LaTeX-Obsidian setup for thesis

This repository provides a custom setup for writing a thesis using LaTeX distribution edited as .tex in a LaTeX editor and Obsidian notes as a literature manager.

LaTeX

LaTeX is a type-setting system. More details at https://www.latex-project.org/. It is widely available. Latex templates can be loaded into different LaTeX editors.

Please fill in both template forms (title file and thesis file) to use auto input where needed. Title file is created separately, and has to be run independently before running the thesis file. A separate title is done to avoid problems with the page count. (It is created normally once and then kept as it is, except for the date. The date is automatically updated to the actual date when the file is re-run.)

Obsidian

Obsidian is a customizable markdown-based editor. For more information visit the official website (https://obsidian.md/)[https://obsidian.md/].

Below is my setup.

Plugins

Custom setup includes community plugins:

• Better Word Count (with disabled standard word count in "Core plugins")
• Editing Toolbar
• File Color
• Regex Find/Replace

CSS

Two additional changes in basic dark theme appearence included in .css file, where --h1-size: changes the size of headings, and --bold-color: is to change the default white bold to a different color for contrast:

body.theme-dark { 
--bold-color: #ffb6c1 !important; 
}


body {
--h1-size: 1.92em;
--h2-size: 1.63em;
--h3-size: 1.45em;
--h4-size: 1.37em;
--h5-size: 1.32em;
--h6-size: 1.32em;
}

Literature template

Update needed! A better way of templating a literature page would be setting up a proper YAML header. The complete Python extraction pipeline must then also be changed, but this is worth a try since if the information is condensed in the YAML header, one could use the DataView plugin for in-Obsidian summaries.

A literature template is one of the most important parts of the literature research pipeline. Template example:

This is a basic template functionality in Obsidian. In a new folder named Templates create a file with the desired template. Then in a new file, use Alt+T to insert the desired template. Done!

1. It is convenient to keep a separate folder with all the literature.
2. It is convenient to have a Title field in the template.
3. DOI should be consistent as a link, e.g. https://doi.org/10.1093/g3journal/jkab361.

Note: internal link is useful if .pdf files are being kept on the local PC. But when copying the internal link, any white spaces have to be replaced with %20.

.bib literature

Literature file .bib is updated when running the python code presented in the Code.py file for collecting DOIs from the Literature folder and writing .bib file. This code is:

1. Iteratively opens and reads every file in the "Literature" folder.
2. Finds a DOI link of the format "http/https", and cleans tail characters \);,. In case other DOI links are present in the file it will catch them all (it is never worse to have them all and use only some).
3. Extracts the DOI suffix.
4. Can write them in .csv if needed.
5. Links to Crossref to extract the full bib citation.
6. Saves as .bib file.

TeX Studio

TeX Studio is a free software for editing and compiling LaTeX files. This software is similar to the basic Overleaf but doesn't require Internet connection. This software allows to use biber backend and apa style for academic writing. You can access this software via the link https://www.texstudio.org/.

Good luck!