PDF from a jupyter notebook file.ipynb, you would run the command
jupyter nbconvert --to=pdf file.ipynb.
Simple Solution
As we just saw, nbconvert can convert a Jupyter notebook to a PDF directly, so we can just do that:
jupyter nbconvert --to=pdf <notebookfilename>
Then we can just another tool to take the PDF for our main LaTeX document, and add the
Jupyter notebook to the end.
For instance, GNU/Linux distros will likely have the pdfunite utility installable via
some package. So then to create a file final.pdf, we run the following command:
pdfunite <mainpdf> <notebookpdf> final.pdf
On Windows, a friend of mine has used something called "pdfsam" to merge PDF documents.
I have never used this myself (you can also install pdfunite in
WSL2).
Check out the output, see if you are satisfied, otherwise try out the next solution.
More Manual Mode
You may have noticed the latex output option mentioned in the help page for
nbconvert above. This produces a .tex file, complete with own preamble,
which you can compile to a PDF
(I presume this is what happens automatically when converting directly to PDF).
This LaTeX output can be surgically adapted into your main document.
The difficulty is likely dealing with the preamble in conjunction with your
existing one.
I have attempted using the solutions in
overleaf's post
on packages subfiles and standalone with no luck in my particular project.
However yours may be different and it could be worth trying those to avoid the
hackery that is to come.
Extracting the Main Content
This is the easy part, just copy-and-paste the content within the document
environment (between \begin{document} and \end{document}) into your LaTeX project,
in the main file, or another that you \input or \import.
Or...
If you're anything like me and value automation, this is how you would go about it.
Say you have a Jupyter notebook calculations.ipynb which you want to include into
a tex document article.tex.
Add the following in the relevant location in article.tex:
% requires \usepackage{import} in preamle
\begingroup % avoid conflicts from the effects of notebook_tex/newcommands.tex
\import{./notebook_tex/}{newcommands}
\import{./notebook_tex/}{calculations}
\endgroup
% maybe subimport if this file is being imported somewhere else
Next we create a Makefile rule to generate (the currently non-existent) LaTeX file
calculations.tex in the notebook_tex directory, to content the main contents
of calculations.tex converted to tex.
# in Makefile
notebook_tex/calculations.tex: calculations.ipynb
# Create full latex file
jupyter nbconvert --to latex $^ -output-dir=notebook_tex
# delete all lines other than main content
sed \
-e '/\\documentclass/,/\\maketitle/d' \
-e '/\\end{document}/d' \
# optional: demote (sub)sections to use sections
# for different notebooks
# -e 's;\\subsection;\\subsubsection;' \
# -e 's;\\section;\\subsection;' \
-i $@
The above requires the make and sed utilities (gnu implementations)
on top of nbconvert.
Now you can run make notebook_tex/calculations.tex to generate the required file.
Alternatively, if you use the -use-make option with latexmk then this will
automatically be called for you.
TODO DOUBLE CHECK THIS IS TRUE.
Note, this will not compile because we are missing the notebook_tex/newcommands.tex file
imported in article.tex.
This will be created in the next subsection.
Newcommands
Unlike \usepackage commands which need to be in the preamble,
many lines in the generated preamble, such as \newcommands
can be put in the main document, and scoped, to avoid potential conflicts.
So we can copy-paste such lines generated by nbconvert into the file
notebook_tex/newcommands.tex.
This could potentially change between releases, but for me, the contents of this file
has been copied to the appendix at the bottom of this post for reference, and potential
convenience.
Dealing with Required Packages
Obviously, we deleted the whole preamble of the generated tex file in the previous subsection. The reason for not even programmatically putting it aside is that there is almost certainly some conflict with your current preamble. Again, I recommend trying the solutions in overleaf's post to try and circumvent this whole issue. But, what worked for me, was to
- copy-paste all the
\usepackage...lines in the generated preamble tonotebook-preamble.tex - add
\input{notebook-preamble}to your main preamble - iteratively attempt compilations of your document, removing/comment seamingly unneeded packages in
notebook-preamble.texuntil there are no errors
For the last (main) step, Git is your friend. This is a great usecase for branching and commit squashing.
Luckily, the preamble generated by nbconvert does have comments hinting at whether
you likely need the package.
For reference, this is the cut-down notebook-preamble.tex file I ended up with:
\usepackage[breakable]{tcolorbox}
\usepackage{float}
\usepackage{xcolor} % Allow colors to be defined
\usepackage{enumerate} % Needed for markdown enumerations to work
\usepackage{textcomp} % defines textquotesingle
\usepackage{upquote} % Upright quotes for verbatim code
\usepackage{eurosym} % defines \euro
\usepackage{fancyvrb} % verbatim replacement that allows latex
\usepackage{grffile} % extends the file name processing of package graphics
\usepackage[Export]{adjustbox} % Used to constrain images to a maximum size
\usepackage[normalem]{ulem} % ulem is needed to support strikethroughs (\sout)
% normalem makes italics be italics, not underlines
\usepackage{soul} % strikethrough (\st) support for pandoc >= 3.0.0
\usepackage{mathrsfs}
Referencing the Appendix
Now scroll through the generated notebook_tex/calculations.tex file.
You will see that nbconvert will have added \labels to all the (sub)sections.
You can then \ref these labels from the main tex file to link to sections of the notebook
appendix as in the examples suggested in the introduction.
Appendix: Dangers of the Manual Approach
This post is to inspire and comes with no guarantees to the reader that these exact steps
will work when they try (especially further in the future).
The project where I did all this has a good chance of not
compiling correctly if I were to update all my software in a few years.
