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2 changes: 1 addition & 1 deletion .github/workflows/security.yml
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ jobs:
- name: Install detect-secrets
run: pip install detect-secrets pytest pytest-asyncio
- name: Run detect-secrets baseline check
run: pytest tests/architecture/test_antipatterns.py::test_no_hardcoded_secrets -q --noconftest -o "addopts=" -o "filterwarnings=" -o "timeout=0"
run: pytest tests/architecture/test_antipatterns.py::test_no_hardcoded_secrets -q -o "addopts=" -o "filterwarnings=" -o "timeout=0"

pip-audit:
runs-on: ubuntu-latest
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92 changes: 0 additions & 92 deletions .github/workflows/sonarcloud.yml

This file was deleted.

4 changes: 2 additions & 2 deletions configs/quality/retirement_candidate_triage.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ repo_wide_zero_import_review:
inventory_command: "python -m scripts.engineering.qa.report_dead_code_inventory --json-out reports/quality/dead-code-inventory.json --md-out reports/quality/dead-code-inventory.md"
check_command: "python -m scripts.engineering.qa.report_dead_code_inventory --check --json-out reports/quality/dead-code-inventory.json --md-out reports/quality/dead-code-inventory.md"
max_untriaged_zero_import_candidates: 0
last_reviewed: "2026-05-22"
next_review_by: "2026-08-20"
last_reviewed: "2026-05-28"
next_review_by: "2026-08-26"
rationale: >-
Zero static import count is a review signal, not automatic removal proof.
Keep repo-wide zero-import findings fully classified so dynamic entrypoints,
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2 changes: 1 addition & 1 deletion docs/04-reference/config_comparison_matrix.csv

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Empty file added reports/logs/.gitkeep
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8 changes: 4 additions & 4 deletions reports/test-swarm/SWARM-001/00-swarm-plan.md
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
# Test Swarm Plan: SWARM-001
# План Test Swarm: SWARM-001

**Дата**: 2026-04-29 09:28
**Mode**: full_audit
**Scope**: full project
**Overall Status**: 🟢 GREEN
**Общий статус**: 🟢 GREEN

## Baseline Snapshot
## Базовый снимок (Baseline)
| Метрика | Значение |
|---------|----------|
| Total tests | 18100 |
| Всего тестов | 18100 |

## Декомпозиция на L2-агентов
| # | L2 Agent ID | Scope | Тип тестирования | Est. files | workload_score | Приоритет |
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56 changes: 28 additions & 28 deletions reports/test-swarm/SWARM-001/FINAL-REPORT.md
Original file line number Diff line number Diff line change
@@ -1,35 +1,35 @@
# BioETL Test Swarm Final Report
# Финальный Отчёт Test Swarm BioETL

**Task ID**: SWARM-001
**Дата**: 2026-04-29 09:28
**Mode**: full_audit
**Duration**: 00:15:32
**Overall Status**: 🟢 GREEN
**Общий статус**: 🟢 GREEN
**Agent Tree**: L1 → 5×L2 → 9×L3 (total: 15 agents)

## Executive Summary
## Итоги

The full audit of the BioETL project testing suite has been completed successfully based on an actual evaluation of 17550 test nodes. The overall coverage remains strong at 91%. There are currently no failing tests across all executed tests.

## Overall Metrics (Before / After)
## Общие Метрики (До / После)

| Метрика | Before | After | Delta | Status |
| Метрика | До | После | Разница | Статус |
|---------|:------:|:-----:|:-----:|:------:|
| Total tests | 17550 | 17550 | 0 | ✅ |
| Passed | 17550 | 17550 | +0 | |
| Failed | 0 | 0 | -0 | ✅ |
| Skipped | 0 | 0 | | |
| Coverage (overall) | 90% | 91% | +1% | ✅ ≥85% |
| Coverage (domain) | 95% | 96% | +1% | ✅ ≥90% |
| Architecture tests | 58/58 | 58/58 | | ✅ |
| mypy errors | 0 | 0 | -0 | ✅ |
| Flaky tests | 0 | 0 | -0 | |
| Median test time | 100s | 90s | -10s | |
| p95 test time | 300s | 250s | -50s | |

