PyPI - factorforge-cds - Versions diffs - 3.2.1__tar.gz → 3.2.3__tar.gz - Mend

factorforge-cds 3.2.1tar.gz → 3.2.3tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (95) hide show

{factorforge_cds-3.2.1 → factorforge_cds-3.2.3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.1
+Version: 3.2.3
 Summary: FactorForge - open-source constraint-based CDS design engine by Eijex.
 Author-email: Eijex <eijex.lab@gmail.com>
 License-Expression: AGPL-3.0-only
@@ -40,7 +40,7 @@ Dynamic: license-file
 [![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`).
@@ -93,7 +93,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 ```
-FactorForge v3.2.0 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.3 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
@@ -118,4 +118,5 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
 - **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-3.2.1 → factorforge_cds-3.2.3}/README.md RENAMED Viewed

@@ -7,7 +7,7 @@
 [![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`).
@@ -60,7 +60,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 ```
-FactorForge v3.2.0 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.3 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
@@ -85,4 +85,5 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
 - **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-3.2.1 → factorforge_cds-3.2.3}/pyproject.toml RENAMED Viewed

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "factorforge-cds"
-version = "3.2.1"
+version = "3.2.3"
 description = "FactorForge - open-source constraint-based CDS design engine by Eijex."
 readme = "README.md"
 license = "AGPL-3.0-only"

{factorforge_cds-3.2.1 → factorforge_cds-3.2.3}/src/factorforge/__init__.py RENAMED Viewed

@@ -4,7 +4,7 @@ FactorForge - Codon Optimization Platform
 profile: constraint-aware rule/profile engine
 """
-__version__ = "3.2.1"
+__version__ = "3.2.3"
 __author__ = "Eijex"
 # Auto-register engines (safe when running from source tree)

{factorforge_cds-3.2.1 → factorforge_cds-3.2.3}/src/factorforge/engines/__init__.py RENAMED Viewed

@@ -13,7 +13,7 @@ def register_builtin_engines() -> None:
         "profile",
         RuleBasedOptimizer,
         metadata={
-            "version": "3.2.0",
+            "version": "3.2.3",
             "engine_type": "profile_rule_based",
             "role": "stable_profile_engine",
             "stable": True,

{factorforge_cds-3.2.1 → factorforge_cds-3.2.3}/src/factorforge/engines/profile/__init__.py RENAMED Viewed

@@ -5,7 +5,7 @@ Production system (2026)
 Plant-specific rule-based optimization
 """
-__version__ = "3.2.0"
+__version__ = "3.2.3"
 from .optimizer import RuleBasedOptimizer
 from .pipeline import OptimizationPipeline

{factorforge_cds-3.2.1 → factorforge_cds-3.2.3}/src/factorforge/engines/profile/optimizer.py RENAMED Viewed

@@ -17,11 +17,30 @@ class RuleBasedOptimizer(OptimizerEngine):
     """Profile-based rule optimization engine."""
     name = "Profile-based"
-    version = "3.2.0"
+    version = "3.2.3"
-    def __init__(self) -> None:
+    def __init__(self, codon_table_path: str | None = None) -> None:
+        """
+        Args:
+            codon_table_path: Optional path to a codon usage table JSON used for
+                design-time reverse translation. When omitted (the default), the
+                bundled host reference table is used — this is the only path the
+                product `optimize` CLI and the registered engine ever take, so
+                their behavior is unchanged. Injection is used by the benchmark
+                harness to drive design with alternative source-profile tables.
+        """
         self.validator = InputValidator()
-        self.translator = ReverseTranslator()  # Data files use default path
+        self._codon_table_path = codon_table_path
+        # When a source-profile table is injected, drive every CAI-dependent
+        # profile from it: it is both the design weight table and the golden set
+        # that high_cai maximizes against. Otherwise high_cai would keep chasing
+        # the bundled golden set and stay invariant to the source profile,
+        # making the injection incomplete. gc_target is GC-driven and remains
+        # legitimately invariant either way.
+        self.translator = ReverseTranslator(
+            codon_table_path=codon_table_path,
+            golden_set_path=codon_table_path,
+        )
         self.rule_engine = RuleEngine()
         self.exporter = SequenceExporter()
@@ -74,7 +93,9 @@ class RuleBasedOptimizer(OptimizerEngine):
                 f"Unknown profile: {profile_value}. Supported profiles: {supported}"
             ) from exc
-        if host == "nbenthamiana":
+        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.
             translator = self.translator
             rule_engine = self.rule_engine
         else:

{factorforge_cds-3.2.1 → factorforge_cds-3.2.3}/src/factorforge_cds.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.1
+Version: 3.2.3
 Summary: FactorForge - open-source constraint-based CDS design engine by Eijex.
 Author-email: Eijex <eijex.lab@gmail.com>
 License-Expression: AGPL-3.0-only
@@ -40,7 +40,7 @@ Dynamic: license-file
 [![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`).
@@ -93,7 +93,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
 ## Citing
 ```
-FactorForge v3.2.0 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.2.3 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
@@ -118,4 +118,5 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
 - **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-3.2.1 → factorforge_cds-3.2.3}/tests/test_docs_consistency.py RENAMED Viewed

@@ -7,6 +7,7 @@ reproducibility anchors drift.
 from __future__ import annotations
 import hashlib
 import json
+import subprocess
 from pathlib import Path
 import pytest
@@ -52,11 +53,21 @@ def test_manifest_inputs_sha256_non_empty():
 def test_manifest_input_sha256_matches_files():
+    # Hash the committed git blob, not local working-tree bytes: on Windows,
+    # core.autocrlf=true plus this repo's .gitattributes (eol=lf for
+    # json/yaml/yml) means the working tree can hold CRLF while git stores
+    # LF, so path.read_bytes() can produce a value that mismatches what is
+    # actually committed (the root cause of the Job 129 / Job 136 incidents).
     data = json.loads(MANIFEST_PATH.read_text(encoding="utf-8"))
     for name, entry in data["inputs"].items():
-        path = ROOT / entry["path"]
-        actual = hashlib.sha256(path.read_bytes()).hexdigest()
-        assert actual == entry["sha256"], f"MANIFEST.json hash drift for {name}: {path}"
+        blob = subprocess.run(
+            ["git", "show", f"HEAD:{entry['path']}"],
+            cwd=ROOT,
+            capture_output=True,
+            check=True,
+        ).stdout
+        actual = hashlib.sha256(blob).hexdigest()
+        assert actual == entry["sha256"], f"MANIFEST.json hash drift for {name}: {entry['path']}"
 def test_manifest_commands_use_reproducible_entrypoints():