just-dna-compiler 0.4.0

Reference compiler for just-dna annotation modules: spec directory → parquet artifact + manifest

just-dna-compiler

The reference compiler for just-dna annotation modules: it turns an authored spec directory into a deployable parquet artifact plus a manifest.json with integrity digests.

A module composes from optional table kinds: the only always-present file is module_spec.yaml. A SNP module adds variants.csv (+ studies.csv, required whenever variants are present) → the weights / annotations / studies parquets; a PGx / PharmGKB / PRS module instead carries only its own table(s) (diplotypes.csv, pharm_variants.csv, pgs.csv, …) and needs no variants.csv. Each present CSV materializes to its own parquet, so the artifact is the set of parquets the module actually uses (up to twelve), not a fixed three.

It consumes the schema/contract from just-dna-format and is the shared transform called by both just-dna-pipelines (local compile) and just-dna-marketplace (server-side recompile on publish).

from just_dna_compiler.compiler import validate_spec, compile_module

validate_spec(spec_dir)                       # -> ValidationResult (genes/categories lists)
compile_module(spec_dir, out_dir,             # -> CompilationResult (+ manifest.json written)
               resolve_with_ensembl=False,    # inject an Ensembl DuckDB/parquet dir to resolve
               compiled_by="marketplace-server")

Dependencies: just-dna-format, polars, duckdb, pyyaml, platformdirs, python-dotenv — deliberately no Dagster / LLM SDKs. The Ensembl reference is injected by the caller (a .duckdb file or a parquet dir); this package never downloads it.