factorforge-cds 3.5.3__tar.gz → 3.5.10__tar.gz

{factorforge_cds-3.5.3 → factorforge_cds-3.5.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.5.3
+Version: 3.5.10
 Summary: FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex.
 Author-email: Eijex <eijex.lab@gmail.com>
 License-Expression: AGPL-3.0-only
@@ -22,6 +22,7 @@ Requires-Dist: pydantic>=2.0
 Provides-Extra: postgres
 Requires-Dist: psycopg2-binary>=2.9; extra == "postgres"
 Requires-Dist: sqlalchemy>=2.0; extra == "postgres"
+Requires-Dist: eijex-db-core==0.1.2; extra == "postgres"
 Provides-Extra: dev
 Requires-Dist: jsonschema>=4.0; extra == "dev"
 Requires-Dist: pandas>=2.0; extra == "dev"
@@ -51,7 +52,7 @@ Dynamic: license-file
 
 FactorForge performs deterministic 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`).
 
-FactorForge v3.5.1 uses independently versioned engines:
+FactorForge v3.5.10 uses independently versioned engines:
 
 | Generation | Engine | Version | Availability |
 |---|---|---:|---|
@@ -89,6 +90,12 @@ Or use the **[web app](https://factorforge.eijex.com)** — no installation requ
 
 ## Repository Structure
 
+Experimental codon-distribution and evidence-ledger modules in the development
+checkout are scaffolds, not a validated laboratory policy or active learned
+recommendation service. Computational checks do not establish synthesis readiness
+or biological performance. Private inputs and collaborator packages must remain
+outside public repositories and dashboards.
+
 The supported deterministic engines are the profile engine, stable DP v2, and
 the explicit DP v2.1.1 development candidate under:
 
@@ -107,7 +114,7 @@ are available, a separately evaluated 5′ MFE value. It is not the default; its
 single-target calibration does not establish holdout generalization or biological
 performance.
 
-The v3.5.1 discovery-slate surface generates versioned Top-K research candidates,
+The v3.5.x discovery-slate surface generates versioned Top-K research candidates,
 applies a shared deterministic hard-constraint filter, and records generator and
 fallback lineage. The sLLM path is disabled by default. A partial-DP rescue solves
 an exact suffix conditioned on the retained prefix; it is not a claim of global
@@ -127,7 +134,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.5.3 (2026). Open-source constraint-based CDS design and sequence review.
+FactorForge v3.5.10 (2026). Open-source constraint-based CDS design and sequence review.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 
@@ -139,9 +146,20 @@ Mun-Kyu Kim ([@eijex](https://github.com/eijex))
 
 ## Optional PostgreSQL support
 
-Install `pip install "factorforge-cds[postgres]"` only when using the PostgreSQL
-connector. Explicit local SQLite checkpoints do not require a PostgreSQL driver.
-Database integration tests require an explicitly configured `DATABASE_URL`.
+FactorForge design, CLI, Python API, and file export do not require a database.
+PostgreSQL persistence is an explicit Eijex integration path for retaining shared
+campaign and candidate identities; it is not enabled by default.
+
+The extra pins `eijex-db-core==0.1.2`. Supply its approved wheel bundle using
+`pip install --find-links PATH_TO_BUNDLE "factorforge-cds[postgres]"`; the shared
+package is not assumed to have been published on PyPI. Standalone installation
+does not require it.
+The deployment must also provide a compatible `eijex-db-core` package and set
+`FACTORFORGE_DATABASE_URL`. FactorForge contains no default database credentials and
+does not silently fall back to another backend. See [Persistence](docs/persistence.md).
+
+Explicit local SQLite research checkpoints in `factorforge.db.connector` remain a
+separate local-only utility and are not the shared DBTL system of record.
 
