Summary

This PR removes noisy per-contig memory-monitoring messages from normal funannotate2 predict logs.

The underlying monitoring flow is preserved, including structured JSONL memory-record capture and warning/error logging for actual memory-risk conditions.

Changes

• remove contig-processing and memory-prediction chatter from abinitio_wrapper()
• stop runSubprocess() from routing formatted memory reports into normal logger/callable logger output
• preserve dedicated predict-abinitio-memory-monitoring.jsonl output
• add regression tests covering both predict-side and subprocess-side logging behavior

Verification

• tests/unit/test_utilities.py → 19 passed
• tests/unit/test_predict.py → 3 passed
• broader predict-focused selection:
  • tests/unit/test_predict.py
  • tests/unit/test_predict_functions.py
  • tests/unit/test_predict_comprehensive.py
  • result: 7 passed, 8 skipped

Notes

• skipped tests are pre-existing skips for unimplemented predict helpers
• the only warning observed was an existing urllib3 / LibreSSL warning

Pull Request opened by Augment Code with guidance from the PR author