factorforge-cds 3.2.2__tar.gz → 3.2.4__tar.gz

{factorforge_cds-3.2.2/src/factorforge_cds.egg-info → factorforge_cds-3.2.4}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.2
-Summary: FactorForge - open-source constraint-based CDS design engine by Eijex.
+Version: 3.2.4
+Summary: FactorForge - open-source CDS design and pre-synthesis sequence review engine by Eijex.
 Author-email: Eijex <eijex.lab@gmail.com>
 License-Expression: AGPL-3.0-only
 Project-URL: Homepage, https://factorforge.eijex.com
@@ -33,19 +33,19 @@ Dynamic: license-file
 
 # FactorForge
 
-**Open-source constraint-based CDS design engine for sequence-level CDS design, with primary support for *Nicotiana benthamiana* (Tobacco BY-2: experimental).**
+**Open-source constraint-based CDS design and pre-synthesis sequence review engine for plant CDS workflows, with primary support for *Nicotiana benthamiana* (Tobacco BY-2: experimental).**
 
 [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE)
 [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
 [![PyPI](https://img.shields.io/pypi/v/factorforge-cds.svg)](https://pypi.org/project/factorforge-cds/)
 [![CI](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml/badge.svg)](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/eijex/factorforge-cds/branch/main/graph/badge.svg)](https://codecov.io/gh/eijex/factorforge-cds)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20640931.svg)](https://doi.org/10.5281/zenodo.20640931)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20407330.svg)](https://doi.org/10.5281/zenodo.20407330)
 [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
 
-FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
+FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
 
-**→ [Full Documentation](https://eijex.github.io/factorforge-cds/)**
+**→ [Full Documentation](https://eijex.github.io/factorforge-cds/)** · **[Roadmap](https://eijex.github.io/factorforge-cds/roadmap/)**
 
 ---
 
@@ -86,14 +86,14 @@ and are not imported by the installed package or exposed as supported engines.
 
 ## ⚠️ Validation Status
 
-FactorForge outputs are **in-silico only** and have not been experimentally validated in wet-lab conditions. See [Validation](https://eijex.github.io/factorforge-cds/validation/) and [VALIDATION.md](VALIDATION.md).
+FactorForge outputs are **in-silico only** and have not been experimentally validated in wet-lab conditions. These checks support reviewability and reproducibility; they do not guarantee expression, yield, synthesis acceptance, folding, glycosylation, regulatory approval, or downstream biological performance. See [Validation](https://eijex.github.io/factorforge-cds/validation/) and [VALIDATION.md](VALIDATION.md).
 
