New models backend: ESM2-650M + ProtT5 + ProstT5 + ESM3c + ANKH

🚀 Changelog: v3.0.0 — Integration with PIS 2.0.0

This release brings full compatibility with Protein Information System v2.0.0, and introduces major enhancements to model selection, embedding quality, and system robustness.

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🆕 Added

• Support for the ESM3c-600M model for protein embeddings.
• Integration of Poetry into the Docker workflow for improved reproducibility.
• .dockerignore file to reduce Docker image size and speed up builds.

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✨ Changed

• Model upgrades:
  • Replaced small ESM2 model with the larger, more powerful ESM2-650M, improving embedding accuracy.
  • Embedding logic refactored:
    • Removed hard truncation to 512 residues across all models.
    • Special tokens (CLS, PAD, etc.) are now excluded from residue-level embeddings.
    • Revised mean embedding calculation to reflect these changes.
• Unified task logic naming for Prot models.
• Improved log directory management with more robust and flexible path handling.
• Minor formatting and whitespace cleanups throughout the codebase.

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🗑️ Removed

• Obsolete and unused files from the old pipeline.

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🐛 Fixed

• Improved resilience of RabbitMQ connection logic under failure conditions.

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This version is required for seamless operation with PIS v2.0.0, and lays the foundation for future enhancements to functional annotation workflows.