 ## License
 
@@ -168,3 +186,40 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
 - **Eijex MCP** — [mcp.eijex.com](https://mcp.eijex.com)
 - **Lab** — [www.eijex.com](https://www.eijex.com)
 
+
+## Testing status
+
+The web UI now labels watermark as disabled and distinguishes the sequence-only baseline from experimental structure-conditioned testing. The local approved workflow supports explicit 1DP-only or paired 3DP mode. 3DP availability is local research testing; it is not a new public optimization endpoint or a biological-performance claim. See [web UI boundaries](web/README.md).
+
+## Direct 3DP browser testing (unreleased)
+
+The FactorForge form supports explicit 1DP/3DP selection. 3DP uploads a PDB/mmCIF file, selects chain and one-based file model order, and requires reviewed one-based protein positions. The selected observed chain must exactly match the complete protein; partial or homologous structures require the retained local reviewed mapping workflow. Direct requests use `/api/optimize` with `design_mode=paired_3dp` and `structure_context={content,format,chain,model,positions,positions_reviewed,target_adaptiveness,penalty_weight}`.
+
+Limits: 3–300 amino acids, structure content 250 KB, HTTP JSON body 1 MB. Both candidates use the configured codon reference, requested GC and canonical motif exclusions plus custom additions. Invalid inputs and infeasible candidates fail without a baseline fallback. Existing sequence-only settings and API requests remain supported. 3DP uses its explicit DP settings and does not apply Kozak, TpA, template or seed transformations. SOP checks are reported for both candidates; regeneration is manual and never silently changes mode. Watermark stays disabled.
+
+This is stateless computational testing, with no external service dependencies or remote database recording. Those existing integrations remain available for later operational use. The structure file is not retained in the response or browser history; normal design results may be retained in local browser history. Submit only public-safe inputs. Structural conformity metrics are codon-weight proxies, not folding/expression measurements. These source changes are not deployed or a new package release.
+
+## Current public policy UI (2026-10-12)
+
+Custom SOP management is paused. The built-in FactorForge default policy is applied; upload/export/preset/editing controls are hidden and disabled. Their code and previous browser configuration remain available for later reactivation through ENABLE_CUSTOM_SOP. Saved custom SOPs are ignored without deletion. 1DP/3DP mode selection and explicit structure inputs remain active. This supersedes the earlier public SOP upload/export instructions. Public API contracts are retained.
+
+### Scientific web observations
+
+Direct 1DP/3DP browser testing reports sense-CDS RNA motif scans and available initiation-window MFE in results, downloadable reports and local history. Structure confidence observations can suggest positions for explicit acceptance and review; unsupported inputs do not invent positions. These checks do not establish expression, yield or folding benefits. The default policy remains active and custom SOP management remains paused. See `docs/experimental-structure.md` for the API and measurement boundary.
+
+### Local reviewed structure file workflow
+
+`factorforge nbfold annotate` and `factorforge nbfold optimize` provide the experimental local Phase A/B workflow for exact-match structure files and an explicit user review manifest. See [NB-Fold documentation](docs/experimental-structure.md).
+
+Web structure handling now requires exact-match uploaded PDB/mmCIF coordinates and explicit reviewed positions. Automatic external folding, artificial structure/confidence fallback, and auto-approval are disabled. Structure metrics are synthetic reconstruction checks; independent public-structure/DSSP validation remains open.
+
+### Experimental human-reference prototype
+
+`factorforge.engines.stemcell_3dp.StemCell3DPOptimizer` is a local experimental interface using a generic human-frequency reference and provisional Eijex review criteria. It is not an MSC/iPSC-calibrated model or a laboratory-approved SOP. See [prototype boundaries](docs/model_cards/human-reference-prototype.md). It is not a new production web host.
+# Local research candidate: DP v2.2
+
+The opt-in Python `DPV220Optimizer` shares the v2.1.1 DP core and adds reviewed
+position penalties. The experimental generic-human adapter uses this core;
+existing plant web/NB-Fold routes retain their prior objective. See the
+[model card](docs/model_cards/dp_v2_2.md) for usage, relaxation reporting and
+engineering validation boundaries. This is not an expression or folding claim.

{factorforge_cds-3.5.3 → factorforge_cds-3.5.10}/README.md

@@ -14,7 +14,7 @@
 
 FactorForge performs deterministic 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`).
 
