ci(5): run the Job tester (jote) against every job submodule#6
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Add a GitHub Actions workflow that runs 'jote --dry-run' against every manifest in each job-based submodule (virtual-screening, squonk2-cdk, squonk2-chemaxon, squonk2-fragmenstein, squonk2-jaqpot, squonk2-smartcyp). A dry-run validates the Job Definition and Manifest files against the decoder schemas and lint rules without executing any tests or containers. Manifests are auto-discovered by globbing data-manager/manifest*.yaml, and each repository is a separate matrix leg (fail-fast disabled) so one non-compliant repository does not mask the others. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Install im-jote at the version set by the workflow-level JOTE_VERSION variable (default 0.12.0) so the check is reproducible and can be moved in one place. Bump actions/checkout to v7 and actions/setup-python to v6. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
0.13.0 fixes the docker-compose probe on --dry-run (InformaticsMatters/squonk2-data-manager-job-tester#10), removing the transient flake on job repositories that have tests. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Fixes #5
What this adds
A GitHub Actions workflow (
.github/workflows/test-jobs.yaml) that runs the Job Tester (jote) against every job-based submodule using its--dry-runoption — validating the Job Definition and Manifest files against the decoder schemas (and lint rules) without executing any tests or containers.virtual-screening,squonk2-cdk,squonk2-chemaxon,squonk2-fragmenstein,squonk2-jaqpot,squonk2-smartcyp.fail-fast: falseso one repo's failure doesn't mask the others.data-manager/manifest*.yaml, so new manifests are picked up without editing the workflow.joteis installed fresh from PyPI (im-jote) so the check always reflects the current tester and schemas. Run with--dry-run --allow-no-teststo keep it a pure definition/schema check.main, all PRs, weekly schedule, and manual dispatch.Expected result: virtual-screening is red
As requested, no manifests are excluded.
virtual-screeningwill fail becausemanifest-moldb.yaml→moldb.yamlusesmaxValue/minValueproperties the (deliberately incomplete) decoder schema rejects:virtual-screening's own CI currently side-steps this by omitting
moldb; this workflow surfaces it instead. The other five repositories pass. Fixing it means either extending the decoder schema to cover these properties or correctingmoldb.yaml— a separate piece of work.Verification
Ran the exact per-repo step logic locally with
im-joteagainst all six submodules:virtual-screening → exit 1(moldb), the other five →exit 0. Workflow YAML parses cleanly.🤖 Generated with Claude Code