factorforge-cds 3.4.3__tar.gz → 3.4.5__tar.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 (114) hide show
  1. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/PKG-INFO +6 -2
  2. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/README.md +5 -1
  3. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/pyproject.toml +1 -1
  4. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/__init__.py +1 -1
  5. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/__init__.py +1 -1
  6. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/__init__.py +1 -1
  7. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/optimizer.py +1 -1
  8. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge_cds.egg-info/PKG-INFO +6 -2
  9. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/LICENSE +0 -0
  10. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/setup.cfg +0 -0
  11. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/__main__.py +0 -0
  12. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/analysis/__init__.py +0 -0
  13. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/analysis/feasibility.py +0 -0
  14. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/analysis/metrics.py +0 -0
  15. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/cli/__init__.py +0 -0
  16. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/cli/legacy_cli.py +0 -0
  17. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/cli/main.py +0 -0
  18. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/core/interfaces/__init__.py +0 -0
  19. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/core/interfaces/exporter.py +0 -0
  20. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/core/interfaces/optimizer.py +0 -0
  21. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/core/interfaces/validator.py +0 -0
  22. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/nbenthamiana_codons.json +0 -0
  23. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/nbenthamiana_golden_set.json +0 -0
  24. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/ntabacum_codons.json +0 -0
  25. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/nbev11_cds_all_derived_codons.json +0 -0
  26. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/nbev11_cds_all_derived_filtered_stats.json +0 -0
  27. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/nbev11_cds_all_derived_manifest.json +0 -0
  28. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/nbev11_cds_hc_derived_codons.json +0 -0
  29. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/nbev11_cds_hc_derived_filtered_stats.json +0 -0
  30. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/nbev11_cds_hc_derived_manifest.json +0 -0
  31. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/qld183_v103_derived_codons.json +0 -0
  32. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/qld183_v103_derived_manifest.json +0 -0
  33. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/profiles/qld183_v103_filtered_stats.json +0 -0
  34. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/reference/reference_policy_manifest.json +0 -0
  35. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/templates/high_expression.json +0 -0
  36. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/templates/standard_expression.json +0 -0
  37. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/data/wolffia_globosa_codons.json +0 -0
  38. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/database.py +0 -0
  39. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/design_review.py +0 -0
  40. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/codon_table_builder.py +0 -0
  41. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/construct_builder.py +0 -0
  42. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/exporter.py +0 -0
  43. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/pipeline.py +0 -0
  44. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/rules/__init__.py +0 -0
  45. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/rules/domesticator.py +0 -0
  46. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/rules/reverse_translator.py +0 -0
  47. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/rules/rule_engine.py +0 -0
  48. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/scoring.py +0 -0
  49. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/scoring_ml.py +0 -0
  50. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/utils.py +0 -0
  51. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/validator.py +0 -0
  52. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/registry.py +0 -0
  53. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/io/__init__.py +0 -0
  54. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/io/fasta.py +0 -0
  55. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/io/validation.py +0 -0
  56. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/protein_risk/__init__.py +0 -0
  57. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/protein_risk/annotate.py +0 -0
  58. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/protein_risk/kd_scale.py +0 -0
  59. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/protein_risk/risk_classifier.py +0 -0
  60. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/protein_risk/sp_predict.py +0 -0
  61. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/protein_risk/tm_predict.py +0 -0
  62. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/registry/__init__.py +0 -0
  63. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/registry/registry_loader.py +0 -0
  64. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/review/__init__.py +0 -0
  65. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/schemas/__init__.py +0 -0
  66. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/schemas/design_package.py +0 -0
  67. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/schemas/design_package.schema.json +0 -0
  68. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/utils/__init__.py +0 -0
  69. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/utils/construct_id.py +0 -0
  70. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/utils/exceptions.py +0 -0
  71. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/utils/restriction_sites.py +0 -0
  72. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/utils/sequence_validator.py +0 -0
  73. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/utils/validation.py +0 -0
  74. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/validation/__init__.py +0 -0
  75. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/validation/cli.py +0 -0
  76. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/validation/package_generator.py +0 -0
  77. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/validation_registry.py +0 -0
  78. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/validation_report.py +0 -0
  79. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge_cds.egg-info/SOURCES.txt +0 -0
  80. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge_cds.egg-info/dependency_links.txt +0 -0
  81. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge_cds.egg-info/entry_points.txt +0 -0
  82. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge_cds.egg-info/requires.txt +0 -0
  83. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge_cds.egg-info/top_level.txt +0 -0
  84. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_baselines.py +0 -0
  85. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_benchmark_cli_output_guard.py +0 -0
  86. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_benchmark_codon_table_metadata.py +0 -0
  87. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_benchmark_regression.py +0 -0
  88. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_benchmark_scoring.py +0 -0
  89. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_benchmark_smoke.py +0 -0
  90. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_cai.py +0 -0
  91. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_codon_table_manifest.py +0 -0
  92. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_database.py +0 -0
  93. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_design_package_schema.py +0 -0
  94. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_design_package_semantics.py +0 -0
  95. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_design_package_serialization.py +0 -0
  96. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_design_review.py +0 -0
  97. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_docs_consistency.py +0 -0
  98. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_fasta_io.py +0 -0
  99. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_gc_content.py +0 -0
  100. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_host_profile_metadata.py +0 -0
  101. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_iupac_validation.py +0 -0
  102. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_legacy_cli.py +0 -0
  103. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_no_raw_sequence_logging.py +0 -0