 ---
 
 ## Citing
 
 ```
-FactorForge v3.2.2 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.4 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 
@@ -114,8 +114,9 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
 ## Get in Touch
 
 - **Docs** — [eijex.github.io/factorforge-cds](https://eijex.github.io/factorforge-cds/)
-- **Wet-lab Results** — Public-safe validation summaries are welcome. [Share Wet-lab Results (Form)](https://docs.google.com/forms/d/e/1FAIpQLSeSx-wYvF6YwHhSPdLMl-L44frCugdm25X_eDz50OaqTD66qA/viewform) or [Share Wet-lab Results (GitHub)](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml) (public-safe summaries only). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. See [VALIDATION.md](VALIDATION.md) before submitting.
+- **Wet-lab Feedback** — Public-safe feedback summaries are welcome via [Share Wet-lab Feedback (GitHub)](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. Email `eijex.lab@gmail.com` for private or sensitive summaries. See [VALIDATION.md](VALIDATION.md) before submitting.
 - **GitHub Issues** — bugs, features: [github.com/eijex/factorforge-cds/issues](https://github.com/eijex/factorforge-cds/issues)
 - **Email** — eijex.lab@gmail.com
 - **FactorForge** — [factorforge.eijex.com](https://factorforge.eijex.com)
+- **Eijex MCP** — [mcp.eijex.com](https://mcp.eijex.com)
 - **Lab** — [www.eijex.com](https://www.eijex.com)

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/README.md

@@ -1,18 +1,18 @@
 # FactorForge
 
-**Open-source constraint-based CDS design engine for sequence-level CDS design, with primary support for *Nicotiana benthamiana* (Tobacco BY-2: experimental).**
+**Open-source constraint-based CDS design and pre-synthesis sequence review engine for plant CDS workflows, with primary support for *Nicotiana benthamiana* (Tobacco BY-2: experimental).**
 
 [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE)
 [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
 [![PyPI](https://img.shields.io/pypi/v/factorforge-cds.svg)](https://pypi.org/project/factorforge-cds/)
 [![CI](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml/badge.svg)](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/eijex/factorforge-cds/branch/main/graph/badge.svg)](https://codecov.io/gh/eijex/factorforge-cds)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20640931.svg)](https://doi.org/10.5281/zenodo.20640931)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20407330.svg)](https://doi.org/10.5281/zenodo.20407330)
 [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
 
-FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
+FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
 
-**→ [Full Documentation](https://eijex.github.io/factorforge-cds/)**
+**→ [Full Documentation](https://eijex.github.io/factorforge-cds/)** · **[Roadmap](https://eijex.github.io/factorforge-cds/roadmap/)**
 
 ---
 
@@ -53,14 +53,14 @@ and are not imported by the installed package or exposed as supported engines.
 
 ## ⚠️ Validation Status
 
-FactorForge outputs are **in-silico only** and have not been experimentally validated in wet-lab conditions. See [Validation](https://eijex.github.io/factorforge-cds/validation/) and [VALIDATION.md](VALIDATION.md).
+FactorForge outputs are **in-silico only** and have not been experimentally validated in wet-lab conditions. These checks support reviewability and reproducibility; they do not guarantee expression, yield, synthesis acceptance, folding, glycosylation, regulatory approval, or downstream biological performance. See [Validation](https://eijex.github.io/factorforge-cds/validation/) and [VALIDATION.md](VALIDATION.md).
 
 ---
 
 ## Citing
 
 ```
-FactorForge v3.2.2 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.4 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 
@@ -81,8 +81,9 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
 ## Get in Touch
 
 - **Docs** — [eijex.github.io/factorforge-cds](https://eijex.github.io/factorforge-cds/)
-- **Wet-lab Results** — Public-safe validation summaries are welcome. [Share Wet-lab Results (Form)](https://docs.google.com/forms/d/e/1FAIpQLSeSx-wYvF6YwHhSPdLMl-L44frCugdm25X_eDz50OaqTD66qA/viewform) or [Share Wet-lab Results (GitHub)](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml) (public-safe summaries only). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. See [VALIDATION.md](VALIDATION.md) before submitting.
+- **Wet-lab Feedback** — Public-safe feedback summaries are welcome via [Share Wet-lab Feedback (GitHub)](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. Email `eijex.lab@gmail.com` for private or sensitive summaries. See [VALIDATION.md](VALIDATION.md) before submitting.
 - **GitHub Issues** — bugs, features: [github.com/eijex/factorforge-cds/issues](https://github.com/eijex/factorforge-cds/issues)
 - **Email** — eijex.lab@gmail.com
 - **FactorForge** — [factorforge.eijex.com](https://factorforge.eijex.com)
+- **Eijex MCP** — [mcp.eijex.com](https://mcp.eijex.com)
 - **Lab** — [www.eijex.com](https://www.eijex.com)

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "factorforge-cds"
-version = "3.2.2"
-description = "FactorForge - open-source constraint-based CDS design engine by Eijex."
+version = "3.2.4"
+description = "FactorForge - open-source CDS design and pre-synthesis sequence review engine by Eijex."
 readme = "README.md"
 license = "AGPL-3.0-only"
 license-files = ["LICENSE"]

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/__init__.py

@@ -4,7 +4,7 @@ FactorForge - Codon Optimization Platform
 profile: constraint-aware rule/profile engine
 """
 
-__version__ = "3.2.2"
+__version__ = "3.2.4"
 __author__ = "Eijex"
 
 # Auto-register engines (safe when running from source tree)

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/analysis/feasibility.py

@@ -15,7 +15,7 @@ from factorforge.analysis.metrics import (
 
 
 # Defaults calibrated to nbenthamiana profile engine output distribution
-# (analysis 004, n=49): avg CAI=0.76, avg GC=60.1% (range 55-71%).
+# (internal benchmark, n=49): avg CAI=0.76, avg GC=60.1% (range 55-71%).
 # DEFAULT_CAI_TARGET=0.82 aligns with industry practice (>0.8) and is achievable.
 # Exported as named constants so tests/test_registry_production_sync.py can
 # strictly compare them against the registry (single source of truth).
@@ -110,7 +110,7 @@ def analyze_feasibility(
     codon weights.
 