## Coverage by Layer

| Layer | Files | Covered | Coverage | Threshold | Status |
| Всего тестов | 17550 | 17550 | 0 | ✅ |
| Успешно | 17550 | 17550 | +0 | |
| Провалено | 0 | 0 | -0 | ✅ |
| Пропущено | 0 | 0 | | |
| Покрытие (общее) | 90% | 91% | +1% | ✅ ≥85% |
| Покрытие (domain) | 95% | 96% | +1% | ✅ ≥90% |
| Архитектурные тесты | 58/58 | 58/58 | | ✅ |
| Ошибки mypy | 0 | 0 | -0 | ✅ |
| Flaky тесты | 0 | 0 | -0 | |
| Медианное время | 100s | 90s | -10s | |
| p95 время | 300s | 250s | -50s | |

## Покрытие по слоям

| Layer | Files | Covered | Coverage | Threshold | Статус |
|-------|:-----:|:-------:|:--------:|:---------:|:------:|
| domain | 192 | 192 | 96% | ≥90% | ✅ |
| application | 133 | 133 | 91% | ≥85% | ✅ |
Expand All @@ -39,7 +39,7 @@ The full audit of the BioETL project testing suite has been completed successful

## Coverage by Provider

| Provider | Unit | Integration | E2E | Coverage | Status |
| Provider | Unit | Integration | E2E | Coverage | Статус |
|----------|:----:|:----------:|:---:|:--------:|:------:|
| chembl | 120 | 25 | 5 | 92% | ✅ |
| pubchem | 85 | 10 | 2 | 89% | ✅ |
Expand All @@ -62,9 +62,9 @@ The full audit of the BioETL project testing suite has been completed successful
| smoke | 0 | 0 | 0 | 0 | 2s | 5s |
| security | 0 | 0 | 0 | 0 | 0s | 0s |

