factorforge-cds 3.1.2__tar.gz → 3.1.3__tar.gz

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Files changed (67) hide show
  1. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/PKG-INFO +3 -3
  2. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/README.md +2 -2
  3. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/pyproject.toml +1 -1
  4. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/__init__.py +1 -1
  5. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/__init__.py +1 -1
  6. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/__init__.py +1 -1
  7. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/optimizer.py +1 -1
  8. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/__init__.py +1 -1
  9. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/pipeline.py +1 -1
  10. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge_cds.egg-info/PKG-INFO +3 -3
  11. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/LICENSE +0 -0
  12. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/setup.cfg +0 -0
  13. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/__main__.py +0 -0
  14. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/cli/__init__.py +0 -0
  15. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/cli/legacy_cli.py +0 -0
  16. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/cli/main.py +0 -0
  17. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/core/interfaces/__init__.py +0 -0
  18. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/core/interfaces/exporter.py +0 -0
  19. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/core/interfaces/optimizer.py +0 -0
  20. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/core/interfaces/validator.py +0 -0
  21. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/database.py +0 -0
  22. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/ml/__init__.py +0 -0
  23. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/ml/plant_optimizer.py +0 -0
  24. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/registry.py +0 -0
  25. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v1_archived/__init__.py +0 -0
  26. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/codon_table_builder.py +0 -0
  27. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/construct_builder.py +0 -0
  28. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/exporter.py +0 -0
  29. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/pipeline.py +0 -0
  30. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/rules/__init__.py +0 -0
  31. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/rules/domesticator.py +0 -0
  32. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/rules/reverse_translator.py +0 -0
  33. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/rules/rule_engine.py +0 -0
  34. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/scoring.py +0 -0
  35. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/utils.py +0 -0
  36. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/validator.py +0 -0
  37. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/explain.py +0 -0
  38. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/inference/__init__.py +0 -0
  39. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/inference/constrained_decoder.py +0 -0
  40. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/inference/v2_adapter.py +0 -0
  41. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/metrics.py +0 -0
  42. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/modeling_bart_decoder.py +0 -0
  43. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/synonym_mask.py +0 -0
  44. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/tokenizer.py +0 -0
  45. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/ml/__init__.py +0 -0
  46. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/ml/feasibility.py +0 -0
  47. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/ml/metrics.py +0 -0
  48. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/schemas/__init__.py +0 -0
  49. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/schemas/design_package.py +0 -0
  50. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/utils/__init__.py +0 -0
  51. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/utils/construct_id.py +0 -0
  52. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/utils/exceptions.py +0 -0
  53. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/utils/restriction_sites.py +0 -0
  54. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/utils/sequence_validator.py +0 -0
  55. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/utils/validation.py +0 -0
  56. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/validation/__init__.py +0 -0
  57. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/validation/cli.py +0 -0
  58. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/validation/package_generator.py +0 -0
  59. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge_cds.egg-info/SOURCES.txt +0 -0
  60. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge_cds.egg-info/dependency_links.txt +0 -0
  61. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge_cds.egg-info/entry_points.txt +0 -0
  62. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge_cds.egg-info/requires.txt +0 -0
  63. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge_cds.egg-info/top_level.txt +0 -0
  64. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/tests/test_compare_v1_v2.py +0 -0
  65. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/tests/test_database.py +0 -0
  66. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/tests/test_restriction_sites.py +0 -0
  67. {factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/tests/test_sequence_validator.py +0 -0
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: factorforge-cds
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- Version: 3.1.2
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+ Version: 3.1.3
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  Summary: FactorForge — open-source constraint-based CDS design engine by Eijex.
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  Author-email: Eijex <eijex.lab@gmail.com>
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  License: Apache License
@@ -238,7 +238,7 @@ Dynamic: license-file
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  [![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
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  [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
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- [![Version](https://img.shields.io/badge/version-3.1.2-green.svg)](https://github.com/eijex/factorforge-cds/releases)
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+ [![Version](https://img.shields.io/badge/version-3.1.3-green.svg)](https://github.com/eijex/factorforge-cds/releases)
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  [![PyPI](https://img.shields.io/pypi/v/factorforge-cds.svg)](https://pypi.org/project/factorforge-cds/)
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  [![Web App](https://img.shields.io/badge/web-factorforge--cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
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@@ -278,7 +278,7 @@ FactorForge predictions are **in-silico only** and have not been experimentally
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  ## Citing
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  ```
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- FactorForge v3.1.2 (2026). Open-source constraint-based CDS design engine.