-FactorForge v3.5.1 uses independently versioned engines:
+FactorForge v3.5.10 uses independently versioned engines:
 
 | Generation | Engine | Version | Availability |
 |---|---|---:|---|
@@ -52,6 +52,12 @@ Or use the **[web app](https://factorforge.eijex.com)** — no installation requ
 
 ## Repository Structure
 
+Experimental codon-distribution and evidence-ledger modules in the development
+checkout are scaffolds, not a validated laboratory policy or active learned
+recommendation service. Computational checks do not establish synthesis readiness
+or biological performance. Private inputs and collaborator packages must remain
+outside public repositories and dashboards.
+
 The supported deterministic engines are the profile engine, stable DP v2, and
 the explicit DP v2.1.1 development candidate under:
 
@@ -70,7 +76,7 @@ are available, a separately evaluated 5′ MFE value. It is not the default; its
 single-target calibration does not establish holdout generalization or biological
 performance.
 
-The v3.5.1 discovery-slate surface generates versioned Top-K research candidates,
+The v3.5.x discovery-slate surface generates versioned Top-K research candidates,
 applies a shared deterministic hard-constraint filter, and records generator and
 fallback lineage. The sLLM path is disabled by default. A partial-DP rescue solves
 an exact suffix conditioned on the retained prefix; it is not a claim of global
@@ -90,7 +96,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.5.3 (2026). Open-source constraint-based CDS design and sequence review.
+FactorForge v3.5.10 (2026). Open-source constraint-based CDS design and sequence review.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 
@@ -102,9 +108,20 @@ Mun-Kyu Kim ([@eijex](https://github.com/eijex))
 
 ## Optional PostgreSQL support
 
-Install `pip install "factorforge-cds[postgres]"` only when using the PostgreSQL
-connector. Explicit local SQLite checkpoints do not require a PostgreSQL driver.
-Database integration tests require an explicitly configured `DATABASE_URL`.
+FactorForge design, CLI, Python API, and file export do not require a database.
+PostgreSQL persistence is an explicit Eijex integration path for retaining shared
+campaign and candidate identities; it is not enabled by default.
+
+The extra pins `eijex-db-core==0.1.2`. Supply its approved wheel bundle using
+`pip install --find-links PATH_TO_BUNDLE "factorforge-cds[postgres]"`; the shared
+package is not assumed to have been published on PyPI. Standalone installation
+does not require it.
+The deployment must also provide a compatible `eijex-db-core` package and set
+`FACTORFORGE_DATABASE_URL`. FactorForge contains no default database credentials and
+does not silently fall back to another backend. See [Persistence](docs/persistence.md).
+
+Explicit local SQLite research checkpoints in `factorforge.db.connector` remain a
+separate local-only utility and are not the shared DBTL system of record.
 
 ## License
 
@@ -131,3 +148,40 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
 - **Eijex MCP** — [mcp.eijex.com](https://mcp.eijex.com)
 - **Lab** — [www.eijex.com](https://www.eijex.com)
 
