diff --git a/.planning/STATE.md b/.planning/STATE.md index 95c7fed..d148788 100644 --- a/.planning/STATE.md +++ b/.planning/STATE.md @@ -9,19 +9,19 @@ See: .planning/PROJECT.md (updated 2026-02-11) ## Current Position -Phase: 4 of 6 (Scoring & Integration) -Plan: 3 of 3 in current phase (phase complete) -Status: Phase 4 complete — verified (14/14 must-haves, 5/5 requirements) -Last activity: 2026-02-11 — Phase 4 verified and complete +Phase: 5 of 6 (Output & CLI) +Plan: 1 of 3 in current phase (plan 05-01 complete) +Status: Phase 5 in progress — 05-01 complete +Last activity: 2026-02-11 — Plan 05-01 executed and verified -Progress: [████████░░] 75.0% (15/20 plans complete across all phases) +Progress: [████████░░] 80.0% (16/20 plans complete across all phases) ## Performance Metrics **Velocity:** -- Total plans completed: 15 -- Average duration: 5.1 min -- Total execution time: 1.3 hours +- Total plans completed: 16 +- Average duration: 5.0 min +- Total execution time: 1.4 hours **By Phase:** @@ -31,16 +31,17 @@ Progress: [████████░░] 75.0% (15/20 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 | 1/3 | 4 min | 4.0 min/plan | **Recent Plan Details:** | Plan | Duration | Tasks | Files | |------|----------|-------|-------| -| Phase 03 P04 | 8 min | 2 tasks | 8 files | | Phase 03 P05 | 10 min | 2 tasks | 8 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 | ## Accumulated Context @@ -111,6 +112,12 @@ Recent decisions affecting current work: - [04-03]: Separate --skip-qc and --skip-validation flags for flexible iteration - [04-03]: Tests use tmp_path fixtures for isolated DuckDB instances - [04-03]: Synthetic test data designed to ensure known genes rank highly (0.8-0.95 scores across all layers) +- [05-01]: Configurable tier thresholds (HIGH: score>=0.7 and evidence>=3, MEDIUM: score>=0.4 and evidence>=2, LOW: score>=0.2) +- [05-01]: EXCLUDED genes filtered out (below LOW threshold or NULL composite_score) +- [05-01]: Deterministic sorting (composite_score DESC, gene_id ASC) for reproducible output +- [05-01]: Dual-format TSV+Parquet with identical data for downstream tool compatibility +- [05-01]: YAML provenance sidecar includes statistics (tier counts) and column metadata +- [05-01]: Fixed deprecated pl.count() -> pl.len() usage for polars 0.20.5+ compatibility ### Pending Todos @@ -122,6 +129,6 @@ None yet. ## Session Continuity -Last session: 2026-02-11 - Phase 4 execution -Stopped at: Phase 4 complete and verified — all 3 plans executed, 14/14 must-haves verified -Resume file: .planning/phases/04-scoring-integration/04-VERIFICATION.md +Last session: 2026-02-11 - Phase 5 execution +Stopped at: Plan 05-01 complete — tiering, evidence summary, and dual-format writer implemented with tests +Resume file: .planning/phases/05-output-cli/05-01-SUMMARY.md diff --git a/.planning/phases/05-output-cli/05-01-SUMMARY.md b/.planning/phases/05-output-cli/05-01-SUMMARY.md new file mode 100644 index 0000000..cc80d04 --- /dev/null +++ b/.planning/phases/05-output-cli/05-01-SUMMARY.md @@ -0,0 +1,151 @@ +--- +phase: 05-output-cli +plan: 01 +subsystem: output +tags: [polars, yaml, tsv, parquet, tiering, evidence-summary] + +# Dependency graph +requires: + - phase: 04-scoring-integration + provides: scored_genes DataFrame with composite_score, evidence_count, and layer contributions +provides: + - Confidence tier classification (HIGH/MEDIUM/LOW) based on composite_score and evidence_count + - Per-gene evidence summary (supporting_layers and evidence_gaps columns) + - Dual-format TSV+Parquet writer with YAML provenance sidecar + - Comprehensive unit test suite for output module +affects: [05-02, 05-03, reporting, visualization, downstream-tools] + +# Tech tracking +tech-stack: + added: [pyyaml] + patterns: [vectorized-polars-expressions, dual-format-output, provenance-sidecars, deterministic-sorting] + +key-files: + created: + - src/usher_pipeline/output/tiers.py + - src/usher_pipeline/output/evidence_summary.py + - src/usher_pipeline/output/writers.py + - src/usher_pipeline/output/__init__.py + - tests/test_output.py + modified: [] + +key-decisions: + - "Configurable tier thresholds (HIGH: score>=0.7 and evidence>=3, MEDIUM: score>=0.4 and evidence>=2, LOW: score>=0.2)" + - "EXCLUDED genes filtered out (below LOW threshold or NULL composite_score)" + - "Deterministic sorting (composite_score DESC, gene_id ASC) for reproducible output" + - "Dual-format TSV+Parquet with identical data for downstream tool compatibility" + - "YAML provenance sidecar includes statistics (tier counts) and column metadata" + - "Fixed deprecated pl.count() -> pl.len() usage for polars 0.20.5+ compatibility" + +patterns-established: + - "Vectorized polars when/then/otherwise chains for tier assignment (not row-by-row)" + - "concat_list + list.drop_nulls + list.join for comma-separated string columns" + - "Provenance YAML sidecars alongside output files for full traceability" + - "Deterministic sorting before writing for reproducible output across runs" + +# Metrics +duration: 4min +completed: 2026-02-11 +--- + +# Phase 05 Plan 01: Output Generation Core Summary + +**Tiered candidate classification with supporting/gap evidence tracking and dual-format TSV+Parquet output with YAML provenance sidecars** + +## Performance + +- **Duration:** 4 minutes +- **Started:** 2026-02-11T19:55:28Z +- **Completed:** 2026-02-11T19:59:31Z +- **Tasks:** 2 +- **Files modified:** 5 + +## Accomplishments +- Implemented configurable confidence tier classification (HIGH/MEDIUM/LOW) with filtering of EXCLUDED genes +- Added per-gene evidence summary columns (supporting_layers and evidence_gaps) tracking which layers contributed +- Created dual-format writer producing identical TSV and Parquet outputs with YAML provenance sidecars +- Built comprehensive test suite with 9 tests covering all functionality (100% pass rate) + +## Task Commits + +Each task was committed atomically: + +1. **Task 1: Tiering logic and evidence summary module** - `d2ef3a2` (feat) + - tiers.py with assign_tiers() and configurable TIER_THRESHOLDS + - evidence_summary.py with add_evidence_summary() and EVIDENCE_LAYERS + - __init__.py with exports + +2. **Task 2: Dual-format writer with provenance sidecar and unit tests** - `4e46b48` (feat) + - writers.py with write_candidate_output() + - tests/test_output.py with 9 comprehensive tests + - Fixed deprecated pl.count() -> pl.len() usage + +## Files Created/Modified + +- `src/usher_pipeline/output/tiers.py` - Confidence tier assignment (HIGH/MEDIUM/LOW) with configurable thresholds +- `src/usher_pipeline/output/evidence_summary.py` - Per-gene supporting_layers and evidence_gaps columns +- `src/usher_pipeline/output/writers.py` - Dual-format TSV+Parquet writer with YAML provenance sidecar +- `src/usher_pipeline/output/__init__.py` - Package exports +- `tests/test_output.py` - 9 unit tests covering tiering, evidence summary, and writers + +## Decisions Made + +- **Configurable thresholds:** TIER_THRESHOLDS dictionary allows CLI configurability later while providing sensible defaults from research +- **EXCLUDED filtering:** Genes below LOW threshold (score < 0.2) or with NULL composite_score are filtered out before output +- **Deterministic sorting:** Sort by composite_score DESC, gene_id ASC for reproducible output across runs +- **Dual-format output:** TSV for human-readability and tools like Excel; Parquet for efficient large-scale data processing +- **YAML provenance:** Sidecar includes statistics (tier counts), column metadata, and timestamp for full reproducibility tracking +- **Polars 0.20.5+ compatibility:** Replaced deprecated pl.count() with pl.len() to eliminate deprecation warnings + +## Deviations from Plan + +### Auto-fixed Issues + +**1. [Rule 1 - Bug] Fixed deprecated polars API usage** +- **Found during:** Task 2 (test execution) +- **Issue:** pl.count() deprecated in polars 0.20.5+, producing warnings +- **Fix:** Replaced all occurrences of pl.count() with pl.len() in tests and writers.py, updated row access from row["count"] to row["len"] +- **Files modified:** tests/test_output.py, src/usher_pipeline/output/writers.py +- **Verification:** Tests run without deprecation warnings +- **Committed in:** 4e46b48 (Task 2 commit) + +--- + +**Total deviations:** 1 auto-fixed (1 bug fix) +**Impact on plan:** Necessary fix for current polars version compatibility. No scope creep. + +## Issues Encountered + +None - plan executed smoothly with only the deprecated API fix needed. + +## User Setup Required + +None - no external service configuration required. + +## Next Phase Readiness + +- Output module core complete with tiering, evidence summary, and dual-format writing +- Ready for visualization module (05-02) and reproducibility reporting (05-03) +- Ready for CLI command integration to generate candidate outputs +- All tests pass, no blockers + +--- +*Phase: 05-output-cli* +*Completed: 2026-02-11* + + +## Self-Check: PASSED + +All files and commits verified: + +**Files created:** +- ✓ src/usher_pipeline/output/tiers.py +- ✓ src/usher_pipeline/output/evidence_summary.py +- ✓ src/usher_pipeline/output/writers.py +- ✓ src/usher_pipeline/output/__init__.py +- ✓ tests/test_output.py + +**Commits:** +- ✓ d2ef3a2 (Task 1: Tiering logic and evidence summary module) +- ✓ 4e46b48 (Task 2: Dual-format writer with provenance and tests) +