factorforge-cds 3.1.6__tar.gz → 3.1.7__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 (62) hide show
  1. {factorforge_cds-3.1.6/src/factorforge_cds.egg-info → factorforge_cds-3.1.7}/PKG-INFO +8 -7
  2. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/README.md +6 -5
  3. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/pyproject.toml +2 -2
  4. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/__init__.py +1 -1
  5. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/data/ntabacum_codons.json +1 -1
  6. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/__init__.py +1 -1
  7. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/__init__.py +1 -1
  8. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/optimizer.py +1 -1
  9. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7/src/factorforge_cds.egg-info}/PKG-INFO +8 -7
  10. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/LICENSE +0 -0
  11. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/setup.cfg +0 -0
  12. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/__main__.py +0 -0
  13. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/analysis/__init__.py +0 -0
  14. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/analysis/feasibility.py +0 -0
  15. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/analysis/metrics.py +0 -0
  16. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/cli/__init__.py +0 -0
  17. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/cli/legacy_cli.py +0 -0
  18. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/cli/main.py +0 -0
  19. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/core/interfaces/__init__.py +0 -0
  20. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/core/interfaces/exporter.py +0 -0
  21. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/core/interfaces/optimizer.py +0 -0
  22. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/core/interfaces/validator.py +0 -0
  23. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/data/nbenthamiana_codons.json +0 -0
  24. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/data/nbenthamiana_golden_set.json +0 -0
  25. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/data/templates/high_expression.json +0 -0
  26. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/data/templates/standard_expression.json +0 -0
  27. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/data/wolffia_globosa_codons.json +0 -0
  28. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/database.py +0 -0
  29. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/codon_table_builder.py +0 -0
  30. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/construct_builder.py +0 -0
  31. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/exporter.py +0 -0
  32. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/pipeline.py +0 -0
  33. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/rules/__init__.py +0 -0
  34. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/rules/domesticator.py +0 -0
  35. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/rules/reverse_translator.py +0 -0
  36. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/rules/rule_engine.py +0 -0
  37. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/scoring.py +0 -0
  38. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/scoring_ml.py +0 -0
  39. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/utils.py +0 -0
  40. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/validator.py +0 -0
  41. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/registry.py +0 -0
  42. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/schemas/__init__.py +0 -0
  43. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/schemas/design_package.py +0 -0
  44. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/schemas/design_package.schema.json +0 -0
  45. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/utils/__init__.py +0 -0
  46. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/utils/construct_id.py +0 -0
  47. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/utils/exceptions.py +0 -0
  48. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/utils/restriction_sites.py +0 -0
  49. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/utils/sequence_validator.py +0 -0
  50. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/utils/validation.py +0 -0
  51. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/validation/__init__.py +0 -0
  52. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/validation/cli.py +0 -0
  53. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/validation/package_generator.py +0 -0
  54. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge_cds.egg-info/SOURCES.txt +0 -0
  55. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge_cds.egg-info/dependency_links.txt +0 -0
  56. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge_cds.egg-info/entry_points.txt +0 -0
  57. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge_cds.egg-info/requires.txt +0 -0
  58. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge_cds.egg-info/top_level.txt +0 -0
  59. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/tests/test_database.py +0 -0
  60. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/tests/test_legacy_cli.py +0 -0
  61. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/tests/test_restriction_sites.py +0 -0
  62. {factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/tests/test_sequence_validator.py +0 -0
{factorforge_cds-3.1.6/src/factorforge_cds.egg-info → factorforge_cds-3.1.7}/PKG-INFO RENAMED
@@ -1,10 +1,10 @@
1
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  Metadata-Version: 2.4
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  Name: factorforge-cds
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- Version: 3.1.6
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+ Version: 3.1.7
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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-Expression: AGPL-3.0-only
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- Project-URL: Homepage, https://factorforge-cds.vercel.app
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+ Project-URL: Homepage, https://factorforge.eijex.com
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  Project-URL: Repository, https://github.com/eijex/factorforge-cds
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  Project-URL: Issues, https://github.com/eijex/factorforge-cds/issues
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  Keywords: codon optimization,CDS design,synthetic biology,bioinformatics,Nicotiana benthamiana,Nicotiana tabacum,Tobacco BY-2,constraint optimization,dynamic programming
@@ -39,7 +39,7 @@ Dynamic: license-file
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  [![CI](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml/badge.svg)](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml)
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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.20407331.svg)](https://doi.org/10.5281/zenodo.20407331)
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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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+ [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
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  FactorForge optimizes protein sequences into host-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs. Supports *N. benthamiana* (agroinfiltration) and Tobacco BY-2 (`--host by2`, bioreactor/cGMP workflows).
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@@ -54,7 +54,7 @@ pip install factorforge-cds
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  factorforge optimize my_protein.fasta -o output.fasta
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  ```
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- Or use the **[web app](https://factorforge-cds.vercel.app)** — no installation required.
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+ Or use the **[web app](https://factorforge.eijex.com)** — no installation required.
