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Architecture

Dependency direction

Dependency direction follows ownership:

CLI / presentation
        ↓
in-memory API and APB integration
        ↓
calculation protocols and workflow
        ↓
diagnostics / scoring / configuration

apb-proteobench → APB2 public in-memory, annotation, and result facades
APB2 -/→ apb-proteobench

Package boundaries

APB2 owns storage-neutral ParsedLevels, result adapters, and generic relational observation annotation. This package owns module semantics, complete ProteoBench coverage, species mapping, diagnostics, scoring, compatibility assets, and presentation.

The public API owns one operation: annotate and score canonical ParsedLevels in memory. It contains no paths, APB2 compiler, FASTA loading, persistence, logging, or command behavior. The CLI is the physical composition root: raw-vendor workflows construct APB2's ParseRuleCompiler, pass canonical parser output to APB FASTA and ProteoBenchAnalyzer, persist the returned ParsedLevels through APB2, and use compiler.parameters for ProteoBot fields without provenance reconstruction. The integration boundary alone extracts scientific input from ParsedLevels or attaches calculation output; presentation receives the completed analysis and explicit command paths and never reopens output files.

Scientific input

Scientific methods receive QuantitativeLevelInput: a pandas observation table, NumPy/SciPy matrix, feature identifiers, protein assignments, and level name. They never receive AnnData, MuData, or ParsedLevels. The integration boundary extracts those values and attaches the completed analysis to a new ParsedLevels; APB2 persists it when the caller requests storage.

Replaceable methods

DiagnosticMethod and ScoringMethod are client-owned protocols. The default composition uses MixedSpeciesDiagnostics and ProteoBenchCompatibleScoring; callers can explicitly substitute another implementation without adding method-name branches. Automatic plugin discovery is not part of this release.

Persisted extension data

ProteoBench owns one tool namespace. Root provenance records annotation configuration and common scoring methods; the module-selected level records annotation matching evidence and scoring[quantity_name]. Aligned diagnostics remain in that level's varm. APB2's writers map these logical owners to H5AD, H5MU, Parquet or DuckDB without tool-specific branches; calculations remain storage-independent. See Result layout.