factorforge-cds 3.2.7__tar.gz → 3.2.8__tar.gz

{factorforge_cds-3.2.7/src/factorforge_cds.egg-info → factorforge_cds-3.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.7
+Version: 3.2.8
 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
@@ -93,7 +93,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.2.7 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.8 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/README.md

@@ -60,7 +60,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.2.7 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.8 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "factorforge-cds"
-version = "3.2.7"
+version = "3.2.8"
 description = "FactorForge - open-source CDS design and pre-synthesis sequence review engine by Eijex."
 readme = "README.md"
 license = "AGPL-3.0-only"

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/__init__.py

@@ -4,7 +4,7 @@ FactorForge - Codon Optimization Platform
 profile: constraint-aware rule/profile engine
 """
 
-__version__ = "3.2.7"
+__version__ = "3.2.8"
 __author__ = "Eijex"
 
 # Auto-register engines (safe when running from source tree)

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/analysis/feasibility.py

@@ -14,18 +14,19 @@ from factorforge.analysis.metrics import (
 )
 
 
-# DEFAULT_CAI_TARGET=0.82 aligns with industry practice (>0.8) and is achievable
-# (internal benchmark, n=49, avg CAI=0.76).
-# DEFAULT_GC_LOW/HIGH = native genome-composition anchor for N. benthamiana CDS
-# (_analysis/025 STEP 2: 004 endogenous n=10 measured range 40-47%, cross-checked
-# against nbev11_cds_hc/all and qld183_v103 derived-asset GC ~42.8-43.1% and
-# external ground truth ~44%). NOT an empirically validated expression optimum —
-# this is a composition anchor, not a target to maximize toward.
+# Defaults calibrated to nbenthamiana profile engine output distribution
+# (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).
+#
+# DEFAULT_GC_LOW/HIGH provisionally reverted from the Job 168/v3.3.0
+# native-genome-composition anchor (40-47%, released as part of v3.2.7) back
+# to the legacy engine-output-calibrated band, pending an MFE re-sensitivity +
+# 2x2 factorial recheck. See scoring.py's GC_OPT_MIN/MAX comment.
 DEFAULT_CAI_TARGET: float = 0.82
-DEFAULT_GC_LOW: float = 40.0
-DEFAULT_GC_HIGH: float = 47.0
+DEFAULT_GC_LOW: float = 55.0
+DEFAULT_GC_HIGH: float = 65.0
 
 
 AA_TO_CODONS: dict[str, list[str]] = {}
@@ -120,11 +121,7 @@ def analyze_feasibility(
     if not protein:
         raise ValueError("protein_sequence must not be empty")
 
-    # Default exploration ranges: genome-grounded native anchor first, then
-    # progressively wider windows. (55.0, 65.0) is retained ONLY as an explicit
-    # non-native/high-GC option (matches legacy engine-output-calibrated band) —
-    # callers must opt in explicitly to it, it is not the production default.
-    ranges = gc_ranges or [(40.0, 47.0), (35.0, 50.0), (55.0, 65.0)]
+    ranges = gc_ranges or [(55.0, 65.0), (50.0, 65.0), (40.0, 65.0)]
     normalized_ranges = [
         (_normalize_gc_bound(low), _normalize_gc_bound(high)) for low, high in ranges
     ]

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/cli/main.py

@@ -164,8 +164,8 @@ def list_engines():
     type=click.Choice(["feasibility_best"], case_sensitive=False),
     help="DP objective",
 )
-@click.option("--gc-min", type=float, default=40.0, help="Minimum target GC percentage")
-@click.option("--gc-max", type=float, default=47.0, help="Maximum target GC percentage")
+@click.option("--gc-min", type=float, default=55.0, help="Minimum target GC percentage")
+@click.option("--gc-max", type=float, default=65.0, help="Maximum target GC percentage")
 @click.option("--template", "construct_template", help="Construct template name")
 @click.option("--output", "-o", help="Output file")
 @click.option("--format", "output_format", default="fasta", help="Output format (fasta, genbank)")

