docs(05-03): complete CLI report command plan
- Create 05-03-SUMMARY.md with comprehensive execution report - Update STATE.md: Phase 5 complete (3/3 plans), progress 90% (18/20) - Record decisions: CLI pattern, configurable thresholds, skip flags, graceful degradation - Document deviations: 2 auto-fixed bugs (tier threshold format, parameter name) - Update metrics: Phase 05 total 12 min (4.0 min/plan avg) - All tests pass (9/9 CliRunner integration tests)
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@@ -10,17 +10,17 @@ See: .planning/PROJECT.md (updated 2026-02-11)
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## Current Position
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Phase: 5 of 6 (Output & CLI)
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Plan: 2 of 3 in current phase (plans 05-01, 05-02 complete)
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Status: Phase 5 in progress — 05-02 complete
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Last activity: 2026-02-11 — Plan 05-02 executed and verified
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Plan: 3 of 3 in current phase (plans 05-01, 05-02, 05-03 complete)
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Status: Phase 5 complete — 05-03 complete
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Last activity: 2026-02-11 — Plan 05-03 executed and verified
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Progress: [█████████░] 85.0% (17/20 plans complete across all phases)
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Progress: [█████████░] 90.0% (18/20 plans complete across all phases)
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## Performance Metrics
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**Velocity:**
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- Total plans completed: 17
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- Average duration: 5.0 min
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- Total plans completed: 18
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- Average duration: 4.9 min
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- Total execution time: 1.5 hours
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**By Phase:**
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@@ -31,17 +31,17 @@ Progress: [█████████░] 85.0% (17/20 plans complete across al
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| 02 - Prototype Evidence Layer | 2/2 | 8 min | 4.0 min/plan |
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| 03 - Core Evidence Layers | 6/6 | 52 min | 8.7 min/plan |
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| 04 - Scoring Integration | 3/3 | 10 min | 3.3 min/plan |
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| 05 - Output & CLI | 2/3 | 9 min | 4.5 min/plan |
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| 05 - Output & CLI | 3/3 | 12 min | 4.0 min/plan |
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**Recent Plan Details:**
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| Plan | Duration | Tasks | Files |
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|------|----------|-------|-------|
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| Phase 03 P06 | 13 min | 2 tasks | 10 files |
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| Phase 04 P01 | 4 min | 2 tasks | 4 files |
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| Phase 04 P02 | 3 min | 2 tasks | 4 files |
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| Phase 04 P03 | 3 min | 2 tasks | 4 files |
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| Phase 05 P01 | 4 min | 2 tasks | 5 files |
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| Phase 05 P02 | 5 min | 2 tasks | 6 files |
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| Phase 05 P03 | 3 min | 2 tasks | 3 files |
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## Accumulated Context
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@@ -124,6 +124,10 @@ Recent decisions affecting current work:
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- [05-02]: Graceful degradation (individual plot failures don't block batch generation)
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- [05-02]: Dual-format reproducibility reports (JSON machine-readable + Markdown human-readable)
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- [05-02]: Optional validation metrics in reproducibility reports (report generates whether or not validation provided)
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- [05-03]: Report command follows established CLI pattern (config load, store init, checkpoint, steps, summary, cleanup)
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- [05-03]: Configurable tier thresholds via CLI flags (--high-threshold, --medium-threshold, --low-threshold, --min-evidence-high, --min-evidence-medium)
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- [05-03]: Skip flags for flexible iteration (--skip-viz, --skip-report) allow faster output generation
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- [05-03]: Graceful degradation for visualization and reproducibility report failures (warnings, not errors)
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### Pending Todos
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@@ -136,5 +140,5 @@ None yet.
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## Session Continuity
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Last session: 2026-02-11 - Phase 5 execution
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Stopped at: Plan 05-02 complete — visualization and reproducibility report modules implemented with tests
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Resume file: .planning/phases/05-output-cli/05-02-SUMMARY.md
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Stopped at: Plan 05-03 complete — CLI report command implemented with comprehensive CliRunner integration tests, Phase 5 complete
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Resume file: .planning/phases/05-output-cli/05-03-SUMMARY.md
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.planning/phases/05-output-cli/05-03-SUMMARY.md
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@@ -0,0 +1,166 @@
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---
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phase: 05-output-cli
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plan: 03
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subsystem: cli
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tags: [click, cli, report, integration-testing, clir unner]
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# Dependency graph
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requires:
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- phase: 05-01
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provides: assign_tiers, add_evidence_summary, write_candidate_output
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- phase: 05-02
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provides: generate_all_plots, generate_reproducibility_report
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- phase: 04-03
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provides: scored_genes table in DuckDB
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provides:
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- CLI report command orchestrating full output pipeline
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- CliRunner integration tests for report command
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affects: [unified-cli, end-to-end-workflow, user-experience]
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# Tech tracking
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tech-stack:
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added: []
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patterns: [cli-checkpoint-restart, dual-format-output, graceful-degradation, integration-testing-with-synthetic-fixtures]
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key-files:
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created:
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- src/usher_pipeline/cli/report_cmd.py
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- tests/test_report_cmd.py
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modified:
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- src/usher_pipeline/cli/main.py
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key-decisions:
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- "Report command follows established score_cmd.py pattern (config load, store init, checkpoint check, pipeline steps, summary, cleanup)"
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- "Support --output-dir, --force, --skip-viz, --skip-report, and configurable tier threshold flags"
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- "Tier thresholds passed as uppercase keys (HIGH/MEDIUM/LOW) with composite_score and evidence_count fields"
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- "Default output directory: {data_dir}/report if --output-dir not specified"
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- "Checkpoint pattern: warn and skip if candidates.tsv exists without --force"
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- "Integration tests use synthetic DuckDB fixtures with isolated tmp_path instances (no external dependencies)"
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patterns-established:
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- "CliRunner integration tests with test_config and populated_db fixtures"
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- "Synthetic test data designed to validate tier distribution (3 HIGH, 5 MEDIUM, 5 LOW, 4 EXCLUDED, 3 NULL)"
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- "Each test uses isolated tmp_path to avoid cross-test contamination"
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- "Graceful degradation: visualization and reproducibility report failures logged as warnings, not errors"
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# Metrics
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duration: 3min
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completed: 2026-02-11
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---
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# Phase 05 Plan 03: CLI Report Command Summary
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**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.
