nirs4all-io-cli 0.2.2

Command-line front end for nirs4all-io: infer / to-spec / validate / load / emit-dag-ml-data.
nirs4all-io-cli-0.2.2 is not a library.

nirs4all-io

Dataset-assembly bridge. Turn any user input — a directory, a list of files, a glob, a config dict/JSON/YAML, in-memory arrays, a folder of vendor spectra + a reference table — into a pipeline-ready dataset.

nirs4all-io owns the dataset-level concepts that the low-level reader library nirs4all-formats deliberately does not: X/Y/metadata roles, train/test/folds, multi-source, relational joins, signal/task-type inference, and a declarative convention system. It matches the expressiveness of nirs4all's DatasetConfig/DatasetLoader and adds a score-based inference engine.

Part of the open-source NIRS tools ecosystem: file readers, datasets, methods, browser modelling, reproducible pipelines, papers, benchmarks, and release dashboards for near-infrared spectroscopy.

any input ──► RESOLVE ──► INFER ──► CONFIGURE ──► MATERIALIZE ──► SpectroDataset / DatasetPackage
              (InputSet)  (DatasetPlan, scored)   (DatasetSpec)    or dag-ml-data envelope (Rust bridge)

Status

Phase 1 (Python MVP) — complete and parity-verified. load() and infer() work end-to-end and target SpectroDataset, AssembledDataset, and the target-agnostic DatasetPackage; the build is byte-equivalent to nirs4all's own DatasetConfigs on the supported topologies (pytest -m parity).

Phase 2 (Rust rewrite + dag-ml-data bridge) — complete. The Rust workspace ports the same pipeline and the dag-ml-data emit lives in crates/nirs4all-io-dagml (to_dag_ml_data + the emit-dagml binary). The main nirs4all-io CLI keeps an emit-dag-ml-data discovery subcommand that points to that bridge crate. Its bounded DATA-002 path builds a typed provider directly from a Rust DatasetPackage: from_package accepts one dense numeric source, while from_package_source selects one named source without fusing the others. The provider retains package identity, target names, and a typed row-major f64 feature projection. There is intentionally no Python load(..., target="dag-ml-data") surface. See docs/API.md for the seam, docs/IO_XLG_QUALIFICATION.md for binding qualification, and docs/development.md for contributor references and the private development archive policy.

Quick start (target API)

import nirs4all_io as nio

# Inspect a directory and get a scored recommendation
plan = nio.infer("data/mango/", conventions=["nirs4all-classic"])
print(plan.recommendations)

# Materialize a spec/plan/input into a SpectroDataset or target-agnostic package
ds = nio.load(plan, target="spectrodataset")
ds = nio.load({"sources": [{"id": "x", "role": "features", "input": "X.csv"}]})
pkg = nio.to_dataset_package(plan)

# Vendor corpus + reference table (headline new capability)
plan = nio.infer(["spectra/*.0", "reference.csv"], conventions=["vendor-corpus"])

What can it load?

docs/DATASET_CONFIGURATIONS.md is the complete reference: every input form, DatasetSpec field, column selector, merge mode, relational join, partition, fold and loading parameter — with a use-case cookbook and an honest ✅/🟡/📋 implementation status on each option.

Language bindings

One Rust core, thin wrappers per language (all over the same canonical-JSON contract). See COMPAT.md for the full operation matrix.

  • CLI — nirs4all-io (infer / to-spec / validate / load; emit-dag-ml-data points to the bridge crate).
  • dag-ml-data bridge — crates/nirs4all-io-dagml (to_dag_ml_data / emit-dagml), validated by the cross-CLI conformance gate.
  • Rust DATA package provider — PackageProvider::from_package or from_package_source, for one selected dense numeric source plus aligned target tables; multi-source fusion and N-D payloads stay on explicit dag-ml-data provider paths.
  • Python (pyo3/maturin) — bindings/python; the only surface that builds a real SpectroDataset.
  • R (.Call over the C ABI) — bindings/r. R-universe can lag the latest RC tag until its rebuild catches up; use the GitHub Release source tarball for exact-version validation, or install the current R-universe build with: 
    install.packages("nirs4allio", repos = c("https://gbeurier.r-universe.dev", getOption("repos")))
  • MATLAB / Octave (MEX over the C ABI) — bindings/matlab.
  • WASM / JS (wasm-bindgen, fs-free) — bindings/wasm.

Design principles

  • Self-contained: no runtime dependency on nirs4all. The only touch-point is a lazy import of the SpectroDataset class at materialization.
  • Parsers live in nirs4all-formats: vendor byte-decoding is never reimplemented here; tabular loading logic is copied from nirs4all (see COPY_PROVENANCE.md).
  • Versioned, machine-validatable DatasetSpec is the canonical contract.

License

nirs4all-io is dual-licensed open-source — CeCILL-2.1 OR AGPL-3.0-or-later (your choice) — with an optional commercial license for closed-source / SaaS use. For any commercial use, contact nirs4all-admin@cirad.fr. See LICENSING.md, the texts under LICENSES/, and THIRD_PARTY_NOTICES.md.