--- 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)