uvilla.github.io

Personal academic site for Umberto Villa. Jekyll, hosted on GitHub Pages.

Updating the publication list

The single source of truth is files/uvilla.bib (maintained in JabRef). Everything on the Publications page is generated from it:

files/uvilla.bib  ──scripts/bib2yaml.py──►  _data/publications.yml  ──Liquid──►  publications.html

files/ is published, so the bib is also downloadable at https://uvilla.github.io/files/uvilla.bib.

On GitHub, this is automatic: .github/workflows/pages.yml regenerates _data/publications.yml on every push, before Jekyll runs. Edit the .bib, push, and the publications page updates — nothing else to do.

_data/publications.yml is therefore generated, not committed (it is in .gitignore). Build it locally before serving:

make pubs          # or: python3 scripts/bib2yaml.py
make serve         # runs `make pubs` first

make check parses the bib and reports problems (missing years, missing journal names, articles with no classification, unrecognised topic slugs, entries where "Umberto Villa" is not among the authors) without writing anything.

The script needs only Python 3.8+ — no third-party packages.

What the script does

• de-duplicates entries that share a DOI, an arXiv id, or a title
• normalizes LaTeX accents to Unicode (Cram\'er → Cramér)
• collapses co-author name variants to their most complete spelling (M. A. Anastasio, Mark Anastasio → Mark A Anastasio)
• moves generational suffixes after the family name (Hormuth, David A. II → David A Hormuth II)
• classifies each entry as article / preprint / conference / dataset / software / thesis, and reads its research topics from classification

Topics

Topics come from the non-standard classification field in the .bib — one or more comma-separated slugs:

@article{MyCiteKey2026,
  ...
  classification = {pact, dlirm}
}

Slug	Topic
vi	Virtual imaging studies
pact	Photoacoustic computed tomography
usct	Ultrasound computed tomography
iqa	Image quality assessment
dlirm	Deep learning-based image reconstruction
ipuq	Inverse problems, uncertainty quantification, digital twins
amg	Preconditioners, multigrid and numerical upscaling
cfd	Computational fluid dynamics
health	Data science for public health

This table mirrors TOPICS in scripts/bib2yaml.py, which is the single place to edit. Adding a slug there (and using it in the .bib) is all that is needed — the filter chips, the tags on each entry, and their ordering all come from it.

The order of TOPICS in scripts/bib2yaml.py sets both the order of the filter chips and the order of tags on each entry; edit it there to add or rename a topic.

An article with no classification still appears in the list, but only under the "All" filter — make check reports those, along with any slug that isn't in the table above.

Showing more than journal articles

publications.html currently renders only kind: "article". All other kinds are already in _data/publications.yml; to show conference papers too, change the filter near the top of the file:

{% assign articles = site.data.publications.entries | where: "kind", "article" %}

Citing papers elsewhere on the site

Reference lists on the Research page come from the same data, by cite key:

{% include pub_refs.html keys="LiVillaLiEtAl24, ZhouVillaAnastasio23" %}

An unknown key renders an HTML comment rather than a broken citation, so a renamed key shows up as a gap.

Deployment

.github/workflows/pages.yml replaces GitHub's built-in pages-build-deployment pipeline, so that the bib can be turned into _data/publications.yml before Jekyll runs:

push  ─►  bib2yaml.py  ─►  jekyll-build-pages  ─►  deploy-pages

One-time setup: Settings → Pages → Build and deployment → Source → GitHub Actions. While the source is still "Deploy from a branch", the deploy job fails (the build job still runs and reports).

The run summary for each deploy shows the entry counts per topic, and any entry needing attention is raised as a job warning — so a missing DOI or classification is visible from the Actions tab without opening the log.

The generate step passes --min-articles 60. The bib parser is deliberately lenient, so a truncated or malformed .bib would otherwise produce a nearly empty publication list and deploy it without complaint; below that floor the script writes nothing and fails the build instead.

Local development

bundle exec jekyll serve      # or: make serve

There is no Gemfile; GitHub Pages builds with its own gem set. To build locally, gem install jekyll (or add a Gemfile with github-pages).

Structure

Path	What it is
files/uvilla.bib	the publication source of truth (also served as a download)
_config.yml	site metadata, affiliations, profile links
_data/navigation.yml	top navigation
_data/publications.yml	generated, gitignored — built on every deploy
.github/workflows/pages.yml	regenerate → build → deploy
_layouts/	base, default (page + header band), home (hero), wide
_includes/	head, header, footer, pub_refs
assets/css/style.scss	the whole design system (plain CSS, no theme gem)
scripts/bib2yaml.py	bib → YAML generator
material/	drafts and working notes, excluded from the build
images/optimized/	web-sized images; originals kept alongside

Design notes

• No theme gem. assets/css/style.scss is self-contained plain CSS built on custom properties.
• Careful with clamp(). GitHub Pages compiles this file with Ruby Sass 3.7 (jekyll-sass-converter 1.5.2), which predates clamp()/min()/max() and tries to evaluate arithmetic in function arguments. Writing font-size: clamp(2rem, 1.35rem + 2.6vw, 3rem) fails the build with Incompatible units: 'vw' and 'rem'. Sass leaves custom property values alone, so every fluid value lives in a --token in :root and is used via var(). Keep new fluid values in tokens too. (Switching Pages to a custom Actions workflow with your own Gemfile would let you use modern Dart Sass and drop this constraint.)
• The site keeps the filename assets/css/style.scss on purpose: with no theme: in _config.yml, GitHub Pages falls back to jekyll-theme-primer, and a file at that exact path shadows the theme's stylesheet.
• Light and dark themes, following the OS by default with a manual toggle in the header (stored in localStorage).
• Navigation collapses to a CSS-only hamburger below 900px.
• Page container defaults to a reading measure (.prose); pages that lay out grids set container: full in their front matter.