Dynamica Lab website

Source of the Dynamica Research Lab website, built with Quarto.

The pages are not written by hand: create-pages.py reads the YAML files in data/ and generates the Quarto pages (home.qmd, news.qmd, team.qmd, pubs.qmd and one <id>.qmd per member with a personal page), which Quarto then renders to HTML in docs/. The generated .qmd files and docs/ are git-ignored, so to change the site, edit the files in data/ (or create-pages.py for the layout), never the .qmd files.

Cloning the repository

Binary files (*.pdf, *.png, *.jpg and *.zip, see .gitattributes) are stored with Git LFS. Without it, a clone only contains small text "pointer" files in their place, and the site renders with broken pictures and PDFs.

1. Install Git LFS (e.g. brew install git-lfs on macOS, sudo apt install git-lfs on Debian/Ubuntu), then enable it for your user account, only needed once per machine:

   git lfs install

2. Clone the repository (the LFS files are downloaded automatically):

   git clone git@github.com:dynamicalab/dynamicalab.github.io.git
   cd dynamicalab.github.io

   or, without an SSH key, git clone https://github.com/dynamicalab/dynamicalab.github.io.git.

If the repository was cloned before Git LFS was installed, run git lfs install and then git lfs pull inside it to replace the pointer files with the actual files. git lfs ls-files lists the files tracked by LFS.

New binary files matching the patterns above are stored with LFS automatically on git add, as long as git lfs install was run. To track another file type, run git lfs track "*.ext" and commit the updated .gitattributes.

Building the site locally

Requirements: a local clone with its LFS files (see above), uv and Quarto (Quarto is not a Python package and must be installed separately).

1. Install Python and the dependencies (Python version taken from .python-version):

   uv sync

2. Install the Quarto extensions (icons), only needed once:

   quarto add quarto-ext/fontawesome --no-prompt
   quarto add schochastics/academicons --no-prompt

3. Generate the .qmd pages from data/:

   uv run python create-pages.py

4. Render and browse the site, with live reload while editing:

   quarto preview

   This serves the site at a local URL.

Re-run step 3 every time a file in data/ changes: quarto preview does not re-run create-pages.py by itself.

Deployment

Every push to main triggers .github/workflows/publish.yml, which runs steps 1–3 above on GitHub Actions, renders the site and publishes docs/ to GitHub Pages. It can also be started manually from the Actions tab (workflow_dispatch). Nothing needs to be built or committed locally to deploy. If a deployment fails (e.g. YAML syntax error or unknown role in data/), the error is shown in the logs of the failed run in the Actions tab, and the previously published site stays online.

Updating the website directly on GitHub

Text changes can be made from the browser, without cloning the repository or installing anything:

1. Open the file to change on github.com/dynamicalab/dynamicalab.github.io, usually one of the files in data/ (see Editing the content).
2. Click the pencil icon (Edit this file), make the changes and click Commit changes…, committing directly to main.
3. The commit triggers the deployment workflow; follow its progress in the Actions tab. The site is updated after a few minutes if the run succeeds.

Since every commit to main is published, double-check the YAML indentation before committing: a syntax error makes the deployment fail.

Warning

Binary files (pictures, PDFs, ZIP archives, i.e. *.pdf, *.png, *.jpg, *.zip) are stored with Git LFS and cannot be added or replaced from the GitHub web interface (Add file → Upload files): they would not be stored with LFS. Adding a member picture, a thesis, a CV, slides or a poster must be done from a local clone (see Cloning the repository), followed by git add, git commit and git push. The corresponding entry in data/ can be committed in the same push.