+
+## Testing status
+
+The web UI now labels watermark as disabled and distinguishes the sequence-only baseline from experimental structure-conditioned testing. The local approved workflow supports explicit 1DP-only or paired 3DP mode. 3DP availability is local research testing; it is not a new public optimization endpoint or a biological-performance claim. See [web UI boundaries](web/README.md).
+
+## Direct 3DP browser testing (unreleased)
+
+The FactorForge form supports explicit 1DP/3DP selection. 3DP uploads a PDB/mmCIF file, selects chain and one-based file model order, and requires reviewed one-based protein positions. The selected observed chain must exactly match the complete protein; partial or homologous structures require the retained local reviewed mapping workflow. Direct requests use `/api/optimize` with `design_mode=paired_3dp` and `structure_context={content,format,chain,model,positions,positions_reviewed,target_adaptiveness,penalty_weight}`.
+
+Limits: 3–300 amino acids, structure content 250 KB, HTTP JSON body 1 MB. Both candidates use the configured codon reference, requested GC and canonical motif exclusions plus custom additions. Invalid inputs and infeasible candidates fail without a baseline fallback. Existing sequence-only settings and API requests remain supported. 3DP uses its explicit DP settings and does not apply Kozak, TpA, template or seed transformations. SOP checks are reported for both candidates; regeneration is manual and never silently changes mode. Watermark stays disabled.
+
+This is stateless computational testing, with no external service dependencies or remote database recording. Those existing integrations remain available for later operational use. The structure file is not retained in the response or browser history; normal design results may be retained in local browser history. Submit only public-safe inputs. Structural conformity metrics are codon-weight proxies, not folding/expression measurements. These source changes are not deployed or a new package release.
+
+## Current public policy UI (2026-10-12)
+
+Custom SOP management is paused. The built-in FactorForge default policy is applied; upload/export/preset/editing controls are hidden and disabled. Their code and previous browser configuration remain available for later reactivation through ENABLE_CUSTOM_SOP. Saved custom SOPs are ignored without deletion. 1DP/3DP mode selection and explicit structure inputs remain active. This supersedes the earlier public SOP upload/export instructions. Public API contracts are retained.
+
+### Scientific web observations
+
+Direct 1DP/3DP browser testing reports sense-CDS RNA motif scans and available initiation-window MFE in results, downloadable reports and local history. Structure confidence observations can suggest positions for explicit acceptance and review; unsupported inputs do not invent positions. These checks do not establish expression, yield or folding benefits. The default policy remains active and custom SOP management remains paused. See `docs/experimental-structure.md` for the API and measurement boundary.
+
+### Local reviewed structure file workflow
+
+`factorforge nbfold annotate` and `factorforge nbfold optimize` provide the experimental local Phase A/B workflow for exact-match structure files and an explicit user review manifest. See [NB-Fold documentation](docs/experimental-structure.md).
+
+Web structure handling now requires exact-match uploaded PDB/mmCIF coordinates and explicit reviewed positions. Automatic external folding, artificial structure/confidence fallback, and auto-approval are disabled. Structure metrics are synthetic reconstruction checks; independent public-structure/DSSP validation remains open.
+
+### Experimental human-reference prototype
+
+`factorforge.engines.stemcell_3dp.StemCell3DPOptimizer` is a local experimental interface using a generic human-frequency reference and provisional Eijex review criteria. It is not an MSC/iPSC-calibrated model or a laboratory-approved SOP. See [prototype boundaries](docs/model_cards/human-reference-prototype.md). It is not a new production web host.
+# Local research candidate: DP v2.2
+
+The opt-in Python `DPV220Optimizer` shares the v2.1.1 DP core and adds reviewed
+position penalties. The experimental generic-human adapter uses this core;
+existing plant web/NB-Fold routes retain their prior objective. See the
+[model card](docs/model_cards/dp_v2_2.md) for usage, relaxation reporting and
+engineering validation boundaries. This is not an expression or folding claim.

{factorforge_cds-3.5.3 → factorforge_cds-3.5.10}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "factorforge-cds"
-version = "3.5.3"
+version = "3.5.10"
 description = "FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex."
 readme = "README.md"
 license = "AGPL-3.0-only"
@@ -30,6 +30,7 @@ dependencies = [
 postgres = [
     "psycopg2-binary>=2.9",
     "sqlalchemy>=2.0",
+    "eijex-db-core==0.1.2",
 ]
 dev = [
     "jsonschema>=4.0",
@@ -56,6 +57,7 @@ factorforge-validate = "factorforge.validation.cli:main"
 
 [tool.setuptools.packages.find]
 where = ["src"]
+include = ["factorforge*"]
 
 [tool.setuptools.package-data]
 "factorforge" = ["data/*.json", "data/templates/*.json", "data/profiles/*.json", "data/reference/*.json", "schemas/*.json", "registry/*.json"]
@@ -68,4 +70,10 @@ pythonpath = ["src"]
 [tool.ruff]
 line-length = 100
 target-version = "py310"
-exclude = ["archive"]
+# Versioned reproducibility deposits are immutable evidence, not maintained code.
+exclude = ["archive", "reproducibility"]
+
+[tool.ruff.lint.per-file-ignores]
+# Tests initialize paths/optional-dependency skips before importing modules.
+"tests/**" = ["E402"]
+"benchmarks/test_data/test_toy_flip.py" = ["E402"]

