Add BuildCompiler.plating: generate PUDU/Opentrons plating protocol from transformation results

[Gonza10V]

Motivation

• Provide a public BuildCompiler.plating(...) entry point to map transformation outputs into a PUDU-compatible plating protocol and simulate it with Opentrons tooling.
• Accept multiple transformation output shapes (thermocycler wells, strain mapping, or raw well map) and normalize them into PUDU's bacterium_locations format for downstream protocol generation.

Description

• Added BuildCompiler.plating(...) which: normalizes transformation_results, writes plating_input.json containing plating_data and advanced_params, generates a self-contained run_plating.py that from pudu.plating import Plating and calls Plating(plating_data=PLATING_DATA, json_params=ADVANCED_PARAMS), invokes the simulation helper, and returns paths for plating_json, protocol_script, and simulation_zip.
• Added helpers in src/buildcompiler/robotutils.py: load_json_or_dict, normalize_plating_data, write_plating_protocol_script, and run_opentrons_script_to_zip (creates a temp working dir, runs opentrons_simulate, captures stdout/stderr/returncode, and zips protocol+JSON+logs).
• Normalization accepts {'bacterium_locations': {...}}, {'strain_locations': {...}}, {'thermocycler_wells': {...}}, or a raw well map like {'A1': 'strain_1'} and returns {'bacterium_locations': {...}}.
• Updated imports and JSON/filesystem usage in BuildCompiler and added an optional automation dependency pudupy under [project.optional-dependencies] in pyproject.toml.
• Documentation: added a minimal example usage to README.md demonstrating input shape, advanced_params, and calling compiler.plating(...).

Testing

• Ran unit tests for the new plating behavior with python -m unittest tests/test_plating.py, which executed 7 tests and completed successfully (all tests passed).
• Simulated Opentrons execution behavior by monkeypatching subprocess.run in tests to validate run_opentrons_script_to_zip writes simulate_stdout.txt, simulate_stderr.txt, and simulate_returncode.txt into the zip (test passed).
• Ran static checks with ruff on modified files and received no issues.
• The tests do not require a physical OT-2; actual opentrons_simulate invocation is exercised in production usage but is mocked in unit tests.

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Codex Task

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Serialize script constants as Python literals

write_plating_protocol_script embeds plating_data/advanced_params into a Python file using json.dumps, which emits JSON tokens like true, false, and null. Those are not Python literals, so when users pass booleans or None in advanced_params (a common config case), the generated run_plating.py crashes with NameError during module evaluation under opentrons_simulate.

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[chatgpt-codex-connector]

Parse JSON strings before probing filesystem paths

load_json_or_dict treats every string as a path first and calls Path.exists() before json.loads; for large but valid JSON strings (e.g., many well mappings), this can raise OSError: [Errno 36] File name too long and abort parsing. The function should attempt JSON parsing (or catch OSError and fall back) so valid JSON string input does not fail based on filename limits.

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