Updates to opencloning_datamodels

[manulera]

The auto-summary from copilot is pretty good.

@BjornFJohansson

This builds on top of the cloning history branch you started working on. Several tests still fails and are related to the future you added, so you can fix them after merging this.

[Copilot]

Pull request overview

This PR updates the pydna opencloning data models to support additional DNA source types and refactors the serialization approach for better maintainability. The changes expand the library's ability to track provenance for oligonucleotide hybridization and various DNA sequence repositories, while also fixing an edge case bug in CRISPR integration.

Key changes:

• Adds oligonucleotide hybridization functionality with corresponding source tracking
• Introduces multiple new repository source classes (Addgene, Benchling, SnapGene, EUROSCARF, etc.)
• Refactors source serialization from _kwargs methods to Pydantic field_serializer decorators
• Fixes an off-by-one error in CRISPR integration repair end calculation

Reviewed changes

Copilot reviewed 7 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/pydna/opencloning_models.py	Adds new source classes (DatabaseSource, repository sources, OligoHybridizationSource, etc.) and refactors serialization using field_serializer
src/pydna/oligonucleotide_hybridization.py	New module implementing oligonucleotide hybridization with overhang calculation
src/pydna/assembly2.py	Fixes CRISPR integration repair end calculation with +1 offset
tests/test_module_opencloning_models.py	Adds tests for oligonucleotide hybridization and updates history string expectations
tests/test_module_assembly2.py	Adds edge case test for CRISPR integration
pyproject.toml	Changes opencloning-linkml dependency from exact version to caret constraint
poetry.lock	Lock file updates reflecting dependency changes
docs/notebooks/history.ipynb	Updates expected source type names in history display

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[manulera]

In this commit I have commented out the location from the repository. I will have to re-organize the data model to see where this fits best, but we can re-add it once that is done.