Changes in version 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.

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 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).