{factorforge_cds-3.5.3 → factorforge_cds-3.5.10}/src/factorforge/analysis/metrics.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import collections
 import json
 import math
 from collections import Counter
@@ -434,9 +435,6 @@ def detect_invalid_codons(sequence: str) -> list[dict[str, Any]]:
         elif codon not in STANDARD_GENETIC_CODE:
             findings.append({"start": start, "end": start + 3, "codon": codon, "reason": "unknown"})
     return findings
-import math
-import collections
-
 def calculate_synonymous_entropy(sequence, codon_to_aa):
     from factorforge.analysis.metrics import _codons
     codons = _codons(sequence)

{factorforge_cds-3.5.3 → factorforge_cds-3.5.10}/src/factorforge/analysis/sequence_risks.py

@@ -3,7 +3,7 @@
 Extracted from legacy RuleEngine to serve as shared evaluation metrics.
 """
 import re
-from typing import Dict, Any, List, Set, Tuple
+from typing import Dict, Any, List
 
 # Polyadenylation signals (true biological motifs)
 POLYA_PATTERNS = {

{factorforge_cds-3.5.3 → factorforge_cds-3.5.10}/src/factorforge/benchmark/runner.py

@@ -1,4 +1,4 @@
-from typing import List, Dict, Any, Type
+from typing import List, Dict
 import time
 import hashlib
 
@@ -108,7 +108,6 @@ class BenchmarkRunner:
         pass_counts = {}
         total_targets = len(set(r.target_id for r in results))
         
-        cai_sums = {}
         cai_vals = {}
         gc_sums = {}
         engine_counts = {}

{factorforge_cds-3.5.3 → factorforge_cds-3.5.10}/src/factorforge/cli/main.py

@@ -7,18 +7,18 @@ Usage:
   factorforge list-engines
 """
 
-from pathlib import Path
 import hashlib
 import json
 import sys
+from pathlib import Path
 
 import click
 
 from factorforge import __version__
 from factorforge.analysis.feasibility import DEFAULT_CAI_TARGET
 from factorforge.engines import register_builtin_engines
-from factorforge.engines.registry import EngineRegistry
 from factorforge.engines.profile.utils import parse_fasta_records
+from factorforge.engines.registry import EngineRegistry
 
 register_builtin_engines()
 
@@ -710,7 +710,10 @@ def evaluate_model(model_id, train_snapshot, eval_snapshot, input_sequence):
     mock_train_seqs = ["ATGGCTAAATGGTAA", "ATGCGTACGTGCTAG"]
     mock_eval_seqs = ["ATGCCCGGGAAATTT"]
     
-    from factorforge.review.evaluation_integrity import DatasetLeakageAuditor, GenerationMemorizationAuditor
+    from factorforge.review.evaluation_integrity import (
+        DatasetLeakageAuditor,
+        GenerationMemorizationAuditor,
+    )
     
