Zotero

Even if you have no interest in using LaTeX, Zotero is a must for managing your PDF database as well as bibliographic data. Zotero is an open-source reference management software which does all the work for you of saving bibliography data, pdfs, notes, or other files. Rather than ending up with an dizzying array of folders on your hard drive (or desktop!) crammed with documents, Zotero lets you easily create and destroy project folders without creating multiple versions of each paper (unless you want that). Additionally, Zotero will download and organize the associated pdf with the reference, all with the click of a single button in your web browser. That way, building your reference database is the passive result of sorting through papers that interest you online. Most importantly, this software allows you to generate bibliographies from any selected project folders or files, and is compatible with most word processors. I’ve given detailed instructions below on how to install Zotero. (Cost: 3 minute installation, with another 10 minutes to get it linked to your LaTeX editor. Installation instructions can be found here.)

LaTeX

Writing formal symbols is by no means the only reason to use LaTeX which is an extremely powerful and flexible typesetting tool, allowing you to separate composition from formatting. Additionally, by writing in LaTeX, you can take advantage of the extremely powerful tools included in text editors such as NeoVim and VSCodium (see below). In order to write in LaTeX, you will have to install an text editor. Although it is common to use TexShop or TexMaker, or else Overleaf leaving you stuck working in the browser, I recommend starting with VSCodium which will make writing in LaTeX and Markdown a lot easier. Alternatively, see the section on NeoVim below. (Cost: Learning to write in LaTeX is about as hard as learning to barely speak a foreign language while travelling. You will need to learn some vocabulary and new ways of doing things. I provide templates in the repositories linked below to make it easy to get started. If you like the way I have things formatted, then it will not take much to learn enough to write papers using these templates. Modifying the templates is more advanced, and will likely require some troubleshooting online.)

VSCodium

An easy way to get going without spending too much time in the weeds is to use an IDE like VSCodium to write LaTeX (this is the private, community maintained version of Microsoft’s VS Code). Using VSCodium is a huge step up from TexShop with not much more work required to get it configured to your needs. In order to streamline the process of configuring this tool, I have provided a number of resources with detailed installation instructions. (Cost: If you follow the instructions, it shouldn’t take more than ten minutes to install and configure VSCodium for writing LaTeX, Markdown, and the like. From there it may take a little getting used to, learning all of its features, but hopefully pretty intuitive and much nicer to use than some of the more austere editors.)

NeoVim

Although an IDE like VSCodium or Sublime is much nicer to use than TexShop with not much more work required to get it configured to your needs, NeoVim (henceforth ‘Vim’) takes this a lot further, providing a lightweight and highly customization stock text editor which can be configured to your exact needs without including extra bells and whistles. As a result, Vim is much faster than Sublime, or some of the other IDEs like VSCodium. I have provided my configuration files on my GitHub repository along with extensive installation instructions so that you can recreate the Vim setup that I have optimized for writing LaTeX and Markdown without going through the difficulty of cobbling together a collections of plugins and settings for yourself. I also explain how to customize the config, tailoring the setup to your needs. You can preview that setup here and some further evangelizing here. (Cost: If you follow my configuration instructions, it should take no more than an afternoon to get Vim installed and configured. It took me a couple of weeks to get comfortable enough using the Vim key-bindings to feel a net increase in productivity. More than just an increase in speed, Vim provides an enjoyable writing and editing experience perhaps comparable to learning to touch type. It eliminates the tedium of constantly having to switch between using the mouse and the keyboard, and provides so many useful tools.)

Git

Git is a powerful version control software which can help you manage your workflow, track changes as you work, leaving yourself or others notes, and backing up a complete history of your project as it progresses. (Cost: The hardest part about Git for a beginner is the install, requiring some use of the terminal. VSCodium makes using Git very easy, allowing you to avoid using the terminal altogether. Otherwise, you can use LazyGit in the terminal, or else inside Vim which I have integrated into my config.)

Markdown

Instead of taking notes in LaTeX, Word, or some other note-taking application, you can recover some of the elegance of LaTeX without any of the trouble by writing in Markdown. The syntax for Markdown is designed to be as simple as possible while still producing a good looking document which you can then convert via Pandoc into other formats. (Cost: 10 minutes to install and another 10 minutes to learn how to use.)

Annotation

Instead of hand typing quotes, or cutting and pasting quotes and notes from pdfs files, pdfannots is a convenient utility for exporting all highlighted text and notes from a pdf to markdown, organised by page number. I have included a key-binding in my Vim config for using pdfannots in conjunction with vimtex which looks up and export all highlights and notes from the pdf corresponding to the citation-key that your cursor is hovering over, creating a new markdown file in an annotations folder in your project directory. (Cost: 1 second, assuming that you have already installed my Vim config and that your cursor is over a citation-key in a LaTeX document which includes a path to your Zotero.bib file. Simply enter the key-binding specified here in order to export all highlights and notes included in that pdf.)

Pandoc

Pandoc is a convenient utility for converting between different text formats. I have included key-bindings for using Pandoc in my Vim config which I demonstrate here. (Cost: 10 minutes to install, 2 minutes to use inside my Vim config, and 10 minutes to learn how to use in the terminal.)