factorforge-cds 3.2.4__tar.gz → 3.2.6__tar.gz

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.4
+Version: 3.2.6
 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
@@ -17,14 +17,14 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: biopython>=1.81
 Requires-Dist: requests>=2.31
-Requires-Dist: click>=8.0
+Requires-Dist: click>=8.4.1
 Requires-Dist: pydantic>=2.0
 Provides-Extra: dev
 Requires-Dist: jsonschema>=4.0; extra == "dev"
 Requires-Dist: pandas>=2.0; extra == "dev"
-Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest>=9.1.1; extra == "dev"
 Requires-Dist: pytest-cov>=4.0; extra == "dev"
-Requires-Dist: ruff>=0.1; extra == "dev"
+Requires-Dist: ruff>=0.15.18; extra == "dev"
 Requires-Dist: pyyaml>=6.0; extra == "dev"
 Provides-Extra: ml
 Requires-Dist: transformers>=4.40; extra == "ml"
@@ -93,7 +93,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.2.4 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.6 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/README.md

@@ -60,7 +60,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.2.4 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.6 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "factorforge-cds"
-version = "3.2.4"
+version = "3.2.6"
 description = "FactorForge - open-source CDS design and pre-synthesis sequence review engine by Eijex."
 readme = "README.md"
 license = "AGPL-3.0-only"
@@ -22,7 +22,7 @@ classifiers = [
 dependencies = [
     "biopython>=1.81",
     "requests>=2.31",
-    "click>=8.0",
+    "click>=8.4.1",
     "pydantic>=2.0",
 ]
 
@@ -30,9 +30,9 @@ dependencies = [
 dev = [
     "jsonschema>=4.0",
     "pandas>=2.0",
-    "pytest>=7.0",
+    "pytest>=9.1.1",
     "pytest-cov>=4.0",
-    "ruff>=0.1",
+    "ruff>=0.15.18",
     "pyyaml>=6.0",
 ]
 ml = [

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/src/factorforge/__init__.py

@@ -4,7 +4,7 @@ FactorForge - Codon Optimization Platform
 profile: constraint-aware rule/profile engine
 """
 
-__version__ = "3.2.4"
+__version__ = "3.2.6"
 __author__ = "Eijex"
 
 # Auto-register engines (safe when running from source tree)

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/src/factorforge/engines/__init__.py

@@ -13,7 +13,7 @@ def register_builtin_engines() -> None:
         "profile",
         RuleBasedOptimizer,
         metadata={
-            "version": "3.2.4",
+            "version": "3.2.6",
             "engine_type": "profile_rule_based",
             "role": "stable_profile_engine",
             "stable": True,

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/src/factorforge/engines/profile/__init__.py

@@ -5,7 +5,7 @@ Production system (2026)
 Plant-specific rule-based optimization
 """
 
-__version__ = "3.2.4"
+__version__ = "3.2.6"
 
 from .optimizer import RuleBasedOptimizer
 from .pipeline import OptimizationPipeline

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/src/factorforge/engines/profile/optimizer.py

@@ -20,7 +20,7 @@ class RuleBasedOptimizer(OptimizerEngine):
     """Profile-based rule optimization engine."""
 
     name = "Profile-based"
-    version = "3.2.4"
+    version = "3.2.6"
 
     def __init__(self, codon_table_path: str | None = None) -> None:
         """

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/src/factorforge_cds.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.4
+Version: 3.2.6
 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
@@ -17,14 +17,14 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: biopython>=1.81
 Requires-Dist: requests>=2.31
-Requires-Dist: click>=8.0
+Requires-Dist: click>=8.4.1
 Requires-Dist: pydantic>=2.0
 Provides-Extra: dev
 Requires-Dist: jsonschema>=4.0; extra == "dev"
 Requires-Dist: pandas>=2.0; extra == "dev"
-Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest>=9.1.1; extra == "dev"
 Requires-Dist: pytest-cov>=4.0; extra == "dev"
-Requires-Dist: ruff>=0.1; extra == "dev"
+Requires-Dist: ruff>=0.15.18; extra == "dev"
 Requires-Dist: pyyaml>=6.0; extra == "dev"
 Provides-Extra: ml
 Requires-Dist: transformers>=4.40; extra == "ml"
@@ -93,7 +93,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 
 ```
-FactorForge v3.2.4 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.6 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.2.4 → factorforge_cds-3.2.6}/src/factorforge_cds.egg-info/requires.txt

@@ -1,14 +1,14 @@
 biopython>=1.81
 requests>=2.31
-click>=8.0
+click>=8.4.1
 pydantic>=2.0
 
 [dev]
 jsonschema>=4.0
 pandas>=2.0
-pytest>=7.0
+pytest>=9.1.1
 pytest-cov>=4.0
-ruff>=0.1
+ruff>=0.15.18
 pyyaml>=6.0
 
 [ml]