  104. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_openbio_missing_metric_contract.py +0 -0
  105. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_parameter_registry.py +0 -0
  106. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_protein_risk.py +0 -0
  107. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_registry_production_sync.py +0 -0
  108. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_restriction_sites.py +0 -0
  109. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_sequence_validator.py +0 -0
  110. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_translation_integrity.py +0 -0
  111. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_validation_contract_compat.py +0 -0
  112. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_validation_registry.py +0 -0
  113. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_validation_report.py +0 -0
  114. {factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/tests/test_worked_example.py +0 -0
{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/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: 3.4.3
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+ Version: 3.4.5
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  Summary: FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex.
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  Author-email: Eijex <eijex.lab@gmail.com>
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  License-Expression: AGPL-3.0-only
@@ -42,6 +42,8 @@ Dynamic: license-file
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  [![codecov](https://codecov.io/gh/eijex/factorforge-cds/branch/main/graph/badge.svg)](https://codecov.io/gh/eijex/factorforge-cds)
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  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20407330.svg)](https://doi.org/10.5281/zenodo.20407330)
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  [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
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+ [![Sponsor](https://img.shields.io/badge/Sponsor-EA4AAA?style=flat&logo=github-sponsors&logoColor=white)](https://github.com/sponsors/eijex)
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+
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  FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
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  ## Citing
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  ```
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- FactorForge v3.4.3 (2026). Open-source constraint-based CDS design and sequence review.
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+ FactorForge v3.4.5 (2026). Open-source constraint-based CDS design and sequence review.
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  Eijex. https://github.com/eijex/factorforge-cds
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  ```
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  ## Get in Touch
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+ - **Sponsor** — Support our research via [GitHub Sponsors](https://github.com/sponsors/eijex) or [PayPal](https://paypal.me/munkyukim)
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  - **Docs** — [eijex.github.io/factorforge-cds](https://eijex.github.io/factorforge-cds/)
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  - **Wet-lab Feedback** — Public-safe feedback summaries are welcome via [Share Wet-lab Feedback (GitHub)](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. Email `eijex.lab@gmail.com` for private or sensitive summaries. See [VALIDATION.md](VALIDATION.md) before submitting.
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  - **GitHub Issues** — bugs, features: [github.com/eijex/factorforge-cds/issues](https://github.com/eijex/factorforge-cds/issues)
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  - **FactorForge** — [factorforge.eijex.com](https://factorforge.eijex.com)
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  - **Eijex MCP** — [mcp.eijex.com](https://mcp.eijex.com)
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  - **Lab** — [www.eijex.com](https://www.eijex.com)
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{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/README.md RENAMED
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  [![codecov](https://codecov.io/gh/eijex/factorforge-cds/branch/main/graph/badge.svg)](https://codecov.io/gh/eijex/factorforge-cds)
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  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20407330.svg)](https://doi.org/10.5281/zenodo.20407330)
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  [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
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+ [![Sponsor](https://img.shields.io/badge/Sponsor-EA4AAA?style=flat&logo=github-sponsors&logoColor=white)](https://github.com/sponsors/eijex)
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  FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
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  ## Citing
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  ```
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- FactorForge v3.4.3 (2026). Open-source constraint-based CDS design and sequence review.
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+ FactorForge v3.4.5 (2026). Open-source constraint-based CDS design and sequence review.
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  Eijex. https://github.com/eijex/factorforge-cds
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  ```
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  ## Get in Touch
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+ - **Sponsor** — Support our research via [GitHub Sponsors](https://github.com/sponsors/eijex) or [PayPal](https://paypal.me/munkyukim)
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  - **Docs** — [eijex.github.io/factorforge-cds](https://eijex.github.io/factorforge-cds/)
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  - **Wet-lab Feedback** — Public-safe feedback summaries are welcome via [Share Wet-lab Feedback (GitHub)](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. Email `eijex.lab@gmail.com` for private or sensitive summaries. See [VALIDATION.md](VALIDATION.md) before submitting.
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  - **GitHub Issues** — bugs, features: [github.com/eijex/factorforge-cds/issues](https://github.com/eijex/factorforge-cds/issues)
@@ -87,3 +90,4 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
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  - **FactorForge** — [factorforge.eijex.com](https://factorforge.eijex.com)
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  - **Eijex MCP** — [mcp.eijex.com](https://mcp.eijex.com)
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  - **Lab** — [www.eijex.com](https://www.eijex.com)
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{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/pyproject.toml RENAMED
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  [project]
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  name = "factorforge-cds"
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- version = "3.4.3"
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  description = "FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex."
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  readme = "README.md"
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  license = "AGPL-3.0-only"
{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/__init__.py RENAMED
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  profile: constraint-aware rule/profile engine
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  """
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  __author__ = "Eijex"
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  # Auto-register engines (safe when running from source tree)
{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/__init__.py RENAMED
@@ -13,7 +13,7 @@ def register_builtin_engines() -> None:
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  "profile",
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  RuleBasedOptimizer,
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  metadata={
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- "version": "3.4.3",
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+ "version": "3.4.5",
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  "engine_type": "profile_rule_based",
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  "role": "stable_profile_engine",
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  "stable": True,
{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/__init__.py RENAMED
@@ -5,7 +5,7 @@ Production system (2026)
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5
  Plant-specific rule-based optimization
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  """
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7
 
