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feat: add experiment resume support and improve robustness#90

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YihanJIANG-lab wants to merge 1 commit intoSakanaAI:mainfrom
YihanJIANG-lab:feat/resume-and-robustness-improvements
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feat: add experiment resume support and improve robustness#90
YihanJIANG-lab wants to merge 1 commit intoSakanaAI:mainfrom
YihanJIANG-lab:feat/resume-and-robustness-improvements

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Adds the ability to resume experiments from a checkpoint, plus several robustness improvements:

Resume support:

  • --resume flag in launch_scientist_bfts.py to resume from a previous experiment directory
  • AgentManager.from_checkpoint() classmethod for state restoration
  • Automatic checkpoint discovery in perform_experiments_bfts

Robustness improvements:

  • Robust PDF discovery (find_pdf_path_for_review) — guards against None return
  • Dynamic log directory discovery (find_run_log_dir) instead of hardcoded logs/0-run/
  • psutil import guard for environments without it
  • max_tries=8 on Semantic Scholar backoff decorators
  • Multi-source literature search tool (OpenAlex → Crossref → arXiv → S2 cascade fallback)
  • mkdir(parents=True, exist_ok=True) for log directories

Major features:
- Add --resume flag to launch_scientist_bfts.py for resuming from a
  previous experiment's checkpoint
- Add AgentManager.from_checkpoint() classmethod for state restoration
- Add perform_experiments_bfts resume_dir parameter with checkpoint
  discovery

Robustness improvements:
- launch_scientist_bfts.py: robust PDF discovery (find_pdf_path_for_review),
  dynamic log dir discovery (find_run_log_dir), guard against missing
  experiment_results dir, psutil import guard
- semantic_scholar.py: add max_tries=8 to backoff decorators, fix
  duplicate __init__ assignments
- Add literature_search.py: multi-source search (OpenAlex, Crossref,
  arXiv, S2) with cascade fallback
- Add github_models_config.yaml: example config for GitHub Models API
- perform_ideation_temp_free.py: use MultiSourceLiteratureSearchTool
  for more reliable literature search
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