SynBioHub PartShop client, collection pulls, and stricter Golden Gate digest handling

[Gonza10V]

Motivation

• Provide a thin adapter for SynBioHub sbol2.PartShop to enable authenticated and anonymous repository access and automatic collection pulls into the in-memory SBOL document using the BuildCompiler convenience constructor.
• Wire identity-based pulls into planning/execution so resolver misses can be fulfilled from the same repository client instance.
• Make Golden Gate assembly simulation more deterministic by enforcing an exact two-fragment digest and clearer error messages for unexpected digests.

Description

• Add PartShopRepositoryClient in src/buildcompiler/sbol/repository.py implementing auth-token and email/password login, pull_identity, and a safe __repr__ that does not expose secrets.
• Extend the public API in src/buildcompiler/api/compiler.py to accept repository_url, email, and password in BuildCompiler.from_synbiohub and full_build, create an sbol2.Document when needed, instantiate PartShopRepositoryClient, and pull configured collections; expose the client on the BuildCompiler instance as repository_client.
• Pass a pull_client callback into FullBuildExecutor.from_dependencies so the SbolResolver can use the repository pull function during planning/execution, and export PartShopRepositoryClient from buildcompiler.sbol.
• Replace ad-hoc digest selection logic in src/buildcompiler/sbol2build.py with _select_expected_digest_fragment to require exactly two digest fragments and to explicitly choose the insert (smaller) or backbone (larger) fragment, with improved error messages.
• Add example usage to README.md and include a new authenticated SynBioHub tutorial notebook under notebooks/ demonstrating login and collection pulls.
• Add unit tests: tests/unit/sbol/test_repository.py to validate PartShopRepositoryClient behaviors and extend tests/unit/api/test_compiler_api.py to test repository integration and authentication edge cases.

Testing

• Added and ran unit tests in tests/unit/sbol/test_repository.py, which exercise anonymous pulls, token auth, login flow, and __repr__, and they passed.
• Extended and ran tests/unit/api/test_compiler_api.py to validate BuildCompiler.from_synbiohub argument validation and collection pulls with a fake PartShop, and the tests passed.
• Ran the test suite with pytest for the modified areas and observed success for the new and adjusted tests.

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[chatgpt-codex-connector]

Forward caller-provided SBOL document to SynBioHub path

When full_build takes the SynBioHub constructor branch, it only forwards sbol_doc and drops the sbol_document argument; if callers pass repository_url/auth options together with sbol_document (the other public parameter), from_synbiohub receives None and creates a new sbol2.Document, so the user’s preloaded SBOL content is silently ignored during planning/execution. This is a regression in mixed local+remote workflows and can cause missing inventory/component resolution.

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