Release 0.6.0: prebuilt simulator images (+ deploy config)

[jcschaff]

Release PR for 0.6.0. It does what make tag / tag.sh would commit, plus the production config that enables the first prebuilt simulator, as a reviewable PR instead of a direct push.

Contents

• Version 0.6.0: pyproject.toml, compose_api/version.py and uv.lock. The OpenAPI spec is regenerated, picking up 0.6.0 and feat: run a submission in a listed prebuilt simulator image #190's simulator query parameter.
  • The checked-in generated client (compose_api/api/client/) isn't regenerated here. make clients needs LIB_DIR, and the new parameter is optional.
• Overlays: ghcr.io/biosimulations/compose-api:0.6.0 in compose-api-rke, compose-api-rke-db-migration, compose-api-local and compose-api-local-db-migration.
• kustomize/config/compose-api-rke/api.env: lists the first prebuilt simulator, pinned by digest:

  PREBUILT_SIMULATORS={"viva-pde-particle": "ghcr.io/vivarium-collective/viva-pde-particle-compose@sha256:f3ddef47…95b6"}
  

  • The image is public (an anonymous manifest fetch gives 200).
  • Its CI ran compose-api's exact job command under apptainer run --compat before publishing it (feat(compose): ensemble documents and a container image for compose-api vivarium-collective/viva-pde-particle#46).

Checked

• kubectl kustomize kustomize/overlays/compose-api-rke renders image: …compose-api:0.6.0 and PREBUILT_SIMULATORS in the api-config ConfigMap.
• The value parses to the expected mapping through compose_api.config.Settings.
• make check is clean.

Since 0.5.0

155 commits, including:

• Build and run containers on the test cluster, and a plan for OCI runtimes #167 / Build a real deployed simulator definition on the container, and survey the associated repositories #170: SLURM container build;
• fix: pin the simulator library list instead of fetching it per request #182: the pinned simulator registry;
• feat: run a submission in a listed prebuilt simulator image #190: prebuilt simulator images.

There are no Alembic migrations since 0.5.0, so the deploy needs no migration job.

Before merging

• feat: registry manifest, and refuse unregistered process addresses at submission #184 / feat: list every viva-catalog wrapper in the registry at level listed #185 (registry manifest enforcement): I'll bring main in here once they merge, so 0.6.0 ships with them. feat: registry manifest, and refuse unregistered process addresses at submission #184 already exempts listed prebuilt-simulator submissions from the address check.

After merging

1. Tag the merge commit 0.6.0 and push the tag. build-containers.yml builds and pushes ghcr.io/biosimulations/compose-api:0.6.0.
2. Deploy: make deploy, which applies kustomize/overlays/compose-api-rke. This needs explicit go-ahead.
3. Optionally, publish a GitHub release, which archives it to Zenodo.

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