     # 2. Dataset Leakage Audit
     ds_auditor = DatasetLeakageAuditor(mock_train_seqs, mock_eval_seqs)
@@ -914,82 +917,22 @@ def audit(sequence_fasta, reference_codon_profile, exclude_region, output):
     Run generic sequence audit to report codon usage, CAI, GC, and AA distribution.
     """
     _configure_stdio()
-    from factorforge.engines.profile.utils import parse_fasta_records
-    from factorforge.analysis.metrics import load_codon_usage_table, calculate_cai, calculate_gc, codon_usage_profile, translate_dna
     import hashlib
     import json
-    
     from pathlib import Path
-    fasta_records = parse_fasta_records(Path(sequence_fasta).read_text(encoding='utf-8'))
-    if not fasta_records:
-        raise click.UsageError(f"No FASTA records found in {sequence_fasta}")
-    
-    results = {}
-    for header, sequence in fasta_records:
-        seq = sequence.upper().replace("U", "T")
-        seq = "".join(seq.split())
-        
-        if exclude_region:
-            parts = exclude_region.split(":")
-            range_str = parts[-1]
-            try:
-                start, end = map(int, range_str.split("-"))
-                seq = seq[end:] # Naively assume we're removing the N-terminal SP 1-N.
-            except ValueError:
-                click.echo(f"Warning: Could not parse exclude region {exclude_region}", err=True)
-                
-        table = load_codon_usage_table()
-        
-        cai = calculate_cai(seq, table.codon_weights)
-        gc = calculate_gc(seq)
-        usage = codon_usage_profile(seq)
-        
-        aa_seq = translate_dna(seq)
-        aa_counts = {}
-        for aa in aa_seq:
-            aa_counts[aa] = aa_counts.get(aa, 0) + 1
-            
-        res = {
-            "input_sha256": hashlib.sha256(sequence.encode('utf-8')).hexdigest(),
-            "codon_table_sha256": hashlib.sha256(json.dumps(table.codon_weights, sort_keys=True).encode()).hexdigest(),
-            "tool_version": "1.0",
-            "cai": cai,
-            "gc_percent": gc,
-            "length": len(seq),
-            "aa_counts": aa_counts,
-            "codon_counts": usage,
-        }
-        results[header or "Sequence"] = res
-
-    if output:
-        with open(output, "w", encoding="utf-8") as f:
-            json.dump(results, f, indent=2)
-        click.echo(f"Audit report saved to: {output}")
-    else:
-        click.echo(json.dumps(results, indent=2))
 
-
-@cli.command("audit")
-@click.argument("sequence_fasta", type=click.Path(exists=True))
-@click.option("--reference-codon-profile", default="nbev11", help="Reference codon profile to use")
-@click.option("--exclude-region", help="Region to exclude from analysis (e.g., SP:1-60 or 1-60)")
-@click.option("--output", "-o", type=click.Path(), help="Output path for JSON report")
-def audit(sequence_fasta, reference_codon_profile, exclude_region, output):
-    """
-    Run generic sequence audit to report codon usage, CAI, GC, and AA distribution.
-    """
-    _configure_stdio()
-    from factorforge.engines.profile.utils import parse_fasta_records
     from factorforge.analysis.metrics import (
-        load_codon_usage_table, calculate_cai, calculate_gc, codon_usage_profile, 
-        translate_dna, calculate_synonymous_entropy, calculate_max_synonymous_share,
-        calculate_reference_distance
+        calculate_cai,
+        calculate_gc,
+        calculate_max_synonymous_share,
+        calculate_reference_distance,
+        calculate_synonymous_entropy,
+        codon_usage_profile,
+        load_codon_usage_table,
+        translate_dna,
     )
     from factorforge.engines.balanced_optimizer import STANDARD_GENETIC_CODE
-    
-    import hashlib
-    import json
-    from pathlib import Path
+    from factorforge.engines.profile.utils import parse_fasta_records
     
     fasta_records = parse_fasta_records(Path(sequence_fasta).read_text(encoding='utf-8'))
     if not fasta_records:
@@ -1053,6 +996,13 @@ def audit(sequence_fasta, reference_codon_profile, exclude_region, output):
     else:
         click.echo(json.dumps(results, indent=2))
 
+
+from factorforge.nbfold.cli import nbfold_cli
+
+cli.add_command(nbfold_cli)
+
+
 if __name__ == "__main__":
     cli()
 
+

factorforge_cds-3.5.10/src/factorforge/closed_loop/__init__.py

@@ -0,0 +1,27 @@
+"""FactorForge Closed-Loop Codon Evidence Foundation Package."""
+
+from factorforge.closed_loop.contracts import (
+    ConstructRecord,
+    ConstructSetRecord,
+    ExperimentRecord,
+    MeasurementRecord,
+    PolicyRecord,
+)
+from factorforge.closed_loop.ledger import EvidenceLedger
+from factorforge.closed_loop.readiness import (
+    ModelRecommendationGate,
+    ReadinessEvaluator,
+    ReadinessStatus,
+)
+
+__all__ = [
+    "ConstructRecord",
+    "ConstructSetRecord",
+    "EvidenceLedger",
+    "ExperimentRecord",
+    "MeasurementRecord",
+    "ModelRecommendationGate",
+    "PolicyRecord",
+    "ReadinessEvaluator",
+    "ReadinessStatus",
+]