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+ FactorForge v3.1.3 (2026). Open-source constraint-based CDS design engine.
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  Eijex. https://github.com/eijex/factorforge-cds
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  ```
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{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/README.md RENAMED
@@ -4,7 +4,7 @@
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  [![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
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  [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
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- [![Version](https://img.shields.io/badge/version-3.1.2-green.svg)](https://github.com/eijex/factorforge-cds/releases)
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+ [![Version](https://img.shields.io/badge/version-3.1.3-green.svg)](https://github.com/eijex/factorforge-cds/releases)
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  [![PyPI](https://img.shields.io/pypi/v/factorforge-cds.svg)](https://pypi.org/project/factorforge-cds/)
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  [![Web App](https://img.shields.io/badge/web-factorforge--cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
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@@ -44,7 +44,7 @@ FactorForge predictions are **in-silico only** and have not been experimentally
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  ## Citing
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  ```
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- FactorForge v3.1.2 (2026). Open-source constraint-based CDS design engine.
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+ FactorForge v3.1.3 (2026). Open-source constraint-based CDS design engine.
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  Eijex. https://github.com/eijex/factorforge-cds
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  ```
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{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "factorforge-cds"
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- version = "3.1.2"
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+ version = "3.1.3"
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  description = "FactorForge — open-source constraint-based CDS design engine by Eijex."
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  readme = "README.md"
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  license = { file = "LICENSE" }
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/__init__.py RENAMED
@@ -5,7 +5,7 @@ v2: Rule-based engine (Production)
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  v3: ML engine (ESM2 + BART)
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  """
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- __version__ = "3.1.2"
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+ __version__ = "3.1.3"
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  __author__ = "Eijex"
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  # Auto-register engines (safe when running from source tree)
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/__init__.py RENAMED
@@ -29,7 +29,7 @@ def register_builtin_engines() -> None:
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  "v2",
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  RuleBasedOptimizer,
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  metadata={
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- "version": "3.1.2",
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+ "version": "3.1.3",
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  "engine_type": "rule_based",
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  "role": "legacy_fallback",
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  "stable": True,
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/__init__.py RENAMED
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  Plant-specific rule-based optimization
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  """
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- __version__ = "3.1.2"
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  from .optimizer import RuleBasedOptimizer
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  from .pipeline import OptimizationPipeline
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v2/optimizer.py RENAMED
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  """Rule-based optimization engine"""
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  name = "Rule-based"
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- version = "3.1.2"
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+ version = "3.1.3"
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  def __init__(self) -> None:
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  self.validator = InputValidator()
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/__init__.py RENAMED
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  from __future__ import annotations
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  from .pipeline import V3Optimizer, V3Pipeline
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  from .tokenizer import AATokenizer, CodonTokenizer
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge/engines/v3/pipeline.py RENAMED
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  """Optimizer wrapper for v3 pipeline."""
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  name = "v3 BART Decoder"
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  def __init__(self, pipeline: V3Pipeline | None = None) -> None:
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  self.pipeline = pipeline or V3Pipeline()
{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/src/factorforge_cds.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: factorforge-cds
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- Version: 3.1.2
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+ Version: 3.1.3
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  Summary: FactorForge — open-source constraint-based CDS design engine by Eijex.
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  Author-email: Eijex <eijex.lab@gmail.com>
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  License: Apache License
@@ -238,7 +238,7 @@ Dynamic: license-file
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  [![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
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  [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
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- [![Version](https://img.shields.io/badge/version-3.1.2-green.svg)](https://github.com/eijex/factorforge-cds/releases)
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+ [![Version](https://img.shields.io/badge/version-3.1.3-green.svg)](https://github.com/eijex/factorforge-cds/releases)
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  [![PyPI](https://img.shields.io/pypi/v/factorforge-cds.svg)](https://pypi.org/project/factorforge-cds/)
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  [![Web App](https://img.shields.io/badge/web-factorforge--cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
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@@ -278,7 +278,7 @@ FactorForge predictions are **in-silico only** and have not been experimentally
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  ## Citing
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  ```
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- FactorForge v3.1.2 (2026). Open-source constraint-based CDS design engine.
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+ FactorForge v3.1.3 (2026). Open-source constraint-based CDS design engine.
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  Eijex. https://github.com/eijex/factorforge-cds
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  ```
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{factorforge_cds-3.1.2 → factorforge_cds-3.1.3}/LICENSE RENAMED
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