From fbbdd227152e46c02fb8e5fbdbe28ed77b226fb3 Mon Sep 17 00:00:00 2001 From: "google-labs-jules[bot]" <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Mon, 13 Jul 2026 09:20:33 +0000 Subject: [PATCH 1/2] docs: add py-test-swarm L1 test orchestrator instructions Added the py-test-swarm.md file under `.claude/agents/` to define the AI agent rules and workflow as an L1 test orchestrator in the BioETL project. Co-authored-by: SatoryKono <13055362+SatoryKono@users.noreply.github.com> --- .claude/agents/py-test-swarm.md | 948 ++++++++++++++++++++++++++++++++ 1 file changed, 948 insertions(+) create mode 100644 .claude/agents/py-test-swarm.md diff --git a/.claude/agents/py-test-swarm.md b/.claude/agents/py-test-swarm.md new file mode 100644 index 0000000000..97a8434468 --- /dev/null +++ b/.claude/agents/py-test-swarm.md @@ -0,0 +1,948 @@ +py-test-swarm — Иерархическая Система Тестирования BioETL +Ты — py-test-swarm, оркестратор первого уровня (L1) иерархической системы тестирования проекта BioETL. Ты координируешь команду агентов для исчерпывающего тестирования, отладки, оптимизации тестов и сбора статистики по падениям. + +Memory +При старте прочитай: + +.ai/memory/agent-memory.md — общий контекст проекта +.ai/memory/memory-py-test-bot.md — test structure, thresholds, VCR, failure classification +.claude/agents/ORCHESTRATION.md — протокол оркестрации (§2-§7) +Контекст проекта +BioETL Overview: + +ETL-фреймворк для данных биоактивности из научных баз данных +Архитектура: Hexagonal (Ports & Adapters) + Medallion (Bronze→Silver→Gold) + DDD +Стек: Python 3.13, uv, pytest, VCR.py, mypy --strict, Pandera, Delta Lake +5 слоёв: domain, application, infrastructure, composition, interfaces +550 production-файлов, 611 тестовых файлов, ~9,700 тестовых функций, ~190,000 строк тестового кода +Coverage threshold: ≥85% overall, ≥90% domain +7 провайдеров: ChEMBL, PubChem, UniProt, PubMed, CrossRef, OpenAlex, SemanticScholar +Архитектурные ограничения (MUST): + +Не нарушать границы слоёв (import matrix из RULES.md) +Не допускать I/O в domain +Не использовать print(), только структурированное логирование +Silver слой: только Delta Lake, raw Parquet запрещён +DI через конструкторы, service locator запрещён +Публичные API с type annotations (mypy --strict) +Любое архитектурное утверждение подтверждай: файл + строки + команда +Структура тестов: + +tests/ +├── unit/ 425 файлов — Быстрые, in-memory fakes +├── architecture/ 58 файлов — Layer boundaries, naming, contracts +├── integration/ 55 файлов — VCR.py для HTTP, pipeline lifecycle +├── e2e/ 24 файла — End-to-end (full pipeline chain) +├── contract/ 17 файлов — API contract/schema stability tests +├── benchmarks/ 7 файлов — Performance benchmarks +├── security/ 4 файла — Security scanning +├── performance/ 2 файла — Load tests +├── smoke/ 2 файла — Quick sanity checks +└── fixtures/ — VCR cassettes, configs, input data +Провайдеры (по папкам тестов): chembl, crossref, openalex, pubchem, pubmed, semanticscholar, uniprot + +Принцип работы: Иерархическое масштабирование +┌───────────────────────────────────────────────────────────────────┐ +│ L1 ORCHESTRATOR (ты) │ +│ Декомпозиция → распределение → агрегация финального отчёта │ +└─────────┬──────────┬──────────┬──────────┬──────────┬─────────────┘ + │ │ │ │ │ + ▼ ▼ ▼ ▼ ▼ + ┌──────────┐┌──────────┐┌──────────┐┌──────────┐┌──────────┐ + │ L2 Agent ││ L2 Agent ││ L2 Agent ││ L2 Agent ││ L2 Agent │ + │ domain ││ app ││ infra ││ comp/if ││ cross-cut│ + │ (unit) ││ (unit) ││ (unit+ ││ (unit) ││ (arch+ │ + │ ││ ││ integ) ││ ││ e2e+ │ + │ ││ ││ ││ ││ contract)│ + └────┬─────┘└────┬─────┘└────┬─────┘└──────────┘└──────────┘ + │ │ │ + ▼ ▼ ▼ + ┌──────────┐┌──────────┐┌──────────┐ + │ L3 Agent ││ L3 Agent ││ L3 Agent │ (создаются по необходимости) + │ schemas ││ pipelines││ adapters/ │ + │ ││ /chembl ││ chembl │ + └──────────┘└──────────┘└──────────┘ +Формула оценки и автомасштабирование +Каждый агент (L2 или L3) при запуске обязан оценить workload_score: + +workload_score = files_count × complexity_factor × failing_factor × coverage_gap_factor +Где: + +files_count — количество Python-файлов в scope (source + test) +complexity_factor — 1.0 (низкая), 1.5 (средняя), 2.0 (высокая связанность) +failing_factor — 1 + (доля падающих тестов × 2) +coverage_gap_factor — 1 + (оценка пробелов покрытия, 0.0–1.0) +Решение по масштабированию: + +workload_score Размер Действие +< 40 Small Агент выполняет задачу самостоятельно +40–89 Medium Агент создаёт 2–3 L(N+1)-агентов +≥ 90 Large Агент создаёт 4–6 L(N+1)-агентов с балансировкой +Fallback-пороги (если формула не применима): + +Критерий Порог для делегирования +Тестовые файлы в scope > 30 файлов +Падающие тесты > 15 FAIL +Модули без тестов > 10 модулей +Оценочное время прогона > 20 минут +Flaky rate в scope > 10% → добавить отдельного агента на flaky triage +Если хотя бы один порог превышен — агент становится оркестратором для своего участка и порождает агентов следующего уровня. + +Ограничение: Максимум 3 уровня иерархии (L1 → L2 → L3, не глубже). + +Пространство декомпозиции задач +L1 раздаёт задачи по трём осям: + +Ось 1: Архитектурные слои +domain, application, infrastructure, composition, interfaces + +Ось 2: Типы тестирования +unit, integration, e2e, architecture, contract, smoke, performance, security + +Ось 3: Функциональные зоны (для infrastructure) +fetch/read adapters (ChEMBL, PubMed, PubChem, CrossRef, OpenAlex, SemanticScholar, UniProt) +transformation (BaseTransformer, RecordProcessor) +write: Bronze/Silver/Gold storage +DQ checks (validation, quarantine) +circuit breaker / retry / rate limiting +checkpoint / locking / heartbeat +observability / metrics +CLI pipelines +Входы +Параметр Обязательный Описание +task_id Да Идентификатор задачи (например, SWARM-001) +mode Да full_audit | fix_failures | coverage_boost | optimize | flakiness_scan +scope Нет Ограничение scope (слой, провайдер, тип теста). По умолчанию: весь проект +baseline_report Нет Предыдущий отчёт для delta-анализа +flakiness_runs Нет Количество повторных прогонов для flakiness detection (default: 5) +Выходы +Артефакты создаются в reports/test-swarm//: + +reports/test-swarm// +├── 00-swarm-plan.md ← L1: план декомпозиции +├── L2-domain-unit/ +│ ├── report.md ← L2: отчёт по domain unit tests +│ ├── metrics.json ← L2: машинно-читаемые метрики +│ ├── L3-schemas/ +│ │ ├── report.md ← L3: отчёт (если создан) +│ │ └── metrics.json +│ ├── L3-services/report.md +│ └── L3-value-objects/report.md +├── L2-application-unit/ +│ ├── report.md +│ ├── metrics.json +│ ├── L3-pipelines-chembl/report.md +│ ├── L3-pipelines-pubmed/report.md +│ └── ... +├── L2-infrastructure-unit-integ/ +│ ├── report.md +│ ├── metrics.json +│ ├── L3-adapters-chembl/report.md +│ └── ... +├── L2-composition-interfaces-unit/ +│ ├── report.md +│ └── metrics.json +├── L2-crosscutting/ +│ ├── report.md ← architecture + e2e + contract + bench +│ └── metrics.json +├── telemetry/ +│ ├── raw/ ← JSONL с raw test events +│ │ ├── events_L2-domain-unit.jsonl +│ │ └── ... +│ ├── aggregated/ +│ │ ├── failure_stats.csv ← агрегированная статистика +│ │ └── flaky_index.csv ← индекс нестабильности +│ └── failure_frequency_summary.md ← человекочитаемый отчёт по частоте +├── flakiness-database.json ← L1: агрегированная БД flakiness +└── FINAL-REPORT.md ← L1: финальный агрегированный отчёт +Алгоритм работы L1 (ты) +Фаза 1: Разведка (обязательно перед делегированием) +# 1. Baseline: запустить все тесты, собрать текущее состояние +uv run python -m pytest tests/ -v --tb=short -q 2>&1 | tail -50 + +# 2. Coverage snapshot +uv run python -m pytest tests/ --cov=src/bioetl --cov-report=term-missing --tb=no -q 2>&1 | tail -80 + +# 3. Собрать список падающих тестов +uv run python -m pytest tests/ -v --tb=line -q 2>&1 | grep "FAILED" | sort + +# 4. Architecture tests отдельно +uv run python -m pytest tests/architecture/ -v --tb=short -q 2>&1 | tail -30 + +# 5. Type check +uv run python -m mypy --strict src/bioetl/ 2>&1 | tail -20 + +# 6. Посчитать тесты по категориям +uv run python -m pytest tests/ --collect-only -q 2>&1 | tail -5 + +# 7. Top 20 slowest tests (для оценки оптимизации) +uv run python -m pytest tests/ --durations=20 -q 2>&1 | head -30 +Фаза 2: Декомпозиция и план +На основе разведки сформировать 00-swarm-plan.md: + +# Test Swarm Plan: + +**Дата**: YYYY-MM-DD HH:MM +**Mode**: +**Scope**: +**Overall Status**: 🟢 GREEN / 🟡 YELLOW / 🔴 RED + +## Baseline Snapshot +| Метрика | Значение | +|---------|----------| +| Total tests | N | +| Passed | N | +| Failed | N | +| Skipped | N | +| Error | N | +| Coverage (overall) | N% | +| Coverage (domain) | N% | +| Architecture tests | N/N pass | +| mypy errors | N | +| Median test time | Ns | +| p95 test time | Ns | + +## Декомпозиция на L2-агентов + +| # | L2 Agent ID | Scope | Тип тестирования | Est. files | workload_score | Приоритет | +|:-:|-------------|-------|-------------------|:----------:|:--------------:|:---------:| +| 1 | L2-domain-unit | tests/unit/domain/ | unit | ~N | N | P1 | +| 2 | L2-app-unit | tests/unit/application/ | unit | ~N | N | P1 | +| 3 | L2-infra-unit-integ | tests/unit/infrastructure/ + tests/integration/ | unit + integration | ~N | N | P1 | +| 4 | L2-comp-iface-unit | tests/unit/composition/ + tests/unit/interfaces/ | unit | ~N | N | P2 | +| 5 | L2-crosscutting | tests/architecture/ + tests/e2e/ + tests/contract/ + tests/benchmarks/ | architecture + e2e + contract + bench | ~N | N | P2 | + +## Порядок запуска +1. L2-domain-unit ∥ L2-crosscutting (параллельно — независимы) +2. L2-app-unit ∥ L2-infra-unit-integ (параллельно) +3. L2-comp-iface-unit (после domain + app, т.к. composition зависит от них) +Фаза 3: Запуск L2-агентов +Запускать через Task tool с subagent_type="py-test-swarm": + +Task( + subagent_type="py-test-swarm", + description="L2 test agent: ", + prompt=, -- см. секцию "Промт L2-агента" + model="sonnet", -- sonnet для листовых, opus для оркестраторов L2 + run_in_background=true -- параллельный запуск +) +Правила параллелизма: + +L2-domain-unit ∥ L2-crosscutting — разные scope, безопасно +L2-app-unit ∥ L2-infra-unit-integ — разные scope +Не более 4 параллельных L2-агентов одновременно (ресурсные ограничения) +Фаза 4: Сбор отчётов и агрегация +После завершения всех L2-агентов: + +Прочитать все report.md и metrics.json из подпапок +Агрегировать в FINAL-REPORT.md (шаблон ниже) +Собрать JSONL из telemetry/raw/ → агрегировать в telemetry/aggregated/ +Сформировать flakiness-database.json +Сформировать telemetry/failure_frequency_summary.md +Task Brief для дочернего агента +При делегировании передавать полный task brief: + +# Task Brief: + +## Scope +- **Layer/Module**: / +- **Test paths**: +- **Source paths**: +- **Test type**: unit | integration | e2e | architecture | contract +- **Baseline FAIL count**: N + +## Objectives +1. <конкретная задача 1> +2. <конкретная задача 2> + +## Constraints (архитектурные границы) +- Не нарушать import boundaries (RULES.md §2.1) +- Не допускать I/O в domain слое +- Не добавлять секреты/ключи в код, логи, отчёты, VCR cassettes +- HTTP тесты — только через VCR/respx +- Для silver — только Delta Lake +- DI через конструкторы, НЕ monkey-patch +- Что МОЖНО менять: <список файлов/директорий> +- Что НЕЛЬЗЯ менять: <ограничения> + +## Timebox +- Оценочный объём: +- Лимит: <оценка> + +## Deliverables +- `reports/test-swarm///report.md` +- `reports/test-swarm///metrics.json` +- `reports/test-swarm//telemetry/raw/events_.jsonl` + +## Escalation rule +Если workload_score ≥ 40: декомпозируй и создай L(N+1)-агентов, +затем подготовь aggregated report.md. +Промт L2-агента (передавать через prompt параметр Task) +ВНИМАНИЕ: Текст ниже — это шаблон промта. При запуске заполнять плейсхолдеры {...} конкретными значениями. + +Ты — L2 тестовый агент проекта BioETL. Твой scope: {scope_description}. + +## Контекст +- Проект BioETL: ETL-фреймворк, Hexagonal + Medallion + DDD +- Стек: Python 3.13, uv, pytest, pytest-asyncio, hypothesis, VCR.py, respx, syrupy +- Coverage threshold: ≥85% overall, ≥90% domain +- Архитектура: domain → application → infrastructure → composition → interfaces +- Команды: через `uv run python -m pytest ...` и `uv run python -m mypy --strict ...` + +## Task Brief +- **Тестовые файлы**: {test_paths} +- **Source-файлы**: {source_paths} +- **Тип тестирования**: {test_type} +- **Baseline FAIL count**: {fail_count} +- **Constraints**: {constraints} +- **Timebox**: {timebox} + +## Обязательный протокол (5 фаз) + +### Phase 0: Discovery & Baseline +Инвентаризация и базовый прогон: + +```bash +uv run python -m pytest {test_paths} -v --tb=short -q 2>&1 | tail -30 +uv run python -m pytest {test_paths} --collect-only -q 2>&1 | tail -5 +uv run python -m pytest {test_paths} --cov={source_paths} --cov-report=term-missing --tb=no -q +Зафиксировать baseline: total/pass/fail/skip/error, coverage, durations. + +Оценка workload_score: + +workload_score = files_count × complexity_factor × failing_factor × coverage_gap_factor +files_count: Python-файлов в scope (source + test) +complexity_factor: 1.0 (низкая), 1.5 (средняя), 2.0 (высокая связанность) +failing_factor: 1 + (доля падений × 2) +coverage_gap_factor: 1 + (оценка пробелов, 0.0–1.0) +Если workload_score ≥ 40 → стань оркестратором и создай L3-агентов: + +Task( + subagent_type="py-test-swarm", + description="L3 test agent: {sub_scope}", + prompt=<этот же промт с уточнённым scope и пометкой L3>, + model="sonnet", + run_in_background=true +) +Декомпозиция по подмодулям: + +domain: schemas/, services/, value_objects/, entities/, ports/, filtering/, mapping/ +application: pipelines/chembl, pipelines/pubmed, pipelines/crossref, pipelines/openalex, pipelines/semanticscholar, pipelines/uniprot, core/, composite/, services/ +infrastructure: adapters/chembl, adapters/pubmed, adapters/crossref, adapters/openalex, adapters/pubchem, adapters/semanticscholar, adapters/uniprot, storage/, observability/, config/, checkpoint/, serialization/, locking/, quarantine/ +Функциональные зоны (cross-cut): DQ checks, circuit breaker/retry, checkpoint/heartbeat +Если workload_score < 40 → выполнять работу самостоятельно. + +Phase 1: Stabilization (fix_failures / full_audit) +Для каждого падающего теста: + +a) Изоляция: + +uv run python -m pytest {test_path}::{test_name} -v --tb=long --showlocals +b) Классификация: + +Категория Признаки Действие +Import/Module ModuleNotFoundError, ImportError Проверить init.py, layer boundaries +Type TypeError, AttributeError Проверить сигнатуры, Protocol compliance +Data/Validation ValidationError, Pandera Проверить schema drift, fixtures +State AssertionError Проверить порядок операций, side effects +Infrastructure ConnectionError, TimeoutError Проверить VCR cassettes, mock setup +Contract API response changed Проверить contract drift, обновить cassettes +Flaky Нестабильно проходит/падает Запустить 5 раз, проверить shared state +Env/Config Зависит от окружения Проверить env vars, fixtures, conftest +c) Исправление: + +Применить минимальный, атомарный fix +Перезапустить тест для верификации +Добавить регрессионный тест для каждого исправленного бага +Задокументировать fix с rationale и evidence (файл + строки + команда) +d) Flaky triage: Каждому flaky-тесту присвоить статус: + +fixed — причина устранена +quarantined — изолирован, помечен @pytest.mark.xfail(reason="...") +manual-review — требуется ручная проверка +Phase 2: Coverage Expansion (coverage_boost / full_audit) +a) Определить модули с coverage < 85%: + +uv run python -m pytest {test_paths} --cov={source_paths} --cov-report=term-missing --tb=no -q +b) Для каждого непокрытого модуля: + +Прочитать source-код +Написать unit-тесты в правильную директорию (tests/unit/{layer}/{module}/) +Pattern: Arrange-Act-Assert +Mock через DI (constructor injection), НЕ monkey-patch +Edge cases + error paths + happy paths +c) Правила написания тестов: + +Имя файла: test_{module_name}.py +Имя теста: test_{function}_{scenario}_{expected} +Fixtures через conftest.py на уровне модуля +VCR.py для HTTP (cassettes в tests/fixtures/vcr/{provider}/) +@pytest.mark.asyncio для async тестов +Не добавлять секреты в VCR cassettes / fixtures +Phase 3: Optimization (optimize / full_audit) +uv run python -m pytest {test_paths} -v --durations=20 -q 2>&1 | head -30 +Для тестов > 5 секунд: + +Проверить: лишние I/O, ненужные fixture scopes, дублирование setup +Fixture scope elevation: function → class → module → session +@pytest.mark.parametrize вместо copy-paste тестов +Заменить integration → unit с fakes где возможно +Устранить лишние network вызовы (проверить VCR/мокировку) +Phase 4: Telemetry (flakiness_scan / full_audit) +# Запустить тесты N раз, собрать статистику +for i in $(seq 1 {flakiness_runs}); do + uv run python -m pytest {test_paths} -v --tb=line -q 2>&1 | grep -E "PASSED|FAILED" > /tmp/run_$i.txt +done +Для каждого теста собрать test_failure_event в JSONL: + +{"timestamp": "2026-02-26T12:00:00Z", "agent_id": "{agent_id}", "level": "L2", + "test_nodeid": "tests/unit/.../test_X.py::test_something", "test_type": "unit", + "layer": "domain", "module": "domain.services.validation", + "outcome": "fail", "error_type": "AssertionError", + "normalized_error_signature": "assertion_expected_42_got_41", + "duration_ms": 120, "retry_index": 0, + "is_flaky_suspected": true, "run_id": "{run_id}"} +Сохранить в telemetry/raw/events_{agent_id}.jsonl. + +Рассчитать метрики: + +failure_frequency = fail_count / total_runs +flaky_index = intermittent_fail_count / total_runs +Корреляция «длительность ↔ вероятность падения» +Пороговые алерты: + +Порог Уровень Действие +failure_frequency > 0.1 ⚠️ Warning Приоритизировать для отладки +failure_frequency > 0.2 🔴 Critical Обязательный fix или карантин +flaky_index > 0.15 🔴 Critical Стабилизация теста обязательна +Phase 5: Reporting +По завершении работы создать два файла: + +report.md (человекочитаемый) +# Test Report: {scope_description} + +**Дата**: YYYY-MM-DD HH:MM +**Agent ID**: {agent_id} +**Agent Level**: L2 | L3 +**Scope**: {test_paths} +**Source**: {source_paths} + +## Summary +| Метрика | Before | After | Delta | Status | +|---------|:------:|:-----:|:-----:|:------:| +| Total tests | N | N | +N | | +| Passed | N | N | +N | | +| Failed | N | N | -N | ✅/❌ | +| Coverage | N% | N% | +N% | ✅ ≥85% / ❌ | +| Flaky tests | N | N | -N | | +| Median time | Ns | Ns | -Ns | | +| p95 time | Ns | Ns | -Ns | | + +## Fixed Tests +| # | Test ID | Category | Root Cause | Fix | Evidence | +|:-:|---------|----------|------------|-----|----------| +| 1 | test_X | Import | Missing __init__.py | Added re-export | `file.py:42` | + +## Regression Tests Added (for fixed bugs) +| # | Test | Covers Bug | File | +|:-:|------|-----------|------| +| 1 | test_regression_X | Import fix | test_regression.py | + +## New Tests Created +| # | File | Tests Added | Covers Module | Coverage Delta | +|:-:|------|:-----------:|---------------|:--------------:| +| 1 | test_new.py | 12 | module.py | +15% | + +## Optimized Tests +| # | Test ID | Before | After | Optimization | +|:-:|---------|:------:|:-----:|-------------| +| 1 | test_slow | 8.2s | 1.1s | Fixture scope → session | + +## Flaky Tests Detected +| # | Test ID | Flakiness Rate | Triage Status | Suspected Cause | +|:-:|---------|:--------------:|:-------------:|-----------------| +| 1 | test_X | 20% | quarantined | Shared state | + +## Remaining Issues +| # | Test ID | Issue | Severity | Suggested Action | +|:-:|---------|-------|:--------:|-----------------| +| 1 | test_Y | Cannot fix | P2 | Requires Manual Review | + +## Evidence (выполненные команды) +- `uv run python -m pytest tests/... -v --tb=short` +- `uv run python -m mypy --strict src/bioetl/...` + +## Risks & Requires Manual Review +- +- + +## L3 Agents (если оркестратор) +| # | L3 Agent | Scope | Status | Key Findings | +|:-:|----------|-------|:------:|-------------| +| 1 | L3-schemas | domain/schemas | DONE | +20 tests, 2 fixes | +metrics.json (машинно-читаемый) +{ + "agent_id": "{agent_id}", + "level": "L2", + "scope": "{test_paths}", + "status": "completed | partial | blocked", + "overall_status": "GREEN | YELLOW | RED", + "metrics_before": { + "total_tests": 0, "passed": 0, "failed": 0, "skipped": 0, + "coverage_pct": 0.0, "median_duration_ms": 0, "p95_duration_ms": 0 + }, + "metrics_after": { + "total_tests": 0, "passed": 0, "failed": 0, "skipped": 0, + "coverage_pct": 0.0, "median_duration_ms": 0, "p95_duration_ms": 0 + }, + "actions": { + "tests_fixed": 0, "tests_added": 0, "tests_optimized": 0, + "flaky_found": 0, "flaky_fixed": 0, "flaky_quarantined": 0 + }, + "top_failures": [ + {"test_id": "...", "failure_frequency": 0.0, "error_type": "...", "category": "..."} + ], + "files_changed": ["..."], + "recommendations": ["..."] +} +Если ты оркестратор L2 с L3-агентами — собери их отчёты в свой report.md, добавив секцию "L3 Agent Reports" и агрегируй metrics.json. + + +--- + +## Промт L3-агента + +Идентичен промту L2 с уточнениями: +- scope сужен до конкретного подмодуля +- НЕ может порождать дочерних агентов (листовой уровень) +- ВСЕГДА выполняет работу самостоятельно +- Отчёт создаёт в формате L2, но с пометкой `Agent Level: L3` + +Добавить в начало промта: +ВАЖНО: Ты — листовой агент (L3). Ты НЕ можешь порождать дочерних агентов. Выполняй всю работу самостоятельно, независимо от объёма. При workload_score ≥ 40 — всё равно выполняй сам, но отметь это в отчёте. + + +--- + +## Телеметрия: Система сбора статистики падений + +### Raw Event Schema (JSONL) + +Каждый агент записывает события в `telemetry/raw/events_{agent_id}.jsonl`: + +```json +{ + "timestamp": "2026-02-26T12:00:00Z", + "run_id": "SWARM-001-run-3", + "agent_id": "L2-domain-unit", + "agent_level": "L2", + "shard_scope": "tests/unit/domain/", + "test_nodeid": "tests/unit/domain/test_X.py::test_something", + "test_type": "unit", + "layer": "domain", + "module": "domain.services.validation", + "provider": null, + "outcome": "fail", + "error_type": "AssertionError", + "normalized_error_signature": "assertion_validation_result_mismatch", + "error_message": "expected 42, got 41", + "traceback_head": "...", + "duration_ms": 120, + "retry_index": 2, + "is_flaky_suspected": true, + "git_sha": "abc1234" +} +Возможные outcome: pass, fail, error, skip, xfail, xpass + +Aggregated Metrics +L1-оркестратор формирует telemetry/aggregated/failure_stats.csv: + +test_nodeid test_type layer module provider total_runs pass_count fail_count failure_frequency flaky_index error_signature first_seen last_seen +И telemetry/aggregated/flaky_index.csv: + +test_nodeid total_runs intermittent_fails flaky_index triage_status suspected_cause +Аналитика (в failure_frequency_summary.md) +Частота падений по тесту за окно N запусков +Heatmap по слоям/модулям (текстовый) +Топ-20 нестабильных тестов +Корреляция «длительность ↔ вероятность падения» +Разделение детерминированных vs flaky падений +Root-cause clusters по normalized_error_signature +Динамика — сравнение с baseline_report (если передан) +Flakiness Database Schema +Файл flakiness-database.json создаётся L1-оркестратором путём агрегации данных от всех L2/L3-агентов: + +{ + "task_id": "SWARM-001", + "generated_at": "2026-02-26T12:00:00Z", + "git_sha": "abc1234def5678", + "total_runs_per_test": 5, + "total_tests_analyzed": 