Update assembly data types

[emilylm]

📌 Summary

This PR introduces an assembly intent/reservation flow so manifest generation can reserve a version without prematurely creating an assembly record, and hardens error handling for invalid experiment/platform combinations.

The goal is to avoid long-running pipeline race conditions (duplicate provisional versions) while preserving strict assembly schema requirements for final assembly creation.

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🔄 Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to change)
• 🧹 Refactor (code change that neither fixes a bug nor adds a feature)
• 📚 Documentation update
• ⚙️ CI / build / tooling change

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🧩 Key Changes

• Added assembly_run reservation model/table (+ migration) to persist manifest intent state and reserve version numbers safely before final assembly creation.
• Added POST /api/v1/assemblies/intent/{tax_id} to reserve version + return manifest; updated GET /api/v1/assemblies/manifest/{tax_id} to require sample_id and return the latest (or requested) reserved manifest.
• Added support for tol_id on assembly creation/schema/model and included tolid + version in generated manifest output.
• Added placeholder endpoint/function for optimal sample selection by tax ID (/api/v1/assemblies/optimal-sample/{tax_id}). Logic is TBD - on hold whilst requirements are being fleshed out.
• Standardized error handling in assembly intent path: ValueError from data-type detection is now mapped to AppError with unified error envelope (instead of 500).
• Updated unit tests across assemblies/manifest/intent and helper/service paths;

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✅ Checklist

• Tests are passing locally / in CI
• New tests have been added for new or changed functionality
• Self-review completed
• Documentation updated (if needed)
• No sensitive data or secrets included

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🔍 Review Notes

• Review the new assembly_run lifecycle and version reservation logic (assembly max version + assembly_run max version).
• Confirm API contract changes for manifest endpoints:
  • GET /assemblies/manifest/{tax_id} now requires sample_id
  • POST /assemblies/intent/{tax_id} is the reservation entrypoint
• Migration uses CREATE TABLE IF NOT EXISTS / DROP TABLE IF EXISTS; please confirm this is acceptable for your migration policy.

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📎 Related Issues / Tickets

• Closes #AP-351
• Related to #AP-64, AP-341