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/engines/__init__.py

@@ -13,7 +13,7 @@ def register_builtin_engines() -> None:
         "profile",
         RuleBasedOptimizer,
         metadata={
-            "version": "3.2.7",
+            "version": "3.2.8",
             "engine_type": "profile_rule_based",
             "role": "stable_profile_engine",
             "stable": True,

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/engines/profile/__init__.py

@@ -5,7 +5,7 @@ Production system (2026)
 Plant-specific rule-based optimization
 """
 
-__version__ = "3.2.7"
+__version__ = "3.2.8"
 
 from .optimizer import RuleBasedOptimizer
 from .pipeline import OptimizationPipeline

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/engines/profile/optimizer.py

@@ -20,7 +20,7 @@ class RuleBasedOptimizer(OptimizerEngine):
     """Profile-based rule optimization engine."""
 
     name = "Profile-based"
-    version = "3.2.7"
+    version = "3.2.8"
 
     def __init__(self, codon_table_path: str | None = None) -> None:
         """

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/engines/profile/rules/reverse_translator.py

@@ -374,11 +374,12 @@ class ReverseTranslator:
         Balanced profile: CAI first, GC balanced
 
         - Preferred codon ratio: 70%
-        - Target GC: host composition band (nbenthamiana: 40-47%, native
-          genome-composition anchor; see _analysis/025 STEP 2 and
-          engines/profile/scoring.py GC_OPT_MIN/MAX. Not an empirically
-          validated expression optimum. Other hosts: resolve_host_gc_range()
-          default, unchanged from pre-v3.3.0 behavior.)
+        - Target GC: host composition band, resolved via
+          resolve_host_gc_range() (engines/profile/scoring.py
+          GC_OPT_MIN/MAX). nbenthamiana currently uses the legacy 55-65%
+          band; the native genome-composition anchor (40-47%, _analysis/025)
+          was provisionally reverted on 2026-06-29 pending an MFE
+          re-sensitivity + 2x2 factorial recheck.
         """
         _host_gc_min, _host_gc_max = resolve_host_gc_range(self.host)
         target_gc_min = kwargs.get("target_gc_min", _host_gc_min)

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/engines/profile/rules/rule_engine.py

@@ -358,12 +358,14 @@ class RuleEngine:
 
         This is a LOCAL synthesis/extreme-window guard (default 25-75% over a
         50 bp window), NOT the global GC target. Global GC is governed separately
-        by the scoring band (GC_OPT_MIN/MAX, native genome-composition anchor
-        ~40-47%, see _analysis/025 STEP 2) and the API/DP gc_min/gc_max
-        constraints. The wide 25-75% local band is an independent synthesis/
-        hairpin-risk guard (registry `gc_extreme_local_window`), not derived from
-        or coupled to the global GC target — narrowing it is a separate decision
-        from the global band retarget and is out of scope here.
+        by the scoring band (GC_OPT_MIN/MAX, currently 55-65% for nbenthamiana
+        — the native genome-composition anchor, ~40-47%, _analysis/025, was
+        provisionally reverted on 2026-06-29 pending an MFE re-sensitivity +
+        2x2 factorial recheck) and the API/DP gc_min/gc_max constraints. The
+        wide 25-75% local band is an independent synthesis/hairpin-risk guard
+        (registry `gc_extreme_local_window`), not derived from or coupled to
+        the global GC target — narrowing it is a separate decision from the
+        global band retarget and is out of scope here.
 
