Add Snapshots/Read Model

[sygao]

Revision of PR 152.

• Add ref.snapshot.index

  • Add .SnapshotIndex
    • .id_to_taxid maps Virtool id to taxid
    • index_by_taxid, .index_by_name and .index_by_legacy_id maps to Virtool id
    • .snapshot() creates a new set of snapshots from a list of EventSourcedRepoOTU
  • Add .OTUKeys dataclass to hold indexable information

• Add ref.snapshot.otu

  • Add .OTUSnapshot
    • OTUSnapshot.load() returns snapshot data
    • OTUSnapshot.cache() writes snapshot data for a whole OTU
  • Add OTUSnapshotToC: Loads and writes table of contents data
  • Add OTUSnapshotDataStore: Handles the data subdirectory, writes isolates and sequences

• Add ref.snapshot.models:

  • OTUSnapshotSequence, OTUSnapshotIsolate, OTUSnapshotOTU base models parse, validate and serialize repo data
  • OTUSnapshotToCIsolate base model handles table of contents entries for each isolate
  • OTUSnapshotMeta holds metadata for the OTU, namely .at_event

• Add tests/snapshot

[virtool-bot]

:tada: This PR is included in version 2.0.0-alpha.31 :tada:

The release is available on GitHub release

Your semantic-release bot :package::rocket: