[SPRINT-02-06] Add canonical SBOL fixture collections for indexing and assembly tests

[Gonza10V]

Parent sprint: #87
Depends on: #88, #89, #90, #91, #92
Recommended order: 6
Codex-ready: yes

Goal

Add small canonical SBOL2 fixture documents for software tests of indexing, selection, assembly-artifact generation, and transformation/plating boundaries.

Background

The current implementation needs known-good local SBOL fixtures before debugging higher-level behavior. Without deterministic fixtures, failures may come from malformed SBOL, missing implementations, inconsistent roles, missing fusion-site metadata, or missing antibiotic metadata rather than from BuildCompiler logic.

Scope

Create minimal fixtures under a path such as:

tests/fixtures/sbol/

Fixtures should cover:

• a complete local inventory fixture sufficient for lvl1 route-selection tests;
• a minimal design fixture that references the inventory fixture;
• an incomplete inventory fixture for missing-input/audit tests;
• a metadata-defect fixture for audit diagnostics.

Requirements

• Fixtures are local/offline and load with sbol2.Document().read(...) or an equivalent helper.
• Fixture identities and display IDs are deterministic.
• Fixture structure matches current BuildCompiler indexing expectations.
• Add small fixture-loader helpers if helpful.

Non-goals

• Do not use live SynBioHub.
• Do not add large real-world inventory dumps.
• Do not add PUDU or Opentrons dependencies.
• Do not add wet-lab protocol instructions.

Acceptance criteria

• Fixture files or deterministic fixture builders are committed under tests.
• At least one complete fixture indexes the expected plasmid/backbone/reagent counts.
• At least one incomplete fixture produces expected audit diagnostics.
• Fixture-read tests pass offline.
• The fixtures are documented enough for future tests to reuse them.

Verification

pytest -k "fixture or sbol or index"
ruff check .

Codex implementation notes

Keep fixtures minimal. The goal is deterministic software regression coverage, not realistic experimental design.