[ISSUE-09] Implement lvl1 assembly stage and PUDU assembly JSON adapter

[Gonza10V]

Motivation

• Provide a thin orchestration stage for level-1 assembly that glues route selection, reagent/backbone resolution, and the SBOL AssemblyService into a StageResult while emitting a compiler-only PUDU-compatible JSON intermediate.
• Surface expected missing inputs as structured MissingBuildInput blockers and preserve planner ordering/cardinality warnings instead of raising exceptions.
• Keep digestion/ligation and route selection responsibilities in AssemblyService and CompatibilitySelector respectively, avoiding changes to those internals.

Description

• Added AssemblyLvl1Stage in src/buildcompiler/stages/assembly_lvl1.py which: extracts ordered part identities from request constraints, calls CompatibilitySelector.select_lvl1_route, produces MissingBuildInput records for missing parts/backbone/reagents, resolves default reagents from BuildOptions/Inventory, delegates assembly to AssemblyService.run, appends request.source_identity to generated product insert_identities, indexes generated products via Inventory.add_generated_product, and attaches an in-memory PUDU JSON intermediate via assembly_route_to_pudu_json.
• Implemented PUDU adapter assembly_route_to_pudu_json and batch helper assembly_routes_to_pudu_json in src/buildcompiler/adapters/pudu/assembly_json.py which produce in-memory dictionaries with keys Product, Backbone, PartsList, and Restriction Enzyme using stable identities/names.
• Exported AssemblyLvl1Stage and PUDU adapter functions by updating src/buildcompiler/stages/__init__.py and src/buildcompiler/adapters/pudu/__init__.py.
• Added unit tests: tests/unit/adapters/pudu/test_assembly_json.py to validate adapter shape/values and tests/unit/stages/test_assembly_lvl1.py to cover success (product + JSON intermediate + warning propagation + inventory indexing) and blocked paths (structured missing kinds for promoter/rbs/cds/terminator/backbone/restriction_enzyme/ligase).

Testing

• Import smoke checks: python -c "from buildcompiler.stages import AssemblyLvl1Stage" and python -c "from buildcompiler.adapters.pudu import assembly_route_to_pudu_json" succeeded.
• Unit tests: pytest tests/unit/stages/test_assembly_lvl1.py tests/unit/adapters/pudu/test_assembly_json.py passed (all tests green).
• Lint/format: ruff check and ruff format were run against changed files and succeeded after formatting (no remaining failures).
• Optional uv workflow: uv run pytest tests/unit/stages/test_assembly_lvl1.py tests/unit/adapters/pudu/test_assembly_json.py was attempted but the uv bootstrap failed to fetch an external SBOLInventory git dependency (HTTP 403), so local pytest was used as a fallback and succeeded.

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Accept planner part_order in lvl1 part extraction

The new stage only reads ordered_part_identities/part_identities, but planner-produced level-1 requests currently provide parts under constraints["part_order"] for combinatorial designs (src/buildcompiler/planning/combinatorial.py) and no alternate key normalization is present before execution. In this state, _extract_part_identities returns an empty list and run() immediately returns StageStatus.FAILED, so valid planner outputs cannot reach route selection or assembly. Please include part_order (or normalize planner constraints) when extracting part identities.

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[Gonza10V]

@codex good catch, please fix this issue

[chatgpt-codex-connector]

Summary

• Updated lvl1 part extraction to recognize planner-provided constraints["part_order"] as a supported fallback, so valid planner requests no longer fail early when ordered_part_identities is absent. src/buildcompiler/stages/assembly_lvl1.pyL203-L213
• Added a regression test that uses only part_order in request constraints and verifies lvl1 assembly proceeds successfully. tests/unit/stages/test_assembly_lvl1.pyL172-L186

Testing

• ✅ pytest tests/unit/stages/test_assembly_lvl1.py

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