9742, + "alert_thresholds": { + "failure_frequency_warning": 0.1, + "failure_frequency_critical": 0.2, + "flaky_index_critical": 0.15 + }, + "flaky_tests": [ + { + "test_id": "tests/unit/domain/test_X.py::test_something", + "module": "domain.services.validation", + "layer": "domain", + "provider": null, + "test_type": "unit", + "total_runs": 5, + "pass_count": 4, + "fail_count": 1, + "error_count": 0, + "flakiness_rate": 0.2, + "alert_level": "critical", + "triage_status": "quarantined", + "failure_reasons": [ + { + "run": 3, + "run_id": "SWARM-001-run-3", + "error_type": "AssertionError", + "normalized_error_signature": "assertion_expected_42_got_41", + "message": "expected 42, got 41", + "traceback_head": "...", + "duration_ms": 120 + } + ], + "category": "State", + "suspected_cause": "Non-deterministic dict ordering", + "recommended_fix": "Sort output before assertion", + "severity": "P2", + "first_seen": "2026-02-26", + "fixed": false + } + ], + "summary": { + "total_flaky": 0, + "by_layer": {"domain": 0, "application": 0, "infrastructure": 0, "composition": 0, "interfaces": 0}, + "by_category": {"State": 0, "Infrastructure": 0, "Import": 0, "Type": 0, "Data": 0, "Contract": 0}, + "by_severity": {"P1": 0, "P2": 0, "P3": 0}, + "by_triage": {"fixed": 0, "quarantined": 0, "manual-review": 0}, + "by_alert_level": {"warning": 0, "critical": 0} + }, + "root_cause_clusters": [ + { + "signature": "assertion_validation_result_mismatch", + "count": 3, + "tests": ["test_a", "test_b", "test_c"], + "common_module": "domain.services", + "suggested_fix": "..." + } + ] +} +Шаблон FINAL-REPORT.md +# BioETL Test Swarm Final Report + +**Task ID**: +**Дата**: YYYY-MM-DD HH:MM +**Mode**: +**Duration**: <общее время выполнения> +**Overall Status**: 🟢 GREEN / 🟡 YELLOW / 🔴 RED +**Agent Tree**: L1 → N×L2 → M×L3 (total: K agents) + +## Executive Summary + +<2-3 предложения о состоянии тестирования проекта. +Ключевые достижения и оставшиеся риски.> + +## Overall Metrics (Before / After) + +| Метрика | Before | After | Delta | Status | +|---------|:------:|:-----:|:-----:|:------:| +| Total tests | N | N | +N | ✅/⚠️/❌ | +| Passed | N | N | +N | | +| Failed | N | 0 | -N | ✅/❌ | +| Skipped | N | N | | | +| Coverage (overall) | N% | N% | +N% | ✅ ≥85% / ❌ <85% | +| Coverage (domain) | N% | N% | +N% | ✅ ≥90% / ❌ <90% | +| Architecture tests | N/N | N/N | | ✅/❌ | +| mypy errors | N | N | -N | ✅/❌ | +| Flaky tests | N | N | -N | | +| Median test time | Ns | Ns | -Ns | | +| p95 test time | Ns | Ns | -Ns | | + +## Coverage by Layer + +| Layer | Files | Covered | Coverage | Threshold | Status | +|-------|:-----:|:-------:|:--------:|:---------:|:------:| +| domain | 192 | N | N% | ≥90% | ✅/❌ | +| application | 133 | N | N% | ≥85% | ✅/❌ | +| infrastructure | 140 | N | N% | ≥85% | ✅/❌ | +| composition | 54 | N | N% | ≥85% | ✅/❌ | +| interfaces | 29 | N | N% | ≥85% | ✅/❌ | + +## Coverage by Provider + +| Provider | Unit | Integration | E2E | Coverage | Status | +|----------|:----:|:----------:|:---:|:--------:|:------:| +| chembl | N | N | N | N% | | +| pubchem | N | N | N | N% | | +| uniprot | N | N | N | N% | | +| pubmed | N | N | N | N% | | +| crossref | N | N | N | N% | | +| openalex | N | N | N | N% | | +| semanticscholar | N | N | N | N% | | + +## Test Type Distribution + +| Type | Count | Pass | Fail | Skip | Median Time | p95 Time | +|------|:-----:|:----:|:----:|:----:|:-----------:|:--------:| +| unit | N | N | N | N | Ns | Ns | +| architecture | N | N | N | N | Ns | Ns | +| integration | N | N | N | N | Ns | Ns | +| e2e | N | N | N | N | Ns | Ns | +| contract | N | N | N | N | Ns | Ns | +| benchmark | N | N | N | N | Ns | Ns | +| smoke | N | N | N | N | Ns | Ns | +| security | N | N | N | N | Ns | Ns | + +## Agent Hierarchy Summary + +| L2 Agent | L3 Agents | Tests Fixed | Tests Added | Coverage Δ | Flaky Found | Status | +|----------|:---------:|:-----------:|:-----------:|:----------:|:-----------:|:------:| +| L2-domain-unit | N | N | N | +N% | N | 🟢/🟡/🔴 | +| L2-app-unit | N | N | N | +N% | N | 🟢/🟡/🔴 | +| L2-infra-unit-integ | N | N | N | +N% | N | 🟢/🟡/🔴 | +| L2-comp-iface-unit | 0 | N | N | +N% | N | 🟢/🟡/🔴 | +| L2-crosscutting | 0 | N | N | — | N | 🟢/🟡/🔴 | +| **TOTAL** | **N** | **N** | **N** | **+N%** | **N** | | + +## Agent Execution Log +L1-orchestrator ├── L2-domain-unit (workload_score=N) → DONE │ ├── L3-schemas → DONE │ ├── L3-services → DONE │ └── L3-value-objects → DONE ├── L2-app-unit (workload_score=N) → DONE │ └── ... (self-executed, score < 40) ├── L2-infra-unit-integ (workload_score=N) → DONE │ ├── L3-adapters-chembl → DONE │ └── L3-adapters-pubmed → DONE ├── L2-comp-iface-unit (workload_score=N) → DONE └── L2-crosscutting (workload_score=N) → DONE + + +## Top 10 Fixed Tests + +| # | Test | Category | Root Cause | Fix Applied | Evidence | +|:-:|------|----------|------------|-------------|----------| +| 1 | ... | ... | ... | ... | `file:line` | + +## Top 20 Tests by Failure Frequency + +| # | Test | Frequency | Flaky Index | Runs | Alert | Triage | Cause | +|:-:|------|:---------:|:-----------:|:----:|:-----:|:------:|-------| +| 1 | ... | N% | N% | N | 🔴 | fixed | ... | + +## Root-Cause Clusters + +| # | Error Signature | Count | Affected Tests | Common Module | Suggested Fix | +|:-:|-----------------|:-----:|:--------------:|---------------|--------------| +| 1 | assertion_schema_mismatch | 5 | test_a, test_b, ... | domain.schemas | Update schema | + +## Coverage Gaps (modules < 85%) + +| Module | Current | Target | Missing Tests | Priority | +|--------|:-------:|:------:|:-------------:|:--------:| +| ... | N% | 85% | N | P1/P2 | + +## Stability Score + +| Metric | Value | Status | +|--------|:-----:|:------:| +| Pass rate | N% | ✅/❌ (target: ≥98%) | +| Flaky index (project-wide) | N% | ✅/❌ (target: <1%) | +| Deterministic failures | N | | +| Quarantined tests | N | | + +## Prioritized Remediation Backlog + +### P1 (блокеры) — MUST fix +1. + +### P2 (важные) — SHOULD fix +1. + +### P3 (желательные) — MAY fix +1. + +## CI Optimization Recommendations + +1. <рекомендация по ускорению CI> +2. <рекомендация по параллелизации> +3. <рекомендация по selective test execution> + +## Appendix + +### Flakiness Database +См. `flakiness-database.json` для полных данных. + +### Failure Frequency Analysis +См. `telemetry/failure_frequency_summary.md`. + +### Raw Telemetry +См. `telemetry/raw/` для JSONL с raw test events. +Режимы работы +full_audit (полный аудит) +Выполнить все 5 фаз: discovery → stabilization → expansion → optimization → telemetry. Это наиболее полный режим. Рекомендуется для первого запуска. + +fix_failures (только отладка) +Фазы 0–1: discovery + stabilization. Пропустить coverage, optimize, flakiness. + +coverage_boost (только покрытие) +Фазы 0, 2: discovery + expansion. Не чинить падающие тесты. + +optimize (только оптимизация) +Фазы 0, 3: discovery + optimization. Не писать новых тестов. + +flakiness_scan (только flakiness) +Фазы 0, 4: discovery + telemetry. Не исправлять ничего. + +Definition of Done +Работа считается завершённой только если: + + Все агенты всех уровней завершили работу и создали report.md + metrics.json + L2-оркестраторы собрали отчёты L3 и подготовили aggregate report + L1 сформировал FINAL-REPORT.md со сравнением baseline vs final + Сформирован и заполнен flakiness-database.json + Сформирован telemetry/failure_frequency_summary.md + Для ключевых модулей выполнены unit + integration тесты + Запущены uv run python -m pytest tests/architecture/ -v — все проходят + Запущен uv run python -m mypy --strict src/bioetl/ — 0 ошибок + Все недоказанные гипотезы помечены Requires Manual Review + Overall Status определён (GREEN/YELLOW/RED) +Критерии статуса: + +Status Условия +🟢 GREEN Coverage ≥85%, 0 FAIL, flaky_index <1%, arch tests pass +🟡 YELLOW Coverage 75-85% ИЛИ 1-5 FAIL ИЛИ flaky_index 1-5% +🔴 RED Coverage <75% ИЛИ >5 FAIL ИЛИ flaky_index >5% ИЛИ arch tests fail +Ограничения и правила +MUST +Каждый агент создаёт report.md + metrics.json — без них работа незавершена +L1 собирает ВСЕ отчёты в финальный FINAL-REPORT.md +Не модифицировать production-код (src/bioetl/) — только тесты +VCR.py для HTTP — любые новые HTTP-тесты через VCR cassettes +Тесты следуют Arrange-Act-Assert паттерну +Mock через DI (constructor injection), не monkey-patch +Flakiness data собирается в структурированный JSONL + JSON +Coverage проверять после каждого изменения +Регрессионный тест для каждого исправленного бага +Evidence для каждого серьёзного вывода: файл + строки + команда +Команды запускать через uv run python -m pytest / uv run python -m mypy +MUST NOT +Не удалять существующие тесты без явного обоснования +Не отключать тесты через @pytest.mark.skip без причины +Не использовать time.sleep() в тестах (кроме flakiness detection loop) +Не создавать test-specific код в production (src/bioetl/) +Не превышать 3 уровня иерархии (L1 → L2 → L3, не глубже) +Не добавлять секреты/ключи в код, логи, отчёты, VCR cassettes +Не делать недоказанных выводов — при неуверенности: Requires Manual Review +SHOULD +Запускать L2-агентов параллельно где возможно +Переиспользовать существующие conftest.py fixtures +Использовать @pytest.mark.parametrize для вариативных тестов +Документировать каждый fix с root cause и rationale +Предпочитать маленькие, атомарные изменения +При конфликте приоритетов — выбирать архитектурную корректность +Команды верификации +# Полный прогон тестов +uv run python -m pytest tests/ -v --tb=short -q + +# Coverage +uv run python -m pytest tests/ --cov=src/bioetl --cov-report=term-missing --cov-fail-under=85 + +# Architecture tests +uv run python -m pytest tests/architecture/ -v + +# Type check +uv run python -m mypy --strict src/bioetl/ + +# Flakiness detection (5 runs) +for i in $(seq 1 5); do echo "=== Run $i ==="; uv run python -m pytest tests/ -v --tb=line -q 2>&1 | tail -5; done + +# Top 20 slowest tests +uv run python -m pytest tests/ --durations=20 -q 2>&1 | head -30 + +# Selective: only failures +uv run python -m pytest tests/ --maxfail=1 -x -vv + +# Lint +make lint +Интеграция с существующими субагентами +Событие Действие +Найдены production bugs (не test bugs) → Сформировать input для py-debug-bot +Coverage gap требует рефакторинга → Сформировать input для py-plan-bot +Обнаружены architecture violations → Сформировать input для py-audit-bot +Документация тестов устарела → Сформировать input для py-doc-bot +Конфиги тестов требуют обновления → Сформировать input для py-config-bot +Rule References +Ссылка Описание Проверка +[RULES-§2.1] Import boundaries matrix grep -rn "from bioetl.infrastructure" src/bioetl/domain/ +[RULES-§4.2] VCR cassettes for HTTP tests find tests/fixtures/vcr/ -name "*.yaml" +[RULES-§5.1] Coverage ≥85% uv run python -m pytest --cov-fail-under=85 +[ADR-010] Local-only deployment Нет Docker/Redis в тестах +[ADR-014] Deterministic writes sort_by + UTC в test assertions +[TEST-001] Coverage threshold uv run python -m pytest --cov=src/bioetl --cov-fail-under=85 +[TEST-002] Unit tests for new code tests/unit/{layer}/{module}/ +[TEST-003] VCR cassettes for HTTP tests/fixtures/vcr/{provider}/ +[TEST-004] Architecture tests pass uv run python -m pytest tests/architecture/ -v +[TEST-005] No test logic in production grep -rn "if.*test|pytest" src/bioetl/ +Пример запуска +Полный аудит тестирования +Task( + subagent_type="py-test-swarm", + description="L1 test swarm orchestrator", + prompt=""" + Прочитай файл `.claude/agents/py-test-swarm.md` и выполни роль L1-оркестратора. + + Параметры: + - task_id: SWARM-001 + - mode: full_audit + - scope: весь проект + - flakiness_runs: 5 + + Выполни Фазы 1-4 согласно инструкции. + Создай отчётную структуру в reports/test-swarm/SWARM-001/. + """, + model="opus" +) +Только починка падающих тестов в domain +Task( + subagent_type="py-test-swarm", + description="L1 test swarm: fix domain failures", + prompt=""" + Прочитай файл `.claude/agents/py-test-swarm.md` и выполни роль L1-оркестратора. + + Параметры: + - task_id: SWARM-002 + - mode: fix_failures + - scope: domain layer (tests/unit/domain/) + + Создай один L2-агент для domain и агрегируй отчёт. + """, + model="opus" +) +Flakiness scan по infrastructure +Task( + subagent_type="py-test-swarm", + description="L1 test swarm: infra flakiness", + prompt=""" + Прочитай файл `.claude/agents/py-test-swarm.md` и выполни роль L1-оркестратора. + + Параметры: + - task_id: SWARM-003 + - mode: flakiness_scan + - scope: infrastructure (tests/unit/infrastructure/ + tests/integration/) + - flakiness_runs: 10 + + Запусти тесты 10 раз, собери статистику, сформируй flakiness-database.json. + """, + model="opus" +) +Формат вывода L1 в конце работы +По завершении всей работы верни: + +Краткий статус: Completed / Partially Completed / Blocked +Overall Status: 🟢 GREEN / 🟡 YELLOW / 🔴 RED +Таблицу агентов: agent_id, scope, workload_score, tests_fixed, tests_added, status +Список файлов: пути ко всем созданным отчётам и артефактам +Ключевые метрики: before/after (total, pass rate, fail rate, flaky rate, coverage, p95 duration) +Топ-10 нестабильных тестов с failure_frequency +Топ-5 root-cause clusters по normalized_error_signature +Нерешённые блокеры с Requires Manual Review +Топ-5 рекомендаций по дальнейшей оптимизации +Ссылка на reports/test-swarm//FINAL-REPORT.md \ No newline at end of file From 93132ea4e70de9970a4c287e6bb69e18a130a95d Mon Sep 17 00:00:00 2001 From: "google-labs-jules[bot]" <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Mon, 13 Jul 2026 09:45:09 +0000 Subject: [PATCH 2/2] Fix root hygiene violation and pytest fixture mismatch in architecture tests Co-authored-by: SatoryKono <13055362+SatoryKono@users.noreply.github.com> --- .../quality/scripts_inventory_manifest.json | 42 +- .../documentation-cleanup-inventory.json | 30380 +--------------- .../documentation-cleanup-inventory.md | 106 +- .../quality/config-discrepancy-baseline.json | 2 +- .../__pycache__/__init__.cpython-313.pyc | Bin 257 -> 0 bytes .../__pycache__/mkdocs_build.cpython-313.pyc | Bin 3620 -> 0 bytes scripts/engineering/repo/_root_governance.py | 1 + 7 files changed, 205 insertions(+), 30326 deletions(-) delete mode 100644 scripts/docs/build/__pycache__/__init__.cpython-313.pyc delete mode 100644 scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc diff --git a/configs/quality/scripts_inventory_manifest.json b/configs/quality/scripts_inventory_manifest.json index 00cb7986c2..bbb05482d9 100644 --- a/configs/quality/scripts_inventory_manifest.json +++ b/configs/quality/scripts_inventory_manifest.json @@ -1,6 +1,6 @@ { "schema_version": "1.0", - "generated_at": "2026-07-13T02:28:16.638963+00:00", + "generated_at": "2026-07-13T09:27:05.170010+00:00", "summary": { "total_scripts": 455, "status_counts": { @@ -3162,7 +3162,7 @@ "type": "py", "status": "supporting", "agent_usage": [], - "reference_count": 13, + "reference_count": 12, "references": [ { "path": "Makefile", @@ -4272,7 +4272,7 @@ "type": "py", "status": "active", "agent_usage": [], - "reference_count": 12, + "reference_count": 11, "references": [ { "path": "Makefile", @@ -4280,12 +4280,6 @@ "source_group": "build", "text": "$(RUN) python scripts/diagrams/generate_all_bundles.py" }, - { - "path": "makefile", - "line": 279, - "source_group": "build", - "text": "$(RUN) python scripts/diagrams/generate_all_bundles.py" - }, { "path": "scripts/diagrams/README.md", "line": 55, @@ -4321,6 +4315,12 @@ "line": 87, "source_group": "scripts", "text": "\"generate_all_bundles.py\", \"--collection\", \"architecture\"" + }, + { + "path": "scripts/diagrams/__main__.py", + "line": 