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  ---
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@@ -62,9 +62,10 @@ Or use the **[web app](https://factorforge-cds.vercel.app)** — no installation
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  | Method | Description | Link |
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  |--------|-------------|------|
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- | **Web App** | No installation, demo & light use | [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app) |
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+ | **Web App** | No installation, demo & light use | [factorforge.eijex.com](https://factorforge.eijex.com) |
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  | **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge-cds` |
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  | **Docker** | Full web interface locally | `docker pull ghcr.io/eijex/factorforge-cds:latest` |
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+ | **Eijex MCP** | AI agent access (Claude Code, Cursor) | [mcp.eijex.com](https://mcp.eijex.com) |
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  ---
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@@ -106,7 +107,7 @@ FactorForge predictions are **in-silico only** and have not been experimentally
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  ## Citing
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108
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  ```
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- FactorForge v3.1.6 (2026). Open-source constraint-based CDS design engine.
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+ FactorForge v3.1.7 (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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@@ -136,4 +137,4 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
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  - **Wet-lab Results** — [Submit via Google Form](https://docs.google.com/forms/d/e/1FAIpQLSeSx-wYvF6YwHhSPdLMl-L44frCugdm25X_eDz50OaqTD66qA/viewform?usp=header) (recommended) or [GitHub Issue](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml)
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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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  - **Email** — eijex.lab@gmail.com
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- - **Web** — [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app)
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+ - **Web** — [factorforge.eijex.com](https://factorforge.eijex.com)
{factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/README.md RENAMED
@@ -8,7 +8,7 @@
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  [![CI](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml/badge.svg)](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml)
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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.20407331.svg)](https://doi.org/10.5281/zenodo.20407331)
11
- [![Web App](https://img.shields.io/badge/web-factorforge--cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
11
+ [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
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13
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  FactorForge optimizes protein sequences into host-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs. Supports *N. benthamiana* (agroinfiltration) and Tobacco BY-2 (`--host by2`, bioreactor/cGMP workflows).
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@@ -23,7 +23,7 @@ pip install factorforge-cds
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  factorforge optimize my_protein.fasta -o output.fasta
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  ```
25
25
 
26
- Or use the **[web app](https://factorforge-cds.vercel.app)** — no installation required.
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+ Or use the **[web app](https://factorforge.eijex.com)** — no installation required.
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  ---
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@@ -31,9 +31,10 @@ Or use the **[web app](https://factorforge-cds.vercel.app)** — no installation
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  | Method | Description | Link |
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  |--------|-------------|------|
34
- | **Web App** | No installation, demo & light use | [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app) |
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+ | **Web App** | No installation, demo & light use | [factorforge.eijex.com](https://factorforge.eijex.com) |
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  | **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge-cds` |
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  | **Docker** | Full web interface locally | `docker pull ghcr.io/eijex/factorforge-cds:latest` |
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+ | **Eijex MCP** | AI agent access (Claude Code, Cursor) | [mcp.eijex.com](https://mcp.eijex.com) |
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38
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  ---
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@@ -75,7 +76,7 @@ FactorForge predictions are **in-silico only** and have not been experimentally
75
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  ## Citing
76
77
 
77
78
  ```
78
- FactorForge v3.1.6 (2026). Open-source constraint-based CDS design engine.
79
+ FactorForge v3.1.7 (2026). Open-source constraint-based CDS design engine.
79
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  Eijex. https://github.com/eijex/factorforge-cds
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  ```
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@@ -105,4 +106,4 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
105
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  - **Wet-lab Results** — [Submit via Google Form](https://docs.google.com/forms/d/e/1FAIpQLSeSx-wYvF6YwHhSPdLMl-L44frCugdm25X_eDz50OaqTD66qA/viewform?usp=header) (recommended) or [GitHub Issue](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml)
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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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  - **Email** — eijex.lab@gmail.com
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- - **Web** — [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app)
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+ - **Web** — [factorforge.eijex.com](https://factorforge.eijex.com)
{factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/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 = "3.1.6"
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+ version = "3.1.7"
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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 = "AGPL-3.0-only"
@@ -39,7 +39,7 @@ ml = [
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  ]
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  [project.urls]
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- Homepage = "https://factorforge-cds.vercel.app"
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+ Homepage = "https://factorforge.eijex.com"
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  Repository = "https://github.com/eijex/factorforge-cds"
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  Issues = "https://github.com/eijex/factorforge-cds/issues"
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{factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/__init__.py RENAMED
@@ -4,7 +4,7 @@ FactorForge - Codon Optimization Platform
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  profile: constraint-aware rule/profile engine
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  """
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- __version__ = "3.1.6"
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+ __version__ = "3.1.7"
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  __author__ = "Eijex"
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  # Auto-register engines (safe when running from source tree)
{factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/data/ntabacum_codons.json RENAMED
@@ -1,7 +1,7 @@
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  {
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  "organism": "Nicotiana tabacum",
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  "source": "Kazusa Codon Usage Database (species 4097); 1,534 CDS, 609,684 codons, GenBank release 160 (2007)",
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- "description": "N. tabacum codon usage for BY-2 suspension culture optimization. Kazusa 2007 data; CAI difference vs N. benthamiana < 0.05. Experimental host profile — not wet-lab validated for BY-2 expression.",
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+ "description": "N. tabacum codon usage for BY-2 suspension culture optimization. Kazusa 2007 data. N. tabacum and N. benthamiana share highly similar codon preferences within the Nicotiana genus. Experimental host profile — not wet-lab validated for BY-2 expression.",
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  "codons": {
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  "TTT": {
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  "aa": "F",
{factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/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": "3.1.6",
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+ "version": "3.1.7",
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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-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/__init__.py RENAMED
@@ -5,7 +5,7 @@ Production system (2026)
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  Plant-specific rule-based optimization
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  """
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- __version__ = "3.1.6"
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+ __version__ = "3.1.7"
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  from .optimizer import RuleBasedOptimizer
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  from .pipeline import OptimizationPipeline
{factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/src/factorforge/engines/profile/optimizer.py RENAMED
@@ -17,7 +17,7 @@ class RuleBasedOptimizer(OptimizerEngine):
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  """Profile-based rule optimization engine."""