         Args:
             seq: DNA sequence

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/engines/profile/scoring.py

@@ -12,22 +12,26 @@ from typing import Any
 logger = logging.getLogger(__name__)
 
 # GC band for N. benthamiana codon-optimized sequences.
-# Native genome-composition anchor (_analysis/025 STEP 2: 004 endogenous CDS
-# n=10 measured range 40-47%; cross-checked against nbev11_cds_hc/all and
-# qld183_v103 derived-asset GC ~42.8-43.1% and external ground truth ~44%).
-# NOT an empirically validated expression optimum — this is a composition
-# anchor, not a target to maximize toward. Sequences within [GC_OPT_MIN,
-# GC_OPT_MAX] receive full GC score; outside the band the score decays linearly.
-GC_OPT_MIN = 40.0
-GC_OPT_MAX = 47.0
-GC_OPT_MID = 43.5  # kept for gc_target point-scoring and viral_delivery centering
+# 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]
+# receive full GC score; outside the band the score decays linearly.
+#
+# Job 168/v3.3.0 (released as part of v3.2.7, see CHANGELOG) moved this band to
+# 40-47% (native genome-composition anchor, _analysis/025). Provisionally
+# reverted here pending an MFE re-sensitivity + 2x2 factorial recheck
+# (_analysis, scope TBD as of 2026-06-29) — see eijex-workspace
+# _version/factorforge-version-sequencing-plan.md. Not a rejection of the
+# 40-47% anchor, just not yet re-confirmed as the production default.
+GC_OPT_MIN = 55.0
+GC_OPT_MAX = 65.0
+GC_OPT_MID = 60.0  # kept for gc_target point-scoring and viral_delivery centering
 GC_DECAY_WIDTH = 20.0  # percentage points outside band before score reaches 0.0
 
-# Job 168 / v3.3.0 (_analysis/025) scoped the genome-composition re-derivation
-# to N. benthamiana only. Other hosts (e.g. ntabacum/BY-2) keep the pre-v3.3.0
-# global default (55-65%, internal benchmark n=49 avg GC=60.1%) until they get
-# their own host-specific genome-composition analysis — they must NOT silently
-# inherit GC_OPT_MIN/MAX, which is an N.-benthamiana-specific anchor.
+# Host-isolation fix (Job 168/v3.3.0, kept): ntabacum/BY-2 must not silently
+# inherit whatever band nbenthamiana uses. Both currently resolve to the same
+# GC_RANGE_DEFAULT band pending the nbenthamiana re-check above.
 GC_RANGE_DEFAULT: tuple[float, float] = (55.0, 65.0)
 GC_RANGES_BY_HOST: dict[str, tuple[float, float]] = {
     "nbenthamiana": (GC_OPT_MIN, GC_OPT_MAX),

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/src/factorforge/engines/profile/utils.py

@@ -115,14 +115,13 @@ def calculate_dinucleotide_ratio(sequence: str, dinucleotide: str = "CG") -> flo
     return observed / expected
 
 
-# Job 168 / v3.3.0 (_analysis/025): host -> production-default codon table file
-# overrides. nbenthamiana moved from the legacy {host}_codons.json convention to
-# the NbeV1.1 LAB-strain derived table. See data/reference/active_codon_reference.json.
-# The legacy file itself (nbenthamiana_codons.json) is left untouched on disk for
-# historical benchmark replay (benchmarks/run_benchmark.py --codon-table-path).
-_HOST_CODON_TABLE_OVERRIDES: dict[str, str] = {
-    "nbenthamiana": "profiles/nbev11_cds_hc_derived_codons.json",
-}
+# Job 168 / v3.3.0 (_analysis/025) introduced a host -> production-default
+# codon table file override mechanism and pointed nbenthamiana at the NbeV1.1
+# LAB-strain derived table (released as part of v3.2.7). Provisionally
+# reverted to empty (falls back to the legacy {host}_codons.json convention)
+# pending an MFE re-sensitivity + 2x2 factorial recheck. The NbeV1.1 table
+# remains on disk and selectable; see data/reference/active_codon_reference.json.
+_HOST_CODON_TABLE_OVERRIDES: dict[str, str] = {}
 
 
 def resolve_host_codon_table_path(host: str, codon_tables_dir: Path) -> Path:

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8/src/factorforge_cds.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.7
+Version: 3.2.8
 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
@@ -93,7 +93,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.2.7 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.8 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/tests/test_registry_production_sync.py