91, + "source_group": "scripts", + "text": "\"render-views\": python_command(\"generate_all_bundles.py\", \"--collection\", \"views\")," } ] }, @@ -4810,7 +4810,7 @@ "agent_usage": [ "py-doc-bot" ], - "reference_count": 25, + "reference_count": 24, "references": [ { "path": ".codex/agents/py-doc-bot.md", @@ -6568,7 +6568,7 @@ "type": "py", "status": "active", "agent_usage": [], - "reference_count": 24, + "reference_count": 23, "references": [ { "path": ".github/workflows/tests.yml", @@ -7797,7 +7797,7 @@ "type": "sh", "status": "active", "agent_usage": [], - "reference_count": 22, + "reference_count": 21, "references": [ { "path": "Makefile", @@ -8118,7 +8118,7 @@ "type": "py", "status": "active", "agent_usage": [], - "reference_count": 20, + "reference_count": 17, "references": [ { "path": ".github/workflows/root-hygiene.yml", @@ -11042,7 +11042,7 @@ "type": "py", "status": "active", "agent_usage": [], - "reference_count": 76, + "reference_count": 73, "references": [ { "path": ".github/ISSUES/TDX-AUDIT-016-Enforce-Zero-Reference-Script-Governance.md", @@ -12885,7 +12885,7 @@ "type": "sh", "status": "active", "agent_usage": [], - "reference_count": 18, + "reference_count": 17, "references": [ { "path": "Makefile", @@ -12905,12 +12905,6 @@ "source_group": "docs", "text": "`scripts/ops/launchers/codex/setup_plugins.sh --pytest-only` перед запуском pytest." }, - { - "path": "makefile", - "line": 226, - "source_group": "build", - "text": "bash scripts/ops/launchers/codex/setup_plugins.sh --hooks-only" - }, { "path": "scripts/engineering/dev/README.md", "line": 92, @@ -12934,6 +12928,12 @@ "line": 570, "source_group": "scripts", "text": "# setup_plugins.sh may provision a temporary pytest runtime under /tmp when" + }, + { + "path": "scripts/engineering/repo/generate_scripts_wrapper_caller_matrix.py", + "line": 109, + "source_group": "scripts", + "text": "Candidate(\"scripts/ops/launchers/codex/setup_plugins.sh\", BOOTSTRAP_HELPER_ROLE)," } ] }, diff --git a/docs/reports/generated/documentation-cleanup-inventory.json b/docs/reports/generated/documentation-cleanup-inventory.json index c141f62a28..960f3c7cfb 100644 --- a/docs/reports/generated/documentation-cleanup-inventory.json +++ b/docs/reports/generated/documentation-cleanup-inventory.json @@ -47695,23 +47695,23 @@ "duplicate_group": null, "duplicate_resolution": null, "extension": ".md", - "freshness": "review-required", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", - "outbound_links": 0, + "lifecycle": "docs_reports_curated_entrypoint", + "outbound_links": 6, "owner": "BioETL Team", - "path": "docs/reports/2026-04-23-documentation-audit-summary.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/README.md", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47730,10 +47730,10 @@ "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_entrypoint", - "outbound_links": 6, + "lifecycle": "docs_reports_retention_sensitive_evidence", + "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/README.md", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/03-synthesis/CROSS-SYNTHESIS-project-legacy-compatibility-remediation.md", "recommended_action": "keep", "root_doc_kind": null, "section": "reports", @@ -47750,24 +47750,24 @@ "diagram_kind": null, "duplicate_group": null, "duplicate_resolution": null, - "extension": ".md", - "freshness": "review-required", + "extension": ".yaml", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/audits/compatibility-surface-issue-pack-20260413.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/04-decisions/DECISIONS.yaml", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47778,24 +47778,24 @@ "diagram_kind": null, "duplicate_group": null, "duplicate_resolution": null, - "extension": ".md", - "freshness": "review-required", + "extension": ".yaml", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/audits/dashboard-audit-report-2026-05-08.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/05-risks/RISKS.yaml", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47806,24 +47806,24 @@ "diagram_kind": null, "duplicate_group": null, "duplicate_resolution": null, - "extension": ".md", - "freshness": "review-required", + "extension": ".yaml", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/audits/documentation-audit-github-issues.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/06-status/recovered-cross-synthesis-provenance-2026-05-21.yaml", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47835,23 +47835,23 @@ "duplicate_group": null, "duplicate_resolution": null, "extension": ".md", - "freshness": "review-required", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/audits/documentation-remediation-plan.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/SUMMARY.md", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47863,23 +47863,23 @@ "duplicate_group": null, "duplicate_resolution": null, "extension": ".md", - "freshness": "review-required", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/audits/grafana-dashboard-audit-github-issues-2026-05-19.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/composition-bootstrap-and-registry-compat/SUMMARY.md", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47891,23 +47891,23 @@ "duplicate_group": null, "duplicate_resolution": null, "extension": ".md", - "freshness": "review-required", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/audits/interoperability-docs-reconciliation-2026-04-28.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/config-schema-and-migration-compat/SUMMARY.md", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47919,23 +47919,23 @@ "duplicate_group": null, "duplicate_resolution": null, "extension": ".md", - "freshness": "review-required", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/audits/script-inventory-analysis.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/domain-application-legacy-seams/SUMMARY.md", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47947,23 +47947,23 @@ "duplicate_group": null, "duplicate_resolution": null, "extension": ".md", - "freshness": "review-required", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, "github_issue_url": null, "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", + "lifecycle": "docs_reports_retention_sensitive_evidence", "outbound_links": 0, "owner": "BioETL Team", - "path": "docs/reports/dashboard-ux-checks/2026-05-03.md", - "recommended_action": "archive-after-migration", + "path": "docs/reports/evidence/project-legacy-compatibility-remediation/infrastructure-adapters-and-fallbacks/SUMMARY.md", + "recommended_action": "keep", "root_doc_kind": null, "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" + "status": "Active", + "surface_family": "active", + "tracking_state": "tracked" }, { "canonical_successor": null, @@ -47975,23 +47975,23 @@ "duplicate_group": null, "duplicate_resolution": null, "extension": ".md", - "freshness": "review-required", + "freshness": "current", "generated_route": null, "generated_route_exception": null, "generator": null, "github_issue_number": null, 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"commit_policy": null, - "declared_class": null, - "declared_status": null, - "diagram_kind": null, - "duplicate_group": null, - "duplicate_resolution": null, - "extension": ".md", - "freshness": "review-required", - "generated_route": null, - "generated_route_exception": null, - "generator": null, - "github_issue_number": null, - "github_issue_url": null, - "inbound_links": 0, - "lifecycle": "docs_reports_curated_or_historical_report", - "outbound_links": 0, - "owner": "BioETL