This could be avoided by being able to reproduce the environment used to build the project.
Solutions in this case would include conda environment files with version numbers
specified, or maybe Docker containers.
I may write in the future on the practicalities of Linux containers and devcontainers
specifically in a later post, so consider taking a look back to the
blog page in the future!
Appendix: Notebook Setup Commands
As of the time of writing (2024) these were the lines of the preamble in the LaTeX file
generated by nbconvert (version 7.12.0) which did not need to be in the preamble...
But could be move to the main document.
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\adjustboxset{max size={0.9\linewidth}{0.9\paperheight}}
\def\PYZsq{\textquotesingle}% Upright quotes in Pygmentized code
% Colors for the hyperref package
\definecolor{urlcolor}{rgb}{0,.145,.698}
\definecolor{linkcolor}{rgb}{.71,0.21,0.01}
\definecolor{citecolor}{rgb}{.12,.54,.11}
% ANSI colors
\definecolor{ansi-black}{HTML}{3E424D}
\definecolor{ansi-black-intense}{HTML}{282C36}
\definecolor{ansi-red}{HTML}{E75C58}
\definecolor{ansi-red-intense}{HTML}{B22B31}
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\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
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% Define a nice break command that doesn't care if a line doesn't already
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% Math Jax compatibility definitions
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\def\PYGZdl{\discretionary{}{\Wrappedafterbreak\char`\$}{\char`\$}}%
\def\PYGZhy{\discretionary{\char`\-}{\Wrappedafterbreak}{\char`\-}}%
\def\PYGZsq{\discretionary{}{\Wrappedafterbreak\textquotesingle}{\textquotesingle}}%
\def\PYGZdq{\discretionary{}{\Wrappedafterbreak\char`\"}{\char`\"}}%
\def\PYGZti{\discretionary{\char`\~}{\Wrappedafterbreak}{\char`\~}}%
}
% Some characters . , ; ? ! / are not pygmentized.
% This macro makes them "active" and they will insert potential linebreaks
\newcommand*\Wrappedbreaksatpunct {%
\lccode`\~`\.\lowercase{\def~}{\discretionary{\hbox{\char`\.}}{\Wrappedafterbreak}{\hbox{\char`\.}}}%
\lccode`\~`\,\lowercase{\def~}{\discretionary{\hbox{\char`\,}}{\Wrappedafterbreak}{\hbox{\char`\,}}}%
\lccode`\~`\;\lowercase{\def~}{\discretionary{\hbox{\char`\;}}{\Wrappedafterbreak}{\hbox{\char`\;}}}%
\lccode`\~`\:\lowercase{\def~}{\discretionary{\hbox{\char`\:}}{\Wrappedafterbreak}{\hbox{\char`\:}}}%
\lccode`\~`\?\lowercase{\def~}{\discretionary{\hbox{\char`\?}}{\Wrappedafterbreak}{\hbox{\char`\?}}}%
\lccode`\~`\!\lowercase{\def~}{\discretionary{\hbox{\char`\!}}{\Wrappedafterbreak}{\hbox{\char`\!}}}%
\lccode`\~`\/\lowercase{\def~}{\discretionary{\hbox{\char`\/}}{\Wrappedafterbreak}{\hbox{\char`\/}}}%
\catcode`\.\active
\catcode`\,\active
\catcode`\;\active
\catcode`\:\active
\catcode`\?\active
\catcode`\!\active
\catcode`\/\active
\lccode`\~`\~
}
\makeatother
\let\OriginalVerbatim=\Verbatim
\makeatletter
\renewcommand{\Verbatim}[1][1]{%
%\parskip\z@skip
\sbox\Wrappedcontinuationbox {\Wrappedcontinuationsymbol}%
\sbox\Wrappedvisiblespacebox {\FV@SetupFont\Wrappedvisiblespace}%
\def\FancyVerbFormatLine ##1{\hsize\linewidth
\vtop{\raggedright\hyphenpenalty\z@\exhyphenpenalty\z@
\doublehyphendemerits\z@\finalhyphendemerits\z@
\strut ##1\strut}%
}%
% If the linebreak is at a space, the latter will be displayed as visible
% space at end of first line, and a continuation symbol starts next line.
% Stretch/shrink are however usually zero for typewriter font.
\def\FV@Space {%
\nobreak\hskip\z@ plus\fontdimen3\font minus\fontdimen4\font
\discretionary{\copy\Wrappedvisiblespacebox}{\Wrappedafterbreak}
{\kern\fontdimen2\font}%
}%
% Allow breaks at special characters using \PYG... macros.
\Wrappedbreaksatspecials
% Breaks at punctuation characters . , ; ? ! and / need catcode=\active
\OriginalVerbatim[#1,codes*=\Wrappedbreaksatpunct]%
}
\makeatother
% Exact colors from NB
\definecolor{incolor}{HTML}{303F9F}
\definecolor{outcolor}{HTML}{D84315}
\definecolor{cellborder}{HTML}{CFCFCF}
\definecolor{cellbackground}{HTML}{F7F7F7}
% prompt
\makeatletter
\newcommand{\boxspacing}{\kern\kvtcb@left@rule\kern\kvtcb@boxsep}
\makeatother
\newcommand{\prompt}[4]{
{\ttfamily\llap{{\color{#2}[#3]:\hspace{3pt}#4}}\vspace{-\baselineskip}}
}
% Prevent overflowing lines due to hard-to-break entities
\sloppy
% Setup hyperref package
\hypersetup{
breaklinks=true, % so long urls are correctly broken across lines
colorlinks=true,
urlcolor=urlcolor,
linkcolor=linkcolor,
citecolor=citecolor,
}