0.1.1

tiledbsc now uses the enhanced Group API's introduced in TileDB v2.8 and TileDB-R 0.12.0.

Note: The next version of tiledbsc will migrate to the new SOMA-based naming scheme described here.

On-disk changes

Group-level metadata is now natively supported by TileDB so TileDBGroup-based classes no longer create nested __tiledb_group_metadata arrays for the purpose of storing group-level metadata.

See TileDB 2.8 release notes for additional changes.

API changes

For TileDBGroup and its child classes:

• the arrays field has been replaced with members, which includes both TileDB arrays and groups
• get_array() has been replaced with get_member() which add a type argument to filter by object type
• gain the following methods: count_members(), list_members(), list_member_uris(), and add_member()

SCGroup

• the scgroup_uris argument has been dropped from SCDataset's initialize method (add_member() should now be used instead to add additional SCGroups)

SCDataset

• SCDataset's scgroups field is now an active binding that filters members for SCGroup objects

Other changes

• added a NEWS.md file to track changes to the package
• the fs package is now a dependency
• SCGroup's from_seurat_assay() method gained two new arguments: layers, to specify which Seurat Assay slots should be ingested, and var, to control whether feature-level metadata is ingested
• SCGroup's from_seurat_assay() method will no longer ingest the data slot if it is identical to counts
• Internally group members are now added with names
• New internal TileDBURI class for handling various URI formats
• The uri field for all TileDB(Array|Group)-based classes is now an active binding that retrieves the URI from the private tiledb_uri field
• Several default parameters have been changed to store the the X, obs, and var arrays more efficiently on disk (#50)
• Seurat cell identities are now stored in the active_ident attribute of the obs array (#56)
• Require at least version 0.13.0 of tiledb-r to support retrieval of group names