qmd-runner

What problem does it solve?

It eliminates the slow, frustrating cycle of finding one failing Quarto chunk at a time when quarto render stops early and the error message is hard to interpret.

Core Features & Use Cases

• Chunk-level isolation: Extracts each {r} chunk into a generated sibling .R runner and wraps execution in tryCatch so failures don’t hide downstream issues.
• Fast iterative repair loop: Repeatedly regenerates the runner from the source .qmd, fixes the real root cause in the .qmd, and re-runs until every chunk is PASS / FAIL / SKIP.
• Workflow-aware debugging: Supports dependency-order debugging for notebook DAGs (e.g., Seurat/Bioconductor/GSEA/biomaRt/clusterProfiler pipelines) and reduces cascading failures from stale checkpoints.

Quick Start

Use the qmd-runner skill to debug a failing notebook by generating per-chunk tryCatch runners from your .qmd, running the runner to get a PASS/FAIL/SKIP table, then editing the source .qmd to fix each failing chunk and regenerating until everything is green.