Fix Apptainer CI: replace obsolete flag and modernize workflow - #25
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…refix, update action versions, add caching and workflow_dispatch Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
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[WIP] Check CI status for Apptainer and assess obsolescence
Fix Apptainer CI: replace obsolete flag and modernize workflow
Mar 20, 2026
cokelaer
marked this pull request as ready for review
March 20, 2026 09:27
Pull Request Test Coverage Report for Build 23334950165Details
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The Apptainer CI workflow was failing because
--use-apptainerno longer exists insequana_pipetools; the replacement is--apptainer-prefix <path>. The workflow also had stale action versions and no caching, making runs slow and unreliable.Changes
--use-apptainer→--apptainer-prefix ~/.apptainer/cachecheckout@v3→v4,setup-python@v3→v5workflow_dispatch: enables manual trigger from the GitHub UI~/.apptainer/cache) to avoid redundant installs/downloads across runs3.9(keep3.10only), consistent with other active sequana pipeline repos💬 Send tasks to Copilot coding agent from Slack and Teams to turn conversations into code. Copilot posts an update in your thread when it's finished.