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  name = "Profile-based"
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- version = "3.1.6"
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+ version = "3.1.7"
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  def __init__(self) -> None:
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  self.validator = InputValidator()
{factorforge_cds-3.1.6 → factorforge_cds-3.1.7/src/factorforge_cds.egg-info}/PKG-INFO RENAMED
@@ -1,10 +1,10 @@
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  Metadata-Version: 2.4
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2
  Name: factorforge-cds
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- Version: 3.1.6
3
+ Version: 3.1.7
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  Summary: FactorForge - open-source constraint-based CDS design engine by Eijex.
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5
  Author-email: Eijex <eijex.lab@gmail.com>
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  License-Expression: AGPL-3.0-only
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- Project-URL: Homepage, https://factorforge-cds.vercel.app
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+ Project-URL: Homepage, https://factorforge.eijex.com
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  Project-URL: Repository, https://github.com/eijex/factorforge-cds
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  Project-URL: Issues, https://github.com/eijex/factorforge-cds/issues
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  Keywords: codon optimization,CDS design,synthetic biology,bioinformatics,Nicotiana benthamiana,Nicotiana tabacum,Tobacco BY-2,constraint optimization,dynamic programming
@@ -39,7 +39,7 @@ Dynamic: license-file
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  [![CI](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml/badge.svg)](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml)
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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.20407331.svg)](https://doi.org/10.5281/zenodo.20407331)
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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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+ [![Web App](https://img.shields.io/badge/web-factorforge.eijex.com-brightgreen.svg)](https://factorforge.eijex.com)
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  FactorForge optimizes protein sequences into host-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs. Supports *N. benthamiana* (agroinfiltration) and Tobacco BY-2 (`--host by2`, bioreactor/cGMP workflows).
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@@ -54,7 +54,7 @@ pip install factorforge-cds
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  factorforge optimize my_protein.fasta -o output.fasta
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  ```
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- Or use the **[web app](https://factorforge-cds.vercel.app)** — no installation required.
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+ Or use the **[web app](https://factorforge.eijex.com)** — no installation required.
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  ---
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@@ -62,9 +62,10 @@ Or use the **[web app](https://factorforge-cds.vercel.app)** — no installation
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  | Method | Description | Link |
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  |--------|-------------|------|
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- | **Web App** | No installation, demo & light use | [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app) |
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+ | **Web App** | No installation, demo & light use | [factorforge.eijex.com](https://factorforge.eijex.com) |
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  | **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge-cds` |
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  | **Docker** | Full web interface locally | `docker pull ghcr.io/eijex/factorforge-cds:latest` |
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+ | **Eijex MCP** | AI agent access (Claude Code, Cursor) | [mcp.eijex.com](https://mcp.eijex.com) |
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  ---
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@@ -106,7 +107,7 @@ 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 v3.1.6 (2026). Open-source constraint-based CDS design engine.
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+ FactorForge v3.1.7 (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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@@ -136,4 +137,4 @@ GNU Affero General Public License v3.0 — see [LICENSE](LICENSE).
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  - **Wet-lab Results** — [Submit via Google Form](https://docs.google.com/forms/d/e/1FAIpQLSeSx-wYvF6YwHhSPdLMl-L44frCugdm25X_eDz50OaqTD66qA/viewform?usp=header) (recommended) or [GitHub Issue](https://github.com/eijex/factorforge-cds/issues/new?template=wet_lab_result.yml)
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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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  - **Email** — eijex.lab@gmail.com
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- - **Web** — [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app)
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+ - **Web** — [factorforge.eijex.com](https://factorforge.eijex.com)
{factorforge_cds-3.1.6 → factorforge_cds-3.1.7}/LICENSE RENAMED
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