Repository layout

Path	Content
create-pages.py	Generates the .qmd pages from data/. Constants at the top control role ordering, icons, labels, etc.
data/team.yml	Members and alumni, their positions and theses.
data/pubs.yml	Journal articles, proceedings, other writings and presentations.
data/news.yml	News items.
data/home-about-us.md, data/home-group-picture.md	Markdown blocks inserted in the home page.
images/members/	Member pictures (default.png is used when none is given). Git LFS.
images/logos/	Lab logo (also used as favicon).
images/	Other pictures (e.g. the group picture of the home page). Git LFS.
pdf/	PDFs of papers and theses. Git LFS.
cv/, slides/, posters/	Files linked from member cards and publication entries (CVs, slides as PDF or zipped PPTX, posters). Git LFS.
assets/js/	Scripts used by the pages (e.g. truncation of news excerpts on the home page).
custom.scss	Site styles (on top of the simplex Bootswatch theme).
_quarto.yml	Quarto configuration: navbar, theme, output directory.
pyproject.toml, uv.lock, .python-version	Python version and dependencies (pyyaml, jinja2), managed with uv.
.github/workflows/publish.yml	Build and deployment workflow (see Deployment).
.gitattributes	File patterns stored with Git LFS.

Editing the content

Each of data/team.yml, data/pubs.yml and data/news.yml starts with a commented example showing the supported fields; use them as the reference (copying an example is the easiest way to add an entry). The main rules are summarized below.

Team (data/team.yml)

Each member has an id (lastname-firstname, used everywhere else to refer to them), a name and a list of positions, each with a role, a start year and an end year (no end means the position is still held).

• role must be one of the roles listed in ROLE_ORDER in create-pages.py (Group leader, Honorary member, Postdoctoral fellow, PhD student, MSc student, Intern), otherwise create-pages.py stops with a KeyError. The exception is BSc student, which is only used for the education section of personal pages and should be flagged outside-of-dynamica: true (see below).
• Current members are shown as cards, ordered by role. Members with alumnus: true are listed under Alumni, most recent departures first; nowat or movedto adds their current whereabouts.
• Optional fields: picture (file in images/members/, see the warning about binary files above), email (shown only for some roles, see ROLE_WITH_EMAIL), and links with any of website, ul, orcid, gscholar, github, twitter, cv (file in cv/).
• A PhD student or MSc student position can carry a thesis (title, doi, pdf, and tableau-d-honneur: true for theses added to the Board of Honor). Theses appear in the Theses section of the Publications page; their year is the position's end year.
• A position can list its supervisors under supervisor and its cosupervisors under cosupervisor. Both are lists of entries with a name (a member id or a plain name) and, for people who are not members of Dynamica, an optional university (defaults to SUPERVISOR_UNIVERSITY_DEFAULT, i.e. U. Laval). On personal pages, they are shown under the corresponding education entry as "Supervised by A, B and C (University)", supervisors first.
• Education entries on personal pages use the optional university (defaults to UNIVERSITY_DEFAULT, i.e. Université Laval) and degree (defaults to DEGREE_DEFAULT, i.e. Physics) fields of the position.

Publications and presentations (data/pubs.yml)

Each entry has a type, a title, authors and a year. Authors are given either as a member id (highlighted as a lab member) or as a plain name (collaborator).

• Types shown under Journal Articles & Writings: article (journal, volume, pages), conference-proceeding (conference, location), book-chapter, other-writing (reference).
• Types shown under Presentations: invited-presentation, oral-presentation, poster-presentation (conference, location). presenters lists who presented; it defaults to the first author.
• Optional links: doi (plus open-access: true), pdf (file in pdf/), fulltext, arxiv, biorxiv, medrxiv, slides (file in slides/), poster (file in posters/).
• Optional extras: keywords (list of tags) and highlights (list of short distinctions, shown with a star).
• Theses are not listed in pubs.yml: they are taken from the positions in team.yml (see above).

News (data/news.yml)

Each item has a date (YYYY-MM-DD) and a text (Markdown). members lists the ids of the members involved, so the item also appears on their personal pages. draft: true hides an item everywhere. The home page shows the 10 most recent items (NUMBER_NEWS_ITEMS); the News page shows all of them, grouped by year.

Personal pages

Setting personal-page: true on a member generates a CV-style page (<id>.html), linked from their name on the team page. It shows their bio (free text), education (degrees, theses and internships), publications, presentations and news.

Work done outside Dynamica can be added to a personal page without appearing on the lab's pages: any position, pubs.yml entry or news.yml item can be flagged outside-of-dynamica: true. It is then hidden from the home, news, team and publications pages and shown only on the personal pages of the members it belongs to (positions and publications get a "Not completed as a member of Dynamica" badge). Publications and presentations always go in pubs.yml, never in team.yml.