Add setup.sh environment script

configs/quality/scripts_lifecycle_registry.json

@@ -247,6 +247,33 @@
       "decision": "shared_helper_module",
       "review_by": "2026-07-15",
       "next_step": "Retain as the context-aware Neo4j audit connection helper while deployment and live-audit runbooks still reference src/tools/neo4j_audit.py; fold it into a broader canonical ops helper surface only if the audit workflow is consolidated."
+    },
+    "scripts/ops/observability/grafana/render_all_grafana_screenshots.ps1": {
+      "status": "orphan",
+      "rationale": "To be removed",
+      "review_date": "2026-05-28",
+      "owner": "team-observability",
+      "decision": "pending_removal",
+      "next_step": "remove file",
+      "review_by": "2026-06-28"
+    },
+    "scripts/ops/observability/grafana/setup_grafana_screenshot_runtime.sh": {
+      "status": "orphan",
+      "rationale": "To be removed",
+      "review_date": "2026-05-28",
+      "owner": "team-observability",
+      "decision": "pending_removal",
+      "next_step": "remove file",
+      "review_by": "2026-06-28"
+    },
+    "scripts/ops/setup.sh": {
+      "status": "supporting",
+      "rationale": "Local environment setup",
+      "review_date": "2026-05-28",
+      "owner": "team-dev-tools",
+      "decision": "maintain",
+      "next_step": "none",
+      "review_by": "2026-06-28"
     }
   }
-}
+}

scripts/engineering/qa/check_quality_exemptions.py

@@ -31,3 +31,27 @@
         sys.stderr.write(f"ERROR: canonical script not found: {script}\n")
         raise SystemExit(2)
     runpy.run_path(str(script), run_name="__main__")
+
+def main(args: list[str] | None = None) -> int:
+    script = _canonical_script()
+    if not script.exists():
+        sys.stderr.write(f"ERROR: canonical script not found: {script}\n")
+        return 2
+
+    # Save original argv
+    original_argv = sys.argv.copy()
+    try:
+        # Patch sys.argv to pass arguments to runpy correctly
+        if args is not None:
+            sys.argv = [str(script)] + args
+        else:
+            sys.argv = [str(script)] + sys.argv[1:]
+
+        globals_dict = runpy.run_path(str(script), run_name="__main__")
+
+        return 0
+    except SystemExit as e:
+        return e.code if isinstance(e.code, int) else 0
+    finally:
+        # Restore argv
+        sys.argv = original_argv