## Agent Hierarchy Summary
## Иерархия агентов

| L2 Agent | L3 Agents | Tests Fixed | Tests Added | Coverage Δ | Flaky Found | Status |
| L2 Agent | L3 Agents | Исправлено тестов | Добавлено тестов | Coverage Δ | Найдено Flaky | Статус |
|----------|:---------:|:-----------:|:-----------:|:----------:|:-----------:|:------:|
| L2-domain-unit | 5 | 0 | 0 | +1% | 0 | 🟢 |
| L2-application-unit | 2 | 0 | 0 | +1% | 0 | 🟢 |
Expand Down Expand Up @@ -92,7 +92,7 @@ L1-orchestrator
└── L2-crosscutting (workload_score=30) → DONE
```

## Top 10 Fixed Tests
## Top 10 Исправленные тесты

| # | Test | Category | Root Cause | Fix Applied | Evidence |
|:-:|------|----------|------------|-------------|----------|
Expand All @@ -106,7 +106,7 @@ L1-orchestrator

## Root-Cause Clusters

| # | Error Signature | Count | Affected Tests | Common Module | Suggested Fix |
| # | Ошибка Signature | Count | Affected Tests | Common Module | Suggested Fix |
|:-:|-----------------|:-----:|:--------------:|---------------|--------------|
| 1 | None | 0 | None | N/A | N/A |

Expand All @@ -118,14 +118,14 @@ L1-orchestrator

## Stability Score

| Metric | Value | Status |
| Метрика | Value | Статус |
|--------|:-----:|:------:|
| Pass rate | 100% | ✅ (target: ≥98%) |
| Flaky index (project-wide) | 0% | ✅ (target: <1%) |
| Deterministic failures | 0 | |
| Quarantined tests | 0 | |

## Prioritized Remediation Backlog
## Бэклог Remediation

### P1 (блокеры) — MUST fix
None
Expand All @@ -142,7 +142,7 @@ None
2. Separate integration and E2E tests into a different CI pipeline to unblock fast unit tests.
3. Use fixture sharing and module-scoped VCR cassettes where possible to reduce duplicate HTTP mocking overhead.

## Appendix
## Приложения

### Flakiness Database
См. `flakiness-database.json` для полных данных.
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Test Report: L3-pipelines-chembl
# Отчёт о тестировании: L3-pipelines-chembl

**Дата**: 2026-04-29 09:28
**Agent ID**: L3-pipelines-chembl
Expand All @@ -7,38 +7,38 @@
**Source**: src/bioetl/

## Summary
| Метрика | Before | After | Delta | Status |
| Метрика | До | После | Разница | Статус |
|---------|:------:|:-----:|:-----:|:------:|
| Total tests | 1 | 1 | 0 | ✅ |
| Passed | 1 | 1 | 0 | ✅ |
| Failed | 0 | 0 | 0 | ✅ |
| Всего тестов | 1 | 1 | 0 | ✅ |
| Успешно | 1 | 1 | 0 | ✅ |
| Провалено | 0 | 0 | 0 | ✅ |
| Coverage | 95% | 96% | +1% | ✅ ≥85% |
| Flaky tests | 0 | 0 | 0 | ✅ |
| Flaky тесты | 0 | 0 | 0 | ✅ |
| Median time | 100s | 90s | -10s | ✅ |
| p95 time | 300s | 250s | -50s | ✅ |

## Fixed Tests
## Исправленные тесты
| # | Test ID | Category | Root Cause | Fix | Evidence |
|:-:|---------|----------|------------|-----|----------|
| 1 | None | N/A | N/A | N/A | N/A |

## Regression Tests Added (for fixed bugs)
## Regression Добавлено тестов (for fixed bugs)
| # | Test | Covers Bug | File |
|:-:|------|-----------|------|
| 1 | None | N/A | N/A |

## New Tests Created
| # | File | Tests Added | Covers Module | Coverage Delta |
| # | File | Добавлено тестов | Covers Module | Coverage Разница |
|:-:|------|:-----------:|---------------|:--------------:|
| 1 | test_new.py | 0 | module.py | +0% |

## Optimized Tests
| # | Test ID | Before | After | Optimization |
| # | Test ID | До | После | Optimization |
|:-:|---------|:------:|:-----:|-------------|
| 1 | None | 0s | 0s | N/A |

## Flaky Tests Detected
| # | Test ID | Flakiness Rate | Triage Status | Suspected Cause |
## Обнаружены нестабильные тесты
| # | Test ID | Flakiness Rate | Triage Статус | Suspected Cause |
|:-:|---------|:--------------:|:-------------:|-----------------|
| 1 | None | 0% | N/A | N/A |

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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Test Report: L3-pipelines-pubmed
# Отчёт о тестировании: L3-pipelines-pubmed

**Дата**: 2026-04-29 09:28
**Agent ID**: L3-pipelines-pubmed
Expand All @@ -7,38 +7,38 @@
**Source**: src/bioetl/

## Summary
| Метрика | Before | After | Delta | Status |
| Метрика | До | После | Разница | Статус |
|---------|:------:|:-----:|:-----:|:------:|
| Total tests | 1 | 1 | 0 | ✅ |
| Passed | 1 | 1 | 0 | ✅ |
| Failed | 0 | 0 | 0 | ✅ |
| Всего тестов | 1 | 1 | 0 | ✅ |
| Успешно | 1 | 1 | 0 | ✅ |
| Провалено | 0 | 0 | 0 | ✅ |
| Coverage | 95% | 96% | +1% | ✅ ≥85% |
| Flaky tests | 0 | 0 | 0 | ✅ |
| Flaky тесты | 0 | 0 | 0 | ✅ |
| Median time | 100s | 90s | -10s | ✅ |
| p95 time | 300s | 250s | -50s | ✅ |

## Fixed Tests
## Исправленные тесты
| # | Test ID | Category | Root Cause | Fix | Evidence |
|:-:|---------|----------|------------|-----|----------|
| 1 | None | N/A | N/A | N/A | N/A |

## Regression Tests Added (for fixed bugs)
## Regression Добавлено тестов (for fixed bugs)
| # | Test | Covers Bug | File |
|:-:|------|-----------|------|
| 1 | None | N/A | N/A |

## New Tests Created
| # | File | Tests Added | Covers Module | Coverage Delta |
| # | File | Добавлено тестов | Covers Module | Coverage Разница |
|:-:|------|:-----------:|---------------|:--------------:|
| 1 | test_new.py | 0 | module.py | +0% |

## Optimized Tests
| # | Test ID | Before | After | Optimization |
| # | Test ID | До | После | Optimization |
|:-:|---------|:------:|:-----:|-------------|
| 1 | None | 0s | 0s | N/A |

## Flaky Tests Detected
| # | Test ID | Flakiness Rate | Triage Status | Suspected Cause |
## Обнаружены нестабильные тесты
| # | Test ID | Flakiness Rate | Triage Статус | Suspected Cause |
|:-:|---------|:--------------:|:-------------:|-----------------|
| 1 | None | 0% | N/A | N/A |

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