Python Library Release Notes#
Version 1.5.0: August 29, 2023#
Updated schema set and examples to v1.5.
Officially dropped support for Python 2.
Added check for valid enum values to schema validation routines.
Set enum values to first defined value during template generation routines.
Removed mock dependency installation in ReadTheDocs environments from setup.
Improved package import time.
Version 1.4.1: August 27, 2022#
Updated pandas requirement to 0.24.0 or higher.
Added support for missing integer values (
load_rearrangementby casting to the pandas
Added gzip support to
Significant internal refactoring to improve schema generalizability, harmonize behavior between the python and R libraries, and prepare for AIRR Standards v2.0.
Fixed a bug in the
airr-toolscausing validation errors to only be reporting for the first invalid file when multiple files were specified on the command line.
Data Model and Schema:
Added support for arrays of objects in a single JSON or YAML file.
Added support for the AIRR Data File and associated schema (DataFile, Info). The Data File data format holds AIRR object of multiple types and is backwards compatible with Repertoire metadata.
Added support for the new germline and genotyping schema (GermlineSet, GenotypeSet) and associated schema.
Deprecated the commandline tool
airr-tools validate repertoire. Use
airr-tools validate airrinstead.
Version 1.3.1: October 13, 2020#
merge_rearrangementto allow for larger number of files.
Improved error handling in format validation operations.
Version 1.3.0: May 30, 2020#
Updated schema set to v1.3.
airr.interfaceto read, write and validate Repertoire metadata, respectively.
airr.interfacewhich will return a complete repertoire object where all fields have
airr.schemathat will validate a single repertoire object against the schema.
airr-toolscommandline program to validate both rearrangement and repertoire files.
Version 1.2.1: October 5, 2018#
Fixed a bug in the python reference library causing start coordinate values to be empty in some cases when writing data.
Version 1.2.0: August 17, 2018#
Updated schema set to v1.2.
Several improvements to the
Changed behavior of all airr.interface functions to accept a file path (string) to a single Rearrangement TSV, instead of requiring a file handle as input.
RearrangementWriterto support optional conversion of 1-based closed intervals in the TSV to python-style 0-based half-open intervals. Defaults to conversion.
Added the custom exception
ValidationErrorfor handling validation checks.
RearrangementReaderwhich will raise a
ValidationErrorexception when reading files with missing required fields or invalid values for known field types.
validateargument to all type conversion methods in
Schema, which will now raise a
ValidationErrorexception for value that cannot be converted when set to
True. When set
False(default), the previous behavior of assigning
Noneas the converted value is retained.
Schemaand removed validations methods from
Removed automatic closure of file handle upon reaching the iterator end in
Version 1.1.0: May 1, 2018#