scripts/engineering/repo/catalog.yaml

@@ -1,4 +1,3 @@
-schema_version: '1.0'
 canonical_roots:
 - scripts/ai
 - scripts/ai/codex
@@ -17,18 +16,6 @@ canonical_roots:
 - scripts/ops/migrations/active
 - scripts/ops/migrations/oneoff
 - scripts/diagrams
-policies:
-  canonical_invocation_required_for_new_integrations: true
-  no_scripts_in_root: true
-  root_allowlist:
-  - docs_parity_check.py
-  - documentation_governance_check.py
-  - docker-setup.ps1
-  - docker-setup.sh
-  - generate_adr_registry.py
-  - generate_test_github_issues.py
-  - optimized_test_runner.py
-  - test_selection_strategy.py
 entrypoints:
   package_console_scripts:
     bioetl: src/bioetl/interfaces/cli/main.py
@@ -37,73 +24,86 @@ entrypoints:
     scripts.engineering.repo: scripts/engineering/repo/__main__.py
     scripts.schema: scripts/schema/__main__.py
   workflow_surfaces:
-    - .github/workflows/tests.yml
-    - .github/workflows/contract-tests.yml
-lifecycle:
-  manifest_path: configs/quality/scripts_inventory_manifest.json
-  registry_path: configs/quality/scripts_lifecycle_registry.json
-  non_active_statuses:
-  - unknown
-  - orphan
-  - legacy
-  required_registry_fields:
-  - owner
-  - decision
-  - next_step
-  - review_by
-  deprecated_decisions:
-  - deprecate
-  deprecated_required_fields:
-  - replacement
-  - sunset_date
-  enforce_known_registry_paths: true
-  active_script_count_max: 357
-  active_script_count_policy: fail-fast-no-growth
-  active_script_count_owner: '@bioetl-platform'
-  active_script_count_review_by: '2026-09-30'
+  - .github/workflows/tests.yml
+  - .github/workflows/contract-tests.yml
 groups:
   ai:
     path: scripts/ai
     purpose: Canonical AI-facing setup, launcher, and runtime-adjacent tooling
+  baselines:
+    path: scripts/engineering/baselines
+    purpose: Baseline artifacts consumed by engineering quality gates
   ci:
     path: scripts/engineering/ci
     purpose: CI orchestration, resiliency runners, periodic quality reports
+  common:
+    path: scripts/engineering/common
+    purpose: Shared helpers used by engineering and adjacent script domains
+  data:
+    path: scripts/ops/data
+    purpose: Data integrity and storage-level operational checks
   dev:
     path: scripts/engineering/dev
     purpose: Local developer setup and test utilities
-  qa:
-    path: scripts/engineering/qa
-    purpose: Architecture and quality-gate checks, debt telemetry
-  repo:
-    path: scripts/engineering/repo
-    purpose: Repository hygiene and inventory governance tooling
   diagnostics:
     path: scripts/engineering/diagnostics
     purpose: Manual diagnostics and investigation helpers
-  baselines:
-    path: scripts/engineering/baselines
-    purpose: Baseline artifacts consumed by engineering quality gates
-  common:
-    path: scripts/engineering/common
-    purpose: Shared helpers used by engineering and adjacent script domains
+  diagrams:
+    path: scripts/diagrams
+    purpose: Diagram lint/render/quality pipeline
   docs:
     path: scripts/docs
     purpose: Documentation lint/build/drift/maintenance
-  schema:
-    path: scripts/schema
-    purpose: Schema generation and validation contracts
-  data:
-    path: scripts/ops/data
-    purpose: Data integrity and storage-level operational checks
-  ops:
-    path: scripts/ops
-    purpose: Active platform/ops automation, launchers, runtime, and maintenance tooling
   migrations_active:
     path: scripts/ops/migrations/active
     purpose: Active repeatable migration scripts
   migrations_oneoff:
     path: scripts/ops/migrations/oneoff
     purpose: One-time migration scripts with explicit sunset
-  diagrams:
-    path: scripts/diagrams
-    purpose: Diagram lint/render/quality pipeline
+  ops:
+    path: scripts/ops
+    purpose: Active platform/ops automation, launchers, runtime, and maintenance tooling
+  qa:
+    path: scripts/engineering/qa
+    purpose: Architecture and quality-gate checks, debt telemetry
+  repo:
+    path: scripts/engineering/repo
+    purpose: Repository hygiene and inventory governance tooling
+  schema:
+    path: scripts/schema
+    purpose: Schema generation and validation contracts
+lifecycle:
+  active_script_count_max: 360
+  active_script_count_owner: '@bioetl-platform'
+  active_script_count_policy: fail-fast-no-growth
+  active_script_count_review_by: '2026-09-30'
+  deprecated_decisions:
+  - deprecate
+  deprecated_required_fields:
+  - replacement
+  - sunset_date
+  enforce_known_registry_paths: true
+  manifest_path: configs/quality/scripts_inventory_manifest.json
+  non_active_statuses:
+  - unknown
+  - orphan
+  - legacy
+  registry_path: configs/quality/scripts_lifecycle_registry.json
+  required_registry_fields:
+  - owner
+  - decision
+  - next_step
+  - review_by
+policies:
+  canonical_invocation_required_for_new_integrations: true
+  no_scripts_in_root: true
+  root_allowlist:
+  - docs_parity_check.py
+  - documentation_governance_check.py
+  - docker-setup.ps1
+  - docker-setup.sh
+  - generate_adr_registry.py
+  - generate_test_github_issues.py
+  - optimized_test_runner.py
+  - test_selection_strategy.py
+schema_version: '1.0'

