Use this as a template for writing your paper. It will automatically build a cool HTML that contains all your citations like here.

1. Install pandoc (prerequisite!)
2. Use this repo as template (!= fork)
3. Copy pre-commit into your .git/hooks folder
4. Write your paper (in paper.md)
5. Add citations by adding
   1. the book/article/.. you cite in bibliography.bib
   2. [@citation_handle] in your text
6. Make a git commit. (The pre-commit hook will generate your HTML automatically.)
7. If you want to rename paper.md, rename it's reference in .git/hooks/pre-commit as well
8. If you want to generate your HTML without commiting, execute pandoc --citeproc paper.md -s --shift-heading-level-by=1 -o index.html
9. If you want your paper to be accessible as a website, activate Github Pages by going to Settings -> GitHub Pages and selecting Master as source branch
10. If the links in your table of contents in the generated HTML don't work, check if they start with a number. If they do, remove the numbers and use an ordered list instead.
11. If you want to generate a PDF out of that markdown, ensure you have a pdfEngine installed (e.g. MacTex by brew cask install mactex), then delete your table of contents from the markdown (it will be generated) and execute pandoc --citeproc --toc paper.md -o paper.pdf

Tooling proposals:

• Visual Studio Code
• VSC Extensions
  • Pandoc Citer
  • Markdown All in One
    • Required to auto-generate the table of contents on saving
    • Set the feature "Toc: Ordered List" to true by opening Preferences -> Settings -> Extensions to avoid broken links in table of contents.
  • bibtexLanguage