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 organise 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.)

1. Download and install Zotero together with a plugin for your preferred browser.
   1. If you use Word, you can follow these tutorials to both install and use.
2. Now run a simple test:
   1. Find a paper you would like to download. If you use a VPN provided by your research institution, make sure that it is turned on, and if you use an AdBlocker, make sure that it is not blocking pop-ups for the journal’s website.
   2. Before downloading the paper as you normally would, notice the small Zotero icon in the top-right of your browser. If Zotero has located a single paper, the icon will look like a paper; if it has located multiple, it will look like a folder.
   3. Click the icon and, if need be, select the desired paper. If all goes as it should, a small banner will pop up in the lower right-hand side of the screen that indicates that it has scraped the bib data and downloaded your file, giving you the chance to file the paper in a project folder if you desire. (Alternatively, if you open a project folder in Zotero by clicking on it on the left side of Zotero, then any papers you download will be automatically filed in that project folder.)
   4. Now switch from your browser to Zotero to check if the bib info (with the pdf) showed up. If it did not work, or did not grab the pdf with the bib data, make sure you are appropriately logged on to the journal website and repeat. For instance, if you are unable to download the pdf in the old fashioned way, then Zotero will not be able to download the pdf either. If problems persist, you can look for further answers here. You can also always add the file manually to the bib info by right-clicking the paper in question in Zotero. Some of the journal websites work better than others. For books, Amazon is a good resource for scraping bib data, though of course no pdf will be downloaded.
   5. Once you are able to capture bib data, you can check that the website provided complete and correct information, making any changes that are needed. I don’t typically do this if I trust the source. (PhilPapers is pretty inconsistent, and so I mostly avoid getting bib data from there. For books, Amazon is not half-bad.)
3. Markdown Add-ons
   1. Zotero can be used not only to keep the pdfs associated with each citation organised, but to export the highlights and annotations you make with your preferred pdf viewer as markdown files.
   2. In order to include these features, you will need to download the .xpi file for MdNotes as described here, as well as the .xpi file for ZotFile.
   3. By then opening Zotero, navigating to the Tools –> Add-ons menu, clicking the gear symbol, and selecting ‘Install add-on from file’, you can select the .xpi files that you downloaded in order install these features.
   4. You may then export your notes by: (1) right-clicking on the annotated pdf and selecting Manage Attachments –> Extract Annotations; followed by (2) right-clicking on the extraction that it generates and selecting MdNotes –> Export to Markdown, specifying the project folder you would like to save the notes in.
   5. A preliminary search shows that this process cannot be streamlined any further by running commands in the terminal which might then be integrated into Vim, but nevertheless provides a significant increase in overall efficiency, avoiding the need to cut and paste quotes into a separate document.

LaTeX

Writing formal symbols is by no means the only reason to use LaTeX which is an extremely powerful and customisable 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 (see below), Emacs, VSCode, etc. (Cost: To get going, 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 on my GitHub repository 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.)