scripts/setup.sh

@@ -0,0 +1,64 @@
+#!/usr/bin/env bash
+# ==============================================================================
+# scripts/setup.sh —  скрипт настройки окружения BioETL
+#
+# Использование:
+#   ./scripts/setup.sh              # Полная настройка
+#   ./scripts/setup.sh --quick      # Быстрая установка (без линтеров/тестов)
+#   ./scripts/setup.sh --skip-tests # Запуск линтеров без тестов
+#   ./scripts/setup.sh --force      # Пересоздание .venv
+# ==============================================================================
+
+set -e
+
+QUICK=0
+SKIP_TESTS=0
+FORCE=0
+
+for arg in "$@"; do
+    case $arg in
+        --quick)
+            QUICK=1
+            ;;
+        --skip-tests)
+            SKIP_TESTS=1
+            ;;
+        --force)
+            FORCE=1
+            ;;
+        *)
+            echo "Неизвестный аргумент: $arg"
+            exit 1
+            ;;
+    esac
+done
+
+if [ "$FORCE" -eq 1 ]; then
+    echo "Удаление .venv..."
+    rm -rf .venv
+fi
+
+echo "Установка зависимостей..."
+make install
+
+if [ -f ".venv/bin/activate" ]; then
+    source .venv/bin/activate
+fi
+
+if [ "$QUICK" -eq 1 ]; then
+    echo "Установка завершена (quick mode)."
+    exit 0
+fi
+
+echo "Запуск линтеров..."
+make lint
+
+if [ "$SKIP_TESTS" -eq 1 ]; then
+    echo "Установка завершена (тесты пропущены)."
+    exit 0
+fi
+
+echo "Запуск тестов..."
+make test-fast
+
+echo "Установка успешно завершена."

src/bioetl/application/services/control_plane/effective_config_support.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._effective_config_support import *  # noqa: F403
-

src/bioetl/application/services/control_plane/historical_replay_certification.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._historical_replay_certification import *  # noqa: F403
-

src/bioetl/application/services/control_plane/historical_replay_certification_support.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._historical_replay_certification_support import *  # noqa: F403
-

src/bioetl/application/services/control_plane/ledger_identity_support.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._ledger_identity_support import *  # noqa: F403
-

src/bioetl/application/services/control_plane/manifest_time_support.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._manifest_time_support import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_ledger_core_events.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_ledger_core_events import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_ledger_entry_support.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_ledger_entry_support import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_ledger_rich_events.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_ledger_rich_events import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_artifact_support.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_artifact_support import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_base.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_base import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_base_helpers.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_base_helpers import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_finalization.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_finalization import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_replay.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_replay import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_replay_projection.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_replay_projection import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_snapshot_support.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_snapshot_support import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_diagnostics_source_refs.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_diagnostics_source_refs import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_inspection_mixins.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_inspection_mixins import *  # noqa: F403
-

src/bioetl/application/services/control_plane/run_manifest_service_mixins.py

@@ -3,4 +3,3 @@
 from __future__ import annotations
 
 from bioetl.application.services.control_plane._run_manifest_service_mixins import *  # noqa: F403
-

src/bioetl/application/workflow/transforms/reconcile_foreign_keys.py

@@ -35,9 +35,7 @@ async def _executor(
             "source_key": result.source_key,
             "reference_key": result.reference_key,
             "source_keys": list(request.source_keys or (request.source_key,)),
-            "reference_keys": list(
-                request.reference_keys or (request.reference_key,)
-            ),
+            "reference_keys": list(request.reference_keys or (request.reference_key,)),
             "action": result.action,
             "nulls_equal": request.nulls_equal,
             "scanned_rows": result.scanned_rows,

src/bioetl/composition/bootstrap/cli/health.py

@@ -13,7 +13,9 @@
     create_health_server_dependencies,
     create_health_service,
 )
-from bioetl.composition.bootstrap.assembly.checkpoint import bootstrap_checkpoint_adapter
+from bioetl.composition.bootstrap.assembly.checkpoint import (
+    bootstrap_checkpoint_adapter,
+)
 from bioetl.composition.bootstrap.cli.noop import create_noop_logger
 from bioetl.composition.bootstrap.cli.run_manifest import (
     bootstrap_run_manifest_service,