claratrue

clarathomas.site

An academic site built with Quarto. Minimal, near-monochrome, five pages.

Files you’ll actually touch

File What it is
index.qmd Home — name, affiliations, short intro.
research.qmd Research — projects, publications, presentations, funding.
about.qmd About — background, community work, tools.
cv.qmd CV — full CV, styled to match.
fieldnotes/index.qmd Fieldnotes — the blog listing page.
fieldnotes/posts/ One folder per post.
theme.scss Colors, fonts, spacing. Palette is at the top.
_quarto.yml Site config — nav links, title, description, favicon.
references.bib Optional BibTeX, if you switch publications to auto-citations.
cv.pdf The printable CV, generated from cv.qmd — see below.

Everything in _site/ is generated — never edit it, never commit it.

First-time setup

  1. Install Quarto: https://quarto.org/docs/get-started/ (It’s a normal installer. No R or Python needed unless you want code chunks.)

  2. Open Terminal and cd into this folder — the one containing this README and _quarto.yml. Every Quarto command below runs from here.

    cd ~/Downloads/site      # or wherever you put it

    Shortcut: type cd (with a space), then drag the folder from Finder into the Terminal window — it fills in the path for you.

    To confirm you’re in the right place, ls should show _quarto.yml, index.qmd, cv.qmd, and theme.scss. If it doesn’t, you’re one level too high or too low.

  3. Start the live preview:

    quarto preview

    A browser opens at localhost:4000 and live-reloads as you save. This is the way to work — leave it running while you edit. Ctrl-C stops it.

  4. When you’re done: quarto render writes the finished site to _site/.

Filling in the placeholders

Everything needing your input is marked PLACEHOLDER or in [BRACKETS]. Search the file for those two strings and you’ll find all of them.

Keeping cv.pdf current

cv.pdf is the printable version, and it’s generated from cv.qmd — so you update the CV in one place, not two. After editing:

  1. quarto render
  2. Open _site/cv.html in your browser
  3. Cmd-P → Save as PDF, margins Default, uncheck headers/footers
  4. Save over cv.pdf in this folder

The print stylesheet handles the rest — the back-link and footer are hidden, type sizes drop, and entries won’t split across pages. A fresh cv.pdf is already included.

Switching publications to BibTeX

When the hand-written list gets tedious:

  1. Export your library to references.bib.
  2. Download a style (e.g. Ecology) from https://www.zotero.org/styles into this folder and uncomment the csl: line in _quarto.yml.
  3. Replace the publications section with ::: {#refs} and add nocite: |\n @* to the frontmatter to list everything.

Writing a Fieldnotes post

One folder per post, each containing an index.qmd:

fieldnotes/posts/2026-09-04-my-post-title/index.qmd

The folder name is only for your own organisation — the date shown on the site comes from the frontmatter. Start each post with:

---
title: "Your title here"
description: "One sentence — this is what shows on the listing page."
date: 2026-09-04
---

Then write in markdown below it. Posts appear on the Fieldnotes page automatically, newest first — there’s no index to update.

An example post is already in there (2026-08-11-dawn-chorus/). Delete it once you’ve written a real one.

Figures from code. Because this is Quarto, a post can run R or Python and embed the result:

```{r}
#| label: fig-detections
#| fig-cap: "Detections per hour at one site."
#| echo: false

library(ggplot2)
# your code here
```

Set echo: true to show the code alongside the figure. Note this requires R (or Python) installed locally — plain markdown posts don’t.

Changing the navigation

The five tabs are defined in _quarto.yml under navbar: right:. Each is two lines:

      - href: research.qmd
        text: Research

Reorder, rename, or delete entries there. To add a page, create newpage.qmd alongside the others and add an entry pointing at it.

Publishing

GitHub Pages — free, and the usual choice for an academic site.

quarto publish gh-pages

That’s the whole deployment. It builds, pushes to a gh-pages branch, and gives you a username.github.io/repo URL. Re-run it any time you want to update.

Netlify — if you’d rather drag-and-drop or auto-deploy from git:

quarto publish netlify

Custom domain — buy the domain anywhere (Namecheap, Cloudflare, ~$12/yr), then point it at your host. On GitHub Pages that’s a CNAME record plus the domain entered in the repo’s Pages settings. HTTPS is automatic and free.

Notes