     See module-level DEFAULT_CAI_TARGET / DEFAULT_GC_LOW / DEFAULT_GC_HIGH for
-    the calibration rationale (analysis 004, n=49).
+    the calibration rationale (internal benchmark, n=49).
     """
     protein = "".join(protein_sequence.upper().split()).rstrip("*")
     if not protein:

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/cli/main.py

@@ -161,7 +161,7 @@ def list_engines():
 @click.option(
     "--objective",
     default="feasibility_best",
-    type=click.Choice(["feasibility_best", "gc_target", "high_cai"], case_sensitive=False),
+    type=click.Choice(["feasibility_best"], case_sensitive=False),
     help="DP objective",
 )
 @click.option("--gc-min", type=float, default=55.0, help="Minimum target GC percentage")
@@ -212,6 +212,13 @@ def optimize(
     if host_was_explicit and engine == "dp" and internal_host != "nbenthamiana":
         engine = "profile"
 
+    if host_was_explicit and internal_host != "nbenthamiana":
+        if profile == "high_cai" or "high_cai" in (compare_profile_list or []):
+            raise click.UsageError(
+                "high_cai requires the N. benthamiana golden-set reference "
+                "and is not available for non-default hosts."
+            )
+
     if compare_profile_list:
         if engine == "dp" and _engine_option_was_explicitly_set():
             raise click.UsageError("--compare-profiles cannot be used with --engine dp.")

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/engines/__init__.py

@@ -13,7 +13,7 @@ def register_builtin_engines() -> None:
         "profile",
         RuleBasedOptimizer,
         metadata={
-            "version": "3.2.2",
+            "version": "3.2.4",
             "engine_type": "profile_rule_based",
             "role": "stable_profile_engine",
             "stable": True,

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/engines/profile/__init__.py

@@ -5,7 +5,7 @@ Production system (2026)
 Plant-specific rule-based optimization
 """
 
-__version__ = "3.2.2"
+__version__ = "3.2.4"
 
 from .optimizer import RuleBasedOptimizer
 from .pipeline import OptimizationPipeline

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/engines/profile/construct_builder.py

@@ -19,10 +19,13 @@ if TYPE_CHECKING:
 class ConstructBuilder:
     """Assemble constructs from JSON templates."""
 
-    def __init__(self, template_dir: Path) -> None:
+    def __init__(self, template_dir: Path | None = None) -> None:
         """
         Args:
-            template_dir: Directory containing construct templates.
+            template_dir: Directory containing construct templates. Optional —
+                omit when only using template-independent methods such as
+                check_internal_overhang_collisions() or validate_overhangs(),
+                which do not read from disk.
         """
         self.template_dir = template_dir
 

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/engines/profile/optimizer.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import logging
 from typing import Any
 
 from factorforge.core.interfaces import OptimizationResult, OptimizerEngine
@@ -12,12 +13,14 @@ from .rules.rule_engine import RuleEngine
 from .scoring import calculate_composite_score, compute_mfe_evidence
 from .validator import InputValidator
 
+logger = logging.getLogger(__name__)
+
 
 class RuleBasedOptimizer(OptimizerEngine):
     """Profile-based rule optimization engine."""
 
     name = "Profile-based"
-    version = "3.2.2"
+    version = "3.2.4"
 
     def __init__(self, codon_table_path: str | None = None) -> None:
         """
@@ -93,6 +96,17 @@ class RuleBasedOptimizer(OptimizerEngine):
                 f"Unknown profile: {profile_value}. Supported profiles: {supported}"
             ) from exc
 
+        if (
+            self._codon_table_path is None
+            and host != "nbenthamiana"
+            and profile_value == "high_cai"
+        ):
+            logger.warning(
+                "high_cai is anchored to the N. benthamiana golden set and "
+                "ignores the requested host=%s; output is host-invariant by design.",
+                host,
+            )
+
         if self._codon_table_path is not None or host == "nbenthamiana":
             # An injected design table (benchmark source-profile runs) is
             # authoritative: it already encodes the host it was derived from.

