The State of BioJulia

JuliaCon 2026 · Mainz, Germany · BioJulia Minisymposium

A Typst + Touying presentation, built on the Bonham Lab talk template.

Usage

• Instantiate the assets/general submodule: git submodule update --init --recursive
• Compile: typst compile --root . main.typ presentation.pdf
• Watch while editing: typst watch --root . main.typ presentation.pdf

Fonts: requires IBM Plex Sans/Serif/Mono installed system-wide (Arch: pacman -S ttf-ibm-plex). CI already handles this — see .github/workflows/*.yml.

Theme

assets/theme/bonham-theme.typ is the lab's Touying theme (see the template repo for the full rationale). This deck runs it in its dark "terminal" palette for the whole talk — main.typ swaps the theme's light/dark color arguments so #focus-slide[..] becomes the one deliberate light "paper" moment instead of the reverse.

Images

images/ holds this talk's figures, referenced directly from main.typ (e.g. image("images/foo.png")). images/cajun/ are figures pulled from third-party BioJulia package docs/repos for illustration.

Supplementary: GitHub stats scripts (code/)

code/ is a standalone Julia/Quarto tool used to generate the GitHub-activity plots (stars, repo health, committer histograms) embedded in the deck as images — it's not part of the Typst build. code/gh-module.jl wraps the gh CLI to pull star history and commit/repo stats for the BioJulia org; code/github-stats.qmd is a Quarto notebook that calls into it with CairoMakie and saves figures to ../images/. Requires the gh CLI authenticated as a BioJulia admin/collaborator and the Julia deps in code/Project.toml. Re-run the .qmd in Quarto to regenerate the plots.

Deployment

To trigger the release GitHub Action (compiles the PDF + title-slide preview and attaches them to a GitHub release), create a release.