# bio-rs

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[![Benchmark](https://img.shields.io/badge/benchmark-UniProt%20FASTA-blue)](benchmarks/fasta_vs_biopython.md)
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bio-rs turns biological sequences into validated, model-ready inputs for bio-AI workflows.

```txt
FASTA -> validated protein sequence -> token ids -> model-ready JSON
```

> Status: pre-1.0 CLI and JSON contract stabilization.

## Why bio-rs?

Most bio-AI models are born in Python, but the tooling around them often needs to run somewhere else:

- local CLIs
- CI pipelines
- servers
- browsers
- agents

bio-rs focuses on the boring but important layer before inference:

- parse biological sequence input
- validate it with structured diagnostics
- tokenize it into stable IDs
- emit machine-readable JSON contracts
- keep preprocessing reproducible outside notebooks

The goal is not to replace Python research workflows.

The goal is to make the input layer around bio-AI models faster, more portable, and easier to trust.

## Quickstart

Tokenize a FASTA file:

```bash
cargo run -p biors -- tokenize examples/protein.fasta
```

Pipe FASTA through stdin:

```bash
printf '>tiny\nACDE\n' | cargo run -p biors -- tokenize -
```

Validate FASTA:

```bash
cargo run -p biors -- fasta validate examples/protein.fasta
```

Verify package fixture outputs:

```bash
cargo run -p biors -- package verify \
  examples/protein-package/manifest.json \
  examples/protein-package/observations.json
```

Build model-ready input records:

```bash
cargo run -p biors -- model-input --max-length 8 examples/protein.fasta
```

## Proof

bio-rs keeps performance claims tied to reproducible in-repo benchmarks.

Latest recorded FASTA benchmark baseline:

| Dataset | Matched workload | bio-rs core mean | Biopython mean | bio-rs speedup |
|---|---|---:|---:|---:|
| Human proteome | Parse + validation | **0.191s** | 0.471s | **2.46x** |
| Human proteome | Parse + tokenization | **0.186s** | 0.471s | **2.54x** |
| 100MB+ FASTA | Parse + validation | **1.712s** | 4.232s | **2.47x** |
| 100MB+ FASTA | Parse + tokenization | **1.659s** | 4.238s | **2.55x** |

Benchmark details:

- Datasets:
  - UniProt human reference proteome (`UP000005640`, `9606`)
  - 100MB+ large FASTA generated by repeating the same real proteome to isolate large-input throughput
- Matched workloads:
  - pure parse
  - parse plus validation
  - parse plus tokenization
- Current best recorded raw throughput:
  - human proteome parse + tokenization: `61.7M residues/s`, `70.6 MB/s`
  - 100MB+ FASTA parse + tokenization: `62.2M residues/s`, `71.1 MB/s`
- Benchmark doc: [benchmarks/fasta_vs_biopython.md](benchmarks/fasta_vs_biopython.md)
- Benchmark script: [scripts/benchmark_fasta_vs_biopython.py](scripts/benchmark_fasta_vs_biopython.py)

This benchmark measures `biors-core` directly and excludes CLI startup and JSON
serialization overhead. It is still workload-specific, not a broad claim that
bio-rs is faster than Biopython across every FASTA workload or researcher input
shape.

## What works today

`biors-core` provides the Rust engine and data contracts.

`biors` provides the CLI surface.

Current capabilities:

- FASTA parsing and normalization
- shared FASTA parser/tokenizer scanner with an ASCII fast path and Unicode fallback
- buffered reader APIs for FASTA parse/validate/tokenize paths
- FASTA validation with line and record-index diagnostics
- FASTA record identifier validation
- protein-20 tokenization
- JSON vocab loading for tokenizer contracts
- positional token alignment preserved with explicit unknown-token IDs for unresolved residues
- residue warning/error reporting
- model-ready input records
- attention masks
- padding/truncation policy
- `model-input` CLI output
- model-input safety checks for unresolved residues
- explicit checked and unchecked model-input builders
- writer-based CLI success JSON serialization to reduce peak allocations for large outputs
- package manifest inspect/validate
- typed package validation issue codes
- typed package manifest enums for schema version, model format, runtime target, and tensor dtypes
- runtime bridge planning reports
- manifest-relative asset validation
- package path escape rejection for manifest and observation assets
- SHA-256 package and fixture checksum verification
- package fixture verification from observed artifact paths
- structured package fixture mismatch issue codes and first-difference reports
- committed FASTA, tokenizer, manifest, and verification fixtures
- JSON success/error envelopes

## CLI examples

Inspect FASTA records:

```bash
cargo run -p biors -- inspect examples/protein.fasta
```

Tokenize FASTA records:

```bash
cargo run -p biors -- tokenize examples/protein.fasta
```

Tokenize a multi-record FASTA file:

```bash
cargo run -p biors -- tokenize examples/multi.fasta
```

Validate FASTA records:

```bash
cargo run -p biors -- fasta validate examples/protein.fasta
```

Emit structured JSON errors:

```bash
printf 'ACDE\n' | cargo run -p biors -- --json tokenize -
```

Build model-ready input records:

```bash
cargo run -p biors -- model-input --max-length 4 examples/protein.fasta
```

Inspect a package manifest:

```bash
cargo run -p biors -- package inspect examples/protein-package/manifest.json
```

Validate a package manifest:

```bash
cargo run -p biors -- package validate examples/protein-package/manifest.json
```

Plan a runtime bridge from a package manifest:

```bash
cargo run -p biors -- package bridge examples/protein-package/manifest.json
```

Verify package fixture observations:

```bash
cargo run -p biors -- package verify \
  examples/protein-package/manifest.json \
  examples/protein-package/observations.json
```

`package verify` expects the observations file to point at observed output artifact paths:

```json
[
  {
    "name": "tiny-protein",
    "path": "observed/tiny.output.json"
  }
]
```

## JSON contracts

Success output uses a stable envelope shape:

```json
{
  "ok": true,
  "biors_version": "0.x.y",
  "input_hash": "fnv1a64:846a502e5067bc21",
  "data": {}
}
```

FASTA-backed commands keep `input_hash` in the legacy `fnv1a64:` format for backward compatibility. Package artifacts and fixture hashes use `sha256:` in manifests and verification reports.