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## Performance
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- **Duration:** 3 minutes
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- **Started:** 2026-02-11T20:04:06Z
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- **Completed:** 2026-02-11T20:07:42Z
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- **Tasks:** 2
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- **Files modified:** 3
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## Accomplishments
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- Implemented CLI report command following established CLI pattern from score_cmd.py and evidence_cmd.py
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- Orchestrates full output pipeline: load scored_genes, apply tiering, add evidence summary, write TSV+Parquet, generate plots, create reproducibility reports
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- Supports configurable tier thresholds (--high-threshold, --medium-threshold, --low-threshold, --min-evidence-high, --min-evidence-medium)
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- Provides skip flags (--skip-viz, --skip-report) for flexible iteration
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- Created 9 comprehensive CliRunner integration tests with synthetic fixtures
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- Unified CLI now has 5 commands: setup, evidence, score, report, info
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## Task Commits
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Each task was committed atomically:
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1. **Task 1: Report CLI command** - `2ab25ef` (feat)
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- report_cmd.py with full pipeline orchestration
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- Registered in main.py CLI entry point
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- Follows established pattern: config load, store init, checkpoint, steps, summary, cleanup
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2. **Task 2: CliRunner integration tests** - `c10d595` (test)
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- test_report_cmd.py with 9 comprehensive tests
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- Fixtures: test_config (minimal YAML), populated_db (synthetic scored_genes)
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- Fixed tier threshold format bug (uppercase keys, composite_score field)
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- Fixed write_candidate_output parameter name bug (filename_base not base_filename)
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## Files Created/Modified
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- `src/usher_pipeline/cli/report_cmd.py` - CLI report command orchestrating output pipeline
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- `src/usher_pipeline/cli/main.py` - Added report command registration
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- `tests/test_report_cmd.py` - 9 CliRunner integration tests
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## Decisions Made
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- **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)
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- **Tier threshold format:** Pass uppercase keys (HIGH/MEDIUM/LOW) with composite_score and evidence_count fields to match assign_tiers() signature
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- **Default output directory:** Use {data_dir}/report if --output-dir not specified (consistent with other evidence commands)
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- **Checkpoint pattern:** Warn and skip if candidates.tsv exists without --force flag (prevents accidental overwrites)
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- **Graceful degradation:** Wrap visualization and reproducibility report generation in try/except to log warnings rather than fail entire command
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- **Integration test strategy:** Use synthetic DuckDB fixtures with isolated tmp_path instances to avoid external API dependencies and ensure fast, reproducible tests
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## Deviations from Plan
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### Auto-fixed Issues
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**1. [Rule 1 - Bug] Fixed tier threshold dictionary format**
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- **Found during:** Task 2 (test execution)
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- **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
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- **Fix:** Changed tier_thresholds dict to use uppercase keys and composite_score field, added evidence_count: 1 for LOW tier
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- **Files modified:** src/usher_pipeline/cli/report_cmd.py
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- **Verification:** All tests pass after fix
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- **Committed in:** c10d595 (Task 2 commit)
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**2. [Rule 1 - Bug] Fixed write_candidate_output parameter name**
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- **Found during:** Task 2 (test execution)
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- **Issue:** write_candidate_output() function parameter is filename_base, not base_filename
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- **Fix:** Changed base_filename="candidates" to filename_base="candidates"
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- **Files modified:** src/usher_pipeline/cli/report_cmd.py
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- **Verification:** All tests pass after fix
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- **Committed in:** c10d595 (Task 2 commit)
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---
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**Total deviations:** 2 auto-fixed (2 bug fixes)
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**Impact on plan:** Both were trivial parameter/key name mismatches discovered during testing. Fixed inline before test commit. No scope creep.
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## Issues Encountered
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None - plan executed smoothly with two minor bugs caught and fixed during test-driven development.
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## User Setup Required
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None - no external service configuration required.
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## Next Phase Readiness
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- Phase 05 (Output & CLI) is now complete
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- All output modules implemented: tiering, evidence summary, dual-format writers, visualizations, reproducibility reports
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- Unified CLI provides complete end-to-end workflow: setup -> evidence -> score -> report
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- Ready for Phase 06 (Final Integration & Validation) if planned
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- All tests pass (9/9 CliRunner integration tests), no blockers
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---
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*Phase: 05-output-cli*
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*Completed: 2026-02-11*
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## Self-Check: PASSED
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All files and commits verified:
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**Files created:**
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- ✓ src/usher_pipeline/cli/report_cmd.py
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- ✓ tests/test_report_cmd.py
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**Files modified:**
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- ✓ src/usher_pipeline/cli/main.py
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**Commits:**
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- ✓ 2ab25ef (Task 1: Report CLI command)
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- ✓ c10d595 (Task 2: CliRunner integration tests)
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**Tests:**
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- ✓ 9/9 tests pass (100% pass rate)
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All verification checks passed successfully.
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