run-pipeline

name	run-pipeline
description	Execute the full Stata pipeline via dofiles/00_master.do. Runs every stage in dependency order, aborts on first error, prints stage timings, and reports final output tree.
disable-model-invocation	true
argument-hint
allowed-tools	["Bash","Read","Grep","Glob"]

Run the Full Pipeline

Execute dofiles/00_master.do end-to-end via scripts/run_pipeline.sh. This is the canonical "rebuild everything" command.

Steps

1. Pre-flight checks:

   • Confirm dofiles/00_master.do exists
   • Confirm data/raw/ is non-empty (otherwise the cleaning stage will fail with no inputs)
   • Confirm Stata is on PATH (which stata or which stata-mp)

2. Run the pipeline:

   bash scripts/run_pipeline.sh
   

   The wrapper:

   • Records start time
   • Runs dofiles/00_master.do in batch mode
   • Streams stage timings as each do dofiles/XX/... call completes
   • Aborts on first non-zero exit code
   • Prints total wall time at the end

3. Inspect the environment snapshot: logs/00_master_environment.log should contain Stata version, flavor, OS, and which of key user-written commands.

4. Validate stage logs: For each logs/<stage>_*.log produced, grep for errors:

   for L in logs/*.log; do
     N=$(grep -c -E "^r\(\d+\);|invalid syntax|not found" "$L")
     [ "$N" -gt 0 ] && echo "$L: $N error matches"
   done
   

5. Verify expected outputs:

   • output/tables/ and output/figures/ populated
   • Spot-check that key tables/figures referenced in reports/*.qmd exist and are newer than the producing do-files (freshness check from single-source-of-truth)

6. Report:

   • Total runtime
   • Per-stage timings (from wrapper output)
   • Logs produced + any errors
   • Output files created
   • Next step (re-run a single stage, render report, commit)

Examples

• /run-pipeline → Builds the entire pipeline; reports timing + outputs.

• After data refresh: /run-pipeline then /render-report reports/analysis_report.qmd.

Troubleshooting

• Pipeline aborts at stage 02_construct — check the log of the LAST do-file in stage 01_clean; merge errors are common when raw data shape changes.
• reghdfe not found — run ssc install reghdfe ftools, replace once. Or run dofiles/00_master.do with the INSTALL_DEPS = 1 flag (see master.do header).
• Stata not found — see /run-stata troubleshooting; the same command -v chain applies.
• Permission denied — chmod +x scripts/run_pipeline.sh.

Notes

• This skill is destructive: it overwrites everything in output/. Commit any in-progress work before running.
• Long-running: for typical empirical work, expect minutes to tens of minutes. The wrapper does not background — run it and wait.
• For partial re-runs (one stage), use /run-stata instead.