LaTeX Notebook Functionality

This package contains tools for running a LaTeX notebook with embedded python code. One can then, for instance, keep an electronic lab notebook where the plots and data are generated and processed in place, immediately from the raw data. (The author of the project has kept an electronic notebook for several years in this way with great success.)

Please note that this is a very different “notebook” than the one supplied by jupyter notebooks (which pyspecdata also supports). In this section, we aim to provide a laboratory notebook with publication-ready figures and a complete path from raw data to those figures.

  • With minimal effort, it is possible to design a notebook that works in a similar fashion with HTML, Markdown, etc. (The main author just has no interest in doing this, since the PDF output looks very nice.)

  • It’s highly recommended to keep a notebook as a series of different files that have no preamble or ending (i.e. only the part that goes inside the document environment), which can then be collected into a gigantic master document with the \input{...} command, or compiled individually (e.g. while you are actually in the lab working on a particular section).

  • It’s also highly recommended to store notes organized by project, which can then be cross-referenced in a separate chronological document (or vice versa) with the \\ref{...} command.

Setting up the notebook

Install the Latex Packages

In order to be able to build a latex notebook where \begin{python}...\end{python} environments are replaced with the code output, we first need some helper latex style files.

To make latex files accessible anywhere on your computer, you place them inside a “texmf” directory tree, and then register them with your latex compiler.

  • Note that, similar to a python package, there are strange requirements on the structure and directory names of a texmf directory tree. You can’t just rename the directories as you would like.

The pyspecdata repo itself now has a subdirectory called texmf that is a ready-to-go texmf tree for this purpose.

How do I register the texmf directory?

  • Under Windows, you can add the texmf tree graphically by opening “miktex console” from the start menu.

  • If the menu options are greyed out, you need to activate administrator mode.

  • Inside miktex, go to “settings” → “directories” and click the plus symbol → select the texmf directory inside your pyspecdata repository ([DIRECTORY ONE UP FROM PYSPECDATA FOLDER]/pyspecdata/texmf) So that the “Folder” box says “texmf” → click select folder. If this works for you, you don’t need to do the next bullet

  • In general (windows or otherwise) you should be able to use the command initexmf --register-root=[DIRECTORY ONE UP FROM PYSPECDATA FOLDER]/pyspecdata/texmf

Once you’ve done this, the shell command kpsewhich mypython.sty should return a result (if you have miktex installed on windows, this should work from either the git bash prompt or the dos or powershell prompt).

Use the pySpecData latex wrapper

The pyspecdata package proves the commands pdflatex_notebook_wrapper and update_notebook_pythonscripts, described below under “Running the notebook.”

It also provies the command pdflatex_notebook_view_wrapper, which is used to determine the output PDF and call an appropriate viewer.

If pyspecdata is installed, and the texmf directory is registered with your latex compiler (e.g. miktex), you should be able to clone and compile the example notebooks repo from the franck lab

You can compile the tex file by typing: pdflatex_notebook_wrapper -synctex=-1 notebook.tex inside the root directory of the notebook_example repo. To get the results of the code to appear, you need to run this command twice the first time.

It might take a few passes, but you should able to run this command without have latex complain about missing packages! * If this happens in miktex, you need to

  • go to miktex settings → general, and set it to automatically download new pages. Be sure to click “for all users”!

  • delete notebook.aux (rm notebook.aux) and the scripts directory, and run again

  • The first time you do this, miktex might need to install many packages, so that you need to keep hitting enter and then reattempting.

  • It’s assumed that your latex files are stored in a “notebook directory.” In some cases, during the first run, an explanatory error will appear – just follow the instructions.

Install a PDF viewer that plays nice with latex

On Windows, you will want to install Sumatrapdf (use the installer version, not the portable version) to view your PDFs, since it automatically updates when the PDF is recompiled.

On Linux, Zathura is very nice.

Running the notebook

If you create figures with the figlist_var class, you should simply be able to write a latex file with embedded python environments (\\begin{python} … \\end{python}) replace the pdflatex command with pdflatex_notebook_wrapper when compiling your latex notebook, to drop the code and plots in place. For clarity, the code output is a slightly different color (a dark brown) than the standard text.

A synctex “jump to source” on the resulting portion of the PDF will send you to the tex output, which is stored in scripts/*.tex, where * is a sequential number corresponding to the script, and the python source used to generate it is stored in scripts/*.py.

Each snippet of unique code is run only once, ever making the notebook fast and efficient. For now, an important drawback to this is that if you change modules or libraries called by the script, the resulting PDF output will not change. To get around this, a command is provided that forces scripts to be re-run. You use it like this: update_notebook_pythonscripts flush 10 21 – which will flush script numbers 10 to 21. Manually deleting the .py files inside the scripts directory will not have the same effect.

Todo

To limit downtime for the PDF, pdflatex_notebook_wrapper currently copies the final pdf to a truncated filename (assuming that the filename consists of words separated by underscores, it drops the last word).

It would be much better to copy the source PDF into a subdirectory, build it there, and then copy the pdf back into the main directory. This would entail changing the paths of the various files

\RequirePackage[log]{snapshot} might be helpful to log files here.

probably we will just want to add commands to renewcommand for input as well as the graphicx root.

How it works

  • Note that the code works a bit differently than in previous versions – while it previously required LaTeX to be run with shell-escape enabled, pdflatex_notebook_wrapper doesn’t require this.

  • pdflatex_notebook_wrapper just calls pdflatex followed by update_notebook_pythonscripts

  • To compile, use pdflatex_notebook_wrapper --xelatex

The file mypython.sty looks for the python environment, it pulls the relevant code, outputs it to scripts/*.py and then writes a command to the .aux file that tells LaTeX where to find the scripts/*.tex output. The scripts/*.tex output is only updated once update_notebook_pythonscripts (without arguments) is run.

update_notebook_pythonscripts runs through the various scripts/*.py files, checks and checks whether or not they have been previously cached (under the same or a different script number). If the python code is in the cache, it just pulls the cached output. If not, it runs the file, and stores the result in the cache.