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/engines/profile/rules/reverse_translator.py

@@ -370,7 +370,7 @@ class ReverseTranslator:
         Balanced profile: CAI first, GC balanced
 
         - Preferred codon ratio: 70%
-        - Target GC: 55-65% (benchmark analysis 004: avg output 60.1%)
+        - Target GC: 55-65% (internal benchmark: avg output 60.1%)
         """
         target_gc_min = kwargs.get("target_gc_min", 55)
         target_gc_max = kwargs.get("target_gc_max", 65)

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/engines/profile/rules/rule_engine.py

@@ -361,7 +361,7 @@ class RuleEngine:
         by the scoring band (GC_OPT_MIN/MAX, ~55-65%) and the API/DP gc_min/gc_max
         constraints. The wide 25-75% band intentionally flags only synthesis-hostile
         local windows; narrowing it toward the global optimum would raise false
-        positives against the engine's own output distribution (analysis 004: 55-71%).
+        positives against the engine's own output distribution (internal benchmark: 55-71%).
 
         Args:
             seq: DNA sequence
@@ -704,7 +704,7 @@ class RuleEngine:
         Reduce CpG and TpA dinucleotide density via greedy synonymous substitution.
 
         Modes:
-            aggressive: dinucleotide reduction only; no CAI check (Job 044 behaviour).
+            aggressive: dinucleotide reduction only; no CAI check.
             balanced: dinucleotide reduction first; rollback each pass if final CAI
                       drops below cai_floor.
             cai_preserving: rollback each pass if CAI drops more than max_cai_drop

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/engines/profile/scoring.py

@@ -12,7 +12,7 @@ from typing import Any
 logger = logging.getLogger(__name__)
 
 # GC band for N. benthamiana codon-optimized sequences.
-# Benchmark (analysis 004, n=49): balanced profile output average GC% = 60.1%
+# Benchmark (internal, n=49): balanced profile output average GC% = 60.1%
 # (range 55-71%). The genome-wide average (~42%) reflects all genes, not the
 # high-expression codon table which exhibits 3rd-position GC bias.
 # These constants define the acceptable band — sequences within [GC_OPT_MIN, GC_OPT_MAX]

{factorforge_cds-3.2.2 → factorforge_cds-3.2.4}/src/factorforge/validation/cli.py

@@ -24,7 +24,7 @@ def _sequence_hash(args: argparse.Namespace) -> str:
 def main() -> None:
     parser = argparse.ArgumentParser(
         prog="factorforge-validate",
-        description="Generate a structured validation package from wet-lab results.",
+        description="Generate a structured public-safe wet-lab feedback package.",
     )
     parser.add_argument(
         "--construct-id",
@@ -58,12 +58,12 @@ def main() -> None:
     parser.add_argument(
         "--comparison",
         required=True,
-        choices=["FactorForge better", "Equivalent", "Worse", "Not compared"],
+        choices=["Improved", "Equivalent", "Reduced", "Inconclusive", "No control", "Not reported"],
     )
     parser.add_argument(
         "--expression-level",
         default=None,
-        choices=["High", "Medium", "Low", "Not detected", "Not measured"],
+        choices=["Detected", "Not detected", "Weak", "Strong", "Inconclusive", "Not reported"],
     )
     parser.add_argument("--notes", default=None)
     parser.add_argument("--institution", default=None)

