Python Library Release Notes#
Version 1.4.1: August 27, 2022#
General:
Updated pandas requirement to 0.24.0 or higher.
Added support for missing integer values (
NaN
) inload_rearrangement
by casting to the pandasInt64
data type.Added gzip support to
read_rearrangement
.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
validate
subcommand ofairr-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:
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.
Renamed
schema.CachedSchema
toschema.AIRRSchema
.Removed
specs/blank.airr.yaml
.
Deprecations:
Deprecated
load_repertoire
. Useread_airr
instead.Deprecated
write_repertoire
. Usewrite_airr
instead.Deprecated
validate_repertoire
. Usevalidate_airr
instead.Deprecated
repertoire_template
. Useschema.RepertoireSchema.template
instead.Deprecated the commandline tool
airr-tools validate repertoire
. Useairr-tools validate airr
instead.
Version 1.3.1: October 13, 2020#
Refactored
merge_rearrangement
to 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.
Added
load_repertoire
,write_repertoire
, andvalidate_repertoire
toairr.interface
to read, write and validate Repertoire metadata, respectively.Added
repertoire_template
toairr.interface
which will return a complete repertoire object where all fields havenull
values.Added
validate_object
toairr.schema
that will validate a single repertoire object against the schema.Extended the
airr-tools
commandline 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
validate_rearrangement
function.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.
Added
base
argument toRearrangementReader
andRearrangementWriter
to 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
ValidationError
for handling validation checks.Added the
validate
argument toRearrangementReader
which will raise aValidationError
exception when reading files with missing required fields or invalid values for known field types.Added
validate
argument to all type conversion methods inSchema
, which will now raise aValidationError
exception for value that cannot be converted when set toTrue
. When setFalse
(default), the previous behavior of assigningNone
as the converted value is retained.Added
validate_header
andvalidate_row
methods toSchema
and removed validations methods fromRearrangementReader
.Removed automatic closure of file handle upon reaching the iterator end in
RearrangementReader
.
Version 1.1.0: May 1, 2018#
Initial release.