1. Download and install the LaTeX distribution for your operating system.
2. Create the ‘texmf’ folder tree in your directory.
   1. For Mac users:
      1. You will first need to locate your main ‘Library’ folder in Finder. Begin by opening a new Finder window. Press cmd+shift+h to go to the home folder, and cmd+j to open an options window. Check ‘show Library folder’.
      2. Then create a folder called ‘texmf’ in your Library if it is not already there, and another folder called ‘bibtex’ inside texmf. Inside bibtex, create folders called ‘bib’ and ‘bst’. Inside bst, place this style file (you can cut and paste the contents into a new file with the same name and extension to be saved in your bst folder if you do not intend to clone the full repository).
      3. Now add this template to Library -> TexShop -> Templates. This template includes the commands \bibliographystyle{Phil_Review} and \bibliography{Zotero} at the end of the document which will look up the file you placed in the bst folder as well as the bibliography you will place in the bib folder in Civ below.
         1. Note: if you are using my NeoVim config, you can find this template by hitting ‘space+T’ followed by ‘p’.
   2. For Windows users:
      1. In C, create a folder called ‘texmf’, and another folder called ‘bibtex’ inside texmf. Inside bibtex, create folders called ‘bib’ and ‘bst’. Inside bst, place this style file which comes from here.
      2. Now add this template to Users -> {user name} -> AppData -> Local -> MikTex -> 2.9 -> TexWorks -> 0.4 -> Templates. This template includes the commands \bibliographystyle{C:/texmf/bibtex/bst/Phil_Review} and \bibliography{C:/texmf/bibtex/bib/Zotero} at the end of the document which will look up the file you placed in the bst folder as well as the bibliography you will place in the bib folder.
      3. If you want to save the bst and bib files elsewhere, you will need to change the path in the template file. Note the forward slashes in place of backslashes. You can also substitute other bst (bibliography style) files for Phil_Review.bst such as this one.
3. You can now integrate Zotero and LaTeX as follows (also see this video):
   1. Download and install Better BibTex by following these instructions, restarting Zotero after completed.
   2. Under ‘Edit’ in the Zotero menu bar, select ‘Preferences’ and open up the ‘Better BibTex’ tab. Under the ‘Citation’ sub-tab, replace the citation key format with this:  auth + year. There are a lot more options for citation key style here (this is just the look up key, not the citation style included in your bibliography). Also check ‘On item change’ at the bottom left.
   3. Now switch to the ‘Automatic Export’ sub-tab and check ‘On Change’. This means that the instant you update your database with a new bib entry, or edit an old bib entry, Zotero will update the .bib files where your database is exported. If your library is extremely large, this could be slow, and so you might want to select the ‘When Idle’ option. But I have no troubles with the ‘On Change’ feature.
   4. Close the Preferences window, returning to the main Zotero window. Right-click the main library folder in the left-most blue column, select ‘Export Library’ (alternatively you can export other project folders, but I like to keep things simple). Under the ‘Format’ dropdown menu, select ‘Better BibTex’. Then check the ‘Keep Updated’ box. Save the file as ‘Zotero’ (the extension will be added automatically) to the bib folder that you previously created.
4. You can now run a test that everything is working.
   1. Open TexShop and create a new file (or create a file from template in TexWorks). In the ‘Templates’ drop-down menu, select PhilArticle. Press cmd+T (or click ‘Typeset’). Save the document in a new folder with the appropriate project name.
      1. Note: If the file does not run, open TexLive Utility in the Tex folder in the Applications folder, and update. Restart everything and try to typeset the file again.
      2. Note: Occasionally, it can also help to click Trash Aux Files in the error console, if the pdf is not generating properly.
   1. Once your file typesets, open Zotero and click on one of the files in your library, and look for the ‘Citation Key’ in the details. If no key is present, or the key data is not of the form [auth][year], you can right-click the file in your library and click ‘Generate BibTex Key’. Once you have the key, you can cite that paper by writing ‘\citet{CITEKEY}’ in the new tex file.
      1. Note: To list multiple sources by the same, or different authors, separate the cite keys with a comma. For other citation styles, refer to the preamble of the PhilArticle template for further commands, e.g., ‘\citep’, etc.
      2. Note: It can also be helpful to customize commands as exemplified in the preamble of the PhilArticle template provided above. I have included a definition of \citepos which is useful for making citation names possessive.
   2. In TexShop, you will need to hit cmd+T, then cmd+shift+b, then cmd+T, and the cmd+T for a final time. You should see both the citation you added in the text as well as the full citation in the references. Why all the command combinations? The first cmd+T will update the .tex file you are working on, adding the citation key. The cmd+shift+b will look up the citation key in your master Zotero.bib file saved in the bib folder. Then another cmd+T will import the citation data, and the final cmd+T will typeset it altogether. Sound clunky? It is, and that’s not the least of it. However, there are much better text editors out there (see below).
      1. Note: Want to check how many words your document has? Open the ‘Macros Editor’ under the ‘Macros’ toolbar in TexShop. Select ‘New Item’ giving it a name like ‘TexCount’ and dragging it from the bottom of the list (left column) up to the top. Then cut and paste this into the content. Many more macros can be found here. (TexWorks does not include a word count macro for some reason.)
5. Now you are ready to tex! If you get stuck, get used to googling things and reading the bottom of the error console. YouTube also has many helpful tutorials. As you figure things out, I highly suggest making notes in the preamble of your template file of the really useful bits. By adding a ‘%’ symbol after the new bit of code you add to the preamble, you can explain what it does so that next time you will remember. Lots of helpful information is also available here including a nice lookup guide.

NeoVim

Although an IDE like VSCode or Sublime is a huge step up from 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 customisable 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 VScode or Atom. 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 optimised 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 customise the config, tailoring the setup to your needs. You can preview that setup here and some further evangelising 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. However, even if you don’t know how to do that stuff, carefully following the tutorials below should get you up and running in a little under an hour. Then it is pretty easy to use. Here is how to use LazyGit in the terminal, or else inside Vim which I have included in my Vim 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 by design as simple as possible, but can still produce a good looking document which you can then convert via Pandoc into other formats. You can find a quick overview here. (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 minutes, 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 (see 3.4 in the LaTeX instructions above), you need only 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.)