factorforge_cds-3.2.4/src/factorforge/validation_registry.py

@@ -0,0 +1,322 @@
+"""Runtime validation-check registry — single source of truth for check_id,
+display metadata, and per-execution-path enforcement.
+
+Frozen reference: validation_contract_v1.yaml, factorforge commit
+4a8be9f053797d5f54154afcbda732eaaf79f8ae (v3.2.3). This module is the
+runtime source of truth; the contract file is a pinned manuscript snapshot
+of what this registry's predecessor behavior was.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+VALIDATION_REGISTRY_VERSION = "1.0"
+
+VALIDATION_CHECKS: tuple[dict[str, Any], ...] = (
+    # --- Domain B: Configured Constraints -----------------------------------
+    {
+        "check_id": "global_gc_range",
+        "display_name": "Global GC% target band",
+        "primary_domain": "configured_constraint",
+        "order": 1,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "metric_only",
+            "pipeline_default": "metric_only",
+            "benchmark_scoring": "component_of_multi_constraint_pass_soft",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": (
+            "Configured optimization target, not a pass/fail biological-risk scanner. "
+            "Only gates in the benchmark scoring path."
+        ),
+    },
+    # --- Domain C: Advisory Sequence Scans (RuleEngine, 9 scanners) ---------
+    {
+        "check_id": "polya",
+        "display_name": "PolyA-like motifs",
+        "primary_domain": "advisory_scan",
+        "order": 2,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": "Advisory finding, not a guarantee of expression impact.",
+    },
+    {
+        "check_id": "are",
+        "display_name": "AU-rich elements (ARE)",
+        "primary_domain": "advisory_scan",
+        "order": 3,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": "Advisory finding.",
+    },
+    {
+        "check_id": "at_runs",
+        "display_name": "AT-rich runs",
+        "primary_domain": "advisory_scan",
+        "order": 4,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": "Advisory finding.",
+    },
+    {
+        "check_id": "homopolymers",
+        "display_name": "Homopolymer runs (synthesis risk)",
+        "primary_domain": "advisory_scan",
+        "order": 5,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": (
+            "Synthesis-difficulty advisory, distinct from the separate expression-stability "
+            "homopolymer threshold used in the unrelated/archived utils/validation.py path."
+        ),
+    },
+    {
+        "check_id": "repeats",
+        "display_name": "Tandem / perfect repeats",
+        "primary_domain": "advisory_scan",
+        "order": 6,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": "Advisory finding.",
+    },
+    {
+        "check_id": "gc_extremes",
+        "display_name": "Local GC extremes (sliding window)",
+        "primary_domain": "advisory_scan",
+        "order": 7,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": "Local synthesis-hostile GC extremes, NOT the global GC optimization target.",
+    },
+    {
+        "check_id": "splice_sites",
+        "display_name": "Cryptic splice-site-like motifs",
+        "primary_domain": "advisory_scan",
+        "order": 8,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": (
+            "Advisory pattern-match finding, low severity by default — not a validated "
+            "splicing prediction."
+        ),
+    },
+    {
+        "check_id": "dinucleotides",
+        "display_name": "CpG / TpA dinucleotide density",
+        "primary_domain": "advisory_scan",
+        "order": 9,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": "Advisory finding.",
+    },
+    {
+        "check_id": "rare_codon_runs",
+        "display_name": "Rare-codon runs",
+        "primary_domain": "advisory_scan",
+        "order": 10,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "advisory_only",
+            "pipeline_default": "advisory_only",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": "Advisory finding, not a validated translation-rate measurement.",
+    },
+    # --- Domain D: Assembly Review -------------------------------------------
+    {
+        "check_id": "restriction_sites",
+        "display_name": "Restriction Site Check (Type IIS)",
+        "primary_domain": "assembly_review",
+        "order": 11,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "not_checked",
+            "pipeline_default": "hard_fail_raise_if_unfixable",
+            "benchmark_scoring": "component_of_assembly_pass_soft",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": None}},
+        "claim_boundary": (
+            "Same biological check enforced at TWO different strengths: production pipeline "
+            "raises and halts; benchmark scoring records a soft boolean."
+        ),
+    },
+    {
+        "check_id": "moclo_overhang",
+        "display_name": "MoClo Level-0 overhang validity",
+        "primary_domain": "assembly_review",
