fix: publish scans [rules.environment] for env files#52
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ShixiangWang merged 1 commit intoJul 17, 2026
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publish scanned each rule for [rules.env].file and a conda_env field, neither of which exists in the schema. The real schema is [rules.environment] (EnvironmentSpec) with conda/pixi/venv/ venv_requirements file paths. As a result publish collected zero env files and bundled none — silently, while reporting success. Scan the environment table's file-bearing fields instead. docker/ singularity (image refs) and modules (HPC module names) are not files and are left out. Adds an integration test covering a conda env declared under [rules.environment].
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publish scanned each rule for
[rules.env].fileand aconda_envfield, neither of which exists in the schema. The real schema is[rules.environment](EnvironmentSpec) withconda/pixi/venv/venv_requirementsfile paths.Result: publish collected zero env files and bundled none — silently, while reporting success. A rule with
[rules.environment]/conda = "envs/fastp.yaml"matched nothing.This scans the environment table's file-bearing fields instead.
docker/singularity(image refs) andmodules(HPC module names) are not files and are left out. Adds an integration test covering a conda env declared under[rules.environment].make cipasses (fmt/clippy/build/test); the audit leg needscargo-auditinstalled locally.Known follow-up (out of scope here)
Referenced env files are still flattened to their basename on copy:
envs/fastp.yamllands in the bundle asfastp.yaml, but the bundled workflow keeps referencingenvs/fastp.yaml, so the path does not resolve. This PR fixes only the schema-scanning bug (envs bundled at all vs. silently dropped); preserving the relative layout is a separate fix to follow.