Deprecation and Removal:
read_alignment, write_alignment, and AlignmentSchema.
Removed "Alignment" from the valid definitions list and AIRRSchema.Tabular Data and Parsing:
read_tabular to initially treat logical columns as character data
to prevent silent NA conversions during parsing, then explicitly casting
valid logical character values.validate_tabular to support character strings representing logical
values (e.g., "TRUE", "T", "False", "F") when validating logical fields.Validation:
validate_entry to support comprehensive validation of arrays
without reference schemas, including item type checking (string, integer,
number, boolean) and enum constraints.validate_entry, providing explicit warnings for unrecognized types.validate_entry to ensure that an
ontology field is structured as a list before performing recursive validation.Data Model and Schema:
AIRRSchema to replace the Acknowledgement schema with the new
Contributor schema.extract_field_content to handle fields with null
properties safely.Significant internal refactoring to improve schema generalizability, harmonize behavior between the python and R libraries, and prepare for AIRR Standards v2.0.
Rearrangement:
aux_types argument to read_tabular, read_rearrangement, and
read_alignment to allow explicit declaration of the type for fields that
are not defined in the schema.read_airr, write_airr, and validate_airr to read_tabular,
validate_tabular, and validate_tabular, respectively.Data Model and Schema:
read_airr, write_airr, and validate_airr functions that
support AIRR Data Model files that store arrays of objects in JSON or YAML.info slot to Schema object containing general schema information.base="1" for read and write functions.germline_alignment data and simplification of sequence_id values.Initial release.