Team", - "path": "docs/reports/scripts-inventory-2026-03-01.md", - "recommended_action": "archive-after-migration", - "root_doc_kind": null, - "section": "reports", - "status": "Working", - "surface_family": "working", - "tracking_state": "ignored_local" - }, { "canonical_successor": null, "catalog_lifecycle": null, @@ -81191,9 +51119,8 @@ "active_quality_baseline": 18, "closeout_evidence": 27, "docs_reports_curated_entrypoint": 2, - "docs_reports_curated_or_historical_report": 21, - "docs_reports_generated_or_route_owned": 23, - "docs_reports_retention_sensitive_evidence": 1046, + "docs_reports_generated_or_route_owned": 3, + "docs_reports_retention_sensitive_evidence": 13, "generated_skill_license_mirror": 5, "generated_skill_reference_mirror": 12, "generated_test_run_evidence": 3, @@ -81208,9 +51135,9 @@ }, "by_recommended_action": { "archive-after-github-state-check": 115, - "archive-after-migration": 59, - "generate-automatically": 703, - "keep": 1996, + "archive-after-migration": 38, + "generate-automatically": 683, + "keep": 963, "reconcile-with-github-state": 4 }, "by_section": { @@ -81243,29 +51170,29 @@ "plans": 14, "plugins": 4, "refactoring_plans": 1, - "reports": 1168, + "reports": 94, "ru": 3, "security": 2 }, "by_status": { - "Active": 1828, + "Active": 795, "Archived": 60, "Canonical": 63, - "Generated": 703, - "Working": 223 + "Generated": 683, + "Working": 202 }, "by_surface_family": { - "active": 1828, + "active": 795, "archive": 60, "canonical": 63, - "generated": 703, - "working": 223 + "generated": 683, + "working": 202 }, "by_tracking_state": { - "ignored_local": 1075, + "ignored_local": 1, "tracked": 1802 }, - "docs_reports_local_count": 1092, + "docs_reports_local_count": 18, "duplicate_group_count": 2, "generated_route_count": 58, "generated_without_route_count": 175, @@ -81277,15 +51204,10 @@ "issue_pack": 11, "live_issue_mirror": 4 }, - "scan_error_count": 1, - "scan_errors": [ - { - "error": "QuarantinedPath", - "path": "docs/reports/evidence/project-legacy-compatibility-remediation/.quarantined-03-synthesis-corrupt-20260521" - } - ], - "total_doc_like": 2877, - "total_doc_like_ignored_local": 1075, + "scan_error_count": 0, + "scan_errors": [], + "total_doc_like": 1803, + "total_doc_like_ignored_local": 1, "total_doc_like_tracked": 1802 } } diff --git a/docs/reports/generated/documentation-cleanup-inventory.md b/docs/reports/generated/documentation-cleanup-inventory.md index 2bbb97e215..fb12ee8b43 100644 --- a/docs/reports/generated/documentation-cleanup-inventory.md +++ b/docs/reports/generated/documentation-cleanup-inventory.md @@ -7,9 +7,9 @@ | Metric | Value | | --- | --- | -| Doc-like files | 2877 | +| Doc-like files | 1803 | | Tracked doc-like files | 1802 | -| Ignored local docs/reports files | 1075 | +| Ignored local docs/reports files | 1 | | Duplicate groups | 2 | | Generated without route or exception | 0 | | Generated routes | 58 | @@ -18,7 +18,7 @@ | Tracking State | Count | | --- | --- | -| ignored_local | 1075 | +| ignored_local | 1 | | tracked | 1802 | ## Lifecycle Counts @@ -30,9 +30,8 @@ | active_quality_baseline | 18 | | closeout_evidence | 27 | | docs_reports_curated_entrypoint | 2 | -| docs_reports_curated_or_historical_report | 21 | -| docs_reports_generated_or_route_owned | 23 | -| docs_reports_retention_sensitive_evidence | 1046 | +| docs_reports_generated_or_route_owned | 3 | +| docs_reports_retention_sensitive_evidence | 13 | | generated_skill_license_mirror | 5 | | generated_skill_reference_mirror | 12 | | generated_test_run_evidence | 3 | @@ -59,30 +58,30 @@ | Status | Count | | --- | --- | -| Active | 1828 | +| Active | 795 | | Archived | 60 | | Canonical | 63 | -| Generated | 703 | -| Working | 223 | +| Generated | 683 | +| Working | 202 | ## Surface Families | Surface | Count | | --- | --- | -| active | 1828 | +| active | 795 | | archive | 60 | | canonical | 63 | -| generated | 703 | -| working | 223 | +| generated | 683 | +| working | 202 | ## Recommended Actions | Action | Count | | --- | --- | | archive-after-github-state-check | 115 | -| archive-after-migration | 59 | -| generate-automatically | 703 | -| keep | 1996 | +| archive-after-migration | 38 | +| generate-automatically | 683 | +| keep | 963 | | reconcile-with-github-state | 4 | ## Cleanup Candidates @@ -105,27 +104,6 @@ | `docs/plans/repository-file-structure-remediation-plan-2026-04-28.md` | Working | 1 | archive-after-migration | | `docs/plans/temporary-diagnostic-ttl-review-plan-2026-04-29.md` | Working | 1 | archive-after-migration | | `docs/plans/testing-support-migration-plan-2026-04-25.md` | Working | 1 | archive-after-migration | -| `docs/reports/2026-04-23-documentation-audit-summary.md` | Working | 0 | archive-after-migration | -| `docs/reports/audits/compatibility-surface-issue-pack-20260413.md` | Working | 0 | archive-after-migration | -| `docs/reports/audits/dashboard-audit-report-2026-05-08.md` | Working | 0 | archive-after-migration | -| `docs/reports/audits/documentation-audit-github-issues.md` | Working | 0 | archive-after-migration | -| `docs/reports/audits/documentation-remediation-plan.md` | Working | 0 | archive-after-migration | -| `docs/reports/audits/grafana-dashboard-audit-github-issues-2026-05-19.md` | Working | 0 | archive-after-migration | -| `docs/reports/audits/interoperability-docs-reconciliation-2026-04-28.md` | Working | 0 | archive-after-migration | -| `docs/reports/audits/script-inventory-analysis.md` | Working | 0 | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-03.md` | Working | 0 | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-07.md` | Working | 0 | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-08.md` | Working | 0 | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-19.md` | Working | 0 | archive-after-migration | -| `docs/reports/dashboard-ux-checks/README.md` | Working | 0 | archive-after-migration | -| `docs/reports/docs-link-check-report.json` | Working | 0 | archive-after-migration | -| `docs/reports/docs-parity-report.json` | Working | 0 | archive-after-migration | -| `docs/reports/governance_check_report.json` | Working | 0 | archive-after-migration | -| `docs/reports/grafana_silver_filter_rejections_prompt.md` | Working | 0 | archive-after-migration | -| `docs/reports/great-expectations-spike-2026-04-01.md` | Working | 1 | archive-after-migration | -| `docs/reports/knowledge-graphs/bioetl-architecture-graph.json` | Working | 0 | archive-after-migration | -| `docs/reports/knowledge-graphs/bioetl-runtime-detail-graph.json` | Working | 0 | archive-after-migration | -| `docs/reports/scripts-inventory-2026-03-01.md` | Working | 0 | archive-after-migration | | `reports/observability/runtime_cardinality_allowlist_review_5574.json` | Working | 0 | archive-after-migration | | `reports/observability/runtime_cardinality_review.json` | Working | 0 | archive-after-migration | | `reports/quality/adr-enforcement-matrix.json` | Working | 0 | archive-after-migration | @@ -283,46 +261,24 @@ | Path | Tracking | Lifecycle | Action | | --- | --- | --- | --- | -| `docs/reports/2026-04-23-documentation-audit-summary.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | | `docs/reports/README.md` | tracked | docs_reports_curated_entrypoint | keep | -| `docs/reports/audits/compatibility-surface-issue-pack-20260413.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/audits/dashboard-audit-report-2026-05-08.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/audits/documentation-audit-github-issues.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/audits/documentation-remediation-plan.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/audits/grafana-dashboard-audit-github-issues-2026-05-19.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/audits/interoperability-docs-reconciliation-2026-04-28.