Add SynBioHub PartShop client, collection pulling, and Golden Gate digestion/ligation simulation

[Gonza10V]

Motivation

• Enable BuildCompiler to load and index SBOL collections from SynBioHub with optional authentication and to allow executor-driven identity pulls during build execution.
• Provide a lightweight repository adapter backed by sbol2.PartShop so credentials (token or email/password) can be reused safely in memory.
• Improve assembly fidelity by simulating Golden Gate digestion/ligation for generated assemblies before invoking the legacy assembly routine.

Description

• Implement PartShopRepositoryClient in src/buildcompiler/sbol/repository.py to support anonymous pulls, token reuse, and email/password login, exposing pull_identity, pull_collection, and auth_token while hiding secrets in __repr__.
• Extend BuildCompiler.from_synbiohub and the full_build wrapper in src/buildcompiler/api/compiler.py to accept repository_url, email, and password, create a PartShopRepositoryClient, pull requested collections, and store the client on the compiler instance; validate incompatible credential combinations and required parameters.
• Pass a pull_client hook into FullBuildExecutor.from_dependencies so the executor can use repository_client.pull_identity during execution, wired through the sbol resolver construction.
• Export PartShopRepositoryClient from buildcompiler.sbol and add a new notebook notebooks/buildcompiler_synbiohub_tutorial.ipynb demonstrating authentication and a full-build workflow against SynBioHub.
• Add Golden Gate digestion/ligation simulation to AssemblyService in src/buildcompiler/sbol/assembly.py using Bio.Restriction and pydna.dseqrecord.Dseqrecord to cut components, verify fragment counts, concatenate inserts into an open backbone, and ensure a circular ligation product is produced before invoking the legacy Assembly routine.
• Add unit tests covering the new API behavior in tests/unit/api/test_compiler_api.py (collection pulling, credential validation) and repository client behavior in tests/unit/sbol/test_repository.py (anonymous pull, token usage, email/password login and pull).
• Update README.md with usage examples for BuildCompiler.from_synbiohub(...) demonstrating anonymous access, token reuse, and email/password login.

Testing

• Ran unit tests for the modified components with pytest targeting tests/unit/api/test_compiler_api.py and tests/unit/sbol/test_repository.py, and they passed.
• Exercised the BuildCompiler.from_synbiohub code paths via tests that mock PartShopRepositoryClient and verify pull_collection was invoked successfully.
• Executed the repository client tests which simulate PartShop and Document behavior and verified login, token exposure, and pull semantics.

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[chatgpt-codex-connector]

Preserve component topology in digestion simulation

_digest_component hard-codes circular=True, so the new Golden Gate pre-simulation ignores whether a plasmid/backbone is actually linear. The legacy assembly path (part_digestion/backbone_digestion) branches on topology and accepts different fragment patterns for linear inputs, but this precheck now computes cuts as circular and can produce different fragment counts/joins, causing false precheck failures (or mismatches) before Assembly.run executes. This affects assemblies where source SBOL marks components as linear or lacks circular topology metadata.

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