`--json` error mode emits structured errors:

```json
{
  "ok": false,
  "error": {
    "code": "fasta.missing_header",
    "message": "FASTA input must start with a header line beginning with '>' at line 1",
    "location": {
      "line": 1,
      "record_index": null
    }
  }
}
```

Tokenization output is record-oriented:

```json
[
  {
    "id": "seq1",
    "length": 4,
    "alphabet": "protein-20",
    "valid": true,
    "tokens": [0, 1, 2, 3],
    "warnings": [],
    "errors": []
  }
]
```

Public contract docs:

- [Quickstart](docs/quickstart.md)
- [CLI contract](docs/cli-contract.md)
- [Error code registry](docs/error-codes.md)
- [1.0 contract candidates](docs/public-contract-1.0-candidates.md)
- [1.0 release candidate path](docs/release-candidate-1.0.md)
- [API and schema review](docs/api-review.md)
- [MSRV policy draft](docs/msrv.md)
- [Versioning policy](docs/versioning.md)
- [JSON schemas](schemas)
- [Changelog](CHANGELOG.md)
- [Citation metadata](CITATION.cff)

## Release history

Delivered:

- `0.12.0`: release-candidate documentation, full workflow e2e coverage, MSRV/citation policy drafts, and changelog
- `0.11.0`: benchmark reproducibility metadata, generated benchmark report checks, and refreshed speed/memory proof assets
- `0.10.0`: fixture and verification hardening with shared byte-aware FASTA scanning, tokenizer invariants, and structured mismatch reports
- `0.9.8`: tokenization lookup and CLI JSON writer performance improvements with refreshed reader-based benchmarks
- `0.9.7`: buffered FASTA reader APIs, typed package validation issues, CLI module refactor, and explicit model-input builder safety
- `0.9.6`: FASTA identifier validation, model-input policy validation, package path escape rejection, and JSON vocab loading
- `0.9.5`: core-throughput benchmark harness, matched-workload benchmark refresh, workflow/cache tightening, and git-hook install helper
- `0.9.4`: tokenizer positional alignment preservation, FASTA single-pass tokenization/validation path, typed package manifest enums, and benchmark refresh
- `0.9.3`: release workflow fix for automatic GitHub Release creation after crates publish
- `0.9.2`: model-input safety hardening for unresolved residues and automated GitHub Release creation
- `0.9.1`: model-input CLI, checksum-backed package validation, benchmark refresh, and contract hardening
- `0.9.0`: CLI and JSON contract freeze baseline
- `0.8.1`: documentation, contribution guide, and benchmark baseline hardening
- `0.8.0`: fixture verification with `package verify`
- `0.7.0`: runtime bridge planning with `package bridge`
- `0.6.0`: package manifest inspect/validate

Next:

- first stable release: stable public contracts and runtime-facing APIs after enough real-world package validation

## Not yet

These are roadmap directions, not current capabilities:

- hosted web workflows
- Python bindings
- model inference backends
- package registry or plugin ecosystem
- general-purpose chemistry tooling
- structure tooling
- no-code or low-code workflows

## Development

Run checks:

```bash
scripts/check.sh
```

Run the faster local commit gate:

```bash
scripts/check-fast.sh
```

The check suite runs:

- `cargo fmt`
- shell and Python syntax checks for repo scripts
- benchmark Markdown regeneration check
- Rust checks
- `biors-core` `wasm32-unknown-unknown` build check
- tests
- `cargo clippy` with warnings denied

Reproduce the FASTA benchmark:

```bash
cargo build --release -p biors-core --example benchmark_fasta
python3 -m venv .venv-bench
. .venv-bench/bin/activate
pip install biopython
python scripts/benchmark_fasta_vs_biopython.py
cat benchmarks/fasta_vs_biopython.json
```

The benchmark script updates both `benchmarks/fasta_vs_biopython.json` and
`benchmarks/fasta_vs_biopython.md`. `scripts/check-benchmark-docs.sh` verifies
that the Markdown report still matches the JSON artifact.

Run the Rust library example:

```bash
cargo run -p biors-core --example tokenize
```

## Workspace

```txt
packages/
  rust/
    biors/       CLI
    biors-core/  Core engine + contracts

schemas/
  cli-error.v0.json
  cli-success.v0.json
  fasta-validation-output.v0.json
  inspect-output.v0.json
  model-input-output.v0.json
  package-bridge-output.v0.json
  package-inspect-output.v0.json
  package-manifest.v0.json
  package-validation-report.v0.json
  package-verify-output.v0.json
  tokenize-output.v0.json

examples/
  protein.fasta
  multi.fasta
  protein-package/
    models/
    manifest.json
    observations.json
    fixtures/
    observed/
    tokenizers/
    vocabs/
```

## Protein-20 alphabet

```txt
A C D E F G H I K L M N P Q R S T V W Y
```

Token IDs follow that order, starting at `0`.

## Contributing

See [CONTRIBUTING.md](CONTRIBUTING.md) for local setup, checks, and PR expectations.

## License

Dual licensed under MIT OR Apache-2.0. If you use bio-rs in research software
or publications, cite the repository and version via [CITATION.cff](CITATION.cff).