+        "order": 12,
+        "default_enabled": False,
+        "enforcement_per_path": {
+            "bare_optimizer": "not_checked",
+            "pipeline_default": "opt_in_non_gating",
+            "benchmark_scoring": "not_included",
+        },
+        "presentation": {"web": {"visible": True, "default_status_when_not_executed": "NOT_RUN"}},
+        "claim_boundary": (
+            "MUST be described as a non-gating, opt-in advisory check. It is not run by "
+            "default, and even when run it never blocks a result — unlike restriction_sites, "
+            "which can halt the pipeline."
+        ),
+    },
+    # --- Domain A: Sequence Integrity (hard, gates pipeline via raise) ------
+    {
+        "check_id": "aa_identity",
+        "display_name": "Amino-acid identity",
+        "primary_domain": "integrity",
+        "order": 13,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "not_checked",
+            "pipeline_default": "hard_fail_raise",
+            "benchmark_scoring": "component_of_biological_pass_soft",
+        },
+        "presentation": {"web": {"visible": False, "default_status_when_not_executed": None}},
+        "claim_boundary": "Hard structural validity check, not a biological-risk prediction.",
+    },
+    {
+        "check_id": "internal_stop",
+        "display_name": "Internal stop codons",
+        "primary_domain": "integrity",
+        "order": 14,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "not_checked",
+            "pipeline_default": "hard_fail_raise_via_final_validation",
+            "benchmark_scoring": "component_of_biological_pass_soft",
+        },
+        "presentation": {"web": {"visible": False, "default_status_when_not_executed": None}},
+        "claim_boundary": "Hard structural validity check.",
+    },
+    {
+        "check_id": "invalid_codon",
+        "display_name": "Invalid / partial codons",
+        "primary_domain": "integrity",
+        "order": 15,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "not_checked",
+            "pipeline_default": "hard_fail_raise_via_final_validation",
+            "benchmark_scoring": "component_of_biological_pass_soft",
+        },
+        "presentation": {"web": {"visible": False, "default_status_when_not_executed": None}},
+        "claim_boundary": "Hard structural validity check.",
+    },
+    {
+        "check_id": "frame_length",
+        "display_name": "Reading-frame / length consistency",
+        "primary_domain": "integrity",
+        "order": 16,
+        "default_enabled": True,
+        "enforcement_per_path": {
+            "bare_optimizer": "not_checked",
+            "pipeline_default": "implicit_validator_stage",
+            "benchmark_scoring": "component_of_biological_pass_soft",
+        },
+        "presentation": {"web": {"visible": False, "default_status_when_not_executed": None}},
+        "claim_boundary": "Hard structural validity check.",
+    },
+    {
+        "check_id": "custom_forbidden_motifs",
+        "display_name": "User-configured forbidden motifs",
+        "primary_domain": "configured_constraint",
+        "order": 17,
+        "default_enabled": False,
+        "enforcement_per_path": {
+            "bare_optimizer": "not_wired",
+            "pipeline_default": "not_wired",
+            "benchmark_scoring": "not_wired",
+        },
+        "presentation": {"web": {"visible": False, "default_status_when_not_executed": None}},
+        "claim_boundary": (
+            "MUST NOT be described as an active product feature. Implemented in a "
+            "legacy/archived code path, not connected to the current optimize()/pipeline()/"
+            "CLI/API surface at the pinned commit."
+        ),
+    },
+)
+
+REVIEW_CONTRACT_CHECK_IDS: tuple[str, ...] = (
+    "polya",
+    "are",
+    "at_runs",
+    "homopolymers",
+    "repeats",
+    "gc_extremes",
+    "splice_sites",
+    "dinucleotides",
+    "rare_codon_runs",
+    "restriction_sites",
+    "moclo_overhang",
+)
+
+PUBLIC_VALIDATION_BADGE_IDS: tuple[str, ...] = ("global_gc_range",) + REVIEW_CONTRACT_CHECK_IDS
+
+LEGACY_VALIDATION_FIELD_MAP: dict[str, str] = {
+    "polya": "polya",
+    "gc": "global_gc_range",
+    # validation.moclo carries the Type IIS restriction-site result, NOT
+    # moclo_overhang.
+    "moclo": "restriction_sites",
+}
+
+_CHECKS_BY_ID: dict[str, dict[str, Any]] = {check["check_id"]: check for check in VALIDATION_CHECKS}
+
+
+def get_check(check_id: str) -> dict[str, Any]:
+    """Return the registry entry for `check_id`.
+
+    Raises:
+        KeyError: If `check_id` is not in the registry.
+    """
+    return _CHECKS_BY_ID[check_id]
+
+
+def public_badge_checks() -> list[dict[str, Any]]:
+    """Return the 12 public-badge checks, sorted by registry `order`."""
+    return sorted(
+        (check for check in VALIDATION_CHECKS if check["check_id"] in PUBLIC_VALIDATION_BADGE_IDS),
+        key=lambda check: check["order"],
+    )