PyPI - factorforge-cds - Versions diffs - 3.2.2__tar.gz → 3.2.3__tar.gz - Mend

factorforge-cds 3.2.2tar.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-3.2.2 → factorforge_cds-3.2.3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.2.2
+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 v3.2.2 (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-3.2.2 → 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 v3.2.2 (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-3.2.2 → factorforge_cds-3.2.3}/pyproject.toml RENAMED Viewed

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "factorforge-cds"
-version = "3.2.2"
+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-3.2.2 → 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__ = "3.2.2"
+__version__ = "3.2.3"
 __author__ = "Eijex"
 # Auto-register engines (safe when running from source tree)

{factorforge_cds-3.2.2 → 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": "3.2.2",
+            "version": "3.2.3",
             "engine_type": "profile_rule_based",
             "role": "stable_profile_engine",
             "stable": True,

{factorforge_cds-3.2.2 → 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__ = "3.2.2"
+__version__ = "3.2.3"
 from .optimizer import RuleBasedOptimizer
 from .pipeline import OptimizationPipeline

{factorforge_cds-3.2.2 → factorforge_cds-3.2.3}/src/factorforge/engines/profile/optimizer.py RENAMED Viewed

@@ -17,7 +17,7 @@ class RuleBasedOptimizer(OptimizerEngine):
     """Profile-based rule optimization engine."""
     name = "Profile-based"
-    version = "3.2.2"
+    version = "3.2.3"
     def __init__(self, codon_table_path: str | None = None) -> None:
         """

{factorforge_cds-3.2.2 → 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: 3.2.2
+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 v3.2.2 (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-3.2.2 → 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():