.github

LidkeLab organization defaults, and the lab's shared Julia CI workflow.

Every lab Julia package, in LidkeLab, JuliaSMLM or a personal account, runs its CI through one reusable workflow kept here, .github/workflows/julia-ci.yml. Each package carries only a short caller, the same in every package except its with: lines. This repository is public because a reusable workflow in a private repository can be called only from private repositories in the same organization. It holds no secrets.

What the workflow runs

GitHub-hosted CI checks that a package installs and works on a clean machine. Correctness tests that need a GPU, lab data, long run times or an instrument run on a lab machine instead.

Job	When	What
test	always	GROUP=Core tests at Julia min (the julia compat lower bound) and 1; a private repository runs 1 only
qa	always	GROUP=QA tests (Aqua, ExplicitImports) at Julia 1
downgrade	registered: true, public repositories	GROUP=Core at Julia min, the oldest supported Julia, with direct dependencies at the lowest versions [compat] allows
pre	registered: true, public repositories, scheduled runs only	GROUP=Core at the Julia prerelease; allowed to fail
format	runic: true	Runic formatting check

All jobs run on ubuntu-latest, x64, with a 60-minute timeout, and skip draft pull requests. There is no coverage upload and no docs job. The GROUP variable is read by the lab's standard test/runtests.jl, which runs the test groups declared in test/test_groups.toml.

Inputs

Input	Type	Default	Meaning
registered	boolean	false	The package is in the General registry: adds downgrade and the monthly pre run, in a public repository.
runic	boolean	false	Adds the Runic formatting check. Runic checks every .jl file in the repository.
project	string	.	Path to the package within the repository.

Adopting it in a package

1. Copy templates/CI.yml to .github/workflows/CI.yml. Change only the with: lines, for example registered: true for a registered package.
2. Copy templates/dependabot.yml to .github/dependabot.yml unchanged. Dependabot then opens a weekly pull request per dependency, covering Julia compat bounds in every environment of the repository and the GitHub Actions versions.
3. Delete .github/workflows/CompatHelper.yml, which Dependabot replaces, and the old CI workflow the caller replaces.
4. The package's tests must follow the lab's test layout: the standard test/runtests.jl, a test/test_groups.toml, and at least the Core and QA groups.

The caller runs on pushes to main or master and on tags, on pull requests (including when a draft is marked ready), on manual dispatch, and monthly. Changes only to Markdown files, dev/ or .claude/ do not start a run. A newer push to a pull request cancels the older run.

In a private repository, whose Actions minutes are paid, the jobs run only on pull requests and manual dispatch and skip every other event (admiral decision 0025: the lab tests on its own machines, and its local record checks the Julia floor). Public repositories run on every event.

A public repository saves its Julia cache only from the default branch, and pull requests restore that cache. A private repository has no push runs, so every one of its runs saves: later runs on the same pull request start warm, and a new pull request restores only the default branch's cache, which a manual workflow_dispatch run on main seeds. GitHub drops a cache unused for 7 days, so the first run after a quiet week starts cold.

Versions

Callers use @v2. The v2 tag is moved forward only for backward-compatible changes: a new input with a default that keeps the old behaviour, an updated action version, a fix. A change that could turn a passing package red, or that removes or renames an input, is released as v3, and packages move to it by editing their caller.

Self-test

.github/workflows/selftest.yml runs the workflow from the same commit, with registered and runic on, against a small fixture package in test/fixture/FixturePkg, on every push and pull request.