factorforge-cds 3.5.3__tar.gz → 3.5.4__tar.gz

{factorforge_cds-3.5.3 → factorforge_cds-3.5.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.5.3
+Version: 3.5.4
 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
@@ -51,7 +51,7 @@ 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 v3.5.4 uses independently versioned engines:
 
 | Generation | Engine | Version | Availability |
 |---|---|---:|---|
@@ -107,7 +107,7 @@ 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 +127,7 @@ 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 v3.5.4 (2026). Open-source constraint-based CDS design and sequence review.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 
@@ -139,9 +139,17 @@ 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.
+
+Install `pip install "factorforge-cds[postgres]"` only when using that integration.
+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
 

{factorforge_cds-3.5.3 → factorforge_cds-3.5.4}/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 v3.5.4 uses independently versioned engines:
 
 | Generation | Engine | Version | Availability |
 |---|---|---:|---|
@@ -70,7 +70,7 @@ 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 +90,7 @@ 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 v3.5.4 (2026). Open-source constraint-based CDS design and sequence review.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 
@@ -102,9 +102,17 @@ 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.
+
+Install `pip install "factorforge-cds[postgres]"` only when using that integration.
+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
 

{factorforge_cds-3.5.3 → factorforge_cds-3.5.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "factorforge-cds"
-version = "3.5.3"
+version = "3.5.4"
 description = "FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex."
 readme = "README.md"
 license = "AGPL-3.0-only"
@@ -56,6 +56,7 @@ 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 +69,10 @@ 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-3.5.4}/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-3.5.4}/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-3.5.4}/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-3.5.4}/src/factorforge/cli/main.py

@@ -904,71 +904,6 @@ def ingest_outcome(dataset_file, measurements_file, output):
 
 
 
-@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
-    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")

{factorforge_cds-3.5.3 → factorforge_cds-3.5.4}/src/factorforge/core/host_model.py

@@ -7,7 +7,6 @@ weights (w_ij), reference GC bounds, and model provenance.
 from __future__ import annotations
 
 from dataclasses import dataclass, field
-import json
 import logging
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple

{factorforge_cds-3.5.3 → factorforge_cds-3.5.4}/src/factorforge/core/reranker.py

@@ -6,9 +6,9 @@ Stage 3 (Real 7-D Normalized Trait Space Furthest-First Diversity Selection).
 
 from __future__ import annotations
 
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 import math
-from typing import Any, Dict, List, Optional, Sequence, Tuple
+from typing import Dict, List, Optional
 
 from factorforge.analysis.metrics import calculate_gc_windows, detect_homopolymers
 from factorforge.core.host_model import HostModel

{factorforge_cds-3.5.3 → factorforge_cds-3.5.4}/src/factorforge/core/slate_engine.py

@@ -11,7 +11,6 @@ Stage 5: Exact Top-K Slate Assembly (Successive Pareto Fronts + Boundary Furthes
 
 from __future__ import annotations
 
-from dataclasses import dataclass, field
 import datetime
 import logging
 import time
@@ -21,7 +20,6 @@ from factorforge.core.host_model import HostModel
 from factorforge.core.reranker import (
     MultiFactorSlateReranker,
     PhenotypeDiversitySelector,
-    ScoredCandidate,
 )
 from factorforge.core.slate_generator import (
     DEFAULT_FORBIDDEN_SITES,

{factorforge_cds-3.5.3 → factorforge_cds-3.5.4}/src/factorforge/core/slate_generator.py

@@ -9,7 +9,6 @@ from __future__ import annotations
 from dataclasses import dataclass, field
 import hashlib
 import random
-import re
 from typing import Any, Dict, List, Optional, Set, Tuple
 
 from factorforge.analysis.metrics import (