rsomics-world

rsomics-world is the control plane for omics-rust: a set of coherent, high-performance Rust bioinformatics products and their shared foundations.

The project previously published hundreds of operation-sized crates. That partition was rejected because it confused a Rust module boundary with a user product, repository, CI pipeline, version, and installation boundary.

The current rule is:

One recognizable product or workflow family per Layer B crate. Operations are subcommands and modules. A public Layer A foundation exists only when at least two products consume it.

Current portfolio

• 30 planned product-family boundaries.
• Nine long-term public foundations.
• rsomics-igzip temporarily retained because a published rsomics-seqio version depends on it.
• Historical operation implementations preserved on external storage as a source pool for consolidation.

The live and planned namespace is indexed in REGISTRY.md.

Repository model

Each public product or foundation is an independent repository under omics-rust. There is no Cargo monorepo, submodule aggregation, or cross-repository path dependency.

Local clones live under:

/Volumes/KIOXIA/Documents/omics-rust/

rsomics-world contains documentation, product dossiers, audit scripts, and durable campaign state. It contains no product implementation.

Reconstruction

Existing implementations are reused rather than discarded. The generated portfolio inventory maps the local source pool to provisional target products. The portfolio reconstruction explains the 30-family model and shared-foundation evidence. The product dossier index tracks the mapping from historical implementations to target products, and the consumer-driven foundation audit records the current public API risks and migration waves.

For each product:

1. survey real upstream operations;
2. deduplicate overlapping tools;
3. map old implementations into target modules and subcommands;
4. preserve compatibility tests, fixtures, and benchmarks;
5. evolve shared foundations through concrete consumers;
6. publish only after the product interface and evidence are complete.

Start here

• AGENTS.md — unattended operating rules
• CONVENTIONS.md — architecture and engineering conventions
• ROADMAP.md — reconstruction phases
• TODO.md — current executable checklist
• REGISTRY.md — live and planned public namespace
• docs/ — upstream surveys and product dossiers