usher-exploring/.planning/phases/05-output-cli/05-03-SUMMARY.md

phase, plan, subsystem, tags, requires, provides, affects, tech-stack, key-files, key-decisions, patterns-established, duration, completed

phase	plan	subsystem	tags	requires	provides	affects	tech-stack	key-files	key-decisions	patterns-established	duration	completed
05-output-cli	03	cli	click cli report integration-testing clir unner	phase provides 05-01 assign_tiers, add_evidence_summary, write_candidate_output phase provides 05-02 generate_all_plots, generate_reproducibility_report phase provides 04-03 scored_genes table in DuckDB	CLI report command orchestrating full output pipeline CliRunner integration tests for report command	unified-cli end-to-end-workflow user-experience	added patterns cli-checkpoint-restart dual-format-output graceful-degradation integration-testing-with-synthetic-fixtures	created modified src/usher_pipeline/cli/report_cmd.py tests/test_report_cmd.py src/usher_pipeline/cli/main.py	Report command follows established score_cmd.py pattern (config load, store init, checkpoint check, pipeline steps, summary, cleanup) Support --output-dir, --force, --skip-viz, --skip-report, and configurable tier threshold flags Tier thresholds passed as uppercase keys (HIGH/MEDIUM/LOW) with composite_score and evidence_count fields Default output directory: {data_dir}/report if --output-dir not specified Checkpoint pattern: warn and skip if candidates.tsv exists without --force Integration tests use synthetic DuckDB fixtures with isolated tmp_path instances (no external dependencies)	CliRunner integration tests with test_config and populated_db fixtures Synthetic test data designed to validate tier distribution (3 HIGH, 5 MEDIUM, 5 LOW, 4 EXCLUDED, 3 NULL) Each test uses isolated tmp_path to avoid cross-test contamination Graceful degradation: visualization and reproducibility report failures logged as warnings, not errors	3min	2026-02-11

Phase 05 Plan 03: CLI Report Command Summary

One-liner: Unified CLI report command orchestrates tiering, evidence summary, dual-format output, visualizations, and reproducibility reports in one invocation with configurable thresholds and skip flags.

Performance

• Duration: 3 minutes
• Started: 2026-02-11T20:04:06Z
• Completed: 2026-02-11T20:07:42Z
• Tasks: 2
• Files modified: 3

Accomplishments

• Implemented CLI report command following established CLI pattern from score_cmd.py and evidence_cmd.py
• Orchestrates full output pipeline: load scored_genes, apply tiering, add evidence summary, write TSV+Parquet, generate plots, create reproducibility reports
• Supports configurable tier thresholds (--high-threshold, --medium-threshold, --low-threshold, --min-evidence-high, --min-evidence-medium)
• Provides skip flags (--skip-viz, --skip-report) for flexible iteration
• Created 9 comprehensive CliRunner integration tests with synthetic fixtures
• Unified CLI now has 5 commands: setup, evidence, score, report, info

Task Commits

Each task was committed atomically:

1. Task 1: Report CLI command - 2ab25ef (feat)

   • report_cmd.py with full pipeline orchestration
   • Registered in main.py CLI entry point
   • Follows established pattern: config load, store init, checkpoint, steps, summary, cleanup

2. Task 2: CliRunner integration tests - c10d595 (test)

   • test_report_cmd.py with 9 comprehensive tests
   • Fixtures: test_config (minimal YAML), populated_db (synthetic scored_genes)
   • Fixed tier threshold format bug (uppercase keys, composite_score field)
   • Fixed write_candidate_output parameter name bug (filename_base not base_filename)

Files Created/Modified

• src/usher_pipeline/cli/report_cmd.py - CLI report command orchestrating output pipeline
• src/usher_pipeline/cli/main.py - Added report command registration
• tests/test_report_cmd.py - 9 CliRunner integration tests

Decisions Made

• Report command pattern: Follow score_cmd.py established pattern for consistency (config load, store init, checkpoint check, pipeline steps with click.style output, summary display, cleanup in finally block)
• Tier threshold format: Pass uppercase keys (HIGH/MEDIUM/LOW) with composite_score and evidence_count fields to match assign_tiers() signature
• Default output directory: Use {data_dir}/report if --output-dir not specified (consistent with other evidence commands)
• Checkpoint pattern: Warn and skip if candidates.tsv exists without --force flag (prevents accidental overwrites)
• Graceful degradation: Wrap visualization and reproducibility report generation in try/except to log warnings rather than fail entire command
• Integration test strategy: Use synthetic DuckDB fixtures with isolated tmp_path instances to avoid external API dependencies and ensure fast, reproducible tests

Deviations from Plan

Auto-fixed Issues

1. [Rule 1 - Bug] Fixed tier threshold dictionary format

• Found during: Task 2 (test execution)
• Issue: assign_tiers() expects uppercase keys "HIGH"/"MEDIUM"/"LOW" and "composite_score" field, but report_cmd.py passed lowercase keys "high"/"medium"/"low" and "score" field
• Fix: Changed tier_thresholds dict to use uppercase keys and composite_score field, added evidence_count: 1 for LOW tier
• Files modified: src/usher_pipeline/cli/report_cmd.py
• Verification: All tests pass after fix
• Committed in: c10d595 (Task 2 commit)

2. [Rule 1 - Bug] Fixed write_candidate_output parameter name

• Found during: Task 2 (test execution)
• Issue: write_candidate_output() function parameter is filename_base, not base_filename
• Fix: Changed base_filename="candidates" to filename_base="candidates"
• Files modified: src/usher_pipeline/cli/report_cmd.py
• Verification: All tests pass after fix
• Committed in: c10d595 (Task 2 commit)

---

Total deviations: 2 auto-fixed (2 bug fixes) Impact on plan: Both were trivial parameter/key name mismatches discovered during testing. Fixed inline before test commit. No scope creep.

Issues Encountered

None - plan executed smoothly with two minor bugs caught and fixed during test-driven development.

User Setup Required

None - no external service configuration required.

Next Phase Readiness

• Phase 05 (Output & CLI) is now complete
• All output modules implemented: tiering, evidence summary, dual-format writers, visualizations, reproducibility reports
• Unified CLI provides complete end-to-end workflow: setup -> evidence -> score -> report
• Ready for Phase 06 (Final Integration & Validation) if planned
• All tests pass (9/9 CliRunner integration tests), no blockers

---

Phase: 05-output-cli Completed: 2026-02-11

Self-Check: PASSED

All files and commits verified:

Files created:

• ✓ src/usher_pipeline/cli/report_cmd.py
• ✓ tests/test_report_cmd.py

Files modified:

• ✓ src/usher_pipeline/cli/main.py

Commits:

• ✓ 2ab25ef (Task 1: Report CLI command)
• ✓ c10d595 (Task 2: CliRunner integration tests)

Tests:

• ✓ 9/9 tests pass (100% pass rate)

All verification checks passed successfully.