Python Library Release Notes#

Version 1.5.0: August 29, 2023#

  1. Updated schema set and examples to v1.5.

  2. Officially dropped support for Python 2.

  3. Added check for valid enum values to schema validation routines.

  4. Set enum values to first defined value during template generation routines.

  5. Removed mock dependency installation in ReadTheDocs environments from setup.

  6. Improved package import time.

Version 1.4.1: August 27, 2022#

General:

  1. Updated pandas requirement to 0.24.0 or higher.

  2. Added support for missing integer values (NaN) in load_rearrangement by casting to the pandas Int64 data type.

  3. Added gzip support to read_rearrangement.

  4. Significant internal refactoring to improve schema generalizability, harmonize behavior between the python and R libraries, and prepare for AIRR Standards v2.0.

  5. Fixed a bug in the validate subcommand of airr-tools causing validation errors to only be reporting for the first invalid file when multiple files were specified on the command line.

Data Model and Schema:

  1. Added support for arrays of objects in a single JSON or YAML file.

  2. 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.

  3. Added support for the new germline and genotyping schema (GermlineSet, GenotypeSet) and associated schema.

  4. Renamed schema.CachedSchema to schema.AIRRSchema.

  5. Removed specs/blank.airr.yaml.

Deprecations:

  1. Deprecated load_repertoire. Use read_airr instead.

  2. Deprecated write_repertoire. Use write_airr instead.

  3. Deprecated validate_repertoire. Use validate_airr instead.

  4. Deprecated repertoire_template. Use schema.RepertoireSchema.template instead.

  5. Deprecated the commandline tool airr-tools validate repertoire. Use airr-tools validate airr instead.

Version 1.3.1: October 13, 2020#

  1. Refactored merge_rearrangement to allow for larger number of files.

  2. Improved error handling in format validation operations.

Version 1.3.0: May 30, 2020#

  1. Updated schema set to v1.3.

  2. Added load_repertoire, write_repertoire, and validate_repertoire to airr.interface to read, write and validate Repertoire metadata, respectively.

  3. Added repertoire_template to airr.interface which will return a complete repertoire object where all fields have null values.

  4. Added validate_object to airr.schema that will validate a single repertoire object against the schema.

  5. Extended the airr-tools commandline program to validate both rearrangement and repertoire files.

Version 1.2.1: October 5, 2018#

  1. 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#

  1. Updated schema set to v1.2.

  2. Several improvements to the validate_rearrangement function.

  3. 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.

  4. Added base argument to RearrangementReader and RearrangementWriter to support optional conversion of 1-based closed intervals in the TSV to python-style 0-based half-open intervals. Defaults to conversion.

  5. Added the custom exception ValidationError for handling validation checks.

  6. Added the validate argument to RearrangementReader which will raise a ValidationError exception when reading files with missing required fields or invalid values for known field types.

  7. Added validate argument to all type conversion methods in Schema, which will now raise a ValidationError exception for value that cannot be converted when set to True. When set False (default), the previous behavior of assigning None as the converted value is retained.

  8. Added validate_header and validate_row methods to Schema and removed validations methods from RearrangementReader.

  9. Removed automatic closure of file handle upon reaching the iterator end in RearrangementReader.

Version 1.1.0: May 1, 2018#

Initial release.