Immuneml

Minor bugfix: updated SequenceMetadata object to convert 'nan' for RegionType to None (manifested before as an error on loading existing ImmuneML-formatted dataset from disk).

- standardized import/export metadata for repertoire datasets to always have field "identifier" instead of mixing it with "repertoire_identifier"

- integrate with Zenodo to make the code citable

Updates in v2.0.1 include minor bug fixes:

- fix path handling and serialization for ImmuneML format
- fix exported metadata for datasets with implanted signals
- minor updates related to Galaxy API

Updates in version 2:

- datasets are now stored using binary numpy and YAML files and do not rely on pickle anymore;
- Pickle import and export is replaced with ImmuneML import and export where datasets are represented as YAML files, while the content (repertoire data, receptors, sequences) are stored in numpy files;
- 'store_encoded_data' option is removed from instructions; to store the encoded data, use DesignMatrixExporter report.

The package is also available at: https://pypi.org/project/immuneML/2.0.0/