diff --git a/.planning/STATE.md b/.planning/STATE.md index e010056..63bbbba 100644 --- a/.planning/STATE.md +++ b/.planning/STATE.md @@ -10,17 +10,17 @@ See: .planning/PROJECT.md (updated 2026-02-11) ## Current Position Phase: 5 of 6 (Output & CLI) -Plan: 2 of 3 in current phase (plans 05-01, 05-02 complete) -Status: Phase 5 in progress — 05-02 complete -Last activity: 2026-02-11 — Plan 05-02 executed and verified +Plan: 3 of 3 in current phase (plans 05-01, 05-02, 05-03 complete) +Status: Phase 5 complete — 05-03 complete +Last activity: 2026-02-11 — Plan 05-03 executed and verified -Progress: [█████████░] 85.0% (17/20 plans complete across all phases) +Progress: [█████████░] 90.0% (18/20 plans complete across all phases) ## Performance Metrics **Velocity:** -- Total plans completed: 17 -- Average duration: 5.0 min +- Total plans completed: 18 +- Average duration: 4.9 min - Total execution time: 1.5 hours **By Phase:** @@ -31,17 +31,17 @@ Progress: [█████████░] 85.0% (17/20 plans complete across al | 02 - Prototype Evidence Layer | 2/2 | 8 min | 4.0 min/plan | | 03 - Core Evidence Layers | 6/6 | 52 min | 8.7 min/plan | | 04 - Scoring Integration | 3/3 | 10 min | 3.3 min/plan | -| 05 - Output & CLI | 2/3 | 9 min | 4.5 min/plan | +| 05 - Output & CLI | 3/3 | 12 min | 4.0 min/plan | **Recent Plan Details:** | Plan | Duration | Tasks | Files | |------|----------|-------|-------| -| Phase 03 P06 | 13 min | 2 tasks | 10 files | | Phase 04 P01 | 4 min | 2 tasks | 4 files | | Phase 04 P02 | 3 min | 2 tasks | 4 files | | Phase 04 P03 | 3 min | 2 tasks | 4 files | | Phase 05 P01 | 4 min | 2 tasks | 5 files | | Phase 05 P02 | 5 min | 2 tasks | 6 files | +| Phase 05 P03 | 3 min | 2 tasks | 3 files | ## Accumulated Context @@ -124,6 +124,10 @@ Recent decisions affecting current work: - [05-02]: Graceful degradation (individual plot failures don't block batch generation) - [05-02]: Dual-format reproducibility reports (JSON machine-readable + Markdown human-readable) - [05-02]: Optional validation metrics in reproducibility reports (report generates whether or not validation provided) +- [05-03]: Report command follows established CLI pattern (config load, store init, checkpoint, steps, summary, cleanup) +- [05-03]: Configurable tier thresholds via CLI flags (--high-threshold, --medium-threshold, --low-threshold, --min-evidence-high, --min-evidence-medium) +- [05-03]: Skip flags for flexible iteration (--skip-viz, --skip-report) allow faster output generation +- [05-03]: Graceful degradation for visualization and reproducibility report failures (warnings, not errors) ### Pending Todos @@ -136,5 +140,5 @@ None yet. ## Session Continuity Last session: 2026-02-11 - Phase 5 execution -Stopped at: Plan 05-02 complete — visualization and reproducibility report modules implemented with tests -Resume file: .planning/phases/05-output-cli/05-02-SUMMARY.md +Stopped at: Plan 05-03 complete — CLI report command implemented with comprehensive CliRunner integration tests, Phase 5 complete +Resume file: .planning/phases/05-output-cli/05-03-SUMMARY.md diff --git a/.planning/phases/05-output-cli/05-03-SUMMARY.md b/.planning/phases/05-output-cli/05-03-SUMMARY.md new file mode 100644 index 0000000..ec0fa24 --- /dev/null +++ b/.planning/phases/05-output-cli/05-03-SUMMARY.md @@ -0,0 +1,166 @@ +--- +phase: 05-output-cli +plan: 03 +subsystem: cli +tags: [click, cli, report, integration-testing, clir unner] + +# Dependency graph +requires: + - phase: 05-01 + provides: assign_tiers, add_evidence_summary, write_candidate_output + - phase: 05-02 + provides: generate_all_plots, generate_reproducibility_report + - phase: 04-03 + provides: scored_genes table in DuckDB +provides: + - CLI report command orchestrating full output pipeline + - CliRunner integration tests for report command +affects: [unified-cli, end-to-end-workflow, user-experience] + +# Tech tracking +tech-stack: + added: [] + patterns: [cli-checkpoint-restart, dual-format-output, graceful-degradation, integration-testing-with-synthetic-fixtures] + +key-files: + created: + - src/usher_pipeline/cli/report_cmd.py + - tests/test_report_cmd.py + modified: + - src/usher_pipeline/cli/main.py + +key-decisions: + - "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)" + +patterns-established: + - "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" + +# Metrics +duration: 3min +completed: 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.