Bibliography

Website: https://lennartwittkuhn.com/bibliography/

About

This repository contains my entire bibliography in a .bib file (here) and several .sty files (here) that I use to customize my LaTeX manuscripts. The bibliography mostly spans publications in cognitive and computational neuroscience, psychology and statistics.

A table of all references in the bibliography.bib file can be reviewed at https://lennartwittkuhn.com/bibliography/ (sorted by last name of first author, year of publication and journal name).

Installation

datalad install --recursive git@github.com:lnnrtwttkhn/bibliography.git

Requirements

Managing the .bib and .sty files

The software below is not a strict requirement but merely a list of tools I use to manage my bibliography. This is just to help the interested reader with the software choice and acknowledge the tools that make this bibliography management possible.

• A text editor (I currently use Atom version 1.60.0 on macOS)
• BibDesk (I currently use BibDesk version 1.8.13 on macOS)

Run Python code

$ python3 --version
Python 3.8.6

To run the Python code in the /code directory, please install the required packages in requirements.txt using pip install -r requirements.txt.

Create environment

mkvirtualenv -p $(which python3) -r requirements.txt bibliography

Usage

Add repo as a submodule

• Add this repo as a submodule using git submodule add https://github.com/lnnrtwttkhn/bibliography
• Update the submodule using git submodule foreach git pull origin master
• To only use the bibliography.tex file, add \bibliography{bibliography/code/bibliography.bib} to your LaTeX document

Note: To use the bibliography as a submodule in git via Overleaf requires the repo to be publicly available. A workaround is to provide the .bib-file as a direct download from a website that synchronized the repo contents (e.g., Dropbox or Seafile). Read the next section for further instructions.

Add /code folder contents as a direct download in Overleaf

If you can't or don't want to add the repo as a submodule to your manuscript repo, you can also sync the files with a cloud storage system (like Dropbox or Seafile) and provide it as a direct download in Overleaf. Here is how I do it:

• I sync the /code directory with a cloud storage provider (I use Seafile)
• In Seafile, I can create a direct download link for a specific file (e.g., the bibliography.bib file)
• In Overleaf, I can select Upload and add files From External URL
• Here, I paste the direct download link as the URL to fetch the file from and set the File Name in this Project to be the same link in the repo

Contributing

If you have any suggestions for improvement, please contact Lennart Wittkuhn or create a new issue on the issue board.

Maintainer

• Lennart Wittkuhn, Max Planck Institute for Human Development, Berlin, Germany

License

This project is licensed under the MIT License. Please see the LICENSE.md file for details.

References and acknowledgements

The following links have helped me to create my own bibliography repo (thank you, internet! 🙏):

• How to manage a bibliography like the Context Lab at Dartmouth College, USA
• How to cite an article from arXiv using bibtex
• How to have DOI hyperlinks in the bibliography
• How to make sure that these hyperlinks can deal with DOIs with special characters
• How to check for common errors and other mistakes before using software-generated bibliographic entries
• How to remove the http://dx.doi.org string from the doi field in BibTeX files
• How to use glossary entries from a separate file
• How to update git submodule to the latest commit on the origin
• How to place preamble packages in a different .tex file
• How to stop apacite from displaying the month in references
• How to integrate BibDesk with Dropbox - a nice tutorial by Matthew J. Sigal
• How to get rid of Not defining \perthousand and Not defining \micro warnings
• How to cite a reference in a figure caption in LaTeX
• How to not mess up your bibliographies with BibTex - guide by Claus Wilke
• How to set up BibDesk with a version control system - blog post by Terrel Russel
• How to use a bibliography in LaTeX with version control - discussion on Stackexchange
• How to keep a master .bib-file with version control - tutorial by Andrius Vylikis
• BibTex Useful Hints
• How to clear the Overleaf cache if you have trouble with references
• How to cite a range of papers using numeric keys so that /cite{a, b, c} becomes [1-3]
• How does one indicate the corresponding author when using the authblk package?
• How to easily convert a doi into a bib entry using doi2bib.org
• How to reset line numbers after every chapter in LaTeX
• How to show differences in lines of LaTex with git
• How to make your git + LaTeX workflow more efficient
• "Academics should ditch Elsevier and Mendeley — here’s how" - article by Steve Chignell on medium.com
• "Why you should not use Mendeley as a reference manager" - article on medium.com
• Pandas dataframe to HTML using pd.to_html()
• The DT R package
• How to remove curly brackets in R
• How to convert URL character strings into hyperlinks in DT tables in R
• Travis CI documentation: Building an R Project
• Travid CI documentation: Building a Python project
• Travis CI Issue discussion: Change default version to Python 3.6
• Documentation on the R DESCRIPTION file
• How to render RMarkdown from the command line
• "Adding CI to RMarkdown documents" - Tutorial by Simon Goring
• StackOverflow discussion: "Installing both Python and R for a Travis build"
• Migrating from BibDesk to Zotero
• Blog post on "BibTeX-friendly PDF management with Zotero" by Richard Zach
• WikiBooks entry on hyphenation in LaTeX
• "How to add global hyphenation rules?"- discussion on StackExchange
• "GitHub issue with cross-referencing DT::datatable"
• "Stack Overflow discussion about cross-referencing DT::datatable"
• "Blog post about separating keywords in Biblatex"
• "GitHub issue discussing keywords in Biblatex and biber"
• "How to not mess up your bibliographies with Bibtex" - blogpost by Claus O. Wilke