Julia "Manifest.toml out of sync" / Pkg.instantiate in CI

Julia found that the manifest no longer matches the project, or that packages the manifest records are not installed. It needs Pkg.instantiate() to download and resolve the exact dependency set before code can load.

What this error means

A run fails with "ERROR: expected package X to be registered" or "The project dependencies or compat requirements have changed; run Pkg.resolve() or Pkg.update()", or a using fails because the manifest was never instantiated.

Julia

ERROR: `/home/runner/work/app/Project.toml` has dependencies but no
corresponding entries in the manifest, or the manifest is out of date.
Run `Pkg.resolve()` or `Pkg.instantiate()` to resolve.

Common causes

The project was never instantiated in CI

The job activated the project but did not download its dependencies, so the manifest packages are absent.

Project.toml changed without re-resolving

A dependency or compat bound changed in Project.toml but Manifest.toml was not regenerated, so the two disagree.

How to fix it

Instantiate the project

Activate the project with --project=..
Run Pkg.instantiate() to install exactly what the manifest records.
Run your code in the same environment.

Terminal

julia --project=. -e 'using Pkg; Pkg.instantiate()'

Resolve and commit the manifest after a change

If Project.toml changed, resolve to regenerate the manifest and commit it so CI installs a consistent set.