@@ -103,16 +103,18 @@ def test_codon_reference_active_sync_with_active_reference_file():
     assert registry_active["sha256"] == hashlib.sha256(table_path.read_bytes()).hexdigest()
 
 
-def test_codon_reference_active_sync_with_v2_manifest():
+def test_codon_reference_active_sync_with_legacy_manifest():
     """registry's codon_reference.active block must match the schema-conformant
-    v2 manifest file's facts (asset_type, sha256, source_status)."""
+    legacy (v1) manifest file's facts (asset_type, sha256, source_status) — v1
+    is the production default again as of the v3.2.7 GC-band/codon-reference
+    revert, pending an MFE re-sensitivity + 2x2 factorial recheck of v2."""
     import json
     from pathlib import Path
 
     registry_active = _resolve("codon_reference.active")
     manifest = json.loads(
         (Path(__file__).resolve().parents[1] / "data" / "reference"
-         / "codon_table_manifest_nbev11_hc_v2.json").read_text(encoding="utf-8")
+         / "codon_table_manifest.json").read_text(encoding="utf-8")
     )
     assert registry_active["id"] == manifest["codon_table_id"]
     assert registry_active["sha256"] == manifest["sha256"]
@@ -120,6 +122,24 @@ def test_codon_reference_active_sync_with_v2_manifest():
     assert registry_active["source_status"] == manifest["source_status"]
 
 
+def test_codon_reference_candidate_sync_with_v2_manifest():
+    """registry's codon_reference.candidate block (the provisionally
+    un-promoted v2 asset) must stay in sync with its own manifest file even
+    while not active."""
+    import json
+    from pathlib import Path
+
+    registry_candidate = _resolve("codon_reference.candidate")
+    manifest = json.loads(
+        (Path(__file__).resolve().parents[1] / "data" / "reference"
+         / "codon_table_manifest_nbev11_hc_v2.json").read_text(encoding="utf-8")
+    )
+    assert registry_candidate["id"] == manifest["codon_table_id"]
+    assert registry_candidate["sha256"] == manifest["sha256"]
+    assert registry_candidate["asset_type"] == manifest["asset_type"]
+    assert registry_candidate["source_status"] == manifest["source_status"]
+
+
 def test_codon_reference_active_table_sha256_matches_production_default():
     """The sha256 recorded for the active codon_reference must match the
     actual file the production engine resolves to by default."""

{factorforge_cds-3.2.7 → factorforge_cds-3.2.8}/tests/test_worked_example.py

@@ -82,10 +82,14 @@ def test_run_example_deterministic():
 
 
 def test_run_example_v2_smoke_succeeds():
-    """run_example_v2_smoke.py (current production default) must exit 0.
-
-    No frozen-output comparison — this only checks that the v2 path runs
-    end-to-end and reports correct provenance (Job 168 / v3.3.0, _analysis/025).
+    """run_example_v2_smoke.py (tracks whatever the current production
+    default actually is) must exit 0 and report a provenance ID that matches
+    data/reference/active_codon_reference.json — not hardcoded to v2, since
+    the default was provisionally reverted to v1 on 2026-06-29 pending an MFE
+    re-sensitivity + 2x2 factorial recheck (Job 168 / v3.3.0, _analysis/025).
+
+    No frozen-output comparison — this only checks that the current-default
+    path runs end-to-end and reports correct provenance.
     """
     result = subprocess.run(
         [sys.executable, str(EXAMPLE_DIR / "run_example_v2_smoke.py")],
@@ -98,7 +102,8 @@ def test_run_example_v2_smoke_succeeds():
         f"stdout:{result.stdout}\nstderr:{result.stderr}"
     )
     assert "OK" in result.stdout
-    assert "nbenthamiana_nbev11_hc_v2" in result.stdout
+    active_ref = _load(ROOT / "data" / "reference" / "active_codon_reference.json")
+    assert active_ref["active_codon_table_id"] in result.stdout
 
 
 # ---------------------------------------------------------------------------