quentinmale.github.io

Personal academic website, built with Jekyll and the Just the Docs theme (loaded via remote_theme, so GitHub Pages builds it automatically — no GitHub Actions needed).

Structure

_config.yml            Site settings, theme config, nav/search options
Gemfile                 Ruby gems needed to preview the site locally

index.md                Home page (uses layout: home)
appointments.md         Appointments page
publications.md         Publications page
codes.md                Codes page
data.md                 "Data" parent page (has_children: true)
data/
  dns-database.md       Child page
  chemistry-database.md Child page, links to the mechanism files in assets/data/
teaching.md             Teaching page
student-projects.md     Student projects page
open-positions.md       Open positions page
gallery.md              Gallery page
acknowledgments.md      Acknowledgments page

research/
  index.md              "Research" parent page (top-level nav item)
  machine-learning.md    Child page (single topic, no further nesting)
  pac.md                 Child page, itself has children (has_children: true)
  pac/
    thermoacoustic-stabilization.md   Grandchild page
    combustion-enhancement.md         Grandchild page
    nox-chemistry.md                  Grandchild page
  hydrogen-combustion.md
  hydrogen-enrichment.md              Child page, has children
  hydrogen-enrichment/
    sequential-combustors.md
    prechamber-ignition-engines.md
  turbulent-jet-ignition.md           Child page, has children
  turbulent-jet-ignition/
    general-purpose.md
    prechamber-ignition-engines.md

assets/
  data/*.cti *.f90         Chemical mechanism files linked from data.md
  images/home/             Homepage images
  images/logos/            Funding-agency logos
  images/research/         Figures used across research pages
  images/codes/             Figures used in codes.md / research pages
  images/gallery/          Gallery images and video

The left sidebar is generated automatically by Just the Docs from each page's front matter — there's no manually maintained nav file.

How the sidebar hierarchy works

Every content page starts with a YAML front matter block. The three keys that control where a page sits in the sidebar are:

• title — the text shown in the sidebar and at the top of the page.
• parent — the exact title of the page one level up. Omit this for a top-level page (e.g. Research, Publications).
• grand_parent — only needed for a third-level (grandchild) page. Must match the title of the top-level page, while parent matches the immediate parent's title.
• has_children: true — set this on any page that itself has children, so Just the Docs turns it into an expandable section.
• nav_order — an integer controlling the order pages appear in among their siblings.
• permalink — the clean URL for the page, e.g. /research/pac/nox-chemistry/.

Example — a grandchild page:

---
title: Nitrogen oxides chemistry
parent: Plasma-Assisted Combustion (PAC)
grand_parent: Research
nav_order: 3
permalink: /research/pac/nox-chemistry/
---

Every content page (except index.md, which sets layout: home) inherits layout: default automatically from the defaults: block at the bottom of _config.yml — you don't need to add layout: yourself.

Adding a new page

A new top-level section (like "Research" or "Publications"):

1. Create my-section.md in the repo root.
2. Add front matter with title, nav_order, and permalink: /my-section/.
3. Write the content below the front matter in normal Markdown.

A new topic under Research (a child page):

1. Create research/my-topic.md.
2. Front matter: title, parent: Research, nav_order, permalink: /research/my-topic/.
3. If this topic will itself have subtopics, also add has_children: true, and list them in the body as a bullet list of links (see research/pac.md for an example).

A new subtopic (a grandchild page, e.g. a new subsection under PAC):

1. Create research/pac/my-subtopic.md (i.e. inside the parent topic's own folder).
2. Front matter: title, parent: Plasma-Assisted Combustion (PAC), grand_parent: Research, nav_order, permalink: /research/pac/my-subtopic/.
3. Add a link to it from research/pac.md's bullet list so it's discoverable from the parent page's body too (the sidebar will pick it up automatically regardless).

Images, PDFs, or other files: drop them in the relevant assets/ subfolder (or create a new one) and reference them with an absolute path, e.g. /assets/images/research/my-figure.png.

Previewing the site locally on macOS

The very first time only:

brew install ruby
echo 'export PATH="/opt/homebrew/opt/ruby/bin:$PATH"' >> ~/.zshrc   # Apple Silicon
# echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.zshrc   # Intel Mac
source ~/.zshrc

cd /path/to/quentinmale.github.io
gem install bundler
bundle install

Every time you want to preview changes:

cd /path/to/quentinmale.github.io
bundle exec jekyll serve --livereload

Then open http://127.0.0.1:4000 in your browser. The page auto-reloads whenever you save a file. Stop the server with Ctrl+C.

If you only change _config.yml, you need to stop and restart the server — livereload doesn't pick up config changes automatically.

You'll see a lot of "Sass @import / darken() deprecated" warnings in the terminal — these come from the theme's own stylesheets and Dart Sass being ahead of them. They're harmless and don't affect the site.

Alternative: Docker (no Ruby install needed)

cd /path/to/quentinmale.github.io
docker run --rm -it -v "$PWD":/srv/jekyll -v "$PWD/vendor/bundle":/usr/local/bundle -p 4000:4000 jekyll/jekyll:latest jekyll serve --livereload

Publishing

Commit and push to main. GitHub Pages rebuilds the site automatically (Settings → Pages should already be set to "Deploy from a branch: main / root" from before — no changes needed there).

Do not commit _site/, .jekyll-cache/, .bundle/, or Gemfile.lock — these are local build artifacts and are already listed in .gitignore.