AIRR Standards v1.6.0

What's Changed

• exclude deprecated by @schristley in #791
• curie resolve, handle undefined, fix deprecate bug by @schristley in #792
• minimums for physical quantities by @schristley in #799
• sync with 2.0 code by @schristley in #807
• AKC updates for v1.6 by @schristley in #814

Full Changelog: v1.5.1...v1.6.0

AIRR Standards v1.5.1

Version 1.5.1 of the AIRR Schema

Minor Schema Changes:

• Corrected schema version number in the Info object.

Minor Python Library Changes:

• Updated versioneer to v0.29.

JavaScript Library

• Initial release.

Full Release Notes:

• Schema release notes

AIRR Standards v1.5.0

Version 1.5 of the AIRR Schema

Major Schema Changes:

• Major cleanup, definition clarification, and attribute fixes in the Germline and Genotype schema.
• Set the default for x-airr.miarr attributes to defined.
• Added “IGI” as a valid value to the locus enum fields in multiple schema.
• Added a property type field to the CellExpression object.
• Updated all enum values to snake_case and added allowance for null enum values when appropriate.

Major R and Python Library Changes:

• Officially dropped support for Python 2.
• Updated enum validation and template handling in the python library.

Full Release Notes:

• Schema release notes
• Python library release notes
• R library release notes

AIRR Standards v1.4.1

Version 1.4 of the AIRR Schema

Major Schema Changes:

• Updated quantification fields in the Rearrangement and Clone schemas for better
  compatibility with single-cell and emerging technologies. Changes include new
  optional fields and modifications to the semantics of existing *_count fields.
• Various new optional fields in the Study, Subject and Rearrangement schemas.
• Modified how time points and template concentrations are stored in Sample and
  NucleicAcidProcessing Schemas.

New Experimental Schema:

• Experimental releases of new single-cell associated schemas.
• Experimental releases of germline reference and genotype schemas.
• Experimental release of data aggregation schemas, including collections of repertoires
  and JSON/YAML files bundling multiple AIRR Data Model objects.

Major R and Python Library Changes:

• Added support for generalized AIRR Data Model files and objects that bundle
  multiple data classes.
• Deprecated support for files storing only Repertoire objects in favor of a general
  AIRR Data Model, which is backwards compatible with Repertoire metadata files.

Full Release Notes:

• Schema release notes
• Python library release notes
• R library release notes

Documentation Updates

Overview

• Improvements to the organization and wording of various documentation pages.
• Added missing deprecation tags for rearrangement_id in the Alignment schema.
• Modified merge_rearrangement in the airr python library so that it can handle a large number of files.
• Improved validation error handling in the airr python library.

Full Release Notes:

• Schema release notes
• Python library release notes

AIRR Schema v1.3

Version 1.3 of the AIRR Schema

Major changes:

• First official release of the Repertoire metadata schema.
• First official release of the AIRR Data Commons API specification.
• Expansion of schema field annotations.
• Extensions to the Rearrangement schema for multiple D regions.
• New experimental schema for clones, lineage trees, and cells.

Full Release Notes:

• Schema release notes
• Python library release notes
• R library release notes

Python reference library fix

Fixed a bug in the python reference library causing start coordinate values to be empty in some cases when writing data.

Python library release notes.

Rearrangement schema v1.2

Schema Release Notes

Definition change for the coordinate fields of the Rearrangement and Alignment schema. Coordinates are now defined as 1-based closed intervals, instead of 0-based half-open intervals (as previously defined in v1.1 of the schema).

Reference Library Release Notes

Several changes to the python and R reference library to support the new schema coordinate definition and improve validation. See the package release notes for details:

• Python library release notes
• R library release notes

Data Representation standards and reference libraries

Initial official release of the AIRR Data Representation standards and associated python and R reference libraries.

Early revision of AIRR definitions

An early revision of the AIRR definitions with corresponding reference library.