Update Dataset (PR → snapshot → steps → grapher)

Use this skill to run a complete dataset update with Claude Code subagents, keep a live progress checklist, and pause for approval at a checkpoint after every numbered workflow step before continuing.

Inputs

• <namespace>/<old_version>/<name>
• Get <new_version> as today's date by running date -u +"%Y-%m-%d"

Optional trailing args:

• branch: The working branch name (defaults to current branch)

Assumptions:

• All artifacts are written to workbench/<short_name>/.
• Persist progress to workbench/<short_name>/progress.md and update it after each step.

Progress checklist (maintain, tick live, and persist to progress.md)

(Checkpoint rule: After you finish each item below that represents a workflow step, immediately run the CHECKPOINT procedure. Do not batch multiple steps before a checkpoint.)

• Parse inputs and resolve: channel, namespace, version, short_name, old_version, branch
• Clean workbench directory: delete workbench/<short_name> unless continuing existing update
• Run ETL update workflow via etl-update subagent (help → dry run → approval → real run)
• Create or reuse draft PR and work branch
• Update snapshot and compare to previous version; capture summary
• Meadow step: run + fix + diff + summarize
• Garden step: run + fix + diff + summarize
• Grapher step: run + verify (skip diffs), or explicitly mark N/A
• CHECKPOINT — present consolidated summary and request approval
• If approved, commit, push, and update PR description
• Optional: run indicator upgrade on staging and persist report

Persistence:

• After ticking each item, update workbench/<short_name>/progress.md with the current checklist state and a timestamp.

CHECKPOINT (mandatory user approval)

Always performed immediately after completing each numbered workflow step (1–6). Never start the next step until approval is granted.

Procedure (each time):

1. Present a concise summary of what just changed, key diffs/issues resolved, and what the next step will do.
2. Ask exactly: Proceed? reply: yes/no
3. Only continue if the user replies exactly yes (case-insensitive). Any other reply = no; stop and wait.
4. On approval:
   • Update progress checklist (tick the completed item) and write workbench/<short_name>/progress.md with timestamp.
   • Commit related changes (if any), push.
   • Update (or append to) the PR description: add a collapsed section titled with the step name (e.g., "Snapshot Update", "Meadow Update") containing the summary.

Mandatory per-step checkpoints (rule)

You MUST:

• Stop after each workflow step (1–6) and run CHECKPOINT before starting the next (step 7 is optional and still requires a checkpoint if executed).
• Never chain multiple steps inside a single approval.
• Treat missing or ambiguous replies as no.

Workflow orchestration

0. Initial setup

   • Check if workbench/<short_name>/progress.md exists to determine if continuing existing update
   • If starting fresh: delete workbench/<short_name> directory if it exists
   • Create fresh workbench/<short_name> directory for artifacts

1. Run ETL update command (etl-update subagent)

   • Inputs: <namespace>/<old_version>/<short_name> plus any required flags
   • Perform help check, dry run, approval, then real execution; capture summary for later PR notes
   • CHECKPOINT (stop → summarize → ask → require yes)

2. Create PR and integrate update via subagent (etl-pr)

   • Inputs: <namespace>/<old_version>/<short_name>
   • Create or reuse draft PR, set up work branch, and incorporate the ETL update outputs
   • CHECKPOINT

3. Snapshot run & compare (snapshot-runner subagent)

   • Inputs: <namespace>/<new_version>/<short_name> and <old_version>
   • CHECKPOINT

4. Meadow step repair/verify (step-fixer subagent, channel=meadow)

   • Run, fix, re-run; produce diffs
   • Save diffs and summaries
   • CHECKPOINT

5. Garden step repair/verify (step-fixer subagent, channel=garden)

   • Run, fix, re-run; produce diffs
   • Save diffs and summaries
   • CHECKPOINT

6. Grapher step run/verify (step-fixer subagent, channel=grapher, add --grapher)

   • Skip diff
   • CHECKPOINT

7. Indicator upgrade (optional, staging only)

   • Use indicator-upgrader subagent with <short_name> <branch>
   • CHECKPOINT (if executed)

Guardrails and tips

• Never return empty tables or comment out logic as a workaround — fix the parsing/transformations instead.
• Column name changes: update garden processing code and metadata YAMLs (garden/grapher) to match schema changes.
• Indexing: avoid leaking index columns from reset_index(); format tables with tb.format(["country", "year"]) as appropriate.
• Metadata validation errors are guidance — update YAML to add/remove variables as indicated.

Artifacts (expected)

• workbench/<short_name>/snapshot-runner.md
• workbench/<short_name>/progress.md
• workbench/<short_name>/meadow_diff_raw.txt and meadow_diff.md
• workbench/<short_name>/garden_diff_raw.txt and garden_diff.md
• workbench/<short_name>/indicator_upgrade.json (if indicator-upgrader was used)

Example usage

• Minimal catalog URI with explicit old version:
  • update-dataset data://snapshot/irena/2024-11-15/renewable_power_generation_costs 2023-11-15 update-irena-costs

Common issues when data structure changes

• SILENT FAILURES WARNING: Never return empty tables or comment code as workarounds!
• Column name changes: If columns are renamed/split (e.g., single cost → local currency + PPP), update:
  • Python code references in the garden step
  • Garden metadata YAML (e.g., food_prices_for_nutrition.meta.yml)
  • Grapher metadata YAML (if it exists)
• Index issues: Check for unwanted index columns from reset_index() — ensure proper indexing with tb.format(["country", "year"]).
• Metadata validation: Use error messages as a guide — they show exactly which variables to add/remove from YAML files.