Run opentrons_simulate inside tempdir and use temp-copied inputs

[Gonza10V]

Motivation

• Ensure any files created by the Opentrons simulator land inside the temporary staging folder so they are included in the produced ZIP archive.
• Simplify log writing into the temp folder and remove an unused os import.

Description

• In run_opentrons_script_with_json_to_zip copy the script and JSON into the temporary directory and call subprocess.run with the temp paths and cwd=tmpdir using [ "opentrons_simulate", str(tmp_script), str(tmp_json) ], so the simulator runs inside the temp folder.
• Save the captured stdout into tmpdir / "build_log.txt" using Path APIs instead of os.path.
• Remove the now-unused import os from src/buildcompiler/robotutils.py.

Testing

• Ran python -m pytest, which exercised the test suite but completed with failures unrelated to this change: 4 failing tests and 3 errors caused by external network/proxy errors when sbol2 attempted validation against remote endpoints (e.g. validator.sbolstandard.org).
• Ran ruff check ., which reported many pre-existing lint issues across notebooks and other files; the change removed a single unused import but the overall lint run did not pass.
• Conclusion: the change to run the simulator in the temp directory and write the log succeeded locally in code, but automated test runs were impeded by external network and preexisting linter problems, not by this change.

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Keep simulator cwd where relative inputs exist

Running opentrons_simulate with cwd=tmpdir means the protocol executes in a directory that does not contain the files/ subfolder, but the protocol script still hardcodes open("files/assemblyplan_output.json", ...) and writes output into files (see files/run_sbol2assembly_libre.py:305–311). Because only assemblyplan_output.json is copied to the tmpdir root, this change causes a FileNotFoundError (or later failure when writing the XLSX) for the standard workflow where the script expects the repo’s files/ directory. Unless you also recreate files/ inside the tempdir or adjust the protocol to use the passed JSON path, the simulator will now fail before producing a zip.

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