0.1.0

immundata 0.1.0

This release introduces manifests as the input-file annotation interface and
makes repertoire, strata, and provenance state more explicit and reliable.

Breaking changes

• Renamed the input repertoire metadata interface to avoid confusion with the
  metadata.json snapshot file. read_metadata() is replaced by
  read_manifest(). In read_repertoires(), use manifest,
  manifest_file_col, and path = "<manifest>" instead of metadata,
  metadata_file_col, and path = "<metadata>". The default manifest file
  column is now "file" rather than "File".
• read_repertoires() now uses repertoire_schema = "<auto>" by default. This
  creates one repertoire per input file, or one per manifest row when paths are
  supplied by a manifest. Set repertoire_schema = NULL to retain the previous
  behavior of leaving repertoires undefined.
• agg_strata() now uses the argument names schema and prefix instead of
  by and strata_name_prefix.
• Removed the ImmunData$metadata accessor. Use idata$repertoires for the
  repertoire definitions and summaries, and use manifests for annotations
  associated with input repertoire files.
• For extension developers, imd_schema("metadata_filename") is now
  imd_schema("manifest_filename"), and the unused imd_files()$receptors
  entry has been removed.

New features and improvements

• read_repertoires() now works approximately 60 times faster by
  combining CSV, TSV, and compressed text inputs into
  one temporary Parquet file before processing by default. This avoids repeated
  text scans in downstream duckplyr queries while retaining original input
  paths in provenance. Use prematerialize = FALSE to disable it or
  prematerialize_folder to select the temporary storage directory. I recommend you
  to use it pretty much always.
• Added read_manifest() for CSV, TSV, TXT, and in-memory manifests. It infers
  common delimiters, resolves file-relative paths, validates file availability,
  and adds normalized source paths for joining to repertoire data. The special
  repertoire_schema = "<manifest>" value defines repertoires from all manifest
  columns.
• Promoted strata to first-class ImmunData state. Objects now expose
  schema_strata and a $strata table; agg_strata() and rename_strata()
  update this state, and snapshots persist and restore it.
• Added grouped mutation through .by in mutate_immundata() and
  dplyr::mutate() methods for ImmunData, including a duckplyr-compatible
  fallback for grouped summary expressions.
• Added conflicts = c("error", "replace") to the annotation functions.
  Existing annotation columns are protected by default, while intentional
  replacement is allowed for columns that do not define core ImmunData
  state.
• mutate(), compute(), and annotation operations now preserve repertoire,
  strata, and provenance state when the biological grouping has not changed.
  Filtering and downsampling rebuild affected repertoire and strata summaries
  and retain existing stratum labels when possible.
• Added consistent progress control to manifest reading, repertoire ingestion
  and aggregation, and snapshot reading and writing. Use verbose = FALSE for
  individual calls or options(immundata.verbose = FALSE) globally.
• Snapshot metadata now stores repertoire and strata definitions and validates
  them against the Parquet annotation columns when loading. Older metadata
  formats remain readable and are upgraded in memory when necessary.
• Provenance now includes derived artifact locations (artifacts_root and
  artifacts_path) associated with the project home and current snapshot.

Bug fixes

• Corrected repertoire-level cell and receptor counts for paired-chain data and
  prevented chain rows from inflating n_barcodes, n_receptors, receptor
  proportions, and repertoire-occurrence counts.
• Made imd_repertoire_id assignment deterministic by ordering repertoire
  schema values before assigning identifiers.
• Scoped single-cell barcodes by source filename during chain selection and
  pairing, preventing identical barcode strings from different input files from
  being treated as the same cell.
• Sequence filters now retain every chain belonging to a matched receptor,
  including exact, regular-expression, Hamming, and Levenshtein matching.
  Distance calculations no longer use the k-mer prefilter, and temporary DuckDB
  table names are unique across repeated operations.
• Fixed downsampling with DuckDB 1.5 and later, preserved annotation columns in
  bulk count mode, retained provenance and strata state, and made n = 1 mean
  an absolute sampling depth of one.
• Hardened ingestion against duplicate manifest paths, negative bulk counts,
  missing argument columns, and collisions between custom and canonical locus
  columns.
• Prevented mutate() and annotation replacement from overwriting system,
  receptor-schema, repertoire-schema, or strata-defining columns.
• Fixed Windows path handling in the test and example infrastructure.

Documentation and maintenance

• Reworked the package documentation around biological units, lazy duckplyr
  workflows, ingestion, aggregation, filtering, annotation, snapshots, and
  provenance, and moved website generation to altdoc.
• Removed the unused ggplot2 dependency and raised the minimum supported dplyr
  version to 1.2.1.