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.