docs(modeling): add cluster-free (non-SGE) run instructions - #2
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The submit_*.sh wrappers are plain bash scripts (the #$ lines are ignored by bash), so a non-SGE user can run `bash scripts/submit_*.sh` for full reproduction (Option B1). Adds a granular per-stage python alternative (B2) with the explicit per-subset input->output mapping and a note that every best model must be evaluated to populate combined_df's holdout columns. Corrects the stale "processed CSVs already provided" claim.
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Makes
scripts/modeling/'s README sufficient to reproduce the pipeline without an SGE cluster.I verified the gap by taking a clean checkout of exactly what ships (code + raw data, no processed CSVs, no models) and following the README in the pinned env. Findings:
submit_*.shwrappers are ordinary bash scripts — the#$lines are SGE directives that plainbashignores. Confirmedbash scripts/submit_preprocess.shruns end-to-end with no scheduler.fullsubset trained, andmerge.pyloaded "0 holdout evaluations" (socombined_df's holdout columns were empty).preprocess.py.Change (docs only, one file)
Rewrites the "without a cluster" section into:
bash scripts/submit_*.shfor full published-run coverage (all subsets, every best model).pythoncalls, now with the explicit per-subset input to output mapping and a note that every best model must be evaluated to populatecombined_df.No code or data changes.
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