BIOMERO.WorkflowSkills

biomero-workflow-skills is a small, framework-neutral catalog for Agent Plugins and Agent Skills stored with BIOMERO workflow repositories. It resolves exact GitHub revisions, validates each package locally, and exposes typed catalog data to OMERO plugins.

Agent Plugins 1.0.0 are discovered from <workflow>_plugin_path (default .). The package uses its bundled schema without network access, reads only immediate skills/*/SKILL.md directories, and materializes only bounded UTF-8 skill files and text references. Repositories without plugin.json retain the 0.x _agents/skills fallback. A present but invalid manifest is reported as an error.

It is an optional provider for OMERO.Analysis. It is not an OMERO.web application and does not modify or import OMERO.biomero.

Basic use

from biomero_workflow_skills import WorkflowSkillCatalog

catalog = WorkflowSkillCatalog()
available = catalog.get_catalog("omero-analysis")
package = catalog.get_package(
    "cisegmentation",
    "analyze-cisegmentation-measurements",
)

For stateless adapters, get_package(..., consumer="omero-analysis") is also supported and performs the consumer-filtered catalog lookup first. Only attachment-analysis skills explicitly declaring omero-analysis are returned. [APPLICATIONS] is intentionally ignored; applications such as BIOMERO.ZarrViewer publish their own skills.

The package reads BIOMERO_WORKFLOW_SKILLS_CONFIG when set. Otherwise it merges the existing files at /etc/slurm-config.ini, /OMERO/slurm-config.ini, and ~/slurm-config.ini, matching BIOMERO's configuration precedence.

Public GitHub repositories need no credential. Set BIOMERO_GITHUB_TOKEN to a read-only token for private repositories or a larger API allowance.

The cache follows configured release pins: tags and commits are immutable, while branches are revalidated hourly with GitHub ETags. Removing a workflow or skill removes it from the next authoritative response; stale content is used only for a transient failure of the same unchanged source.

See Workflow skill authoring and deployment for the repository contract, security model, caching, and plugin integration.