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- __version__ = "3.4.3"
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+ __version__ = "3.4.5"
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9
 
10
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  from .optimizer import RuleBasedOptimizer
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  from .pipeline import OptimizationPipeline
{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge/engines/profile/optimizer.py RENAMED
@@ -21,7 +21,7 @@ class RuleBasedOptimizer(OptimizerEngine):
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  """Profile-based rule optimization engine."""
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  name = "Profile-based"
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- version = "3.4.3"
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+ version = "3.4.5"
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25
 
26
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  def __init__(
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  self,
{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/src/factorforge_cds.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
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  Name: factorforge-cds
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- Version: 3.4.3
3
+ Version: 3.4.5
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4
  Summary: FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex.
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5
  Author-email: Eijex <eijex.lab@gmail.com>
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  License-Expression: AGPL-3.0-only
@@ -42,6 +42,8 @@ Dynamic: license-file
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  [![codecov](https://codecov.io/gh/eijex/factorforge-cds/branch/main/graph/badge.svg)](https://codecov.io/gh/eijex/factorforge-cds)
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  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20407330.svg)](https://doi.org/10.5281/zenodo.20407330)
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  [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
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+ [![Sponsor](https://img.shields.io/badge/Sponsor-EA4AAA?style=flat&logo=github-sponsors&logoColor=white)](https://github.com/sponsors/eijex)
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+
45
47
 
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48
  FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: *N. benthamiana* (agroinfiltration). Experimental host context: Tobacco BY-2 (`--host by2`).
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@@ -93,7 +95,7 @@ FactorForge outputs are **in-silico only** and have not been experimentally vali
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  ## Citing
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96
 
95
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  ```
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- FactorForge v3.4.3 (2026). Open-source constraint-based CDS design and sequence review.
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+ FactorForge v3.4.5 (2026). Open-source constraint-based CDS design and sequence review.
97
99
  Eijex. https://github.com/eijex/factorforge-cds
98
100
  ```
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101
 
@@ -113,6 +115,7 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
113
115
 
114
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  ## Get in Touch
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117
 
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+ - **Sponsor** — Support our research via [GitHub Sponsors](https://github.com/sponsors/eijex) or [PayPal](https://paypal.me/munkyukim)
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  - **Docs** — [eijex.github.io/factorforge-cds](https://eijex.github.io/factorforge-cds/)
117
120
  - **Wet-lab Feedback** — Public-safe feedback summaries are welcome via [Share Wet-lab Feedback (GitHub)](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. Email `eijex.lab@gmail.com` for private or sensitive summaries. See [VALIDATION.md](VALIDATION.md) before submitting.
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121
  - **GitHub Issues** — bugs, features: [github.com/eijex/factorforge-cds/issues](https://github.com/eijex/factorforge-cds/issues)
@@ -120,3 +123,4 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
120
123
  - **FactorForge** — [factorforge.eijex.com](https://factorforge.eijex.com)
121
124
  - **Eijex MCP** — [mcp.eijex.com](https://mcp.eijex.com)
122
125
  - **Lab** — [www.eijex.com](https://www.eijex.com)
126
+
{factorforge_cds-3.4.3 → factorforge_cds-3.4.5}/LICENSE RENAMED
File without changes