bionemo-recipeutils

Shared, framework-agnostic utilities for BioNeMo recipes.

Constraint

This package must not depend on megatron-core, megatron-bridge, or NeMo. Recipe-specific framework adapters (e.g., DatasetProvider wrappers) belong in each recipe, not here.

Contents

• bionemo.recipeutils.data.basecamp — High-performance SQLite-backed genomic dataset (ShardedEdenDataset) and window pre-computation CLI, contributed by BaseCamp Research.
• bionemo.recipeutils.io — File format conversion utilities (FASTA to JSONL).

Installation

pip install bionemo-recipeutils            # core
pip install bionemo-recipeutils[basecamp]   # + polars for window pre-computation

CLI tools

bionemo_fasta_to_jsonl input.fasta output.jsonl
bionemo_precompute_windows precompute split.parquet output.sqlite --window-size 8192