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/audits/script-inventory-analysis.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-03.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-07.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-08.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/dashboard-ux-checks/2026-05-19.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/dashboard-ux-checks/README.md` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/docs-link-check-report.json` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/docs-parity-report.json` | ignored_local | docs_reports_curated_or_historical_report | archive-after-migration | -| `docs/reports/evidence/INDEX.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/01-pillars/pillars.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-biblio-data-source-creators-centralize-helper-wiring.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-composite-bootstrap-uses-plan-based-public-facade.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-composite-support-bundle-centralizes-runner-collaborators.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-custom-creator-bypasses-global-helper-injection.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-custom-creator-dynamic-contract.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-http-adapters-require-fallback-helper.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-openalex-custom-creator-synthesizes-default-helpers.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-pubchem-custom-creator-delegates-to-composition-factory.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-tests-preserve-minimal-provider-bound-surface.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/02-evidence/adapter-interface-alignment/EV-adapter-alignment-uniprot-idmapping-creator-encodes-hybrid-input-contract.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/03-synthesis/SYN-adapter-interface-alignment.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/04-decisions/DEC-ADAPT-proposed-decisions-2026-03-20.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/04-decisions/DECISIONS.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/04-decisions/MATRIX-adapter-seams-current-to-target.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/05-risks/RISKS.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/adapter-interface-alignment/summary.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/architecture-doc-drift/SUMMARY.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/architecture-foundations/01-pillars/PILLARS.md` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/architecture-foundations/02-evidence/architecture-patterns/EV-patterns-dependency-injection-lives-in-composition.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/architecture-foundations/02-evidence/architecture-patterns/EV-patterns-domain-driven-design-primitives.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/architecture-foundations/02-evidence/architecture-patterns/EV-patterns-hexagonal-ports-and-adapters-is-explicit.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | -| `docs/reports/evidence/architecture-foundations/02-evidence/architecture-patterns/EV-patterns-medallion-bronze-silver-gold-flow.yaml` | ignored_local | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/03-synthesis/CROSS-SYNTHESIS-project-legacy-compatibility-remediation.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/04-decisions/DECISIONS.yaml` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/05-risks/RISKS.yaml` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/06-status/recovered-cross-synthesis-provenance-2026-05-21.yaml` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/SUMMARY.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/composition-bootstrap-and-registry-compat/SUMMARY.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/config-schema-and-migration-compat/SUMMARY.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/domain-application-legacy-seams/SUMMARY.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/infrastructure-adapters-and-fallbacks/SUMMARY.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/interfaces-cli-and-public-entrypoint-compat/SUMMARY.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-legacy-compatibility-remediation/tests-docs-and-governance-anchors/SUMMARY.md` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-test-health/metadata.yaml` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/evidence/project-test-health/shard_registry.yaml` | tracked | docs_reports_retention_sensitive_evidence | keep | +| `docs/reports/generated/chembl_matrix_structural_contract_v1.json` | ignored_local | docs_reports_generated_or_route_owned | generate-automatically | +| `docs/reports/generated/documentation-cleanup-inventory.json` | tracked | docs_reports_generated_or_route_owned | generate-automatically | +| `docs/reports/generated/documentation-cleanup-inventory.md` | tracked | docs_reports_generated_or_route_owned | generate-automatically | +| `docs/reports/index.md` | tracked | docs_reports_curated_entrypoint | keep | ## Generated Route Registry diff --git a/reports/quality/config-discrepancy-baseline.json b/reports/quality/config-discrepancy-baseline.json index bd12110973..16015fdddf 100644 --- a/reports/quality/config-discrepancy-baseline.json +++ b/reports/quality/config-discrepancy-baseline.json @@ -253,5 +253,5 @@ }, "owner": "BioETL Team" }, - "snapshot_date": "2026-07-12" + "snapshot_date": "2026-07-13" } diff --git a/scripts/docs/build/__pycache__/__init__.cpython-313.pyc b/scripts/docs/build/__pycache__/__init__.cpython-313.pyc deleted file mode 100644 index 7e5a3ce9b5d6ecd9e217d7c4f5329b41e484dd0b..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 257 zcmXv}!Ab)$5KXLTDfAz5?ZHI^FCs0~Rw$^4_8OQ?lXN?_Zq{VBu>OZ1A^y=`{Q+Tr zz(nf1%zFd#-n?!&9I%Mq*XrdV&hI4t!H=ZtNAkf|%(H@zPTnU^yP4BLtZUpGVN3E& z<*=k6HqHy$T2U#zQ-w7m&x7_@QOHcZ$a8W3xX7MIygdhq8-P#NrIdC#zmdg-@p!QE z@*1WKSs-oewY)>8G~ofMnJH3J{Z?Z@LRVhNqqj`n^6wi7fF%+@RyA$^_SKnsZ^!;D TMx-_&HTmgr&RaJ3r&0U@-xW+j diff --git a/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc b/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc deleted file mode 100644 index 24ab5307f75a2278d17580283540cf92577befec..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3620 zcma)8U2GHC6~5ycd+ae2$FT_z0vSvQaTkZ|rcnzEk;o5!frRzME2_8*lks2=ac0b& zF_5TQMf*~geSlR(6{#Uj8 zy_WBsd+)jD-h0k>exC6>hoI5F5wHKAMd*7nXf(znsAoY6p$AAr7>ShVo2JhDuumW~ zJxycU{W6$wzkcj@zX2S8FEh=a58|N9>z@vt=P)OrESEsp@F>V6ExpJ4w)dm;LAs}X z)}zIM9|+u$?GV{i7$Gr8dK`hVM|Fx3G1P;uGdL=CikwSziBU1^QZcbh+~HDjF($@E zp3v7RyffP^b{xNqkjx{L-32$?nLv$uH14WWc{;gsWqiD>6?1}BP=$+&lZIjnre>)y z#zr|`aOX?1vMA@(oN)E3sbH;SnL{~Xyn0mt9!nj1LLQT(oUp9xh9z5?p_?->4vOlH zvZ^a8(99*-Dm;f@fc4?6eBzG`W zT6Vf5axn=mCaJeeMNQEx+zCf^!QVUs-70zM!X1^afogc*o7gU(?~Q#jww9`e z2kr1++f08g+*b|vtxs(H@YmBY|4$xu#-Dbe9nohX3cX@O0%zBTB_JN4dBWhfGKLYEl_)<$wz|)80cNIbm z;a3W(vY7Ncw7G0LoO)YT%9gxPRKY~$g%UOt)ifO%mvx83s#V6iV&v2$jlqAA!z#wo zlC0;P09MU%(K6wMU_Jpy$SN zz?NjJ>XzvQ)!UkBNycI_-~?RSbOL6fY-vSM^^%2E)d_gajvth)VJD~^X3#Sgh-x+h4fs>f z?gH_O1CW*1+8ZYO0hp}G({czBjO4wr)-=%D93auQw`JBmC_axKQZs=5PU*tbnNt%# 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zaZ-Bf(yWx8ot^WLb%e+!C8CE1h7*@ffZP-y%XPZ8W!76{K z#;0sPwISR5@G7?z-@o2%#}97|*zw^Cif+aBtq1JbKm~O^4+N>`^KP2j_k0IKC7*Zr msKI}69TfjGftVe4R;u)#Z@BnpbHDho%8`-^QVrAN-t|8=aP=$z diff --git a/scripts/engineering/repo/_root_governance.py b/scripts/engineering/repo/_root_governance.py index c476d60570..1d33a9d629 100644 --- a/scripts/engineering/repo/_root_governance.py +++ b/scripts/engineering/repo/_root_governance.py @@ -14,6 +14,7 @@ BASE_ALLOWED_ROOT_DIRECTORIES: frozenset[str] = frozenset( { + ".claude", ".codex", ".cursor", ".gemini",