Bench harness + obs_mobility unit fix#65

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infra/benchmark_fixture

Commits on May 9, 2026

chore(bench): add bench dependency group and gitignore bench_out/
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feat(bench): pydantic schema and loader for fixture TOMLs
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fix(bench): clean up fixture schema (dead tomli fallback, validator types, test tightening)
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feat(bench): polymorphic --db spec classifier
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fix(bench): drop unused fixture, add wrong-extension test, sort suffix tuple
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feat(bench): uniprot REST fetch helpers (proteome + accession batch)
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chore: configure ty to use project .venv
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fix(bench): tighten uniprot test (ty-clean url access, exact chunk count)
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feat(bench): resolve --db specs to concatenated fasta + s3 wrapper
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feat(bench): aho-corasick peptide classification for entrapment
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feat(bench): empirical FDR curve and PNG plot for entrapment
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feat(bench): analyse() entry point returning wandb-ready scalars
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feat(bench): push_fixture.py CLI scaffolding + TOML emitter
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feat(bench): push_fixture.py upload + speclib build pipeline
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feat(bench): rewrite bench runner skeleton with fixture selection
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feat(bench): timsseek invocation + wandb logging + entrapment hook
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fix(bench): pass res_dir as timsseek --output-dir (matches its native layout)
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docs(bench): add default config and README for fixture harness
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style(bench): apply task fmt
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fix(bench): ty-clean field_name access; use real S3 prefix in README
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feat(bench): fixture inputs accept absolute local paths (for staged fixtures)
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feat(bench): --fixtures-dir flag on wandb_bench (for staged fixtures)
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chore: disable patching
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feat(bench): idempotent push_fixture uploads (skip existing s3 objects, --force to override)
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feat(bench): stage_fixture CLI for local cache + offline reruns
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docs(bench): add staging + idempotent uploads sections
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feat(bench): k-mer-based search-space normalization for entrapment FDR
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feat(bench): --request-delay-ms flag for speclib_build_cli throttle
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fix(bench): build speclib from merged target+entrap fasta when entrap_db set
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feat(bench): default fetch_proteome to reviewed-only (Swiss-Prot)
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feat(bench): trypsin digest + algorithm-1 shuffled-entrapment helpers
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feat(bench)!: migrate fixture schema to peptide-list inputs + entrapment metadata
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feat(bench)!: rewrite push_fixture for peptide-list pipeline + SHUFFLED entrapment
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feat(bench)!: rewrite entrapment.py with FDRBench Method 1/1B + score histogram
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feat(bench)!: thread peptide-list schema through wandb_bench + stage_fixture
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docs(bench): peptide-list pipeline + Algorithm 1/2 + FDRBench estimators
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feat(bench): target_peptides optional (only required for entrapment); update gt20peps fixture
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Commits on May 11, 2026

fix(bench): speclib_build_cli flag is --peptide-list, not --peptides
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Commits on May 13, 2026

Commits on May 19, 2026

ci: stuff
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