factorforge_cds-3.5.10/src/factorforge/closed_loop/contracts.py

@@ -0,0 +1,103 @@
+"""Data contracts and schemas for Closed-Loop DBTL Lineage."""
+
+from __future__ import annotations
+
+import hashlib
+import json
+import math
+from datetime import datetime, timezone
+
+from pydantic import BaseModel, Field, model_validator
+
+
+class PolicyRecord(BaseModel):
+    """Metadata record of an approved codon distribution policy."""
+
+    policy_id: str
+    canonical_sha256: str
+    target_distribution: dict[str, dict[str, float]]
+    region_definition: str = "mature_chain"
+    feedback_source_id: str = "unspecified"
+    created_at: str = Field(default_factory=lambda: datetime.now(timezone.utc).isoformat())
+
+
+class ConstructRecord(BaseModel):
+    """Immutable sequence identity record for a designed construct."""
+
+    construct_id: str
+    cds_sha256: str
+    protein_sha256: str
+    chain: str  # "LC" or "HC"
+    watermark_pair_id: str
+    watermark_applied: bool
+    achieved_distribution: dict[str, dict[str, float]]
+    policy_id: str
+    engine_version: str = "FactorForge-v3.3.0"
+
+
+class ConstructSetRecord(BaseModel):
+    """Co-expressed pair of Light Chain and Heavy Chain constructs."""
+
+    construct_set_id: str
+    light_construct_id: str
+    heavy_construct_id: str
+    watermark_applied: bool
+    description: str = ""
+
+
+class ExperimentRecord(BaseModel):
+    """Wet-lab or benchmark experiment metadata."""
+
+    experiment_id: str
+    construct_set_id: str
+    host: str = "Nicotiana benthamiana"
+    expression_system: str = "Agroinfiltration (Transient Leaf Expression)"
+    batch_id: str
+    experiment_date: str
+    protocol_version: str = "unspecified"
+
+
+class MeasurementRecord(BaseModel):
+    """Single empirical or synthetic readout record."""
+
+    measurement_id: str
+    experiment_id: str
+    construct_set_id: str
+    biological_replicate_id: str
+    technical_replicate_id: str
+    measurement_type: str  # "protein_yield", "mrna_abundance", "functional_binding"
+    value: float | None
+    unit: str  # "mg/L", "relative_fold", "%"
+    qc_status: str = "PASS"  # "PASS", "FAIL", "FLAGGED"
+    is_synthetic: bool = (
+        False  # CRITICAL: If True, flagged as test_only and excluded from real training
+    )
+    tag: str = "empirical"
+    notes: str = ""
+    recorded_at: str = Field(default_factory=lambda: datetime.now(timezone.utc).isoformat())
+
+    @model_validator(mode="after")
+    def validate_measurement(self):
+        if self.value is not None and not math.isfinite(self.value):
+            raise ValueError("Measurement value must be finite or null")
+        if self.is_synthetic:
+            self.tag = "test_only"
+        if self.qc_status not in {"PASS", "FAIL", "FLAGGED"}:
+            raise ValueError("Unknown QC status")
+        return self
+
+    @property
+    def record_hash(self) -> str:
+        payload = {
+            "measurement_id": self.measurement_id,
+            "experiment_id": self.experiment_id,
+            "construct_set_id": self.construct_set_id,
+            "biological_replicate_id": self.biological_replicate_id,
+            "technical_replicate_id": self.technical_replicate_id,
+            "measurement_type": self.measurement_type,
+            "value": self.value,
+            "unit": self.unit,
+            "is_synthetic": self.is_synthetic,
+        }
+        encoded = json.dumps(payload, sort_keys=True, separators=(",", ":")).encode("utf-8")
+        return hashlib.sha256(encoded).hexdigest()