Add biology_singlecell benchmarks (PBMC3k/68k) to benchmark knowledge base - #308
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Add biology_singlecell benchmarks (PBMC3k/68k) to benchmark knowledge base#308Tryboy869 wants to merge 1 commit into
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What
Adds a
biology_singlecelldomain entry toresearchclaw/data/benchmark_knowledge.yaml,following the existing schema (keywords / standard_benchmarks / common_baselines).
PBMC3k,PBMC3k-processed,PBMC68k-reduced— all loaded viascanpy.datasets.*(already installed inDockerfile.biology), all tier 1(self-caching calls under 6MB, no separate setup-phase download needed).
packages already present in
Dockerfile.biology(pip: []throughout).Names/sizes/sample counts were checked against current scanpy documentation
rather than assumed. One thing worth a reviewer's eye: despite the name,
pbmc68k_reducedships only a ~700-cell reduced subsample, not the full 68kcells — flagged inline in the YAML comment so it doesn't surprise anyone later.
Why
benchmark_knowledge.yamlcurrently covers 16 ML/DL subfields but no non-MLdomain, even though
Dockerfile.biologyand thebiology_*domain profilesshow biology is an actively sandboxed domain. This is a narrowly-scoped first
increment for single-cell analysis specifically (matching the existing
biology_singlecellprofile). Happy to follow up with other biologysub-domains or other domains as separate PRs per the one-concern-per-PR
guideline in CONTRIBUTING.md.
Tests
TestBiologySingleCellDomain(4 tests) totests/test_benchmark_agent.py:domain presence, keyword matching, tier/API-prefix correctness, and that no
baseline needs a pip package beyond what
Dockerfile.biologyinstalls.pytest tests/passes locally (2868 passed, 56 pre-existing/unrelated skips).Scope
Additive only — no existing domains, agents, or schemas touched.