usher-exploring/.planning/phases/05-output-cli/05-01-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	01	output	polars yaml tsv parquet tiering evidence-summary	phase provides 04-scoring-integration scored_genes DataFrame with composite_score, evidence_count, and layer contributions	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	05-02 05-03 reporting visualization downstream-tools	added patterns pyyaml vectorized-polars-expressions dual-format-output provenance-sidecars deterministic-sorting	created modified 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	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	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	4min	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)