Changes in version 0.99.4                        

  - Added spaMTPdbGeneReference() for a versioned HGNC quarterly archive
    with approved/previous/alias symbols and stable gene identifiers.
    The reference is retrieved from the official fixed archive and
    verified locally or in the cache; no changing current-file or live
    symbol lookup is used.
  - HGNC versions and provenance are separate from the existing
    RaMP 3.0.7 registry. Experiment resources remain owned by
    SpaMTPData.

                       Changes in version 0.99.3                        

  - Added a maintainer-only shared release workflow for annotation
    database and native experimental files in the existing Zenodo
    version family. Logical resource ownership, Hub registries and
    resource versions remain separate.
  - Shared preparation verifies all files and preserves published
    registries. Uploads use an explicit new-version or existing-draft
    target, validate the version family, resume matching files, and
    reject conflicts without deleting or overwriting remote files.
    Default execution is an offline dry run.
  - Removed automatic publication and independent-record creation from
    the legacy upload entry point. Publishing remains a separate manual
    action.

                       Changes in version 0.99.2                        

  - Added explicit roxygen2 importFrom declarations for every Imports
    package and regression coverage for namespace dependency
    declarations.
  - Replaced PascalCase resource exports with spaMTPdbResource(),
    spaMTPdbResources(), spaMTPdbBundle() and spaMTPdbVersion(),
    synchronized with SpaMTP >= 0.99.3. The RaMP 3.0.7 resource contents
    and checksums are unchanged.
  - Verify local files by default, allow explicit unverified development
    fixtures, and reuse a verified download cache before Hub access,
    including offline. Bundle defaults now follow the requested resource
    version.
  - Updated the SMILES recipe to the native deconvolveSMILES() API and
    refuse accidental overwrites of an existing structure resource.
    data-raw entry points delegate to shipped recipes instead of keeping
    duplicate code.
  - Made the vignette offline-reproducible and documented the
    responsibilities and coordinated versions of all three packages.

                       Changes in version 0.99.1                        

  - Version bump only. The Zenodo download fallback shipped
    inside 0.99.0, so an installation cached by version alone could
    still hold the pre-Zenodo build that failed with "AnnotationHub does
    not yet contain ...". Bumping the version lets those caches
    invalidate.

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission scaffold.
  - Added versioned AnnotationHub metadata for RaMP 3.0.7 and legacy
    metabolite annotation resources.
  - Resource files are published on Zenodo rather than in the
    Bioconductor Hub bucket, which no longer accepts data from external
    contributors. Hub records point at the Zenodo copy through
    Location_Prefix and RDataPath.
  - Added a verified download and cache path so a resource can be
    retrieved from its immutable Zenodo URL before the AnnotationHub
    records are published. Downloads are checked against the recorded
    size and MD5 checksum.
  - Added inst/scripts/zenodo_upload.R to deposit staged resources on
    Zenodo, and taught inst/scripts/stage_resources.R and
    inst/scripts/make-metadata.R to regenerate the manifest and Hub
    metadata from a Zenodo record ID.
  - Moved resource_manifest.csv out of inst/extdata, because
    AnnotationHubData::makeAnnotationHubMetadata() reads every CSV in
    that directory as Hub metadata.
  - Recorded RaMP-derived resources with SourceType: MySQL; the Hub
    controlled vocabulary has no SQLite term.
  - Added local-resource support for development before Hub ingestion.
  - Added an independent, precomputed smiles_features resource for
    functional groups and positive-, negative-, neutral-, and
    alkali-adduct priors.