NEWS

---

PhysioLake 0.1.3

Documentation

• A vignette carries one task end to end on synthetic or bundled data, offline, and is built and run by R CMD check.
• Runnable @examples added or corrected across 5 help pages. Each runs offline in seconds, writes nothing outside tempdir(), and is executed by R CMD check; anything needing a device, a download or an optional backend is fenced with the reason stated.
• The README's quick start runs as written: it attaches the package, builds its own inputs, and uses only hard dependencies.

PhysioLake 0.1.2

• OmicsLake moved from Imports to Suggests so PhysioLake builds and installs publicly without the private OmicsLake package. The OmicsLake-backed adapter registration (registerPhysioAdapters()) is guarded with requireNamespace() and errors informatively when OmicsLake is absent; the backend-agnostic provenance/bundle helpers (physioPut/physioProvenance/physioPutBundle) work with any lake object regardless.

PhysioLake 0.1.1

• Tests now build their OmicsLake from a project name under a temporary root instead of passing a tempfile() path as the project identifier. The old form worked on Unix by accident but broke the DuckDB backend on Windows, where the drive-letter colon makes the resolved lake path invalid. No runtime change.

PhysioLake 0.1.0

• Initial draft. Integrates the ecosystem with OmicsLake by inheriting its domain-agnostic core (DuckDB/Arrow/Parquet backend, snapshots/time-travel, cross-dataset lineage, query layer) and registering a physiology-specific adapter through OmicsLake's register_adapter() extension point.
• PhysioExperimentAdapter (inherits OmicsLake::SEAdapter) stores and retrieves PhysioExperiment objects with full fidelity: it preserves the class identity and the samplingRate slot that the generic SummarizedExperiment adapter would drop, and — because provenance rides in metadata() — the W3C-PROV provenance survives the round trip unchanged (provenanceHash() identical before and after). Registered on load via .onLoad; re-runnable with registerPhysioAdapters().
• Verified that the non-SummarizedExperiment physio types (MultiRatePhysioExperiment, PhysioLongitudinal, AnalysisResult) round-trip through the lake with full fidelity via OmicsLake's default object serialization — including nested PhysioExperiment provenance — so no bespoke storage adapters are needed for them (pinned by test-containers.R).
• physioPut() / physioProvenance(): a provenance bridge that stores an object's W3C-PROV op-DAG (from PhysioCore::provenance()) as a queryable companion table and records it as a lineage dependency (put(..., depends_on=)), so the per-object (micro) provenance becomes a first-class node in OmicsLake's cross-dataset (macro) lineage -- lake$tree() / deps() / impact() see it.
• physioPutBundle(): store a reproducibility-substrate / PhysioAgent run bundle (frozen prereg, run manifest, op-DAG, terminal artifact, claims, ...) as individual lake entries wired with internal lineage edges (stored parents-first by topological order), so a whole run becomes a versioned, lineage-tracked lake object queryable via tree() / deps(). Gives the substrate the persistent store it lacks (it content-addresses runs but does not persist them).